[ViewVC] Diff of: group/trunk/OOPSE-2.0/ChangeLog

Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 1712 by tim, Thu Nov 4 20:55:01 2004 UTC vs.
Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC

-<
+-11-04 14:48  tim
->
+-03-11 00:43  chrisfen
->
->
+        * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md,
->
+        src/io/RestReader.cpp, src/restraints/Restraints.cpp,
->
+        src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in
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+        MPI restraints
->
->
+-03-10 23:56  tim
->
->
+        * doc/SelectionExpression.html, src/brains/SimInfo.cpp,
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+        src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody
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+        and cutoff group
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->
+-03-10 22:06  gezelter
->
->
+        * src/types/MorseBondType.hpp: fixed a doxygen problem
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->
+-03-10 21:51  gezelter
->
->
+        * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with
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+        the split dipole test cases
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->
+-03-10 21:51  gezelter
->
->
+        * doc/SelectionExpression.html: updated some documentation
->
->
+-03-10 20:40  gezelter
->
->
+        * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp,
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+        Makefile: LinkedList removal project starts now
->
->
+-03-10 20:28  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
->
+        io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp:
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+        using map to replace link list
->
->
+-03-10 19:11  tim
->
->
+        * samples/dipole/: splitInWater.in, splitInWater.md: adding test
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+        case  of split dipole
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->
+-03-10 19:10  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp,
->
+        src/io/RestWriter.cpp,
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+        src/restraints/ThermoIntegrationForceManager.cpp: Oops...  MPI now
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+        builds...
->
->
+-03-10 18:44  tim
->
->
+        * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in,
->
+        split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md:
->
+        adding test case for split dipole
->
->
+-03-10 17:54  gezelter
->
->
+        * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side
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+        support for split dipoles
->
->
+-03-10 16:27  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md,
->
+        src/restraints/ThermoIntegrationForceManager.cpp: fixes to
->
+        restraints
->
->
+-03-10 16:15  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp,
->
+        src/UseTheForce/ForceFields.hpp,
->
+        src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints
->
->
+-03-10 16:14  tim
->
->
+        * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc,
->
+        src/io/MultipoleAtomTypesSectionParser.cpp,
->
+        src/selection/SelectionEvaluator.cpp: minor change
->
->
+-03-10 15:10  chrisfen
->
->
+        * make/Makefile.in, samples/water/tip3p_ice/tp3.md,
->
+        src/brains/SimCreator.cpp, src/brains/SimInfo.hpp,
->
+        src/integrators/Integrator.cpp, src/integrators/Integrator.hpp,
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+        src/integrators/VelocityVerletIntegrator.cpp,
->
+        src/integrators/VelocityVerletIntegrator.hpp,
->
+        src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp,
->
+        src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp,
->
+        src/io/RestReader.hpp, src/io/RestWriter.cpp,
->
+        src/io/RestWriter.hpp, src/io/RestraintReader.cpp,
->
+        src/io/RestraintWriter.cpp, src/restraints/Makefile,
->
+        src/restraints/Restraints.cpp, src/restraints/Restraints.hpp,
->
+        src/restraints/ThermoIntegrationForceManager.cpp,
->
+        src/restraints/ThermoIntegrationForceManager.hpp: First commit of
->
+        the new restraints code
->
->
+-03-09 18:48  tim
->
->
+        * src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding
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+        IndexFinder
->
->
+-03-09 18:46  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.ggo,
->
+        applications/dump2Xyz/Dump2XYZCmd.c,
->
+        applications/dump2Xyz/Dump2XYZCmd.h,
->
+        selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp:
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+        fix compilation issue
->
->
+-03-09 17:58  tim
->
->
+        * forceFields/DUFF2.frc, scripts/filepp,
->
+        src/UseTheForce/EAM_FF.cpp,
->
+        src/io/MultipoleAtomTypesSectionParser.cpp,
->
+        src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug
->
+        in SectionParser (lineNo is not updated)
->
->
+-03-09 17:30  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.ggo,
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+        applications/dump2Xyz/Dump2XYZCmd.c,
->
+        applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp,
->
+        brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp,
->
+        io/ChargeAtomTypesSectionParser.hpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile,
->
+        io/MultipoleAtomTypesSectionParser.cpp,
->
+        io/MultipoleAtomTypesSectionParser.hpp,
->
+        io/SectionParserManager.cpp, selection/Makefile,
->
+        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
->
+        types/AtomType.cpp, types/DirectionalAtomType.cpp,
->
+        visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp,
->
+        visitors/OtherVisitor.hpp: adding IndexFinder which is used to
->
+        select the molecules; Seperate ElectrostaticAtomTypesSectionParser
->
+        into ChargeAtomTypesSectionParser and
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+        MultipoleAtomTypesSectionParser;remove print dipole option from
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+        Dump2XYZ;
->
->
+-03-09 17:28  tim
->
->
+        * forceFields/DUFF2.frc: change the format of DUFF2
->
->
+-03-09 15:44  gezelter
->
->
+        * src/UseTheForce/DarkSide/: electrostatic.F90,
->
+        electrostatic_interface.F90, electrostatic_interface.h: new
->
+        electrostatic module
->
->
+-03-09 14:26  gezelter
->
->
+        * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
->
+        DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole
->
+        and fixed quadrupole stuff
->
->
+-03-09 14:25  gezelter
->
->
+        * src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines
->
+        for outdated charge and dipole interfaces
->
->
+-03-08 21:08  gezelter
->
->
+        * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in,
->
+        mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun
->
+        charge-dipole test cases
->
->
+-03-08 21:07  gezelter
->
->
+        * src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp,
->
+        OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a
->
+        strange icc8 bug (we think).
->
->
+-03-08 21:07  gezelter
->
->
+        * src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa!
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->
+-03-08 21:07  gezelter
->
->
+        * src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic
->
+        Unification Project
->
->
+-03-08 21:07  gezelter
->
->
+        * src/io/Globals.cpp: Dunno
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->
+-03-08 21:06  gezelter
->
->
+        * src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using
->
+        OOPSE_itoa and checking a NULL left over from the LinkedList days
->
->
+-03-08 21:06  gezelter
->
->
+        * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
->
+        atype_interface.F90, atype_interface.h, charge.F90,
->
+        charge_interface.F90, charge_interface.h, dipole.F90,
->
+        dipole_interface.F90, dipole_interface.h: electrostatic unification
->
+        project fixed an uninitialized variable in Lennard Jones mixing map
->
->
+-03-08 21:05  gezelter
->
->
+        * src/UseTheForce/doForces.F90: electrostatic unification project
->
->
+-03-08 21:05  gezelter
->
->
+        * samples/water/dimer/: two.md, water.md: making some cool test
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+        cases
->
->
+-03-08 21:05  gezelter
->
->
+        * forceFields/DUFF2.frc: Added a charge for Chlorine
->
->
+-03-07 22:39  tim
->
->
+        * src/: brains/SimInfo.cpp, io/DumpReader.cpp,
->
+        math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp,
->
+        primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp:
->
+        Fixing a bug in BitSet.cpp
->
->
+-03-04 15:28  gezelter
->
->
+        * src/config.h.in: Cleaning up config.h.in by adding comments
->
->
+-03-04 15:28  gezelter
->
->
+        * configure, ac-tools/configure.in, make/Makefile.in,
->
+        src/brains/SimCreator.cpp: SPRNG eradication project
->
->
+-03-03 14:40  tim
->
->
+        * src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the
->
+        missing atom type problem)
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->
+-03-02 16:29  tim
->
->
+        * src/math/RandNumGen.hpp: adding base class of Random Number
->
+        generator
->
->
+-03-02 16:28  tim
->
->
+        * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
->
+        math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in
->
+        Velocitizer is not initialized which causes a seg fault
->
->
+-03-02 15:36  tim
->
->
+        * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
->
+        integrators/Velocitizer.hpp, math/Makefile,
->
+        math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp,
->
+        math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp,
->
+        math/SeqRandNumGen.hpp: remove default parameter from
->
+        MersenneTwister.hpp which causes all kinds of trouble.  Refactory
->
+        random number generator
->
->
+-03-02 07:32  tim
->
->
+        * test/math/testRandNumGen.cpp: Adding unit test for random number
->
+        generator
->
->
+-03-01 23:17  tim
->
->
+        * src/brains/Thermo.hpp: fixed a file inclusion problem
->
->
+-03-01 23:17  tim
->
->
+        * test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
->
+        OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp,
->
+        ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp,
->
+        RandNumGenTestCase.hpp: fixed compilation problem
->
->
+-03-01 23:02  tim
->
->
+        * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp,
->
+        integrators/Velocitizer.hpp, math/Makefile,
->
+        math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp,
->
+        math/ParallelRandNumGen.hpp, math/mt19937ar.c,
->
+        math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand
->
->
+-03-01 23:00  tim
->
->
+        * test/math/: Makefile, ParallelandNumGenTestCase.cpp,
->
+        ParallelandNumGenTestCase.hpp: Change the name of test case
->
->
+-03-01 21:00  tim
->
->
+        * test/math/: Makefile, OOPSERandNumGenTestCase.cpp,
->
+        OOPSERandNumGenTestCase.hpp: adding testcase for random number
->
+        generator
->
->
+-03-01 20:10  tim
->
->
+        * src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp,
->
+        integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp,
->
+        math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp,
->
+        math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp,
->
+        math/Vector3.hpp, minimizers/MinimizerCreator.hpp,
->
+        utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp,
->
+        utils/TypeContainer.hpp, visitors/AtomVisitor.cpp,
->
+        visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4
->
->
+-03-01 19:11  tim
->
->
+        * src/: brains/SimCreator.cpp, brains/SimInfo.hpp,
->
+        integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
->
+        math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding
->
+        OOPSERandNumGen
->
->
+-03-01 15:44  gezelter
->
->
+        * make/Makefile.in: Fixed the damned build problem with the
->
+        libraries not being removed in make clean and make distclean (at
->
+        least we think it is fixed).
->
->
+-03-01 15:26  gezelter
->
->
+        * src/math/MersenneTwister.hpp: Making small modifications to allow
->
+        for use on MPI machines
->
->
+-03-01 14:45  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp,
->
+        integrators/Velocitizer.cpp, io/DumpReader.cpp,
->
+        math/MersenneTwister.hpp: adding MersenneTwister random number
->
+        generator
->
->
+-03-01 03:55  tim
->
->
+        * src/math/MersenneTwister.hpp: Adding a modified version of
->
+        MersenneTwister.hpp
->
->
+-02-28 17:24  tim
->
->
+        * doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png,
->
+        definition.jpg: selection expression
->
->
+-02-25 21:22  tim
->
->
+        * src/: UseTheForce/DarkSide/LJ.F90,
->
+        UseTheForce/DarkSide/lj_interface.F90,
->
+        UseTheForce/DarkSide/lj_interface.h,
->
+        io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp,
->
+        types/AtomType.hpp: adding soft potential to LJ Module
->
->
+-02-25 16:38  tim
->
->
+        * doc/SelectionExpression.html: adding documentation for selection
->
+        expression
->
->
+-02-24 20:55  tim
->
->
+        * src/: applications/simpleBuilder/simpleBuilder.cpp,
->
+        integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp,
->
+        io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp:
->
+        adding basic_teebuf which can operate on multiple stream
->
+        simutaneously.
->
->
+-02-22 18:56  tim
->
->
+        * src/: UseTheForce/DarkSide/reactionField.F90,
->
+        primitives/RigidBody.cpp: reactionfield get fixed
->
->
+-02-21 16:57  tim
->
->
+        * src/: applications/staticProps/GofRAngle.cpp,
->
+        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix
->
+        a bug in GofRAngle
->
->
+-02-21 15:28  tim
->
->
+        * src/primitives/Molecule.cpp: Fix for compilation on the Sun
->
->
+-02-21 15:22  tim
->
->
+        * src/utils/next_combination.hpp: fix for compilation on the Sun
->
->
+-02-21 15:21  tim
->
->
+        * src/utils/GenericData.hpp: fix problem in sun
->
->
+-02-18 23:07  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.ggo,
->
+        applications/dump2Xyz/Dump2XYZCmd.c,
->
+        applications/dump2Xyz/Dump2XYZCmd.h,
->
+        applications/dynamicProps/RCorrFunc.cpp,
->
+        applications/staticProps/GofXyz.cpp,
->
+        applications/staticProps/GofXyz.hpp,
->
+        applications/staticProps/StaticProps.cpp,
->
+        applications/staticProps/StaticProps.ggo,
->
+        applications/staticProps/StaticPropsCmd.c,
->
+        applications/staticProps/StaticPropsCmd.h,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp,
->
+        visitors/Makefile: adding LipidTransVisitor, GofXyz is working now
->
->
+-02-18 15:58  gezelter
->
->
+        * src/brains/Register.cpp: Corrected filename collision for EAM on
->
+        Mac OS X
->
->
+-02-18 15:58  gezelter
->
->
+        * src/applications/oopse/oopse.cpp: Updated copyright information
->
->
+-02-18 15:58  gezelter
->
->
+        * src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp,
->
+        Makefile: corrected filename collision for EAM on operating systems
->
+        which are not case sensitive (aka Mac OS X)
->
->
+-02-17 20:15  tim
->
->
+        * src/applications/staticProps/GofXyz.cpp: more bug get fixed
->
->
+-02-17 19:50  tim
->
->
+        * src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug
->
+        in GofXyz
->
->
+-02-17 19:09  tim
->
->
+        * src/applications/staticProps/RadialDistrFunc.hpp: make
->
+        processHistogram non-abstrct function
->
->
+-02-17 18:41  tim
->
->
+        * src/applications/staticProps/GofXyz.cpp: [no log message]
->
->
+-02-17 18:30  tim
->
->
+        * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
->
+        GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp:
->
+        finish GofXyz
->
->
+-02-17 16:21  tim
->
->
+        * src/applications/staticProps/: GofAngle2.cpp, GofR.cpp,
->
+        GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial
->
+        distribution function
->
->
+-02-17 15:23  tim
->
->
+        * src/utils/BitSet.hpp: forget the const correctness for BitSet
->
->
+-02-17 15:18  tim
->
->
+        * src/: brains/BlockSnapshotManager.cpp,
->
+        selection/DistanceFinder.cpp: The change of interface of BitSet
->
+        cause a bug in SelectionEvaluation
->
->
+-02-16 21:13  tim
->
->
+        * src/utils/residentMem.c: return residentMem in byte
->
->
+-02-16 21:00  tim
->
->
+        * src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix
->
+        a bug in writing out the value of cosang
->
->
+-02-16 20:43  tim
->
->
+        * src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to
->
+        estimate avaliable memory
->
->
+-02-16 20:30  tim
->
->
+        * src/: applications/staticProps/GofAngle2.cpp,
->
+        applications/staticProps/GofAngle2.hpp,
->
+        applications/staticProps/GofR.cpp,
->
+        applications/staticProps/GofR.hpp,
->
+        applications/staticProps/GofRAngle.cpp,
->
+        applications/staticProps/GofRAngle.hpp,
->
+        applications/staticProps/GofXyz.cpp,
->
+        applications/staticProps/GofXyz.hpp,
->
+        applications/staticProps/StaticProps.cpp,
->
+        applications/staticProps/StaticProps.ggo,
->
+        applications/staticProps/StaticPropsCmd.c,
->
+        applications/staticProps/StaticPropsCmd.h,
->
+        brains/BlockSnapshotManager.cpp: change the default bin number
->
->
+-02-16 19:36  tim
->
->
+        * src/: applications/dynamicProps/DipoleCorrFunc.cpp,
->
+        applications/dynamicProps/RCorrFunc.cpp,
->
+        applications/dynamicProps/TimeCorrFunc.cpp,
->
+        applications/dynamicProps/VCorrFunc.cpp,
->
+        applications/staticProps/GofAngle2.cpp,
->
+        applications/staticProps/GofR.cpp,
->
+        applications/staticProps/GofR.hpp,
->
+        applications/staticProps/GofRAngle.cpp,
->
+        applications/staticProps/GofRAngle.hpp,
->
+        applications/staticProps/RadialDistrFunc.cpp,
->
+        applications/staticProps/RadialDistrFunc.hpp,
->
+        selection/SelectionManager.cpp, selection/SelectionManager.hpp,
->
+        utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output
->
+        files;fix the problem of counting in staticProps
->
->
+-02-15 19:39  tim
->
->
+        * src/brains/BlockSnapshotManager.cpp: fix a bug in
->
+        BlockSnapshotManager
->
->
+-02-15 19:36  tim
->
->
+        * src/: applications/dynamicProps/TimeCorrFunc.cpp,
->
+        applications/staticProps/RadialDistrFunc.cpp,
->
+        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
->
+        selection/SelectionEvaluator.cpp: BlockSnapshotManager is using
->
+        reference counting now
->
->
+-02-15 17:49  tim
->
->
+        * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
->
+        replace std::make_pair by VariablesType::value_type to make Sun
->
+        Compiler happy
->
->
+-02-15 17:35  tim
->
->
+        * src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to
->
+        TokenMap, using TokenMapType::value_type instead of std::make_pair
->
+        to make Sun compiler happy
->
->
+-02-15 17:24  tim
->
->
+        * src/applications/staticProps/: GofRAngle.cpp,
->
+        RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps
->
->
+-02-15 17:11  tim
->
->
+        * src/: applications/staticProps/GofR.cpp,
->
+        applications/staticProps/RadialDistrFunc.cpp,
->
+        applications/staticProps/RadialDistrFunc.hpp,
->
+        brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding
->
+        #ifdef __RWSTD to make sun compiler happy (2) fix pair density
->
+        calculation problem when two selections intersect with each other
->
->
+-02-15 15:24  gezelter
->
->
+        * src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy
->
+        xlc++
->
->
+-02-15 15:17  gezelter
->
->
+        * configure, ac-tools/configure.in, src/config.h.in,
->
+        src/utils/residentMem.c: [no log message]
->
->
+-02-15 06:17  gezelter
->
->
+        * src/utils/residentMem.c: bug fix for null termination
->
->
+-02-15 06:11  gezelter
->
->
+        * configure, ac-tools/configure.in, src/utils/residentMem.c:
->
+        bugfixing residentMem
->
->
+-02-15 05:59  gezelter
->
->
+        * configure, ac-tools/configure.in, src/config.h.in,
->
+        src/utils/residentMem.c: bugfixes for residentMem on LINUX
->
->
+-02-15 05:08  gezelter
->
->
+        * src/utils/Makefile.in: added residentMem
->
->
+-02-15 05:05  gezelter
->
->
+        * configure, ac-tools/configure.in, make/Makefile.in,
