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

Comparing trunk/OOPSE-4/ChangeLog (file contents):
Revision 2762 by chrisfen, Fri May 19 21:26:41 2006 UTC vs.
Revision 3038 by chrisfen, Tue Oct 10 14:36:02 2006 UTC

-+
+-10-10 10:08  chrisfen
-+
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+        * src/applications/utilities/: affineScale, affineScale.in,
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+        solvator, solvator.in, waterBoxer, waterBoxer.in: who needs .in
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+        files for perl?  using env
-+
-+
+-10-09 22:44  gezelter
-+
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+        * src/: applications/randomBuilder/randomBuilder.cpp,
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+        applications/randomBuilder/randomBuilder.ggo,
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+        applications/randomBuilder/randomBuilderCmd.c,
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+        applications/randomBuilder/randomBuilderCmd.h, utils/MoLocator.cpp:
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+        fixing bugs in randomBuilder
-+
-+
+-10-09 18:16  gezelter
-+
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+        * samples/argon/lj.md,
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+        src/applications/randomBuilder/randomBuilder.cpp,
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+        src/applications/simpleBuilder/Makefile,
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+        src/applications/simpleBuilder/randomBuilder.cpp,
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+        src/applications/simpleBuilder/randomBuilder.ggo,
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+        src/applications/simpleBuilder/randomBuilderCmd.c,
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+        src/applications/simpleBuilder/randomBuilderCmd.h: Fixing the
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+        builders to prepare for OOPSE-4 release
-+
-+
+-10-06 17:29  chuckv
-+
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+        * src/applications/utilities/mdSplit: Added utility to split dump
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+        file frames into md files.
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+-10-03 18:39  chrisfen
-+
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+        * src/applications/utilities/Makefile: forgot to adjust the
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+        makefile
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+-10-03 18:38  chrisfen
-+
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+        * src/applications/utilities/: solvator.in, waterBoxer.in: added
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+        solvator and adjusted waterBoxer
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+-10-02 19:54  chrisfen
-+
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+        * src/applications/utilities/waterBoxer.in: improvements to
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+        waterBoxer
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+-10-02 19:27  chrisfen
-+
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+        * src/applications/utilities/waterBoxer.in: fixed a bug in
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+        waterBoxer for invalid water names
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+-09-26 17:55  gezelter
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+        * AUTHORS, README: Starting cleanup for 4.0 release
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+-09-26 12:08  gezelter
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+        * src/applications/staticProps/: BondOrderParameter.cpp,
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+        BondOrderParameter.hpp: Cleaned up the code for BondOrderParameter
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+        and added a bunch of comments.  Fixed a memory leak or ten.
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+-09-26 10:33  gezelter
-+
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+        * src/applications/staticProps/: BondOrderParameter.cpp,
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+        BondOrderParameter.hpp: Some efficiency fixes (now computes Wigner
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+-j coefficients only once in the constructor).