->
+        src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c,
->
+        src/utils/residentMem.h: modifications to estimate memory in use by
->
+        other processes autoconf fixes ps syntax checking config.h file
->
+        cleaning
->
->
+-02-14 23:26  gezelter
->
->
+        * configure, ac-tools/configure.in, make/Makefile.in: ps niceness
->
->
+-02-14 23:16  gezelter
->
->
+        * configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps
->
+        strangeness
->
->
+-02-14 19:42  tim
->
->
+        * src/brains/BlockSnapshotManager.cpp: fix a bug in
->
+        BlockSnapshotManager.hpp
->
->
+-02-14 18:51  tim
->
->
+        * src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo,
->
+        StaticPropsCmd.c: default length for staticProps is 1/2 smallest
->
+        length of first frame
->
->
+-02-14 18:12  tim
->
->
+        * src/integrators/VelocityVerletIntegrator.cpp: fix a bug in
->
+        VelocityVerletIntegrator : last frame is written twice
->
->
+-02-14 17:57  tim
->
->
+        * src/: applications/dynamicProps/TimeCorrFunc.cpp,
->
+        brains/SimInfo.cpp, primitives/RigidBody.cpp,
->
+        primitives/StuntDouble.hpp: begin bug fix
->
->
+-02-14 17:35  tim
->
->
+        * src/applications/dynamicProps/: CorrelationFunction.cpp,
->
+        CorrelationFunction.hpp, CrossTimeCorrFunc.cpp,
->
+        CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp,
->
+        DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile,
->
+        ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp,
->
+        RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp,
->
+        VCorrFunc.hpp: refactory CorrelationFunction
->
->
+-02-14 15:18  gezelter
->
->
+        * src/applications/dynamicProps/CorrelationFunction.cpp: bug fix
->
+        and start of switch for type of correlation function
->
->
+-02-13 21:18  tim
->
->
+        * src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in
->
+        calculating  bytes per stuntdouble
->
->
+-02-13 21:03  tim
->
->
+        * src/applications/dynamicProps/CorrelationFunction.cpp: more fix
->
->
+-02-13 20:57  tim
->
->
+        * src/applications/dynamicProps/CorrelationFunction.cpp: fixed a
->
+        bug in CorrelationFunction
->
->
+-02-13 20:36  tim
->
->
+        * src/: applications/staticProps/GofR.cpp,
->
+        applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a
->
+        bug in SimInfo::getCutoff()
->
->
+-02-13 20:08  tim
->
->
+        * make/Makefile.in: adding staticProps and dynamicProps into
->
+        Makefile.in
->
->
+-02-13 20:05  tim
->
->
+        * src/: applications/dynamicProps/CorrelationFunction.cpp,
->
+        applications/dynamicProps/CorrelationFunction.hpp,
->
+        applications/staticProps/StaticProps.cpp,
->
+        applications/staticProps/StaticProps.ggo,
->
+        applications/staticProps/StaticPropsCmd.c,
->
+        applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp,
->
+        brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length
->
+        defaults to the cutoff radius
->
->
+-02-13 19:14  tim
->
->
+        * src/utils/Algorithm.hpp: adding Algorithm.hpp
->
->
+-02-13 19:10  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/dynamicProps/CorrelationFunction.cpp,
->
+        applications/dynamicProps/CorrelationFunction.hpp,
->
+        applications/dynamicProps/DynamicProps.cpp,
->
+        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
->
+        integrators/Integrator.cpp, integrators/Integrator.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp,
->
+        io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp,
->
+        utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h,
->
+        visitors/OtherVisitor.cpp: dynamicProps get built
->
->
+-02-13 15:56  tim
->
->
+        * src/: applications/dynamicProps/CorrelationFunction.cpp,
->
+        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
->
+        brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in
->
+        progress
->
->
+-02-13 08:04  tim
->
->
+        * src/: applications/dynamicProps/CorrelationFunction.hpp,
->
+        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
->
+        brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp,
->
+        brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more
->
+        work in dynamicProps
->
->
+-02-13 07:25  tim
->
->
+        * src/applications/dynamicProps/DynamicProps.cpp: adding
->
+        dynamicProps
->
->
+-02-13 07:14  tim
->
->
+        * src/applications/dynamicProps/: DynamicPropsCmd.c,
->
+        DynamicPropsCmd.h: adding command line option to DynamicProps
->
->
+-02-13 07:13  tim
->
->
+        * src/applications/dynamicProps/: DynamicProps.ggo, Makefile:
->
+        adding command line option for DynamicProps
->
->
+-02-13 06:57  tim
->
->
+        * src/: applications/dynamicProps/CorrelationFunction.cpp,
->
+        applications/dynamicProps/CorrelationFunction.hpp,
->
+        applications/dynamicProps/DipoleCorrFunc.cpp,
->
+        applications/dynamicProps/DipoleCorrFunc.hpp,
->
+        applications/dynamicProps/RCorrFunc.cpp,
->
+        applications/dynamicProps/RCorrFunc.hpp,
->
+        applications/dynamicProps/VCorrFunc.cpp,
->
+        applications/dynamicProps/VCorrFunc.hpp,
->
+        applications/staticProps/RadialDistrFunc.cpp,
->
+        brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp,
->
+        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
->
+        brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp,
->
+        primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding
->
+        dynamicProps
->
->
+-02-12 20:09  tim
->
->
+        * src/selection/SelectionManager.cpp: adding SelectionManager.cpp
->
->
+-02-11 22:41  tim
->
->
+        * src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one
->
+        more constructor to Snapshot to create customized DataStorage
->
->
+-02-11 22:39  tim
->
->
+        * src/selection/: DistanceFinder.hpp, Makefile,
->
+        SelectionManager.hpp: adding beginSelected, nextSelected method to
->
+        SelectionManager
->
->
+-02-11 22:36  tim
->
->
+        * src/config.h.in, configure: adding support for physmem
->
->
+-02-11 22:35  tim
->
->
+        * ac-tools/configure.in: adding supprot for physmem
->
->
+-02-11 22:35  tim
->
->
+        * src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding
->
+        physmem
->
->
+-02-10 22:37  tim
->
->
+        * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
->
+        GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp,
->
+        GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp,
->
+        StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
->
+        StaticPropsCmd.h: more work in StaticProps
->
->
+-02-10 18:14  tim
->
->
+        * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp,
->
+        GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp,
->
+        GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp,
->
+        Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp,
->
+        StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
->
+        StaticPropsCmd.h: change the filenames
->
->
+-02-10 14:15  tim
->
->
+        * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp,
->
+        GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp,
->
+        RadialDistrFunc.hpp: adding GofRAngle
->
->
+-02-09 18:21  tim
->
->
+        * src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some
->
+        useless files
->
->
+-02-09 18:12  tim
->
->
+        * src/applications/staticProps/: GofR.cpp, Makefile,
->
+        RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress
->
->
+-02-09 17:08  tim
->
->
+        * src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp,
->
+        GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h,
->
+        RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR
->
->
+-02-07 22:39  tim
->
->
+        * src/primitives/Molecule.hpp: add getRigidBodyAt  function into
->
+        Molecule class
->
->
+-02-07 22:38  tim
->
->
+        * src/applications/dump2Xyz/Dump2XYZCmd.c: update help info
->
->
+-02-07 22:36  tim
->
->
+        * src/selection/: NameFinder.cpp, NameFinder.hpp,
->
+        SelectionCompiler.cpp: support select internal index selection, for
->
+        example, select DMPC.3
->
->
+-02-07 21:11  tim
->
->
+        * src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update
->
+        help info for Dump2XYZ
->
->
+-02-07 20:39  chrisfen
->
->
+        * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
->
+        selection librarys added
->
->
+-02-07 20:31  tim
->
->
+        * src/selection/Makefile, make/Makefile.in: adding Makefile
->
->
+-02-07 20:20  chrisfen
->
->
+        * src/utils/wildcards.hpp: issue commented out in wildcards
->
->
+-02-07 20:06  tim
->
->
+        * src/selection/SelectionEvaluator.cpp: forget to reset the pc
->
+        which cause reevaluate return NULL
->
->
+-02-07 19:14  tim
->
->
+        * src/brains/: SimCreator.cpp, SimSnapshotManager.cpp,
->
+        SimSnapshotManager.hpp: fix a bug in determing the global index for
->
+        rigidbodies
->
->
+-02-07 19:13  tim
->
->
+        * src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change
->
+        in Bitset
->
->
+-02-07 19:13  tim
->
->
+        * src/selection/: DistanceFinder.cpp, DistanceFinder.hpp,
->
+        SelectionCompiler.cpp, SelectionCompiler.hpp,
->
+        SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp,
->
+        TokenMap.cpp: selection library is working
->
->
+-02-04 22:46  tim
->
->
+        * src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor
->
->
+-02-04 22:45  tim
->
->
+        * src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor
->
+        and XYZVisitor now use selection library
->
->
+-02-04 22:44  tim
->
->
+        * src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp:
->
+        adding SelectionManager into SimInfo
->
->
+-02-04 22:43  tim
->
->
+        * src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo,
->
+        Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of
->
+        selection library
->
->
+-02-04 22:42  tim
->
->
+        * src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change
->
+        in BitSet
->
->
+-02-04 22:41  tim
->
->
+        * src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing
->
+        implementation
->
->
+-02-04 22:39  tim
->
->
+        * src/selection/: NameFinder.cpp, NameFinder.hpp,
->
+        SelectionCompiler.cpp, SelectionCompiler.hpp,
->
+        SelectionEvaluator.cpp, SelectionEvaluator.hpp,
->
+        SelectionManager.hpp, Token.hpp: half of the selection utility is
->
+        working need to debug within keyword and atomproperty keyword
->
->
+-02-04 05:42  tim
->
->
+        * src/selection/: NameFinder.cpp, NameFinder.hpp: selection library
->
+        get built
->
->
+-02-04 05:42  tim
->
->
+        * src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet
->
->
+-02-04 05:26  tim
->
->
+        * src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp:
->
+        remove some useless files
->
->
+-02-04 04:57  tim
->
->
+        * src/: primitives/RigidBody.hpp, selection/NameFinder.cpp,
->
+        selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp:
->
+        adding wildcard class; NameFinder is finished
->
->
+-02-03 23:14  tim
->
->
+        * src/selection/: NameFinder.cpp, NameFinder.hpp,
->
+        SelectionCompiler.cpp, SelectionCompiler.hpp,
->
+        SelectionEvaluator.cpp, SelectionEvaluator.hpp,
->
+        SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in
->
+        selection library
->
->
+-02-03 14:04  tim
->
->
+        * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp:
->
+        selection in progress
->
->
+-02-02 23:13  tim
->
->
+        * src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp,
->
+        SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp,
->
+        Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in
->
+        progress, except SelectionEvaluator, other files are compiled
->
->
+-02-02 23:12  tim
->
->
+        * src/utils/: Makefile.in, any.hpp: adding boost::any
->
->
+-02-02 12:51  tim
->
->
+        * src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp
->
->
+-02-01 22:49  tim
->
->
+        * src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp,
->
+        selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp,
->
+        selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp,
->
+        selection/Token.hpp: Selection in progress
->
->
+-02-01 06:55  tim
->
->
+        * src/: selection/SelectionCompiler.hpp,
->
+        selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp,
->
+        selection/SelectionManager.hpp, selection/Token.hpp,
->
+        utils/BitSet.cpp, utils/BitSet.hpp: adding selection library
->
->
+-01-26 15:26  tim
->
->
+        * src/integrators/: Integrator.cpp, Integrator.hpp,
->
+        VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget
->
+        to add eorWriter
->
->
+-01-26 15:15  tim
->
->
+        * src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp:
->
+        (1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the
->
+        wrong column of electroframe
->
->
+-01-25 21:59  tim
->
->
+        * src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in
->
+        SimInfo, use number of cutoff stamp as counter to loop over
->
+        rigidbody stamp
->
->
+-01-25 17:45  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
->
+        brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
->
+        integrators/DLM.cpp, io/AtomTypesSectionParser.cpp,
->
+        io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp,
->
+        io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp,
->
+        io/EAMAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp,
->
+        io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp,
->
+        io/StickyAtomTypesSectionParser.cpp,
->
+        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
->
+        math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp,
->
+        primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp,
->
+        primitives/GhostTorsion.hpp, primitives/Makefile,
->
+        primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete
->
+        section parser's error message (2) add GhostTorsion (3) accumulate
->
+        inertial tensor from the directional atoms before calculate
->
+        rigidbody's inertial tensor
->
->
+-01-17 22:17  tim
->
->
+        * forceFields/DUFF2.frc: forget to set dipole for lipid head group
->
->
+-01-17 16:58  tim
->
->
+        * src/integrators/NVT.cpp: fix a bug in loading initial extended
->
+        system parameters
->
->
+-01-17 16:05  tim
->
->
+        * src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT
->
->
+-01-14 22:02  tim
->
->
+        * src/UseTheForce/WATER.cpp: remove WATER.cpp
->
->
+-01-14 21:37  tim
->
->
+        * forceFields/Makefile: sync Makefile
->
->
+-01-14 21:13  gezelter
->
->
+        * make/Makefile.in, src/Makefile, src/UseTheForce/Makefile,
->
+        src/UseTheForce/DarkSide/Makefile, src/applications/Makefile,
->
+        src/applications/dump2Xyz/Makefile,
->
+        src/applications/oopse/Makefile,
->
+        src/applications/simpleBuilder/Makefile, src/brains/Makefile,
->
+        src/constraints/Makefile, src/integrators/Makefile,
->
+        src/io/Makefile, src/math/Makefile, src/minimizers/Makefile,
->
+        src/primitives/Makefile, src/profiling/Makefile,
->
+        src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in,
->
+        src/visitors/Makefile: moved Package variable into subdirectory
->
+        makefiles to speed up the building process
->
->
+-01-14 20:48  gezelter
->
->
+        * src/applications/oopse/oopse.cpp: Fixed publication details in
->
+        banner
->
->
+-01-14 20:48  gezelter
->
->
+        * src/UseTheForce/DarkSide/: simParallel_interface.F90,
->
+        simParallel_interface.h: added dummy subroutine to avoid empty
->
+        unit, synchronized this dummy routine between C and fortran
->
->
+-01-14 20:31  gezelter
->
->
+        * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90,
->
+        notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90,
->
+        DarkSide/Makefile, DarkSide/atype.F90,
->
+        DarkSide/atype_interface.F90, DarkSide/charge.F90,
->
+        DarkSide/charge_interface.F90, DarkSide/dipole.F90,
->
+        DarkSide/dipole_interface.F90, DarkSide/eam.F90,
->
+        DarkSide/eam_interface.F90, DarkSide/gb.F90,
->
+        DarkSide/gb_interface.F90, DarkSide/lj_interface.F90,
->
+        DarkSide/shapes.F90, DarkSide/shapes_interface.F90,
->
+        DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90,
->
+        DarkSide/simulation.F90, DarkSide/simulation_interface.F90,
->
+        DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating
->
+        modules and C/Fortran interface subroutines
->
->
+-01-14 20:15  gezelter
->
->
+        * configure, ac-tools/aclocal.m4: more fixes for gnugetopt
->
->
+-01-14 20:09  gezelter
->
->
+        * configure, ac-tools/configure.in, src/config.h.in,
->
+        src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt
->
->
+-01-14 16:49  tim
->
->
+        * src/: io/EAMAtomTypesSectionParser.cpp,
->
+        utils/StringTokenizer.cpp, utils/StringTokenizer.hpp,
->
+        utils/StringUtils.hpp: using c library to do conversion instead of
->
+        using iostream due to a bug in libstdc++(GCC 3.2)
->
->
+-01-14 02:40  tim
->
->
+        * src/brains/SimSetup.cpp: no message
->
->
+-01-14 01:56  tim
->
->
+        * src/primitives/Molecule.hpp: fix a bug in global index
->
->
+-01-14 01:04  tim
->
->
+        * src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include
->
+        Integrator.hpp in Minimizer
->
->
+-01-13 22:14  gezelter
->
->
+        * src/utils/Makefile: compile getopt and getopt1 if we need to
->
->
+-01-13 21:56  gezelter
->
->
+        * make/Makefile.in: template flags
->
->
+-01-13 21:48  gezelter
->
->
+        * src/applications/oopse/Makefile: formatting
->
->
+-01-13 21:48  gezelter
->
->
+        * make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir
->
+        target
->
->
+-01-13 19:40  tim
->
->
+        * src/: UseTheForce/fSwitchingFunction.h,
->
+        UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile,
->
+        math/Makefile, math/RectMatrix.hpp, math/Vector.hpp,
->
+        primitives/RigidBody.cpp, types/AtomTypeProperties.h,
->
+        types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform
->
->
+-01-13 18:26  tim
->
->
+        * make/Makefile.in: change the order of linking (object file comes
->
+        first and then follow by user built library)
->
->
+-01-12 23:24  tim
->
->
+        * src/io/DumpWriter.cpp: remove useless debug info
->
->
+-01-12 23:21  tim
->
->
+        * src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix
->
->
+-01-12 23:17  tim
->
->
+        * make/: Makefile.in, Makefile.in: missing tab
->
->
+-01-12 23:15  tim
->
->
+        * src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor
->
+        get fixed
->
->
+-01-12 22:40  gezelter
->
->
+        * make/Makefile.in, src/UseTheForce/DUFF.cpp,
->
+        src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp,
->
+        src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp,
->
+        src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp,
->
+        src/UseTheForce/ForceFieldCreator.hpp,
->
+        src/UseTheForce/ForceFieldFactory.cpp,
->
+        src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp,
->
+        src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp,
->
+        src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h,
->
+        src/UseTheForce/fSwitchingFunction.h,
->
+        src/UseTheForce/mpiComponentPlan.h,
->
+        src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h,
->
+        src/UseTheForce/notifyCutoffs.F90,
->
+        src/UseTheForce/notifyCutoffs_interface.h,
->
+        src/UseTheForce/DarkSide/LJ.F90,
->
+        src/UseTheForce/DarkSide/atype.F90,
->
+        src/UseTheForce/DarkSide/atype_interface.h,
->
+        src/UseTheForce/DarkSide/charge.F90,
->
+        src/UseTheForce/DarkSide/charge_interface.h,
->
+        src/UseTheForce/DarkSide/dipole.F90,
->
+        src/UseTheForce/DarkSide/dipole_interface.h,
->
+        src/UseTheForce/DarkSide/eam.F90,
->
+        src/UseTheForce/DarkSide/eam_interface.h,
->
+        src/UseTheForce/DarkSide/force_globals.F90,
->
+        src/UseTheForce/DarkSide/gb.F90,
->
+        src/UseTheForce/DarkSide/gb_interface.h,
->
+        src/UseTheForce/DarkSide/lj_interface.h,
->
+        src/UseTheForce/DarkSide/neighborLists.F90,
->
+        src/UseTheForce/DarkSide/reactionField.F90,
->
+        src/UseTheForce/DarkSide/shapes.F90,
->
+        src/UseTheForce/DarkSide/shapes_interface.h,
->
+        src/UseTheForce/DarkSide/simParallel.F90,
->
+        src/UseTheForce/DarkSide/simParallel_interface.h,
->
+        src/UseTheForce/DarkSide/simulation.F90,
->
+        src/UseTheForce/DarkSide/simulation_interface.h,
->
+        src/UseTheForce/DarkSide/sticky.F90,
->
+        src/UseTheForce/DarkSide/sticky_interface.h,
->
+        src/UseTheForce/DarkSide/switcheroo.F90,
->
+        src/applications/Makedepend, src/applications/quickLate.c,
->
+        src/applications/dump2Xyz/Dump2XYZ.cpp,
->
+        src/applications/oopse/oopse.cpp,
->
+        src/applications/simpleBuilder/BaseLattice.cpp,
->
+        src/applications/simpleBuilder/BaseLattice.hpp,
->
+        src/applications/simpleBuilder/Lattice.cpp,
->
+        src/applications/simpleBuilder/Lattice.hpp,
->
+        src/applications/simpleBuilder/LatticeCreator.cpp,
->
+        src/applications/simpleBuilder/LatticeCreator.hpp,
->
+        src/applications/simpleBuilder/LatticeFactory.cpp,
->
+        src/applications/simpleBuilder/LatticeFactory.hpp,
->
+        src/applications/simpleBuilder/MoLocator.cpp,
->
+        src/applications/simpleBuilder/MoLocator.hpp,
->
+        src/applications/simpleBuilder/simpleBuilder.cpp,
->
+        src/brains/DataStorage.cpp, src/brains/DataStorage.hpp,
->
+        src/brains/Exclude.cpp, src/brains/Exclude.hpp,
->
+        src/brains/ForceManager.cpp, src/brains/ForceManager.hpp,
->
+        src/brains/Makefile, src/brains/Migrator.hpp,
->
+        src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp,
->
+        src/brains/Register.cpp, src/brains/Register.hpp,
->
+        src/brains/SimCreator.cpp, src/brains/SimCreator.hpp,
->
+        src/brains/SimInfo.cpp, src/brains/SimInfo.hpp,
->
+        src/brains/SimModel.hpp, src/brains/SimSetup.hpp,
->
+        src/brains/SimSnapshotManager.cpp,
->
+        src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp,
->
+        src/brains/SimState.hpp, src/brains/SkipList.cpp,
->
+        src/brains/SkipList.hpp, src/brains/Snapshot.cpp,
->
+        src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp,
->
+        src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp,
->
+        src/brains/Thermo.hpp, src/brains/fSimulation.h,
->
+        src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp,
->
+        src/constraints/AbstractClasses.hpp,
->
+        src/constraints/ConstraintElem.hpp,
->
+        src/constraints/ConstraintPair.hpp, src/constraints/Makefile,
->
+        src/constraints/Rattle.cpp, src/constraints/Rattle.hpp,
->
+        src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
->
+        src/constraints/ZconsStruct.hpp,
->
+        src/constraints/ZconstraintForceManager.cpp,
->
+        src/constraints/ZconstraintForceManager.hpp,
->
+        src/integrators/AbstractClasses.hpp,
->
+        src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp,
->
+        src/integrators/DLM.hpp, src/integrators/Integrator.cpp,
->
+        src/integrators/Integrator.hpp,
->
+        src/integrators/IntegratorCreator.hpp,
->
+        src/integrators/IntegratorFactory.cpp,
->
+        src/integrators/IntegratorFactory.hpp, src/integrators/Makefile,
->
+        src/integrators/NPT.cpp, src/integrators/NPT.hpp,
->
+        src/integrators/NPTf.cpp, src/integrators/NPTf.hpp,
->
+        src/integrators/NPTi.cpp, src/integrators/NPTi.hpp,
->
+        src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp,
->
+        src/integrators/NVE.cpp, src/integrators/NVE.hpp,
->
+        src/integrators/NVT.cpp, src/integrators/NVT.hpp,
->
+        src/integrators/RotationAlgorithm.hpp,
->
+        src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp,
->
+        src/integrators/VelocityVerletIntegrator.cpp,
->
+        src/integrators/VelocityVerletIntegrator.hpp,
->
+        src/io/AtomTypesSectionParser.cpp,
->
+        src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp,
->
+        src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h,
->
+        src/io/BendTypesSectionParser.cpp,
->
+        src/io/BendTypesSectionParser.hpp,
->
+        src/io/BondTypesSectionParser.cpp,
->
+        src/io/BondTypesSectionParser.hpp,
->
+        src/io/DirectionalAtomTypesSectionParser.cpp,
->
+        src/io/DirectionalAtomTypesSectionParser.hpp,
->
+        src/io/DumpReader.cpp, src/io/DumpReader.hpp,
->
+        src/io/DumpWriter.cpp, src/io/DumpWriter.hpp,
->
+        src/io/EAMAtomTypesSectionParser.cpp,
->
+        src/io/EAMAtomTypesSectionParser.hpp,
->
+        src/io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp,
->
+        src/io/Globals.hpp, src/io/InitializeFromFile.cpp,
->
+        src/io/LennardJonesAtomTypesSectionParser.cpp,
->
+        src/io/LennardJonesAtomTypesSectionParser.hpp,
->
+        src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp,
->
+        src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp,
->
+        src/io/Makefile, src/io/SectionParser.cpp,
->
+        src/io/SectionParser.hpp, src/io/SectionParserManager.cpp,
->
+        src/io/SectionParserManager.hpp, src/io/StatWriter.cpp,
->
+        src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp,
->
+        src/io/StickyAtomTypesSectionParser.hpp,
->
+        src/io/TorsionTypesSectionParser.cpp,
->
+        src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp,
->
+        src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
->
+        src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.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/math/ChebyshevPolynomials.cpp,
->
+        src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c,
->
+        src/math/MatVec3.h, src/math/Polynomial.hpp,
->
+        src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp,
->
+        src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp,
->
+        src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
->
+        src/math/Vector.hpp, src/math/Vector3.hpp,
->
+        src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp,
->
+        src/minimizers/CGFamilyMinimizer.cpp,
->
+        src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile,
->
+        src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp,
->
+        src/minimizers/MinimizerCreator.hpp,
->
+        src/minimizers/MinimizerFactory.cpp,
->
+        src/minimizers/MinimizerFactory.hpp,
->
+        src/minimizers/MinimizerParameterSet.cpp,
->
+        src/minimizers/MinimizerParameterSet.hpp,
->
+        src/minimizers/OOPSEMinimizer.cpp,
->
+        src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp,
->
+        src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp,
->
+        src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp,
->
+        src/primitives/Atom.cpp, src/primitives/Atom.hpp,
->
+        src/primitives/Bend.cpp, src/primitives/Bend.hpp,
->
+        src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp,
->
+        src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp,
->
+        src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp,
->
+        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
->
+        src/primitives/GhostBend.hpp, 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/Torsion.hpp, src/primitives/TorsionExtensions.cpp,
->
+        src/primitives/UreyBradleyBend.cpp,
->
+        src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp,
->
+        src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp,
->
+        src/types/AtomStamp.hpp, src/types/AtomType.cpp,
->
+        src/types/AtomType.hpp, src/types/AtomTypeProperties.h,
->
+        src/types/BendStamp.cpp, src/types/BendStamp.hpp,
->
+        src/types/BendType.hpp, src/types/BondStamp.cpp,
->
+        src/types/BondStamp.hpp, src/types/BondType.hpp,
->
+        src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp,
->
+        src/types/Component.cpp, src/types/Component.hpp,
->
+        src/types/CubicBendType.hpp, src/types/CubicBondType.hpp,
->
+        src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp,
->
+        src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp,
->
+        src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp,
->
+        src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp,
->
+        src/types/MakeStamps.cpp, src/types/MakeStamps.hpp,
->
+        src/types/Makefile, src/types/MoleculeStamp.cpp,
->
+        src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp,
->
+        src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp,
->
+        src/types/PolynomialBondType.hpp,
->
+        src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp,
->
+        src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp,
->
+        src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp,
->
+        src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp,
->
+        src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp,
->
+        src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp,
->
+        src/types/ZconStamp.cpp, src/types/ZconStamp.hpp,
->
+        src/utils/GenericData.hpp, src/utils/GenericFactory.hpp,
->
+        src/utils/LocalIndexManager.hpp, src/utils/Makefile,
->
+        src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp,
->
+        src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp,
->
+        src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp,
->
+        src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp,
->
+        src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp,
->
+        src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp,
->
+        src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp,
->
+        src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp,
->
+        src/utils/Utility.cpp, src/utils/Utility.hpp,
->
+        src/utils/definitions.F90, src/utils/fError.c,
->
+        src/utils/next_combination.hpp, src/utils/oopseMPI.F90,
->
+        src/utils/simError.c, src/utils/simError.h, src/utils/status.F90,
->
+        src/utils/vector_class.F90, src/visitors/AtomData.hpp,
->
+        src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp,
->
+        src/visitors/BaseVisitor.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: merging new_design branch into
->
+        OOPSE-2.0
->
->
+-01-12 18:13  tim
->
->
+        * src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp,
->
+        utils/TypeContainer.hpp: forget to include <algorithm>
->
->
+-01-12 17:25  tim
->
->
+        * forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc,
->
+        newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force
->
+        fields
->
->
+-01-12 17:14  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/EAM.cpp, UseTheForce/EAM.hpp,
->
+        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
->
+        UseTheForce/ForceFieldCreator.hpp,
->
+        UseTheForce/ForceFieldFactory.cpp,
->
+        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp,
->
+        UseTheForce/doForces.F90, UseTheForce/doForces_interface.h,
->
+        UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h,
->
+        UseTheForce/notifyCutoffs.F90,
->
+        UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90,
->
+        UseTheForce/DarkSide/atype.F90,
->
+        UseTheForce/DarkSide/atype_interface.h,
->
+        UseTheForce/DarkSide/charge.F90,
->
+        UseTheForce/DarkSide/charge_interface.h,
->
+        UseTheForce/DarkSide/dipole.F90,
->
+        UseTheForce/DarkSide/dipole_interface.h,
->
+        UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h,
->
+        UseTheForce/DarkSide/force_globals.F90,
->
+        UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h,
->
+        UseTheForce/DarkSide/lj_interface.h,
->
+        UseTheForce/DarkSide/neighborLists.F90,
->
+        UseTheForce/DarkSide/reactionField.F90,
->
+        UseTheForce/DarkSide/shapes.F90,
->
+        UseTheForce/DarkSide/shapes_interface.h,
->
+        UseTheForce/DarkSide/simParallel.F90,
->
+        UseTheForce/DarkSide/simParallel_interface.h,
->
+        UseTheForce/DarkSide/simulation.F90,
->
+        UseTheForce/DarkSide/simulation_interface.h,
->
+        UseTheForce/DarkSide/sticky.F90,
->
+        UseTheForce/DarkSide/sticky_interface.h,
->
+        UseTheForce/DarkSide/switcheroo.F90,
->
+        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
->
+        applications/simpleBuilder/BaseLattice.cpp,
->
+        applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.cpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeCreator.cpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/MoLocator.cpp,
->
+        applications/simpleBuilder/MoLocator.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp,
->
+        brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp,
->
+        brains/Exclude.hpp, brains/ForceManager.cpp,
->
+        brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp,
->
+        brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
->
+        brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp,
->
+        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
->
+        brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp,
->
+        brains/Snapshot.cpp, brains/Snapshot.hpp,
->
+        brains/SnapshotManager.hpp, brains/Stats.cpp, brains/Stats.hpp,
->
+        brains/Thermo.cpp, brains/Thermo.hpp, brains/fSimulation.h,
->
+        constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp,
->
+        constraints/Rattle.cpp, constraints/Rattle.hpp,
->
+        constraints/ZconsStruct.hpp,
->
+        constraints/ZconstraintForceManager.cpp,
->
+        constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp,
->
+        integrators/DLM.hpp, integrators/Integrator.cpp,
->
+        integrators/Integrator.hpp, integrators/IntegratorCreator.hpp,
->
+        integrators/IntegratorFactory.cpp,
->
+        integrators/IntegratorFactory.hpp, integrators/NPT.cpp,
->
+        integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp,
->
+        integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp,
->
+        integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
->
+        integrators/NVT.cpp, integrators/NVT.hpp,
->
+        integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp,
->
+        integrators/Velocitizer.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp,
->
+        io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp,
->
+        io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c,
->
+        io/BASS_parse.h, io/BendTypesSectionParser.cpp,
->
+        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
->
+        io/BondTypesSectionParser.hpp,
->
+        io/DirectionalAtomTypesSectionParser.cpp,
->
+        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
->
+        io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp,
->
+        io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp,
->
+        io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp,
->
+        io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp,
->
+        io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.hpp,
->
+        io/SectionParser.cpp, io/SectionParser.hpp,
->
+        io/SectionParserManager.cpp, io/SectionParserManager.hpp,
->
+        io/StatWriter.cpp, io/StatWriter.hpp,
->
+        io/StickyAtomTypesSectionParser.cpp,
->
+        io/StickyAtomTypesSectionParser.hpp,
->
+        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
->
+        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp,
->
+        io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, 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, math/ChebyshevPolynomials.cpp,
->
+        math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h,
->
+        math/Polynomial.hpp, math/Quaternion.hpp,
->
+        math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp,
->
+        math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp,
->
+        math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp,
->
+        math/randomSPRNG.hpp, minimizers/CGFamilyMinimizer.cpp,
->
+        minimizers/CGFamilyMinimizer.hpp, minimizers/Minimizer.cpp,
->
+        minimizers/Minimizer.hpp, minimizers/MinimizerCreator.hpp,
->
+        minimizers/MinimizerFactory.cpp, minimizers/MinimizerFactory.hpp,
->
+        minimizers/MinimizerParameterSet.cpp,
->
+        minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp,
->
+        minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp,
->
+        minimizers/SDMinimizer.hpp, primitives/Atom.cpp,
->
+        primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp,
->
+        primitives/Bond.hpp, primitives/CutoffGroup.hpp,
->
+        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
->
+        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
->
+        primitives/Molecule.cpp, primitives/Molecule.hpp,
->
+        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
->
+        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp,
->
+        primitives/Torsion.cpp, primitives/Torsion.hpp,
->
+        primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp,
->
+        profiling/mdProfile.cpp, profiling/mdProfile.hpp,
->
+        restraints/Restraints.cpp, restraints/Restraints.hpp,
->
+        types/AtomStamp.cpp, types/AtomStamp.hpp, types/AtomType.cpp,
->
+        types/AtomType.hpp, types/AtomTypeProperties.h,
->
+        types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp,
->
+        types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp,
->
+        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
->
+        types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp,
->
+        types/CubicBondType.hpp, types/CubicTorsionType.hpp,
->
+        types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp,
->
+        types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp,
->
+        types/FixedBondType.hpp, types/HarmonicBendType.hpp,
->
+        types/HarmonicBondType.hpp, types/MakeStamps.cpp,
->
+        types/MakeStamps.hpp, types/MoleculeStamp.cpp,
->
+        types/MoleculeStamp.hpp, types/MorseBondType.hpp,
->
+        types/OplsTorsionType.hpp, types/PolynomialBendType.hpp,
->
+        types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp,
->
+        types/QuarticBendType.hpp, types/QuarticBondType.hpp,
->
+        types/QuarticTorsionType.hpp, types/RigidBodyStamp.cpp,
->
+        types/RigidBodyStamp.hpp, types/ShapeAtomType.cpp,
->
+        types/ShapeAtomType.hpp, types/TorsionStamp.cpp,
->
+        types/TorsionStamp.hpp, types/TorsionType.hpp,
->
+        types/UreyBradleyBendType.hpp, types/ZconStamp.cpp,
->
+        types/ZconStamp.hpp, utils/GenericData.hpp,
->
+        utils/GenericFactory.hpp, utils/LocalIndexManager.hpp,
->
+        utils/MemoryUtils.hpp, utils/NumericConstant.hpp,
->
+        utils/OOPSEConstant.hpp, utils/PropertyMap.cpp,
->
+        utils/PropertyMap.hpp, utils/StringTokenizer.cpp,
->
+        utils/StringTokenizer.hpp, utils/StringUtils.cpp,
->
+        utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp,
->
+        utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp,
->
+        utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90,
->
+        utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90,
->
+        utils/simError.c, utils/simError.h, utils/status.F90,
->
+        utils/vector_class.F90, visitors/AtomData.hpp,
->
+        visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp,
->
+        visitors/BaseVisitor.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 license
->
->
+-01-12 17:14  tim
->
->
+        * src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on
->
+        branch new_design.
->
->
+-01-11 21:03  tim
->
->
+        * src/: constraints/ZconstraintForceManager.cpp,
->
+        constraints/ZconstraintForceManager.hpp,
->
+        minimizers/MinimizerParameterSet.cpp,
->
+        minimizers/MinimizerParameterSet.hpp: change const static double
->
+        data member to const double
->
->
+-01-11 20:50  tim
->
->
+        * src/io/basic_ifstrstream.hpp: forget namespace qualifier std::
->
->
+-01-11 20:39  tim
->
->
+        * src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h:
->
+        change data type from logical to integer in AtomTypeProperties.h
->
->
+-01-11 16:36  tim
->
->
+        * forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding
->
+        new format of EAM force field
->
->
+-01-11 16:24  tim
->
->
+        * src/UseTheForce/DUFF.cpp: change default name of DUFF force field
->
+        to DUFF2.frc
->
->
+-01-11 16:23  tim
->
->
+        * forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to
->
+        DUFF2.frc
->
->
+-01-11 16:09  tim
->
->
+        * make/Makefile.in: adding constraints and minimizers into
->
+        Makefile.in
->
->
+-01-11 16:03  tim
->
->
+        * src/io/: ChargeAtomTypesSectionParser.cpp,
->
+        ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp,
->
+        DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless
->
+        files
->
->
+-01-11 15:59  tim
->
->
+        * src/io/ZConsWriter.cpp: [no log message]
->
->
+-01-11 15:53  tim
->
->
+        * src/UseTheForce/EAM.cpp: minor fix
->
->
+-01-11 15:52  tim
->
->
+        * src/constraints/Rattle.hpp: file Rattle.hpp was initially added
->
+        on branch new_design.