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+-09-25 21:30  gezelter
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+        * src/applications/staticProps/: BondOrderParameter.cpp,
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+        BondOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo,
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+        StaticPropsCmd.c, StaticPropsCmd.h: Mostly done with
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+        BondOrderParameter.  Only a few performance tweaks remain
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+-09-25 18:08  gezelter
-+
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+        * src/: applications/staticProps/BondOrderParameter.cpp,
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+        applications/staticProps/BondOrderParameter.hpp,
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+        applications/staticProps/StaticProps.cpp, brains/SimCreator.cpp,
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+        math/SphericalHarmonic.cpp: fixing bond order parameter code
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+-09-22 18:19  chrisfen
-+
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+        * src/: UseTheForce/DarkSide/simulation.F90, brains/SimInfo.cpp,
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+        brains/fSimulation.h, io/ForceFieldOptions.cpp,
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+        io/ForceFieldOptions.hpp, io/Globals.cpp, io/Globals.hpp: refined
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+        the reaction field dielectric passing
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+-09-21 21:41  gezelter
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+        * src/applications/staticProps/: BondOrderParameter.cpp,
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+        BondOrderParameter.hpp: bug fixes (still broken, however)
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+-09-21 21:36  gezelter
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+        * src/applications/staticProps/: BondOrderParameter.cpp,
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+        BondOrderParameter.hpp: Following Rein ten Wolde article
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+-09-21 17:47  gezelter
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+        * src/applications/staticProps/: BondOrderParameter.cpp,
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+        BondOrderParameter.hpp: more bug fixes
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+-09-21 16:43  gezelter
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+        * src/applications/staticProps/BondOrderParameter.cpp: more changes
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+        to BOP and SH
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+-09-21 14:25  chrisfen
-+
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+        * src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp,
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+        io/Globals.cpp: fixed the half self term for wolf electrostatics
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+        and OOPSE now chooses a cutoff radius dependent alpha for damped
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+        electrostatics
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+-09-21 14:04  gezelter
-+
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+        * src/applications/staticProps/BondOrderParameter.cpp: Fixed a bug
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+        in Wl code in BondOrderParameter
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+-09-21 10:45  gezelter
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+        * src/: applications/staticProps/BondOrderParameter.cpp,
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+        math/SphericalHarmonic.cpp, math/SphericalHarmonic.hpp: Bugfixes in
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+        BondOrderParameter and SphericalHarmonic
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+-09-20 18:16  gezelter
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+        * src/: applications/staticProps/BondOrderParameter.cpp,
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+        math/Makefile, math/SphericalHarmonic.cpp,
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+        math/SphericalHarmonic.hpp: added SphericalHarmonics, fixed a few
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+        problems with BondOrderParameter
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+-09-20 16:13  gezelter
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+        * src/applications/staticProps/: BondOrderParameter.cpp,
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+        BondOrderParameter.hpp, GofAngle2.cpp, StaticProps.cpp,
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+        StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: fixed bugs
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+        (mostly in BondOrderParameter)
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+-09-19 17:20  gezelter
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+        * src/applications/staticProps/: BondOrderParameter.cpp,
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+        BondOrderParameter.hpp: Adding BondOrderParameter to StaticProps
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+-09-19 17:14  gezelter
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+        * src/applications/staticProps/: BondOrderParameter.cpp,
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+        BondOrderParameter.hpp, Makefile, StaticProps.cpp, StaticProps.ggo,