->
->
+-01-11 15:52  tim
->
->
+        * src/constraints/Rattle.cpp: file Rattle.cpp was initially added
->
+        on branch new_design.
->
->
+-01-11 15:52  tim
->
->
+        * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm
->
->
+-01-11 15:47  tim
->
->
+        * make/Makefile.in: forget a '$' sign
->
->
+-01-11 15:46  tim
->
->
+        * make/Makefile.in: missing tab in rules
->
->
+-01-10 22:04  tim
->
->
+        * src/: UseTheForce/ForceFieldCreator.cpp,
->
+        UseTheForce/ForceFieldCreator.hpp,
->
+        UseTheForce/ForceFieldFactory.cpp,
->
+        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile,
->
+        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile,
->
+        brains/Register.cpp, brains/Register.hpp,
->
+        integrators/IntegratorCreator.cpp,
->
+        integrators/IntegratorCreator.hpp,
->
+        integrators/IntegratorFactory.cpp,
->
+        integrators/IntegratorFactory.hpp, integrators/Makefile,
->
+        integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp,
->
+        minimizers/Makefile, minimizers/MinimizerCreator.cpp,
->
+        minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp,
->
+        minimizers/MinimizerFactory.hpp: create a register module to
->
+        register force fields, integrators and minimizers
->
->
+-01-10 22:04  tim
->
->
+        * src/brains/Register.cpp: file Register.cpp was initially added on
->
+        branch new_design.
->
->
+-01-10 22:04  tim
->
->
+        * src/brains/Register.hpp: file Register.hpp was initially added on
->
+        branch new_design.
->
->
+-01-10 20:52  tim
->
->
+        * src/: UseTheForce/ForceFieldFactory.cpp,
->
+        applications/oopse/oopse.cpp, brains/ForceManager.hpp,
->
+        constraints/ZconstraintForceManager.cpp,
->
+        constraints/ZconstraintForceManager.hpp,
->
+        integrators/IntegratorFactory.cpp,
->
+        integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp,
->
+        io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp,
->
+        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint
->
+        method is working now
->
->
+-01-10 18:05  tim
->
->
+        * src/: constraints/ConstraintElem.hpp,
->
+        constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp,
->
+        constraints/ZconstraintForceManager.cpp,
->
+        constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp,
->
+        io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp,
->
+        visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in
->
+        zconstraint
->
->
+-01-10 18:05  tim
->
->
+        * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was
->
+        initially added on branch new_design.
->
->
+-01-07 21:50  tim
->
->
+        * src/constraints/ZconstraintForceManager.cpp: file
->
+        ZconstraintForceManager.cpp was initially added on branch
->
+        new_design.
->
->
+-01-07 21:50  tim
->
->
+        * src/constraints/ZconstraintForceManager.hpp: file
->
+        ZconstraintForceManager.hpp was initially added on branch
->
+        new_design.
->
->
+-01-07 21:50  tim
->
->
+        * src/: applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp,
->
+        constraints/ConstraintElem.hpp, constraints/Makefile,
->
+        constraints/ZConstraint.cpp, constraints/ZconsData.hpp,
->
+        constraints/ZconstraintForceManager.cpp,
->
+        constraints/ZconstraintForceManager.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp,
->
+        utils/NumericConstant.hpp: ZConstraintForceManager in progress
->
->
+-01-07 21:50  tim
->
->
+        * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was
->
+        initially added on branch new_design.
->
->
+-01-06 22:31  tim
->
->
+        * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
->
+        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        constraints/ConstraintPair.hpp, integrators/Integrator.cpp,
->
+        integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp,
->
+        io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp:
->
+        constraint is almost working
->
->
+-01-06 00:36  tim
->
->
+        * src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is
->
+        working
->
->
+-01-06 00:16  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/oopse/oopse.cpp,
->
+        applications/simpleBuilder/BaseLattice.cpp,
->
+        applications/simpleBuilder/Lattice.cpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/MoLocator.cpp,
->
+        applications/simpleBuilder/MoLocator.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp,
->
+        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp,
->
+        minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder
->
+        in progress
->
->
+-01-05 17:35  tim
->
->
+        * src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp
->
+        was initially added on branch new_design.
->
->
+-01-05 17:35  tim
->
->
+        * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially
->
+        added on branch new_design.
->
->
+-01-05 17:35  tim
->
->
+        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
->
+        Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp,
->
+        MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp,
->
+        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp,
->
+        SDMinimizer.hpp: minimizer in progress
->
->
+-01-05 17:35  tim
->
->
+        * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp
->
+        was initially added on branch new_design.
->
->
+-01-05 17:35  tim
->
->
+        * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp
->
+        was initially added on branch new_design.
->
->
+-01-05 17:35  tim
->
->
+        * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp
->
+        was initially added on branch new_design.
->
->
+-01-05 17:35  tim
->
->
+        * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially
->
+        added on branch new_design.
->
->
+-01-04 22:18  tim
->
->
+        * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
->
+        brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp,
->
+        brains/Thermo.cpp, constraints/ConstraintPair.hpp,
->
+        constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp,
->
+        integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp,
->
+        primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in
->
+        progress
->
->
+-01-04 22:18  tim
->
->
+        * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was
->
+        initially added on branch new_design.
->
->
+-01-04 22:18  tim
->
->
+        * src/minimizers/MinimizerParameterSet.cpp: file
->
+        MinimizerParameterSet.cpp was initially added on branch new_design.
->
->
+-01-04 22:18  tim
->
->
+        * src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was
->
+        initially added on branch new_design.
->
->
+-01-04 22:18  tim
->
->
+        * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp
->
+        was initially added on branch new_design.
->
->
+-01-04 22:18  tim
->
->
+        * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp,
->
+        Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp,
->
+        OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp,
->
+        SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress
->
->
+-01-04 22:18  tim
->
->
+        * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on
->
+        branch new_design.
->
->
+-12-20 20:50  chuckv
->
->
+        * make/Makefile.in: Fixed Makefile test bug under OSX and possibly
->
+        other BSD's, replaced test -f *.mod with ls function since BSD test
->
+        apparently doesn't support wildcards.
->
->
+-12-20 20:36  tim
->
->
+        * make/Makefile.in: fix a test command incompatiable problem
->
->
+-12-20 19:49  tim
->
->
+        * src/integrators/NPTi.cpp: NPT is working now
->
->
+-12-16 19:20  tim
->
->
+        * src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the
->
+        invalid stamp id
->
->
+-12-16 19:00  tim
->
->
+        * forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc,
->
+        newEAM.u6.frc: adding new EAM force field files
->
->
+-12-16 18:55  tim
->
->
+        * src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays
->
+        in  EAM parameter file is incorrect
->
->
+-12-16 17:27  tim
->
->
+        * src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp,
->
+        brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp,
->
+        utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM
->
->
+-12-15 22:34  tim
->
->
+        * src/: applications/simpleBuilder/BaseLattice.cpp,
->
+        applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.cpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeCreator.cpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp,
->
+        io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream
->
->
+-12-15 21:07  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile,
->
+        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp:
->
+        add EAM Force Field
->
->
+-12-15 19:40  tim
->
->
+        * src/applications/oopse/oopse.cpp: add more force fields
->
->
+-12-15 16:44  tim
->
->
+        * src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget
->
+        to call All_reduce in MPI version)
->
->
+-12-15 16:13  tim
->
->
+        * src/: brains/SimCreator.cpp, brains/SimInfo.cpp,
->
+        io/DumpReader.cpp: MPI in NVE is working
->
->
+-12-14 21:57  tim
->
->
+        * src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader.
->
+        Master nodes does not brocast the total number of frames
->
->
+-12-14 19:08  tim
->
->
+        * src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp,
->
+        integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
->
+        minimizers/CGFamilyMinimizer.cpp,
->
+        minimizers/MinimizerParameterSet.hpp,
->
+        minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp,
->
+        minimizers/SDMinimizer.cpp: more fix in MPI version
->
->
+-12-13 22:30  tim
->
->
+        * src/: UseTheForce/DarkSide/simParallel.F90,
->
+        applications/oopse/oopse.cpp, brains/SimCreator.cpp,
->
+        brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp,
->
+        integrators/DLM.cpp, integrators/Integrator.cpp,
->
+        integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp,
->
+        integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp,
->
+        io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp,
->
+        io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp,
->
+        math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp,
->
+        primitives/RigidBody.cpp, primitives/StuntDouble.cpp,
->
+        primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp,
->
+        utils/LocalIndexManager.hpp, utils/PropertyMap.cpp,
->
+        utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version
->
+        is built
->
->
+-12-10 18:41  tim
->
->
+        * src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp
->
->
+-12-10 16:14  tim
->
->
+        * src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp,
->
+        primitives/StuntDouble.hpp: forget to zero out the torque. Sticky
->
+        and Dipole is working now
->
->
+-12-09 23:15  tim
->
->
+        * src/: UseTheForce/DarkSide/dipole.F90,
->
+        UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp:
->
+        fix an index problem in eFrame matrix
->
->
+-12-09 23:09  tim
->
->
+        * src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when
->
+        initializing the new Charge AtomType
->
->
+-12-09 21:15  tim
->
->
+        * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90,
->
+        types/DirectionalAtomType.cpp: sticky module get compiled
->
->
+-12-09 20:43  gezelter
->
->
+        * src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90,
->
+        reactionField.F90: u_l -> eFrame  for electrostatics u_l -> A for
->
+        GB
->
->
+-12-09 20:42  gezelter
->
->
+        * src/UseTheForce/doForces.F90: u_l -> eFrame
->
->
+-12-09 20:27  gezelter
->
->
+        * src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky
->
+        module now has the option for multiple sticky types
->
->
+-12-09 20:27  gezelter
->
->
+        * src/UseTheForce/doForces.F90: sticky
->
->
+-12-09 16:22  tim
->
->
+        * src/integrators/: NPT.cpp, NVT.cpp: fix an interface
->
+        inconsistency in lab2Bidy
->
->
+-12-09 15:45  tim
->
->
+        * src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug
->
+        in calculating torque in rigid body
->
->
+-12-08 20:37  tim
->
->
+        * src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h,
->
+        brains/SnapShot.cpp, brains/Snapshot.hpp,
->
+        integrators/Integrator.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp:
->
+        fix a parsing bug in ElectroStaticAtomTypesSectionParser
->
->
+-12-08 17:03  tim
->
->
+        * src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane
->
+        in  NVT is working
->
->
+-12-07 23:08  tim
->
->
+        * src/: UseTheForce/Makefile, brains/SimInfo.hpp,
->
+        integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp,
->
+        integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp,
->
+        io/DumpWriter.cpp: NPT in progress
->
->
+-12-07 14:43  tim
->
->
+        * test/utils/: Makefile, NextCombinationTestCase.hpp: [no log
->
+        message]
->
->
+-12-07 05:12  tim
->
->
+        * src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in
->
+        UseInitXSstate
->
->
+-12-07 05:00  tim
->
->
+        * src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message
->
->
+-12-07 04:47  tim
->
->
+        * src/types/DirectionalAtomType.cpp: [no log message]
->
->
+-12-07 02:18  tim
->
->
+        * forceFields/newDUFF.frc: merge WATER force field into DUFF
->
->
+-12-07 01:33  tim
->
->
+        * forceFields/newDUFF.frc: change the force constant of bonds
->
->
+-12-06 23:29  tim
->
->
+        * src/: UseTheForce/DarkSide/charge.F90,
->
+        UseTheForce/DarkSide/charge_interface.h,
->
+        UseTheForce/DarkSide/dipole.F90,
->
+        UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp:
->
+        fix atom type ident in Charge and Dipole Module
->
->
+-12-06 22:56  tim
->
->
+        * src/primitives/Torsion.cpp: butane is working now
->
->
+-12-06 20:15  tim
->
->
+        * src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp,
->
+        primitives/Bond.hpp, primitives/Torsion.cpp: short range
->
+        interaction for butane is correct.Still something wrong with long
->
+        range one
->
->
+-12-06 04:49  tim
->
->
+        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
->
+        brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        io/BendTypesSectionParser.cpp, math/Polynomial.hpp,
->
+        primitives/Atom.hpp, utils/NumericConstant.hpp,
->
+        utils/TypeContainer.hpp: fix a bug in Exclude List
->
->
+-12-05 22:21  tim
->
->
+        * forceFields/newDUFF.frc: minor fix in DUFF
->
->
+-12-05 22:02  tim
->
->
+        * src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp,
->
+        utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp:
->
+        fix a bug in filling MolMembership
->
->
+-12-05 17:12  tim
->
->
+        * forceFields/newDUFF.frc: minor fix in force field file
->
->
+-12-05 17:09  tim
->
->
+        * src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp,
->
+        integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp
->
->
+-12-04 20:09  tim
->
->
+        * src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp,
->
+        math/Vector3.hpp: NVE is working now, get the same result as
->
+        OOPSE-1.0
->
->
+-12-04 19:29  tim
->
->
+        * src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy
->
->
+-12-04 19:24  gezelter
->
->
+        * src/primitives/: Bend.cpp, Torsion.cpp: What?
->
->
+-12-04 19:24  gezelter
->
->
+        * src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion
->
->
+-12-04 05:24  tim
->
->
+        * src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp,
->
+        integrators/Integrator.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp,
->
+        utils/TypeContainer.hpp: NVE conserved energy, however, potential
->
+        is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf
->
+        and NPTxyz to test integrator Step 2 SSD in NVE to test DLM,
->
+        dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step
->
+EAM Step 5 Shape Step 6 Constraint & Restraint
->
->
+-12-04 00:01  tim
->
->
+        * src/: UseTheForce/DarkSide/LJ.F90,
->
+        applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
->
+        io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working,
->
+        energy of NVE is not conserved
->
->
+-12-03 22:36  tim
->
->
+        * src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
->
+        primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running
->
->
+-12-03 21:30  tim
->
->
+        * src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp,
->
+        brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile,
->
+        integrators/NVE.cpp, primitives/Molecule.cpp,
->
+        primitives/Molecule.hpp, primitives/StuntDouble.hpp,
->
+        primitives/Torsion.hpp: more missing function get implemented
->
->
+-12-03 20:30  tim
->
->
+        * src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp,
->
+        SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo
->
->
+-12-03 17:59  tim
->
->
+        * src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp,
->
+        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp,
->
+        io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp,
->
+        io/SectionParserManager.cpp, utils/LocalIndexManager.hpp,
->
+        utils/TypeContainer.hpp: begin to fix bugs
->
->
+-12-03 00:26  tim
->
->
+        * src/utils/Trim.cpp: file Trim.cpp was initially added on branch
->
+        new_design.
->
->
+-12-03 00:26  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/ForceFieldCreator.cpp,
->
+        UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp,
->
+        integrators/IntegratorCreator.cpp,
->
+        integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp,
->
+        io/SectionParserManager.hpp, utils/Makefile,
->
+        utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a
->
+        bug in countTokens in StringTokenizer
->
->
+-12-03 00:06  tim
->
->
+        * forceFields/newDUFF.frc: minor fix
->
->
+-12-02 23:15  tim
->
->
+        * forceFields/newDUFF.frc: new ForceField format
->
->
+-12-02 22:15  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/ForceFieldCreator.cpp,
->
+        UseTheForce/ForceFieldCreator.hpp,
->
+        UseTheForce/ForceFieldFactory.cpp,
->
+        UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile,
->
+        applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp,
->
+        integrators/IntegratorCreator.hpp,
->
+        integrators/IntegratorFactory.cpp,
->
+        integrators/IntegratorFactory.hpp, integrators/Makefile,
->
+        integrators/NPTf.cpp, integrators/NPTf.hpp, integrators/NPTi.cpp,
->
+        integrators/NPTi.hpp, integrators/NPTxyz.cpp,
->
+        integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp,
->
+        integrators/NVT.cpp, integrators/NVT.hpp,
->
+        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
->
+        types/Makefile: refine factory pattern to make it initialized
->
+        correctly
->
->
+-12-02 22:15  tim
->
->
+        * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp
->
+        was initially added on branch new_design.
->
->
+-12-02 22:15  tim
->
->
+        * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp
->
+        was initially added on branch new_design.
->
->
+-12-02 22:15  tim
->
->
+        * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp
->
+        was initially added on branch new_design.
->
->
+-12-02 22:15  tim
->
->
+        * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp
->
+        was initially added on branch new_design.
->
->
+-12-02 16:53  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp,
->
+        types/DirectionalAtomType.cpp, types/Makefile: oopse get built
->
->
+-12-02 16:04  tim
->
->
+        * src/: applications/simpleBuilder/LatticeCreator.cpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp,
->
+        brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
->
+        brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
->
+        brains/SnapshotManager.hpp, brains/Stats.cpp,
->
+        constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp,
->
+        io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp,
->
+        io/basic_ifstrstream.hpp, primitives/Bend.hpp,
->
+        primitives/GhostBend.cpp, primitives/GhostBend.hpp,
->
+        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
->
+        types/OplsTorsionType.hpp, types/ShapeAtomType.hpp,
->
+        utils/PropertyMap.hpp, utils/TypeContainer.hpp,
->
+        visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp,
->
+        visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp,
->
+        visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still
->
+        have two linking problem
->
->
+-12-02 05:17  tim
->
->
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/simpleBuilder/Lattice.cpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp,
->
+        constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp,
->
+        io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp,
->
+        minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp,
->
+        restraints/Restraints.cpp, visitors/AtomVisitor.cpp,
->
+        visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/ZconsVisitor.cpp: change endl to std::endl
->
->
+-12-02 05:14  tim
->
->
+        * src/: UseTheForce/Shapes_FF.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp,
->
+        io/LinkedAssign.hpp, io/basic_ifstrstream.hpp,
->
+        minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp,
->
+        utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp,
->
+        visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/RigidBodyVisitor.hpp: minor fix
->
->
+-12-02 05:09  tim
->
->
+        * src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp:
->
+        remove StreamTokenizer
->
->
+-12-02 05:06  tim
->
->
+        * src/: UseTheForce/Shapes_FF.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp,
->
+        io/ZConsWriter.cpp, math/randomSPRNG.cpp,
->
+        restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using
->
+        namespace std in .cpp file
->
->
+-12-02 05:04  tim
->
->
+        * src/: UseTheForce/Shapes_FF.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.cpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/MoLocator.cpp,
->
+        applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp,
->
+        brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp,
->
+        io/ZConsWriter.cpp, io/ZConsWriter.hpp,
->
+        minimizers/MinimizerParameterSet.hpp,
->
+        minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp,
->
+        minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp,
->
+        restraints/Restraints.cpp, restraints/Restraints.hpp,
->
+        types/MoleculeStamp.cpp, types/MoleculeStamp.hpp,
->
+        types/ShapeAtomType.cpp, types/ShapeAtomType.hpp,
->
+        utils/GenericData.hpp, visitors/CompositeVisitor.cpp,
->
+        visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding
->
+        qulified name prefix std
->
->
+-12-02 04:55  tim
->
->
+        * src/: UseTheForce/Shapes_FF.cpp,
->
+        applications/dump2Xyz/Dump2XYZ.cpp,
->
+        applications/simpleBuilder/BaseLattice.hpp,
->
+        applications/simpleBuilder/Lattice.hpp,
->
+        applications/simpleBuilder/LatticeCreator.hpp,
->
+        applications/simpleBuilder/LatticeFactory.cpp,
->
+        applications/simpleBuilder/LatticeFactory.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp,
->
+        io/LinkedAssign.hpp, io/basic_ifstrstream.hpp,
->
+        minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp,
->
+        utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp,
->
+        visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp,
->
+        visitors/RigidBodyVisitor.hpp: replace string by std::string
->
->
+-12-02 03:12  tim
->
->
+        * make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp,
->
+        src/applications/simpleBuilder/BaseLattice.hpp,
->
+        src/applications/simpleBuilder/Lattice.hpp,
->
+        src/applications/simpleBuilder/LatticeCreator.hpp,
->
+        src/applications/simpleBuilder/LatticeFactory.hpp,
->
+        src/applications/simpleBuilder/MoLocator.hpp,
->
+        src/brains/SimInfo.cpp, src/brains/SkipList.hpp,
->
+        src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp,
->
+        src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp,
->
+        src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp,
->
+        src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp,
->
+        src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp,
->
+        src/utils/Makefile, src/utils/StringUtils.cpp,
->
+        src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp,
->
+        src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp,
->
+        src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp,
->
+        test/brains/RigidBody.cpp: replace misuse of using namespace std in
->
+        header files
->
->
+-12-02 02:23  tim
->
->
+        * src/: primitives/Atom.hpp, primitives/RigidBody.hpp,
->
+        primitives/StuntDouble.hpp, utils/TypeContainer.hpp,
->
+        utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp:
->
+        begin to fix linking problem
->
->
+-12-02 02:08  tim
->
->
+        * src/: applications/oopse/oopse.cpp, brains/Stats.cpp,
->
+        brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile,
->
+        integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp,
->
+        integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp,
->
+        integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp,
->
+        math/SquareMatrix3.hpp, primitives/Atom.hpp,
->
+        primitives/RigidBody.hpp, primitives/StuntDouble.hpp,
->
+        utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled,
->
+        still has some linking problem
->
->
+-12-02 00:26  tim
->
->
+        * src/: integrators/NVT.cpp, integrators/NVT.hpp,
->
+        utils/OOPSEConstant.hpp: NVT get built
->
->
+-12-02 00:09  tim
->
->
+        * src/integrators/DLM.cpp: file DLM.cpp was initially added on
->
+        branch new_design.
->
->
+-12-02 00:09  tim
->
->
+        * src/integrators/DLM.hpp: file DLM.hpp was initially added on
->
+        branch new_design.
->
->
+-12-02 00:09  tim
->
->
+        * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp,
->
+        brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
->
+        brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp,
->
+        integrators/Integrator.hpp, integrators/Makefile,
->
+        integrators/NVE.cpp, integrators/NVE.hpp,
->
+        integrators/RotationAlgorithm.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE
->
+        get built
->
->
+-12-02 00:09  tim
->
->
+        * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp
->
+        was initially added on branch new_design.
->
->
+-12-01 22:45  tim
->
->
+        * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp,
->
+        integrators/IntegratorFactory.cpp,
->
+        integrators/IntegratorFactory.hpp, integrators/Makefile,
->
+        integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp,
->
+        io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp,
->
+        io/StatWriter.hpp: rename DumpWrite to DumpWriter
->
->
+-12-01 22:45  tim
->
->
+        * src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on
->
+        branch new_design.
->
->
+-12-01 20:05  tim
->
->
+        * src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp,
->
+        io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile,
->
+        utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp,
->
+        visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp,
->
+        visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp,
->
+        visitors/ZconsVisitor.hpp: visitors get built
->
->
+-12-01 19:32  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md: fixed a sample
->
->
+-12-01 19:10  tim
->
->
+        * src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp,
->
+        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
->
+        src/types/AtomType.hpp, src/utils/Utility.hpp,
->
+        src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp,
->
+        src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp:
->
+        spell check
->
->
+-12-01 18:42  tim
->
->
+        * src/: UseTheForce/DarkSide/atype.F90,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp,
->
+        primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp,
->
+        primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator
->
+        and constraint, other directories get built
->
->
+-12-01 17:38  tim
->
->
+        * src/: brains/DataStorage.cpp, brains/DataStorage.hpp,
->
+        brains/ForceManager.cpp, brains/MoleculeCreator.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp,
->
+        primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp,
->
+        primitives/GhostBend.cpp, primitives/RigidBody.cpp,
->
+        primitives/RigidBody.hpp, primitives/StuntDouble.hpp,
->
+        types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h,
->
+        types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp:
->
+        refactory AtomType
->
->
+-12-01 03:11  tim
->
->
+        * src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change
->
->
+-12-01 02:30  tim
->
->
+        * src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change
->
+        NumericConstant
->
->
+-12-01 02:24  tim
->
->
+        * src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp,
->
+        primitives/RigidBody.cpp: minor fix
->
->
+-11-30 23:14  tim
->
->
+        * src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp,
->
+        io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile,
->
+        io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io
->
+        get built, next is integrator
->
->
+-11-30 22:43  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/ForceField.hpp, brains/SimCreator.cpp,
->
+        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        io/BASS_interface.cpp, primitives/StuntDouble.hpp,
->
+        utils/StringUtils.hpp: brains get built
->
->
+-11-30 20:50  tim
->
->
+        * src/: brains/ForceManager.cpp, brains/Makefile,
->
+        brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
->
+        primitives/RigidBody.cpp, primitives/RigidBody.hpp,
->
+        utils/StringUtils.hpp: brains get built, io is next
->
->
+-11-30 19:58  tim
->
->
+        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
->
+        brains/ForceManager.cpp, brains/ForceManager.hpp,
->
+        brains/MoleculeCreator.cpp, brains/SimCreator.hpp,
->
+        brains/SimInfo.cpp, brains/SimInfo.hpp,
->
+        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
->
+        brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp,
->
+        brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile,
->
+        math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo
->
->
+-11-30 19:58  tim
->
->
+        * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially
->
+        added on branch new_design.
->
->
+-11-30 17:54  tim
->
->
+        * src/: primitives/Bend.hpp, primitives/Bond.hpp,
->
+        primitives/StuntDouble.hpp, primitives/Torsion.hpp,
->
+        utils/LocalIndexManager.hpp: more get fixed
->
->
+-11-30 05:03  tim
->
->
+        * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was
->
+        initially added on branch new_design.
->
->
+-11-30 05:03  tim
->
->
+        * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename
->
+        LocalndexManager.hpp to LocalIndexManager.hpp
->
->
+-11-30 04:43  tim
->
->
+        * src/: io/BendTypesSectionParser.cpp,
->
+        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
->
+        io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp,
->
+        io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp,
->
+        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
->
+        types/PolynomialTorsionType.hpp: Section Parsers get compiled
->
->
+-11-30 04:14  tim
->
->
+        * src/: io/BendTypesSectionParser.cpp,
->
+        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
->
+        io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp,
->
+        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor
->
+        fixed
->
->
+-11-30 03:49  tim
->
->
+        * src/: io/TorsionTypesSectionParser.cpp,
->
+        io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp,
->
+        types/CubicTorsionType.hpp, types/PolynomialBendType.hpp,
->
+        types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp,
->
+        types/QuarticTorsionType.hpp: minor fixed
->
->
+-11-30 03:32  tim
->
->
+        * src/: io/TorsionTypesSectionParser.cpp,
->
+        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
->
+        types/PolynomialTorsionType.hpp: #inlcude statement can not be
->
+        embedded
->
->
+-11-29 21:42  tim
->
->
+        * test/math/: Makefile, PolynomialTestCase.cpp,
->
+        PolynomialTestCase.hpp: add PolynomialTestCase
->
->
+-11-29 21:42  tim
->
->
+        * src/math/Polynomial.hpp: Polynomial passes unit test
->
->
+-11-29 20:03  tim
->
->
+        * src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename
->
+        QuarticTorsion.hpp to QuarticTorsionType.hpp
->
->
+-11-29 20:03  tim
->
->
+        * src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was
->
+        initially added on branch new_design.
->
->
+-11-29 19:56  tim
->
->
+        * src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was
->
+        initially added on branch new_design.
->
->
+-11-29 19:56  tim
->
->
+        * src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add
->
+        CubicTorsionType and QuarticTorsionType
->
->
+-11-29 19:56  tim
->
->
+        * src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was
->
+        initially added on branch new_design.
->
->
+-11-29 18:00  tim
->
->
+        * src/: brains/DataStorage.hpp, brains/Snapshot.hpp,
->
+        types/CubicBendType.hpp, types/CubicBondType.hpp,
->
+        types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get
->
+        fixed
->
->
+-11-29 17:59  tim
->
->
+        * src/utils/Trim.hpp: file Trim.hpp was initially added on branch
->
+        new_design.
->
->
+-11-29 17:59  tim
->
->
+        * src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim
->
+        Algorithm for std::string
->
->
+-11-29 15:52  tim
->
->
+        * src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove
->
+        some useless files
->
->
+-11-29 15:50  tim
->
->
+        * src/io/: BondTypesSectionParser.cpp,
->
+        ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp,
->
+        ElectrostaticAtomTypesSectionParser.cpp,
->
+        HarmonicBondTypesSectionParser.cpp,
->
+        HarmonicBondTypesSectionParser.hpp,
->
+        LennardJonesAtomTypesSectionParser.cpp, Makefile,
->
+        SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp,
->
+        StickyAtomTypesSectionParser.hpp: more files get fixed
->
->
+-11-29 15:27  tim
->
->
+        * src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp,
->
+        DirectionalAtomTypesSectionParser.cpp,
->
+        EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp,
->
+        Makefile, SectionParser.cpp, SectionParser.hpp,
->
+        SectionParserManager.cpp, SectionParserManager.hpp: part of io get
->
+        built
->
->
+-11-29 14:49  tim
->
->
+        * src/types/UreyBradleyBendType.hpp: types get built
->
->
+-11-29 14:40  tim
->
->
+        * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp:
->
+        types  get built
->
->
+-11-26 02:13  tim
->
->
+        * src/: UseTheForce/ForceField.hpp,
->
+        io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp,
->
+        types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some
->
+        files
->
->
+-11-25 20:18  tim
->
->
+        * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was
->
+        initially added on branch new_design.
->
->
+-11-25 20:18  tim
->
->
+        * src/: io/AtomTypesSectionParser.cpp,
->
+        io/BondTypesSectionParser.cpp,
->
+        io/DirectionalAtomTypesSectionParser.cpp,
->
+        types/QuadraticBendType.hpp, types/QuadraticBondType.hpp,
->
+        types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some
->
+        files
->
->
+-11-25 20:18  tim
->
->
+        * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was
->
+        initially added on branch new_design.
->
->
+-11-24 22:12  tim
->
->
+        * src/: io/AtomTypesSectionParser.cpp,
->
+        io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp,
->
+        io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp,
->
+        io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
->
+        io/ChargeAtomTypesSectionParser.hpp,
->
+        io/DipoleAtomTypesSectionParser.cpp,
->
+        io/DipoleAtomTypesSectionParser.hpp,
->
+        io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp,
->
+        io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp,
->
+        io/EAMAtomTypesSectionParser.hpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp,
->
+        io/HarmonicBondTypesSectionParser.hpp,
->
+        io/LennardJonesAtomTypesSectionParser.cpp,
->
+        io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile,
->
+        io/SectionParser.hpp, io/SectionParserManager.hpp,
->
+        io/StickyAtomTypesSectionParser.cpp,
->
+        io/StickyAtomTypesSectionParser.hpp,
->
+        io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp,
->
+        utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built
->
->
+-11-24 21:33  tim
->
->
+        * src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp,
->
+        ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp,
->
+        LJFF.cpp, Makefile: UseTheForce get built
->
->
+-11-24 20:55  tim
->
->
+        * src/: math/RectMatrix.hpp, primitives/Bend.cpp,
->
+        primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp,
->
+        primitives/Makefile, primitives/Molecule.cpp,
->
+        primitives/Molecule.hpp, primitives/RigidBody.cpp,
->
+        primitives/StuntDouble.hpp, primitives/Torsion.cpp,
->
+        primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp,
->
+        primitives/UreyBradleyBend.hpp: types and primitives get built
->
->
+-11-24 19:49  tim
->
->
+        * test/utils/: Makefile, NextCombinationTestCase.cpp,
->
+        StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint
->
+        StringTokenizerTestCase
->
->
+-11-24 19:49  tim
->
->
+        * src/utils/: GenericData.hpp, StringTokenizer.cpp,
->
+        StringTokenizer.hpp: StringTokenizer passes unit test
->
->
+-11-24 18:20  tim
->
->
+        * ChangeLog, make/Makefile.in, src/UseTheForce/Makefile,
->
+        src/io/Makefile, src/primitives/Makefile, src/utils/Makefile:
->
+        change Makefile
->
->
+-11-24 18:06  chrisfen
->
->
+        * src/io/RestraintReader.cpp: improved restraints - mpi should work
->
+        fine
->
->
+-11-24 18:06  chrisfen
->
->
+        * src/integrators/Integrator.cpp: improved restraints
->
->
+-11-24 18:05  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md: oops...
->
->
+-11-24 17:42  tim
->
->
+        * src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp,
->
+        brains/DataStorage.hpp, brains/SimCreator.cpp,
->
+        brains/SimCreator.hpp, integrators/Integrator.hpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        primitives/DirectionalAtom.cpp: add SetForceManager method to
->
+        integrator
->
->
+-11-23 23:12  tim
->
->
+        * src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp,
->
+        integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp,
->
+        integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp,
->
+        integrators/NPTxyz.cpp, integrators/NPTxyz.hpp,
->
+        integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp,
->
+        integrators/NVT.hpp, integrators/Velocitizer.cpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp,
->
+        types/UreyBradleyBendType.hpp: refactory NPT integrator
->
->
+-11-23 22:50  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md: Back to normal... Oh...
->
+        Restraints should work in parallel now
->
->
+-11-23 22:48  chrisfen
->
->
+        * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
->
+        brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
->
+        integrators/Integrator.cpp, integrators/Integrator.hpp,
->
+        io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp,
->
+        io/RestraintReader.cpp, io/RestraintWriter.cpp,
->
+        restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements
->
+        to restraints
->
->
+-11-23 22:47  chrisfen
->
->
+        * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll
->
+        return to the original on next commit
->
->
+-11-23 17:53  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
->
+        applications/simpleBuilder/simpleBuilder.cpp,
->
+        io/ChargeAtomTypesSectionParser.cpp,
->
+        io/DirectionalAtomTypesSectionParser.hpp,
->
+        io/EAMAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.cpp,
->
+        io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp,
->
+        io/SectionParser.hpp, types/DirectionalAtomType.cpp,
->
+        utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser
->
->
+-11-23 17:53  tim
->
->
+        * src/io/ElectrostaticAtomTypesSectionParser.hpp: file
->
+        ElectrostaticAtomTypesSectionParser.hpp was initially added on
->
+        branch new_design.
->
->
+-11-23 17:53  tim
->
->
+        * src/io/ElectrostaticAtomTypesSectionParser.cpp: file
->
+        ElectrostaticAtomTypesSectionParser.cpp was initially added on
->
+        branch new_design.
->
->
+-11-23 06:03  tim
->
->
+        * src/: io/EAMAtomTypesSectionParser.cpp,
->
+        io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp,
->
+        types/AtomType.hpp, types/DirectionalAtomType.cpp,
->
+        types/DirectionalAtomType.hpp: add EAM AtomType Section Parser
->
->
+-11-23 06:03  tim
->
->
+        * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp
->
+        was initially added on branch new_design.