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+        StaticPropsCmd.c, StaticPropsCmd.h: Working on BondOrderParameter
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+-09-18 17:31  chuckv
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+        * src/applications/staticProps/: BondOrderParameter.cpp,
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+        BondOrderParameter.hpp: Latest Version
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+-09-08 12:13  gezelter
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+        * src/: brains/BlockSnapshotManager.cpp, io/DumpReader.cpp,
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+        utils/residentMem.c: fixed a DumpReader bug, took out extra
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+        printing statements in residentMem and BlockSnapshotManager
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+-09-04 09:37  gezelter
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+        * configure, ac-tools/configure.in,
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+        src/applications/utilities/Makefile: changing configure script to
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+        process the new utilities
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+-09-01 18:58  chrisfen
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+        * src/applications/utilities/waterBoxer.in: added some features to
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+        waterBoxer
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+-09-01 17:08  chrisfen
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+        * src/applications/utilities/: Makefile, affineScale.in,
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+        waterBoxer.in: added the waterBoxer script
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+-09-01 15:22  chrisfen
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+        * src/applications/utilities/affineScale.in: added comment info
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+-09-01 15:16  gezelter
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+        * src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp,
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+        brains/Register.cpp, integrators/Makefile, integrators/NgammaT.cpp,
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+        integrators/NgammaT.hpp, io/Globals.cpp: adding NgammaT integrator
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+-09-01 14:29  chrisfen
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+        * src/applications/utilities/affineScale.in: modified affineScale
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+        to work with the new OOPSE files
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+-09-01 10:15  chrisfen
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+        * src/io/: RestReader.cpp, RestWriter.cpp: fixed TI MPI bug
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+-08-31 18:34  chrisfen
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+        * src/: integrators/VelocityVerletIntegrator.cpp,
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+        restraints/ThermoIntegrationForceManager.cpp: fixes to zang writing
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+-08-31 16:12  chrisfen
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+        * samples/alkane/butane.in, samples/alkane/butane.md,
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+        samples/argon/500.in, samples/argon/500.md, samples/argon/ar864.in,
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+        samples/argon/ar864.md, samples/argon/argonNVT.in,
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+        samples/argon/argonNVT.md, samples/cutoff/GB-Ar-max.md,
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+        samples/cutoff/GB-Ar-mix.md, samples/cutoff/GB-Ar-traditional.md,
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+        samples/cutoff/cutoff_test.in, samples/cutoff/cutoff_test.md,
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+        samples/cutoff/gb-ar.in, samples/cutoff/max.md,
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+        samples/cutoff/mix.md, samples/cutoff/traditional.md,
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+        samples/dipole/splitInWater.in, samples/dipole/splitInWater.md,
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+        samples/dipole/split_SSD.in, samples/dipole/split_SSD.md,
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+        samples/dipole/twoSplitDipole.in, samples/dipole/twoSplitDipole.md,
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+        samples/gbljtest/2gb.in, samples/gbljtest/2gb.md,
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+        samples/gbljtest/gb2lj1.in, samples/gbljtest/gb2lj1.md,
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+        samples/gbljtest/gbRotRoundX.in, samples/gbljtest/gbRotRoundX.md,
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+        samples/gbljtest/gbRotRoundY.in, samples/gbljtest/gbRotRoundY.md,
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+        samples/gbljtest/gbRotRoundZ.in, samples/gbljtest/gbRotRoundZ.md,
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+        samples/lipid/5x5.in, samples/lipid/5x5.md,
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+        samples/metals/EAM/Au_bulk.in, samples/metals/EAM/Au_bulk_FBD.md,
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+        samples/metals/EAM/Au_bulk_voter.md,
-+
+        samples/metals/EAM/nanoparticle/Au-Core-Ag-Shell_Nanoparticle.in,
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+        samples/metals/EAM/nanoparticle/Au-Core-Ag-Shell_Nanoparticle.md,
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+        samples/metals/EAM/nanoparticle/Au_nanoparticle.in,