->
->
+-11-23 06:03  tim
->
->
+        * src/io/EAMAtomTypesSectionParser.hpp: file
->
+        EAMAtomTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-23 06:03  tim
->
->
+        * src/io/EAMAtomTypesSectionParser.cpp: file
->
+        EAMAtomTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-23 04:35  tim
->
->
+        * src/io/TorsionTypesSectionParser.hpp: file
->
+        TorsionTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-23 04:35  tim
->
->
+        * src/io/BendTypesSectionParser.hpp: file
->
+        BendTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-23 04:35  tim
->
->
+        * src/io/BondTypesSectionParser.hpp: file
->
+        BondTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-23 04:35  tim
->
->
+        * src/io/BondTypesSectionParser.cpp: file
->
+        BondTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-23 04:35  tim
->
->
+        * src/io/TorsionTypesSectionParser.cpp: file
->
+        TorsionTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-23 04:35  tim
->
->
+        * src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp,
->
+        BondTypesSectionParser.cpp, BondTypesSectionParser.hpp,
->
+        TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add
->
+        BondTypesSectionParser, BendTypesSectionParser and
->
+        TorsionTypeSectionParser
->
->
+-11-23 04:35  tim
->
->
+        * src/io/BendTypesSectionParser.cpp: file
->
+        BendTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 23:04  tim
->
->
+        * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in
->
+        DUFF and EAM
->
->
+-11-22 23:02  tim
->
->
+        * src/io/: DirectionalAtomTypesParser.hpp,
->
+        DirectionalAtomTypesSectionParser.hpp: adding section parsers
->
->
+-11-22 23:02  tim
->
->
+        * src/io/DirectionalAtomTypesSectionParser.hpp: file
->
+        DirectionalAtomTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/DipoleAtomTypesSectionParser.hpp: file
->
+        DipoleAtomTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/AtomTypesSectionParser.hpp: file
->
+        AtomTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/HarmonicBondTypesSectionParser.hpp: file
->
+        HarmonicBondTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/StickyAtomTypesSectionParser.cpp: file
->
+        StickyAtomTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/LennardJonesAtomTypesSectionParser.hpp: file
->
+        LennardJonesAtomTypesSectionParser.hpp was initially added on
->
+        branch new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/HarmonicBondTypesSectionParser.cpp: file
->
+        HarmonicBondTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/DirectionalAtomTypesSectionParser.cpp: file
->
+        DirectionalAtomTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/SectionParserManager.cpp: file SectionParserManager.cpp
->
+        was initially added on branch new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/AtomTypesSectionParser.cpp: file
->
+        AtomTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/ChargeAtomTypesSectionParser.cpp: file
->
+        ChargeAtomTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/DipoleAtomTypesSectionParser.cpp: file
->
+        DipoleAtomTypesSectionParser.cpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/LennardJonesAtomTypesSectionParser.cpp: file
->
+        LennardJonesAtomTypesSectionParser.cpp was initially added on
->
+        branch new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/ChargeAtomTypesSectionParser.hpp: file
->
+        ChargeAtomTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/StickyAtomTypesSectionParser.hpp: file
->
+        StickyAtomTypesSectionParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/SectionParser.hpp: file SectionParser.hpp was initially
->
+        added on branch new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp,
->
+        brains/SimSnapshotManager.cpp, brains/SnapShot.cpp,
->
+        brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp,
->
+        integrators/NVT.hpp, io/AtomTypesSectionParser.cpp,
->
+        io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp,
->
+        io/ChargeAtomTypesSectionParser.hpp,
->
+        io/DipoleAtomTypesSectionParser.cpp,
->
+        io/DipoleAtomTypesSectionParser.hpp,
->
+        io/DirectionalAtomTypesParser.hpp,
->
+        io/DirectionalAtomTypesSectionParser.cpp,
->
+        io/HarmonicBondTypesSectionParser.cpp,
->
+        io/HarmonicBondTypesSectionParser.hpp,
->
+        io/LennardJonesAtomTypesSectionParser.cpp,
->
+        io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp,
->
+        io/SectionParser.hpp, io/SectionParserManager.cpp,
->
+        io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp,
->
+        io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp,
->
+        types/AtomType.hpp, types/DirectionalAtomType.hpp,
->
+        utils/GenericData.hpp: adding section parsers
->
->
+-11-22 20:55  tim
->
->
+        * src/io/DirectionalAtomTypesParser.hpp: file
->
+        DirectionalAtomTypesParser.hpp was initially added on branch
->
+        new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/SectionParserManager.hpp: file SectionParserManager.hpp
->
+        was initially added on branch new_design.
->
->
+-11-22 20:55  tim
->
->
+        * src/io/SectionParser.cpp: file SectionParser.cpp was initially
->
+        added on branch new_design.
->
->
+-11-19 22:12  tim
->
->
+        * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially
->
+        added on branch new_design.
->
->
+-11-19 22:12  tim
->
->
+        * src/: brains/SimState.cpp, brains/SimState.hpp,
->
+        io/InitializeFromFile.cpp, types/FixBondType.hpp,
->
+        types/FixedBondType.hpp: remove more useless files
->
->
+-11-19 21:47  tim
->
->
+        * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp,
->
+        integrators/Integrator.cpp, applications/Makedepend: remove more
->
+        useless files
->
->
+-11-19 21:38  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
->
+        UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp,
->
+        integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp,
->
+        integrators/NVT.hpp: refactory integrator
->
->
+-11-19 21:38  tim
->
->
+        * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on
->
+        branch new_design.
->
->
+-11-19 21:38  tim
->
->
+        * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on
->
+        branch new_design.
->
->
+-11-19 21:38  tim
->
->
+        * src/integrators/NPT.hpp: file NPT.hpp was initially added on
->
+        branch new_design.
->
->
+-11-19 21:38  tim
->
->
+        * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added
->
+        on branch new_design.
->
->
+-11-19 21:38  tim
->
->
+        * src/integrators/NVT.hpp: file NVT.hpp was initially added on
->
+        branch new_design.
->
->
+-11-19 20:37  tim
->
->
+        * forceFields/newDUFF.frc: new DUFF forcefield
->
->
+-11-19 20:23  tim
->
->
+        * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on
->
+        branch new_design.
->
->
+-11-19 20:23  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp,
->
+        UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp,
->
+        utils/TypeContainer.hpp: add EAM
->
->
+-11-19 20:23  tim
->
->
+        * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on
->
+        branch new_design.
->
->
+-11-19 18:02  tim
->
->
+        * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except
->
+        error checking
->
->
+-11-19 17:56  tim
->
->
+        * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp
->
+        was initially added on branch new_design.
->
->
+-11-19 17:56  tim
->
->
+        * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp
->
+        was initially added on branch new_design.
->
->
+-11-19 17:56  tim
->
->
+        * src/types/FixBondType.hpp: file FixBondType.hpp was initially
->
+        added on branch new_design.
->
->
+-11-19 17:56  tim
->
->
+        * src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp,
->
+        UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp,
->
+        UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp,
->
+        integrators/IntegratorFactory.cpp,
->
+        integrators/IntegratorFactory.hpp, integrators/NVE.hpp,
->
+        integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp,
->
+        utils/StringTokenizer.cpp: DUFF is almost done except error
->
+        checking
->
->
+-11-19 00:11  tim
->
->
+        * src/UseTheForce/DUFF.cpp: adding DUFF parser
->
->
+-11-18 23:26  tim
->
->
+        * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was
->
+        initially added on branch new_design.
->
->
+-11-18 23:26  tim
->
->
+        * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp,
->
+        integrators/Velocitizer.cpp, integrators/Velocitizer.hpp,
->
+        integrators/VelocityVerletIntegrator.cpp,
->
+        integrators/VelocityVerletIntegrator.hpp,
->
+        types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp,
->
+        types/CubicBendType.hpp, types/CubicBondType.hpp,
->
+        types/HarmonicBondType.hpp, types/QuadraticBendType.hpp,
->
+        types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding
->
+        DUFF parser
->
->
+-11-18 21:42  tim
->
->
+        * forceFields/newDUFF.frc: adding new format DUFF force field
->
->
+-11-18 15:57  chrisfen
->
->
+        * src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that
->
+        slowed down the force loop
->
->
+-11-18 05:42  tim
->
->
+        * src/utils/NumericConstant.cpp: file NumericConstant.cpp was
->
+        initially added on branch new_design.
->
->
+-11-18 05:42  tim
->
->
+        * src/utils/NumericConstant.hpp: file NumericConstant.hpp was
->
+        initially added on branch new_design.
->
->
+-11-18 05:42  tim
->
->
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp,
->
+        primitives/Bend.cpp, utils/NumericConstant.cpp,
->
+        utils/NumericConstant.hpp: Adding NumericConstant class
-<
+        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
-<
+        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
-<
+        class
->
+-11-18 04:16  tim
-<
+-11-04 14:48  tim
->
+        * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp,
->
+        UseTheForce/ForceFields.hpp: remove more junk files
-+
+-11-18 04:12  tim
-+
-+
+        * src/: brains/ForceFields.cpp, brains/SimSetup.cpp,
-+
+        brains/SimSetup.hpp, constraints/AbstractClasses.hpp,
-+
+        integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp,
-+
+        primitives/AbstractClasses.hpp, primitives/Bond.cpp,
-+
+        primitives/BondExtensions.cpp, primitives/SRI.hpp,
-+
+        primitives/TorsionExtensions.cpp: remove some junk files
-+
-+
+-11-18 04:07  tim
-+
-+
+        * src/primitives/BendExtensions.cpp: remove some junk files
-+
-+
+-11-18 04:04  tim
-+
-+
+        * src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp,
-+
+        QuadraticBondType.hpp: refine QudraticBond
-+
-+
+-11-18 03:57  tim
-+
-+
+        * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp
-+
-+
+-11-18 03:57  tim
-+
-+
+        * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 21:47  tim
-+
-+
+        * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-17 21:47  tim
-+
-+
+        * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-17 21:47  tim
-+
-+
+        * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-17 21:47  tim
-+
-+
+        * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 21:47  tim
-+
-+
+        * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 21:47  tim
-+
-+
+        * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 21:47  tim
-+
-+
+        * src/types/CubicBondType.hpp: file CubicBondType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-17 21:47  tim
-+
-+
+        * src/: math/ChebyshevPolynomials.cpp,
-+
+        math/ChebyshevPolynomials.hpp, primitives/Bend.cpp,
-+
+        primitives/Bend.hpp, primitives/GhostBend.cpp,
-+
+        primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp,
-+
+        primitives/UreyBradleyBend.hpp, types/BondType.hpp,
-+
+        types/CubicBendType.hpp, types/CubicBondType.hpp,
-+
+        types/HarmonicBondType.hpp, types/MorseBondType.hpp,
-+
+        types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp:
-+
+        UreyBradleyBend and GhostBend
-+
-+
+-11-17 18:58  tim
-+
-+
+        * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-17 18:58  tim
-+
-+
+        * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-17 18:58  tim
-+
-+
+        * src/: math/ChebyshevPolynomials.cpp,
-+
+        math/ChebyshevPolynomials.hpp, math/Polynomial.hpp,
-+
+        primitives/Bond.hpp, types/CharmmTorsionType.hpp,
-+
+        types/OplsTorsionType.hpp, types/PolynomialBondType.hpp,
-+
+        types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types
-+
+        stuff and Chebyshev Polynomial
-+
-+
+-11-17 18:58  tim
-+
-+
+        * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 06:37  tim
-+
-+
+        * src/types/PolynomialTorsionType.hpp: file
-+
+        PolynomialTorsionType.hpp was initially added on branch new_design.
-+
-+
+-11-17 06:37  tim
-+
-+
+        * src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 06:37  tim
-+
-+
+        * src/: math/Polynomial.hpp, primitives/Bend.cpp,
-+
+        primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp,
-+
+        types/BondType.hpp, types/CharmmTorsionType.cpp,
-+
+        types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp,
-+
+        types/HarmonicBondType.hpp, types/MorseBondType.hpp,
-+
+        types/PolynomialBendType.hpp, types/PolynomialBondType.hpp,
-+
+        types/PolynomialTorsionType.hpp, types/TorsionType.hpp,
-+
+        utils/StringTokenizer.hpp: add  PolynomialBondType,
-+
+        PolynomialBendType, PolynomialTorsionType, HarmonicBendType and
-+
+        CharmmTorsionType. Need to refine the design and add document for
-+
+        them
-+
-+
+-11-17 06:37  tim
-+
-+
+        * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 06:37  tim
-+
-+
+        * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 06:37  tim
-+
-+
+        * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-17 01:11  tim
-+
-+
+        * src/types/: BendType.hpp, PolynomialBondType.hpp,
-+
+        TorsionType.hpp: add PolynomialBondType
-+
-+
+-11-17 01:11  tim
-+
-+
+        * src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-16 23:20  tim
-+
-+
+        * src/math/Polynomial.hpp: file Polynomial.hpp was initially added
-+
+        on branch new_design.
-+
-+
+-11-16 23:20  tim
-+
-+
+        * src/math/Polynomial.hpp: Adding Polynomial class
-+
-+
+-11-16 22:04  gezelter
-+
-+
+        * src/types/MorseBondType.hpp: file MorseBondType.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-16 22:04  gezelter
-+
-+
+        * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-16 22:04  gezelter
-+
-+
+        * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp,
-+
+        MorseBondType.hpp, TorsionType.hpp: added some new stuff
-+
-+
+-11-16 20:36  tim
-+
-+
+        * src/: primitives/Bend.cpp, primitives/Bend.hpp,
-+
+        primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp,
-+
+        types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and
-+
+        TorsionType
-+
-+
+-11-16 02:07  tim
-+
-+
+        * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-16 02:07  tim
-+
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
-+
+        UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp,
-+
+        utils/StringTokenizer.cpp: adding DUFF class; adding checking
-+
+        statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
-+
-+
+-11-15 23:00  tim
-+
-+
+        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
-+
+        UseTheForce/ForceFieldFactory.cpp,
-+
+        UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp,
-+
+        UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp,
-+
+        types/AtomType.hpp: adding ForceFieldFactory and LJFF classes
-+
-+
+-11-15 23:00  tim
-+
-+
+        * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-15 23:00  tim
-+
-+
+        * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp
-+
+        was initially added on branch new_design.
-+
-+
+-11-15 23:00  tim
-+
-+
+        * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-15 18:02  tim
-+
-+
+        * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-15 18:02  tim
-+
-+
+        * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-15 18:02  tim
-+
-+
+        * src/io/DumpReader.hpp: file DumpReader.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-15 18:02  tim
-+
-+
+        * src/: brains/SimInfo.cpp, brains/SimInfo.hpp,
-+
+        brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp,
-+
+        integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp,
-+
+        io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader,
-+
+        DumpWriter.Next Step is LJFF and integrators
-+
-+
+-11-13 05:08  tim
-+
-+
+        * src/: brains/ForceManager.cpp, brains/ForceManager.hpp,
-+
+        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
-+
+        brains/SimInfo.hpp, primitives/Molecule.cpp,
-+
+        primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory,
-+
+        refactory, refactory
-+
-+
+-11-12 22:43  tim
-+
-+
+        * src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp,
-+
+        StringTokenizer.cpp: bug fix in hasMoreTokens
-+
-+
+-11-12 22:28  tim
-+
-+
+        * src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-12 22:28  tim
-+
-+
+        * src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding
-+
+        StringUtils, a c-style strtok like class, need unit test
-+
-+
+-11-12 17:40  tim
-+
-+
+        * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp,
-+
+        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
-+
+        brains/SimInfo.hpp: SimCreator and SimInfo are  ready for unit test
-+
-+
+-11-12 07:05  tim
-+
-+
+        * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
-+
+        primitives/CutoffGroup.hpp, primitives/Molecule.cpp:
-+
+        MoleculeCreator forget to create CutoffGroups for free atoms
-+
-+
+-11-12 06:19  tim
-+
-+
+        * src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp,
-+
+        brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
-+
+        brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp,
-+
+        io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp:
-+
+        OOPSE = Object-Obfuscated Parallel Simulation Engine
-+
-+
+-11-11 21:48  chrisfen
-+
-+
+        * samples/water/tip3p_ice/tp3.md: working sample
-+
-+
+-11-11 21:47  chrisfen
-+
-+
+        * src/restraints/Restraints.cpp: working towards parallel
-+
+        restraints
-+
-+
+-11-11 21:47  chrisfen
-+
-+
+        * src/integrators/Integrator.cpp: Commented out some write
-+
+        statements
-+
-+
+-11-11 21:46  chrisfen
-+
-+
+        * src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some
-+
+        write statements
-+
-+
+-11-11 21:46  chrisfen
-+
-+
+        * samples/water/tip3p_ice/tp3.md: Fun with ice
-+
-+
+-11-11 16:41  tim
-+
-+
+        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
-+
+        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
-+
+        brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h,
-+
+        brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp,
-+
+        io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove
-+
+        useless mpiSimulation
-+
-+
+-11-11 16:41  tim
-+
-+
+        * src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-10 22:50  tim
-+
-+
+        * src/: brains/ForceManager.cpp, brains/SimInfo.cpp,
-+
+        brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp,
-+
+        integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo
-+
-+
+-11-10 22:01  tim
-+
-+
+        * src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
-+
+        brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp,
-+
+        brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp,
-+
+        brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp,
-+
+        integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
-+
+        io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp,
-+
+        visitors/AtomVisitor.cpp: another painful day (1) SimCreator,
-+
+        SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom
-+
+        File will be removed) (3) ForceField (at least LJ) and BondType,
-+
+        BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors &
-+
+        Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint
-+
-+
+-11-10 14:52  tim
-+
-+
+        * src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a
-+
+        configurable StatWriter
-+
-+
+-11-10 14:52  tim
-+
-+
+        * src/io/StatWriter.hpp: file StatWriter.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-10 02:58  tim
-+
-+
+        * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation
-+
+        in progress
-+
-+
+-11-09 23:11  tim
-+
-+
+        * src/brains/ForceManager.cpp: file ForceManager.cpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-09 23:11  tim
-+
-+
+        * src/integrators/VelocityVerletIntegrator.cpp: file
-+
+        VelocityVerletIntegrator.cpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-09 23:11  tim
-+
-+
+        * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp,
-+
+        brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
-+
+        brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp,
-+
+        brains/mpiSimulation.hpp, integrators/Integrator.hpp,
-+
+        integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp,
-+
+        integrators/VelocityVerletIntegrator.hpp: adding ForceManager
-+
-+
+-11-09 23:11  tim
-+
-+
+        * src/brains/ForceManager.hpp: file ForceManager.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-09 23:11  tim
-+
-+
+        * src/integrators/NVE.cpp: file NVE.cpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-09 01:08  tim
-+
-+
+        * src/integrators/VelocityVerletIntegrator.hpp: file
-+
+        VelocityVerletIntegrator.hpp was initially added on branch
-+
+        new_design.
-+
-+
+-11-09 01:08  tim
-+
-+
+        * src/integrators/NVE.hpp: file NVE.hpp was initially added on
-+
+        branch new_design.
-+
-+
+-11-09 01:08  tim
-+
-+
+        * src/: brains/Exclude.hpp, brains/Stats.hpp,
-+
+        integrators/Integrator.hpp, integrators/NVE.hpp,
-+
+        integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp,
-+
+        utils/TypeContainer.hpp: More to break
-+
-+
+-11-06 05:21  tim
-+
-+
+        * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-06 05:21  tim
-+
-+
+        * src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp,
-+
+        UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp,
-+
+        utils/TypeContainer.hpp, utils/next_combination.hpp: adding
-+
+        ForceField and TypeContainer classes
-+
-+
+-11-05 23:38  tim
-+
-+
+        * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-05 23:38  tim
-+
-+
+        * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was
-+
+        initially added on branch new_design.
-+
-+
+-11-05 23:38  tim
-+
-+
+        * src/: brains/Exclude.cpp, brains/Exclude.hpp,
-+
+        brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp,
-+
+        brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp,
-+
+        brains/SimInfo.hpp, primitives/Molecule.hpp,
-+
+        utils/LocalndexManager.hpp: Fix Exclude class etc.
-+
-+
+-11-05 21:45  chrisfen
-+
-+
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
-+
+        visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the
-+
+        linear visitor
-+
-+
+-11-05 21:04  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/shapes.F90: current status of the
-+
+        debugging process
-+
-+
+-11-05 21:04  chrisfen
-+
-+
+        * make/Makefile.in: included visitors and minimizer
-+
-+
+-11-05 21:03  chrisfen
-+
-+
+        * ChangeLog: new changes
-+
-+
+-11-05 02:56  tim
-+
-+
+        * src/: brains/SimCreator.cpp, brains/SimCreator.hpp,
-+
+        primitives/Molecule.hpp: Pain......
-+
-+
+-11-04 20:55  tim
-+
-+
+        * ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp,
-+
+        src/brains/SimCreator.hpp, src/brains/SimInfo.hpp,
-+
+        src/brains/Stats.hpp: time to break SimSetup
-+
-+
+-11-04 20:51  gezelter
-+
-+
+        * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new
-+
+        classes in progress
-+
-+
+-11-04 19:48  tim
-+
+        * src/brains/Stats.cpp: file Stats.cpp was initially added on
+        branch new_design.
-<
+-11-04 14:48  tim
->
+-11-04 19:48  tim
+        * src/brains/Stats.hpp: file Stats.hpp was initially added on
+        branch new_design.
-<
+-11-04 11:22  gezelter
->
+-11-04 19:48  tim
-+
+        * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp,
-+
+        SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats
-+
+        class
-+
-+
+-11-04 16:22  gezelter
-+
+        * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp,
+        RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and
+        linearAxis are virtual in StuntDouble, but are implemented by
+        false and "-1" but there should be logic to figure them out in the
+        other two classes
-<
+-11-04 11:20  gezelter
->
+-11-04 16:20  gezelter
+        * src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't
+        remember what I did
-<
+-11-04 11:20  gezelter
->
+-11-04 16:20  gezelter
+        * src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky
-<
+-11-04 11:20  gezelter
->
+-11-04 16:20  gezelter
+        * src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX
+        in the entry_plug so that it only is set if the atoms really are in
+        the simulation
-<
+-11-04 11:20  gezelter
->
+-11-04 16:20  gezelter
+        * samples/water/ssd/ssd.md: testing force fields
-<
+-11-04 11:19  gezelter
->
+-11-04 16:19  gezelter
+        * samples/shape/linear.in: testing shapes
-<
+-11-03 14:56  tim
->
+-11-03 19:56  tim
-–
+        * src/brains/SimCreator.cpp: file SimCreator.cpp was initially
-–
+        added on branch new_design.
-–
-–
+-11-03 14:56  tim
-–
+        * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator
+        class(similar as SimSetup)
-<
+-11-03 14:56  tim
->
+-11-03 19:56  tim
+        * src/brains/SimCreator.hpp: file SimCreator.hpp was initially
+        added on branch new_design.
-<
+-11-03 13:00  tim
->
+-11-03 19:56  tim
-+
+        * src/brains/SimCreator.cpp: file SimCreator.cpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-03 18:00  tim
-+
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
+        UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp,
+        UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp,
+        visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get
+        compiled. Still a long way to go ......
-<
+-11-03 11:08  tim
->
+-11-03 16:08  tim
+        * ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp,
+        src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp,
+        src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp,
+        src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ......
-<
+-11-02 17:41  tim
->
+-11-02 22:41  tim
-+
+        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
-+
+        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
-+
+        Need unit test
-+
-+
+-11-02 22:41  tim
-+
+        * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was
+        initially added on branch new_design.
-<
+-11-02 17:41  tim
->
+-11-02 22:41  tim
+        * src/brains/Migrator.hpp: file Migrator.hpp was initially added on
+        branch new_design.
-<
+-11-02 17:41  tim
->
+-11-02 16:59  tim
-<
+        * src/: brains/Migrator.hpp, brains/SimModel.cpp,
-<
+        utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator.
-<
+        Need unit test
->
+        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
->
+        branch new_design.
-<
+-11-02 11:59  tim
->
+-11-02 16:59  tim
+        * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp,
+        SimSnapshotManager.hpp: SimModel in progress
-<
+-11-02 11:59  tim
->
+-11-02 15:28  chrisfen
-–
+        * src/brains/SimModel.cpp: file SimModel.cpp was initially added on
-–
+        branch new_design.
-–
-–
+-11-02 10:28  chrisfen
-–
+        * src/: UseTheForce/DarkSide/shapes.F90,
+        primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes
+        looks like it's working
-<
+-11-02 10:27  tim
->
+-11-02 15:27  tim
-–
+        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
-–
+        added on branch new_design.
-–
-–
+-11-02 10:27  tim
-–
+        * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some
+        functions for dealing with memory issue
-<
+-11-02 10:23  tim
->
+-11-02 15:27  tim
-+
+        * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially
-+
+        added on branch new_design.
-+
-+
+-11-02 15:23  tim
-+
+        * src/: brains/SimModel.hpp, brains/Snapshot.hpp,
+        brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding
+        SimModel(something similar as SimInfo)
-<
+-11-01 17:52  tim
->
+-11-01 22:52  tim
+        * src/: applications/simpleBuilder/MoLocator.hpp,
+        applications/simpleBuilder/simpleBuilder.cpp,
+        visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom,
+        RigidBody and StuntDouble classes get compiled
-<
+-11-01 16:40  tim
->
+-11-01 21:40  tim
+        * src/primitives/Torsion.hpp: file Torsion.hpp was initially added
+        on branch new_design.
-<
+-11-01 16:40  tim
->
+-11-01 21:40  tim
+        * src/primitives/Bend.hpp: file Bend.hpp was initially added on
+        branch new_design.
-<
+-11-01 16:40  tim
->
+-11-01 21:40  tim
+        * src/primitives/Bond.hpp: file Bond.hpp was initially added on
+        branch new_design.
-<
+-11-01 16:40  tim
->
+-11-01 21:40  tim
+        * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial
+        version of Bond, Bend and Torsion.
-<
+-11-01 16:37  tim
->
+-11-01 21:37  tim
+        * src/types/BendType.hpp: file BendType.hpp was initially added on
+        branch new_design.
-<
+-11-01 16:37  tim
->
+-11-01 21:37  tim
+        * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding
+        BondType, BendType, TorsionType
-<
+-11-01 16:37  tim
->
+-11-01 21:37  tim
+        * src/types/TorsionType.hpp: file TorsionType.hpp was initially
+        added on branch new_design.
-<
+-11-01 16:37  tim
->
+-11-01 21:37  tim
+        * src/types/BondType.hpp: file BondType.hpp was initially added on
+        branch new_design.
-<
+-11-01 15:15  tim
->
+-11-01 20:15  tim
+        * src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp,
+        CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp,
+        RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp:
+        break, break and break.....
-<
+-11-01 14:57  tim
->
+-11-01 19:57  tim
+        * test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp,
+        DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp,
+        StuntDouble.hpp: these core classes get compiled
-<
+-10-29 17:37  tim
->
+-10-29 22:37  tim
+        * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule
+        class
-<
+-10-29 17:28  chrisfen
->
+-10-29 22:28  chrisfen
+        * src/: UseTheForce/DarkSide/atype.F90,
+        UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp,
+        types/ShapeAtomType.cpp: still debugging
-<
+-10-29 17:28  chrisfen
->
+-10-29 22:28  chrisfen
+        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90:
+        shapes rcut calculator added
-<
+-10-29 17:27  chrisfen
->
+-10-29 22:27  chrisfen
+        * samples/shape/linear.md: shorter run
-<
+-10-29 15:54  tim
->
+-10-29 20:54  tim
+        * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class.
-<
+-10-29 11:22  tim
->
+-10-29 16:22  tim
+        * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp,
+        ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove
+        some deprecated files
-<
+-10-29 11:20  tim
->
+-10-29 16:20  tim
+        * test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp,
+        DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp:
+        More painful reconstruction is coming !!!
-<
+-10-28 17:34  tim
->
+-10-28 22:34  tim
+        * src/brains/DataStorage.hpp, src/utils/next_combination.hpp,
+        test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp,
+        test/brains/StuntDouble.hpp: More work on StuntDouble, Atom,
+        DirectionalAtom and RigidBody
-<
+-10-28 17:26  tim
->
+-10-28 22:26  tim
+        * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp,
+        src/applications/simpleBuilder/MoLocator.cpp,
+        src/utils/GenericFactory.hpp, src/utils/next_combination.hpp:
+        remove old Vector3d.hpp from application/simpleBuilder
-<
+-10-28 16:42  tim
->
+-10-28 21:42  tim
+        * src/utils/next_combination.hpp: Minor change in next_combination
-<
+-10-28 16:28  tim
->
+-10-28 21:28  tim
+        * src/utils/next_combination.hpp,
+        test/utils/NextCombinationTestCase.cpp,
+        test/utils/ReplaceWildCardTestCase.cpp: Done with combination
-<
+-10-28 16:11  tim
->
+-10-28 21:11  tim
+        * src/utils/next_combination.hpp: change documentation of
+        next_combination.hpp
-<
+-10-28 15:41  tim
->
+-10-28 20:41  tim
+        * ChangeLog, src/utils/next_combination.hpp,
+        test/utils/NextCombinationTestCase.cpp,
+        test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working
-<
+-10-28 15:01  tim
->
+-10-28 20:01  tim
+        * src/utils/next_combination.hpp: adding replace wildcard function
-<
+-10-28 14:33  tim
->
+-10-28 19:33  tim
+        * src/utils/next_combination.hpp: Minor change
-<
+-10-28 14:06  tim
->
+-10-28 19:06  tim
+        * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp,
+        src/applications/simpleBuilder/simpleBuilder.cpp,
+        test/utils/next_combination.hpp: STL next_permutation like
+        next_combination is working
-<
+-10-28 12:22  chrisfen
->
+-10-28 17:22  chrisfen
+        * src/UseTheForce/WATER.cpp: fix of setDipoles
-<
+-10-28 12:20  gezelter
->
+-10-28 17:20  gezelter
+        * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the
+        shapeFile
-<
+-10-28 12:20  gezelter
->
+-10-28 17:20  gezelter
+        * samples/shape/linear.md: forgot the orientation line
-<
+-10-28 11:56  gezelter
->
+-10-28 16:56  gezelter
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
+        UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
+        UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate
+        declaration foo
-<
+-10-28 11:55  gezelter
->
+-10-28 16:55  gezelter
+        * samples/lipid/5x5.md: uncommented .in line
-<
+-10-28 10:42  tim
->
+-10-28 15:42  tim
+        * test/utils/: Makefile, NextCombinationTestCase.cpp,
+        NextCombinationTestCase.hpp, next_combination.hpp: next_combination
+        in progress
-<
+-10-28 10:15  tim
->
+-10-28 15:15  tim
+        * test/utils/: NextCombinationTestCase.cpp,
+        NextCombinationTestCase.hpp: adding next_combination test case
-<
+-10-28 10:02  tim
->
+-10-28 15:02  tim
+        * test/utils/next_combination.hpp: STL Compatible combination
+        sequence generator
-<
+-10-28 01:23  tim
->
+-10-28 06:23  tim
+        * test/utils/: GenerateCombination.hpp,
+        ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp
-<
+-10-28 01:16  tim
->
+-10-28 06:16  tim
+        * test/utils/GenerateCombination.hpp: a STL next_permutaion like
+        next_combination function.
-<
+-10-27 22:27  tim
->
+-10-28 03:27  tim
+        * test/utils/ReplaceWildCard.hpp: no message
-<
+-10-27 22:14  tim
->
+-10-28 03:14  tim
+        * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp:
+        ReplaceWildCard(recursive version) is working, need refactoring. An
+        iterative version is on the way
-<
+-10-27 21:28  tim
->
+-10-28 02:28  tim
+        * test/utils/: Makefile, ReplaceWildCard.hpp,
+        ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress
-<
+-10-27 21:08  tim
->
+-10-28 02:08  tim
+        * test/utils/: ReplaceWildCardTestCase.cpp,
+        ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard
-<
+-10-27 18:17  tim
->
+-10-27 23:17  tim
+        * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need
+        test
-<
+-10-27 01:25  tim
->
+-10-27 06:25  tim
+        * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild
+        char matching is on the way
-<
+-10-27 01:07  tim
->
+-10-27 06:07  tim
+        * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4
-<
+-10-26 22:00  gezelter
->
+-10-27 03:00  gezelter
+        * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix
-<
+-10-26 21:20  gezelter
->
+-10-27 02:20  gezelter
+        * src/UseTheForce/ForceFields.hpp: subclass foo
-<
+-10-26 21:16  gezelter
->
+-10-27 02:16  gezelter
+        * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* ->
+        string conversion
-<
+-10-26 19:01  gezelter
->
+-10-27 00:01  gezelter
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
+        UseTheForce/ForceFields.hpp, brains/SimSetup.cpp,
+        brains/SimSetup.hpp: char* -> string
-<
+-10-26 17:25  gezelter
->
+-10-26 22:25  gezelter
+        * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp,
+        Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp,
+        ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some
+        isXXX
-<
+-10-26 17:25  gezelter
->
+-10-26 22:25  gezelter
+        * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
+        define name collision
-<
+-10-26 17:24  gezelter
->
+-10-26 22:24  gezelter
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
+        UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
+        UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp:
+        forcefield refactoring for shapes
-<
+-10-26 17:24  gezelter
->
+-10-26 22:24  gezelter
+        * samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape,
+        Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in,
+        linear.md, linear.shape, toluene.shape: adding sample shape
+        directory
-<
+-10-26 17:19  tim
->
+-10-26 22:19  tim
+        * ChangeLog, src/brains/DataStorage.cpp,
+        src/brains/DataStorage.hpp, src/brains/Snapshot.hpp,
+        test/brains/DataStorageTestCase.hpp, test/brains/Makefile:
+        DataStorage passes unit test
-<
+-10-26 13:03  chrisfen
->
+-10-26 18:03  chrisfen
+        * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h:
+        Changes to help advance shapes
-<
+-10-26 13:02  chrisfen
->
+-10-26 18:02  chrisfen
+        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to
+        Shapes force field reader
-<
+-10-26 12:28  tim
->
+-10-26 17:28  tim
+        * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and
+        SnapshotTestCase in progress
-<
+-10-25 17:46  tim
->
+-10-25 22:46  tim
+        * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
+        src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
+        test/math/VectorTestCase.cpp: add getArray function to  RectMatrix
+        and Vector classes
-<
+-10-25 12:03  tim
->
+-10-25 17:03  tim
+        * ChangeLog, src/utils/GenericFactory.hpp,
+        test/utils/GenericFactoryTestCase.cpp,
+        GenericFactory Test Case. GenericFactory now can bed used to creat
+        ForcefieldFactory and IntegratorFactory etc.
-<
+-10-24 23:08  tim
->
+-10-25 04:08  tim
+        * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp,
+        brains/SimSnapshotManager.hpp, brains/Snapshot.hpp,
+        brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes
+        get reconstructed
-<
+-10-24 02:55  tim
->
+-10-24 07:55  tim
+        * src/utils/GenericFactory.hpp: GenericFactory pass unit test
-<
+-10-23 18:09  tim
->
+-10-23 23:09  tim
+        * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp,
+        StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp,
+        RigidBody.cpp: Refactoring in progress
-<
+-10-22 18:09  tim
->
+-10-22 23:09  tim
+        * 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
-<
+-10-22 17:59  chrisfen
->
+-10-22 22:59  chrisfen
+        * src/: UseTheForce/LJFF.cpp,
+        UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear
+        god!  It runs and conserves energy!
-<
+-10-22 17:54  chrisfen
->
+-10-22 22:54  chrisfen
+        * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY
-<
+-10-22 17:53  chrisfen
->
+-10-22 22:53  chrisfen
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
+        UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
+        brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey
+        breakey
-<
+-10-22 17:53  chrisfen
->
+-10-22 22:53  chrisfen
+        * make/Makefile.in: compiler flags
-<
+-10-22 16:20  gezelter
->
+-10-22 21:20  gezelter
+        * 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
-<
+-10-22 15:22  gezelter
->
+-10-22 20:22  gezelter
+        * 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
-<
+-10-22 15:21  gezelter
->
+-10-22 20:21  gezelter
+        * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
+        DirectionalAtomType.hpp, Makefile: More on AtomType and
+        DirectionalAtomType
-<
+-10-22 09:47  gezelter
->
+-10-22 14:47  gezelter
+        * src/types/AtomType.hpp: Adding AtomType
-<
+-10-21 16:31  tim
->
+-10-21 21:31  tim
+        * ChangeLog, src/brains/Snapshot.hpp,
+        src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp,
+        test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp:
+        Snapshot and SnapshotManager in progress
-<
+-10-21 16:30  tim
->
+-10-21 21:30  tim
+        * test/brains/: BrainsTest.cpp, Makefile,
+        SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp,
+        SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for
+        Snapshot and snapshotManager.
-<
+-10-21 15:15  gezelter
->
+-10-21 20:15  gezelter
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
+        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
+        brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky.
+        Fixey Fixey.
-<
+-10-21 11:32  tim
->
+-10-21 16:32  tim
+        * src/utils/GenericData.cpp, src/utils/Makefile,
+        test/utils/Makefile, test/utils/UtilTest: remove some junk files
-<
+-10-21 11:24  tim
->
+-10-21 16:24  tim
+        * test/utils/GenericData.hpp: remove backup of  GenericData.hpp
-<
+-10-21 11:22  tim
->
+-10-21 16:22  tim
+        * ChangeLog, src/brains/SimSetup.cpp,
+        src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
+        src/visitors/ZconsVisitor.hpp: replace old GebericData with  new
+        GenericData
-<
+-10-21 10:25  chuckv
->
+-10-21 15:25  chuckv
+        * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj
+        module.
-<
+-10-21 10:24  chuckv
->
+-10-21 15:24  chuckv
+        * src/UseTheForce/DarkSide/lj_interface.h: Added interface for
+        fortran lj module.
-<
+-10-20 17:54  tim
->
+-10-20 22:54  tim
+        * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp,
+        test/utils/GenericDataTestCase.cpp, test/utils/Makefile,
+        test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest:
+        GenericData and PropertyMap  pass unit test.
-<
+-10-20 16:52  gezelter
->
+-10-20 21:52  gezelter
+        * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90,
+        DarkSide/sticky_interface.h: fixed a fortran name problem
-<
+-10-20 16:38  tim
->
+-10-20 21:38  tim
+        * test/utils/: GenericData.hpp, GenericDataTestCase.cpp,
+        GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp,
+        UtilTest, UtilTest.cpp: adding generic data test case
-<
+-10-20 16:16  chuckv
->
+-10-20 21:16  chuckv
+        * configure, ac-tools/aclocal.m4,
+        src/UseTheForce/DarkSide/Makefile,
+        Fortran/C++ interface de-obfuscation project appears to be
+        complete!  Woo hoo!
-<
+-10-20 15:47  chuckv
->
+-10-20 20:47  chuckv
+        * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp,
+        fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project
+        continues
-<
+-10-20 15:46  chuckv
->
+-10-20 20:46  chuckv
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
+        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
+        brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface
+        de-obfuscation project (It is a very long story)
-<
+-10-20 13:07  tim
->
+-10-20 18:07  tim
+        * 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
-<
+-10-20 00:52  tim
->
+-10-20 05:52  tim
+        * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and
+        SnapshotManager in design phase
-<
+-10-19 23:54  gezelter
->
+-10-20 04:54  gezelter
+        * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace
+        problem prevented linking
-<
+-10-19 23:54  gezelter
->
+-10-20 04:54  gezelter
+        * src/UseTheForce/Shapes_FF.cpp: fixed include
-<
+-10-19 23:26  gezelter
->
+-10-20 04:26  gezelter
+        * src/utils/: Makefile, definitions.F90, definitions_module.F90,
+        oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90:
+        more fortran name mangling
-<
+-10-19 23:23  gezelter
->
+-10-20 04:23  gezelter
+        * src/profiling/timing.F90: yet more fortran renaming
-<
+-10-19 23:19  gezelter
->
+-10-20 04:19  gezelter
+        * 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
-<
+-10-19 23:12  gezelter
->
+-10-20 04:12  gezelter
+        * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some
+        broken fortran stuff
-<
+-10-19 23:02  gezelter
->
+-10-20 04:02  gezelter
+        * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
+        atype_interface.h, atype_module.F90, atype_module_interface.h,
+        sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90:
+        name sanity on the fortran side
-<
+-10-19 19:18  tim
->
+-10-20 00:18  tim
+        * test/math/SquareMatrix3TestCase.hpp: [no log message]
-<
+-10-19 18:01  tim
->
+-10-19 23:01  tim
+        * 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
-<
+-10-19 17:43  chuckv
->
+-10-19 22:43  chuckv
+        * src/UseTheForce/do_Forces.h: Added correct prototypes for
+        C-fortran interface functions.
-<
+-10-19 17:37  chuckv
->
+-10-19 22:37  chuckv
+        * src/UseTheForce/DarkSide/: atype_module_interface.h,
+        eam_module_inteface.h, gb_module_interface.h,
+        sticky_pair_module_interface.h: Added correct prototypes for
+        C-fortran interface functions.
-<
+-10-19 16:28  tim
->
+-10-19 21:28  tim
+        * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp,
+        src/math/SquareMatrix.hpp, src/math/Vector.hpp,
+        test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more
+        bugs get fixed at math library
-<
+-10-19 15:43  chuckv
->
+-10-19 20:43  chuckv
+        * src/UseTheForce/: DarkSide/atype_module_interface.h,
+        DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h,
+        notifycutoffs_module_interface.h: Added new files for fortran
+        interface.
-<
+-10-19 15:43  gezelter
->
+-10-19 20:43  gezelter
+        * src/UseTheForce/Makefile: regressing
-<
+-10-19 15:40  gezelter
->
+-10-19 20:40  gezelter
+        * src/: UseTheForce/DarkSide/calc_shapes.F90,
+        UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp:
+        working on shapes for portability
-<
+-10-19 15:40  gezelter
->
+-10-19 20:40  gezelter
+        * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes
-<
+-10-19 13:21  chrisfen
->
+-10-19 18:21  chrisfen
+        * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around
+        findBegin
-<
+-10-18 23:34  tim
->
+-10-19 04:34  tim
+        * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs
+        are fixed in Vector class
-<
+-10-18 23:28  tim
->
+-10-19 04:28  tim
+        * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix
+        some bugs in RectMatrixTestCase
-<
+-10-18 23:21  tim
->
+-10-19 04:21  tim
+        * 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
-<
+-10-18 18:13  tim
->
+-10-18 23:13  tim
+        * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp,
+        src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
+        test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more
+        tests on math library
-<
+-10-18 16:03  tim
->
+-10-18 21:03  tim
+        * test/math/: Makefile, QuaternionTestCase.cpp,
+        QuaternionTestCase.hpp, RectMatrixTestCase.cpp,
+        Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding
+        more testing units
-<
+-10-18 12:07  tim
->
+-10-18 17:07  tim
+        * 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
-<
+-10-18 11:30  gezelter
->
+-10-18 16:30  gezelter
+        * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
+        Your basic run of the mill real-valued versions of Y_l^m(\theta,
+        \phi)
-<
+-10-18 11:29  gezelter
->
+-10-18 16:29  gezelter
+        * 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
-<
+-10-18 10:21  gezelter
->
+-10-18 15:21  gezelter
+        * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType
-<
+-10-18 00:23  tim
->
+-10-18 05:23  tim
+        * test/math/VectorTestCase.hpp: adding  vector test case
-<
+-10-18 00:23  tim
->
+-10-18 05:23  tim
+        * src/utils/GenericFactory.hpp: adding generic factory and vector
+        test case
-<
+-10-16 20:19  tim
->
+-10-17 01:19  tim
+        * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp,
+        SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in
+        progress
-<
+-10-15 20:31  tim
->
+-10-16 01:31  tim
+        * src/math/Quaternion.hpp: add quaternion class
-<
+-10-15 16:11  tim
->
+-10-15 21:11  tim
+        * test/io/: DUFF.frc, IfstrstreamTestCase.cpp,
+        IfstrstreamTestCase.hpp: adding test file
-<
+-10-15 16:10  tim
->
+-10-15 21:10  tim
+        * src/io/basic_ifstrstream.hpp: fix a bunch of bugs
-<
+-10-15 15:42  tim
->
+-10-15 20:42  tim
+        * src/io/basic_ifstrstream.hpp: change const_cast to statc_const
-<
+-10-15 15:35  tim
->
+-10-15 20:35  tim
+        * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp
-<
+-10-15 15:34  tim
->
+-10-15 20:34  tim
+        * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use
+        namespace oopse
-<
+-10-15 14:38  chuckv
->
+-10-15 19:38  chuckv
+        * configure, ac-tools/aclocal.m4: Changed optimization flags for
+        XLF and XLC.
-<
+-10-15 13:28  tim
->
+-10-15 18:28  tim
+        * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp:
+        adding ifstrstream test case
-<
+-10-15 13:20  tim
->
+-10-15 18:20  tim
+        * src/io/basic_ifstrstream.hpp: fix include
-<
+-10-15 13:18  tim
->
+-10-15 18:18  tim
+        * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi
-<
+-10-15 13:17  tim
->
+-10-15 18:17  tim
+        * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile
-<
+-10-15 13:16  tim
->
+-10-15 18:16  tim
+        * test/io/: Makefile, ifstrstreamTestCase.cpp,
+        ifstrstreamTestCase.hpp: adding test case for ifstrstream
-<
+-10-15 10:37  tim
->
+-10-15 15:37  tim
+        * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp,
+        ifstrstreamTestCase.hpp: add ifstrstreamTestCase
-<
+-10-15 10:20  tim
->
+-10-15 15:20  tim
+        * src/io/basic_ifstrstream.hpp: add checkFilename Option
-<
+-10-15 10:19  tim
->
+-10-15 15:19  tim
+        * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp,
+        SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add
+        SquareMatrixTestCase class
-<
+-10-15 02:52  tim
->
+-10-15 07:52  tim
+        * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream
-<
+-10-14 18:28  tim
->
+-10-14 23:28  tim
+        * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp,
+        Vector.hpp: math library in progress
-<
+-10-14 18:27  tim
->
+-10-14 23:27  tim
+        * src/io/FileReader.hpp: FileReader in progress
-<
+-10-13 18:53  tim
->
+-10-13 23:53  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
->
+-10-13 22:28  tim
+        * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap
+        class
-<
+-10-13 17:27  tim
->
+-10-13 22:27  tim
+        * test/math/: MainTest.cpp, RectMatrixTestCase.cpp,
+        RectMatrixTestCase.hpp: adding testing unit
-<
+-10-13 17:24  tim
->
+-10-13 22:24  tim
+        * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix
-<
+-10-13 01:51  tim
->
+-10-13 06:51  tim
+        * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp,
+        Vector3.hpp: refactory vector and matrix classes
-<
+-10-13 01:50  tim
->
+-10-13 06:50  tim
+        * src/math/Vector3d.hpp: Remove some Makefile.in
-<
+-10-12 18:57  tim
->
+-10-12 23:57  tim
+        * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and
+        Matrix3x3d.hpp
-<
+-10-12 14:08  tim
->
+-10-12 19:08  tim
+        * doc/: cppstyle.html, style.css: adding c++ coding style
-<
+-10-11 17:15  tim
->
+-10-11 22:15  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
->
+-10-11 21:54  tim
+        * scripts/filepp: fix a bug in filepp
-<
+-10-11 16:13  tim
->
+-10-11 21:13  tim
+        * make/Makefile.in: using filepp to generate dependencies instead
+        of compilers
-<
+-10-11 16:10  tim
->
+-10-11 21:10  tim
+        * scripts/filepp: filepp can be used to generate dependencies for
+        c/c++ now
-<
+-10-11 13:40  tim
->
+-10-11 18:40  tim
+        * make/Makefile.in: remove -module from F90Options
-<
+-10-11 13:01  tim
->
+-10-11 18:01  tim
+        * make/Makefile.in: adding rules to move fortran 90 module to
+        target directory
-<
+-10-11 10:43  gezelter
->
+-10-11 15:43  gezelter
+        * make/Makefile.in: fixed makefile.in
-<
+-10-11 09:51  tim
->
+-10-11 14:51  tim
+        * scripts/filepp: remove "use bytes" which causes problem in sgi
+        machine
-<
+-10-11 09:26  tim
->
+-10-11 14:26  tim
+        * forceFields/Makefile: add Makefile
-<
+-10-11 09:23  tim
->
+-10-11 14:23  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
->
+-10-09 06:01  tim
-<
+        * samples/argon/Makefile: remove argon.dump and argon.eor from
-<
+        Makefile
->
+        * samples/: alkane/Makefile.in, lipid/Makefile.in,
->
+        metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in
-<
+-10-09 01:01  tim
->
+-10-08 23:15  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
->
+-10-08 22:51  tim
+        * make/Makefile.in: fix make install
-<
+-10-08 17:10  tim
->
+-10-08 22:10  tim
+        * make/Makefile.in: adding make install
-<
+-10-08 17:04  tim
->
+-10-08 22:04  tim
-<
+        * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
-<
+        metals/Makefile, minimizer/Makefile, water/Makefile.in,
-<
+        water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile,
->
+        * samples/: alkane/Makefile, lipid/Makefile, 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
-<
+-10-06 18:03  gezelter
->
+-10-06 23:03  gezelter
+        * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt
+        stuff
-<
+-10-06 18:03  gezelter
->
+-10-06 23:03  gezelter
+        * 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
-<
+-10-06 17:20  tim
->
+-10-06 22:20  tim
+        * make/: Doxyfile, Makefile.in: adding doxygen configuration file
-<
+-10-06 17:19  tim
->
+-10-06 22:19  tim
+        * scripts/filepp: filepp can handle different fortran module case
+        and suffix
-<
+-10-06 16:27  gezelter
->
+-10-06 21:27  gezelter
+        * src/restraints/Restraints.cpp: Chris doesn't know about the
+        OOPSE-2.0 directory structure yet
-<
+-10-06 16:27  gezelter
->
+-10-06 21:27  gezelter
+        * ChangeLog: Yeah yeah, we'lll get around to it later
-<
+-10-06 16:22  gezelter
->
+-10-06 21:22  gezelter
+        * configure, ac-tools/configure.in, ac-tools/fortran90.m4,
+        make/Makefile.in: cleaning up build process
-<
+-10-06 15:01  chrisfen
->
+-10-06 20:01  chrisfen
+        * src/restraints/Restraints.cpp: made the file reading in
+        restraints more intelligent - no longer gives uninformative seg
+        faults
-<
+-10-06 14:55  gezelter
->
+-10-06 19:55  gezelter
+        * src/applications/simpleBuilder/Make.ftemp.old: cleaning up
-<
+-10-06 14:51  gezelter
->
+-10-06 19:51  gezelter
+        * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy,
+        scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit
-<
+-10-06 13:53  tim
->
+-10-06 18:53  tim
+        * make/: Makefile, Makefile.in: fix make statistics
-<
+-10-06 13:18  tim
->
+-10-06 18:18  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
->
+-10-05 22:57  tim
+        * make/: Makefile, Makefile.in:  adding shared library flag
-<
+-10-05 14:37  tim
->
+-10-05 19:37  tim
+        * src/: Makefile, UseTheForce/Makefile,
+        UseTheForce/mpiSimulation_module.F90,
+        UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move
+        mpiSimulation_module to DarkSide
-<
+-10-05 14:35  tim
->
+-10-05 19:35  tim
+        * make/: Makefile, Makefile.in: building MPI version;using static
+        library instead of shared library
-<
+-10-05 09:14  tim
->
+-10-05 14:14  tim
+        * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90
+        to filepp
-<
+-10-04 15:56  tim
->
+-10-04 20:56  tim
+        * make/: Makefile, Makefile.in: add make cvslog
-<
+-10-04 11:24  gezelter
->
+-10-04 16:24  gezelter
+        * make/: Makefile, Makefile.in: more work on the parallel build
-<
+-10-04 11:06  gezelter
->
+-10-04 16:06  gezelter
+        * make/: Makefile, Makefile.in: changes to backport declare flags
-<
+-10-04 10:27  gezelter
->
+-10-04 15:27  gezelter
+        * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp,
+        DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging
+        shapes
-<
+-10-01 23:40  tim
->
+-10-02 04:40  tim
+        * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree
-<
+-10-01 23:22  tim
->
+-10-02 04:22  tim
+        * make/: Makefile, Makefile.in: add oopse_ as library prefix
-<
+-10-01 16:59  tim
->
+-10-01 21:59  tim
+        * make/: Makefile, Makefile.in: fix a space trimming bug in filepp
-<
+-10-01 16:22  gezelter
->
+-10-01 21:22  gezelter
+        * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A
+        few minor build changes
-<
+-10-01 16:11  tim
->
+-10-01 21:11  tim
+        * scripts/filepp: adding fortran90 make dependency tool
-<
+-09-30 10:41  tim
->
+-09-30 15:41  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
->
+-09-29 21:55  tim
+        * src/: Makefile, UseTheForce/Makefile,
+        UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile,
+        restraints/Makefile, types/Makefile, utils/Makefile,
+        visitors/Makefile: define DEV_ROOT as relative path
-<
+-09-29 16:54  tim
->
+-09-29 21:54  tim
+        * make/: Makefile, Makefile.in: get the relative path by shell
+        script
-<
+-09-29 16:32  tim
->
+-09-29 21:32  tim
+        * make/Makefile: eliminate DEV_ROOT by relative path
-<
+-09-29 13:37  tim
->
+-09-29 18:37  tim
+        * make/Makefile.in: add PackageLibs;  fix dependency rule
-<
+-09-29 12:57  gezelter
->
+-09-29 17:57  gezelter
+        * configure, ac-tools/configure.in: updates
-<
+-09-29 12:56  gezelter
->
+-09-29 17:56  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
->
+-09-29 17:46  tim
+        * Makefile: If makefile does not exist, print error message
-<
+-09-29 12:12  tim
->
+-09-29 17:12  tim
+        * make/: Make.conf.in, Makefile: fix dependencies rule
-<
+-09-29 10:58  gezelter
->
+-09-29 15:58  gezelter
+        * Makefile, make/Makefile: still working on build process
-<
+-09-29 10:00  tim
->
+-09-29 15:00  tim
+        * make/Makefile: add print statment to rules
-<
+-09-29 09:59  tim
->
+-09-29 14:59  tim
+        * src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile,
+        applications/dump2Xyz/Makefile, applications/oopse/Makefile,
+        profiling/Makefile, restraints/Makefile, types/Makefile,
+        utils/Makefile, visitors/Makefile: change Makefile to relative path
-<
+-09-28 21:55  tim
->
+-09-29 02:55  tim
+        * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c
+        which cause headache in bulding libutils
-<
+-09-28 18:24  tim
->
+-09-28 23:24  tim
+        * src/applications/: BaseLattice.cpp, BaseLattice.hpp,
+        Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h,
+        change directory structure of application. Every executable file is
+        replaced in seperate directory
-<
+-09-28 17:15  gezelter
->
+-09-28 22:15  gezelter
+        * lib/dummy: Keep that lib around, please.
-<
+-09-28 17:14  gezelter
->
+-09-28 22:14  gezelter
+        * Makefile, configure, ac-tools/configure.in, make/Make.conf.in:
+        starting a configure version
-<
+-09-28 16:08  tim
->
+-09-28 21:08  tim
+        * src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90,
+        UseTheForce/DarkSide/Makefile,
+        brains/Makefile, brains/simulation_module.F90: move fortran files
+        around to solve dependency problem
-<
+-09-28 15:43  tim
->
+-09-28 20:43  tim
+        * Makefile, src/UseTheForce/ForceFields.hpp,
+        src/UseTheForce/Makefile, src/applications/BaseLattice.hpp,
+        src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp,
+        src/utils/Makefile: [no log message]
-<
+-09-28 15:41  tim
->
+-09-28 20:41  tim
+        * make/Makefile, scripts/sfmakedepend: fix fortran dependency
+        problem
-<
+-09-28 11:13  tim
->
+-09-28 16:13  tim
+        * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y,
+        src/io/Makefile: add yacc and lex rules
-<
+-09-27 15:24  tim
->
+-09-27 20:24  tim
+        * make/Makefile: adding include path to F90Options
-<
+-09-27 15:13  tim
->
+-09-27 20:13  tim
+        * make/Makefile: change suffix from .cc to .cpp
-<
+-09-24 11:27  tim
->
+-09-24 16:27  tim
+        * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
+        UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
+        visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
+        visitors/ZconsVisitor.hpp: change the #include in source files
-<
+-09-23 23:16  gezelter
->
+-09-24 04:16  gezelter
+        * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
+        src/Makefile, src/config.h.in, src/constraints/AbstractClasses.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, 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,
+        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,
+        forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
+        forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0
-<
+-09-23 23:16  gezelter
->
+-09-24 04:16  gezelter
+        * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
+        src/Makefile, src/config.h.in, src/constraints/AbstractClasses.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, 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,
+        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,

Diff Legend

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

Comparing trunk/OOPSE-2.0/ChangeLog (file contents): Revision 1712 by tim, Thu Nov 4 20:55:01 2004 UTC vs. Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC

Diff Legend

Comparing trunk/OOPSE-2.0/ChangeLog (file contents):
Revision 1712 by tim, Thu Nov 4 20:55:01 2004 UTC vs.
Revision 2116 by tim, Fri Mar 11 15:00:20 2005 UTC