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+        samples/metals/EAM/nanoparticle/Au_nanoparticle.md,
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+        samples/metals/EAM/nanorod/Au_nanoparticle.in,
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+        samples/metals/EAM/nanorod/Au_nanoparticle_FCC.md,
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+        samples/metals/Sutton-Chen/Au_bulk.in,
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+        samples/metals/Sutton-Chen/Au_bulk_QSC.md,
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+        samples/metals/Sutton-Chen/Au_bulk_SC.md,
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+        samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in,
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+        samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.md,
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+        samples/thermoIntegration/liquid/ssde.in,
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+        samples/thermoIntegration/liquid/ssde.md,
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+        samples/thermoIntegration/solid/ssde.in,
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+        samples/thermoIntegration/solid/ssde.md, samples/water/dimer/cl.in,
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+        samples/water/dimer/cl.md, samples/water/dimer/mix.in,
-+
+        samples/water/dimer/mix.md, samples/water/dimer/mix2.in,
-+
+        samples/water/dimer/mix2.md, samples/water/dimer/ssd.in,
-+
+        samples/water/dimer/ssd.md, samples/water/dimer/tap.in,
-+
+        samples/water/dimer/tap.md, samples/water/dimer/two.in,
-+
+        samples/water/dimer/two.md, samples/water/spce/spce.in,
-+
+        samples/water/spce/spce.md, samples/water/ssd/ssd.in,
-+
+        samples/water/ssd/ssd.md, samples/water/ssd-ion/ssd-ion.md,
-+
+        samples/water/ssd-ion/ssdCl.in, samples/water/ssd-ion/ssdCl.md,
-+
+        samples/water/ssde/ssde.in, samples/water/ssde/ssde.md,
-+
+        samples/water/ssdrf/ssdrf.in, samples/water/ssdrf/ssdrf.md,
-+
+        samples/water/tap/tap.in, samples/water/tap/tap.md,
-+
+        samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md,
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+        samples/water/tip4p/tp4.in, samples/water/tip4p/tp4.md,
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+        samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md,
-+
+        samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md,
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+        src/restraints/ThermoIntegrationForceManager.cpp: converted samples
-+
+        over to the OOPSE-4 file format
-+
-+
+        Fixed an MPI bug in thermodynamic integration
-+
-+
+-08-30 17:13  gezelter
-+
-+
+        * src/applications/hydrodynamics/Hydro.cpp: removed extra file in
-+
+        Hydro.cpp
-+
-+
+-08-30 17:04  gezelter
-+
-+
+        * src/: applications/dump2Xyz/Dump2XYZ.cpp,
-+
+        applications/dynamicProps/DynamicProps.cpp,
-+
+        applications/staticProps/StaticProps.cpp,
-+
+        applications/utilities/dumpConverter, openbabel/oopseformat.cpp:
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+        Changing utility programs to use the new file format
-+
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+-08-30 16:33  gezelter
-+
-+
+        * src/: brains/SimCreator.cpp, io/DumpReader.cpp,
-+
+        io/DumpWriter.cpp: fixed some bugs in DumpWriter, eliminated some
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+        extra printing of debugging information
-+
-+
+-08-30 14:42  tim
-+
-+
+        * configure, ac-tools/OOPSE.m4, forceFields/Au.u3.funcfl,
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+        forceFields/Ni.u3.funcfl, samples/argon/lj.md,
-+
+        src/brains/Register.cpp, src/brains/SimCreator.cpp,
-+
+        src/brains/SimCreator.hpp, src/brains/SimInfo.cpp,
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+        src/brains/SimInfo.hpp, src/io/DumpReader.cpp,
-+
+        src/io/DumpReader.hpp, src/io/DumpWriter.cpp,
-+
+        src/io/DumpWriter.hpp, src/io/Globals.cpp, src/io/Globals.hpp,
-+
+        src/mdParser/SimplePreprocessor.hpp, src/openbabel/Makefile,
-+
+        src/openbabel/oopseformat.cpp, src/primitives/StuntDouble.cpp,
-+
+        src/primitives/StuntDouble.hpp, src/utils/StringUtils.cpp,
-+
+        src/utils/StringUtils.hpp: Massive changes preparing for release of
-+
+        OOPSE-4: The main difference is that the new MD file format (.md,
-+
+        .dump, .eor) now contains meta-data information along with the
-+
+        configuration information.
-+
-+
+-08-24 13:42  xsun
-+
-+
+        * src/io/Globals.cpp: change the globals.cpp to make sure we can
-+
+        set targetPressure and surfaceTension to be negative.
-+
-+
+-08-14 16:32  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/electrostatic.F90: fixed an ordering
-+
+        issue in quadrupole-charge interactions
-+
-+
+-08-02 15:40  gezelter
-+
-+
+        * make/Makefile.in, samples/water/ssde/ssde.md, src/config.h.in,
-+
+        src/antlr/Makefile, src/applications/atom2md/atom2md.cpp,
-+
+        src/brains/Snapshot.cpp, src/brains/Snapshot.hpp,
-+
+        src/openbabel/Makefile, src/openbabel/oopseformat.cpp,
-+
+        src/openbabel/oopseformat.hpp: starting change of file formats
-+
-+
+-08-02 14:06  gezelter
-+
-+
+        * src/applications/: atom2md/Makefile, atom2md/atom2md.cpp,
-+
+        atom2mdin/Makefile, atom2mdin/atom2mdin.cpp: Changing atom2mdin
-+
+        into atom2md to reflect new unified file format
-+
-+
+-07-27 17:02  chrisfen
-+
-+
+        * src/applications/utilities/dumpConverter: fixed a pvf bug
-+
-+
+-07-27 16:36  tim
-+
-+
+        * src/applications/utilities/dumpConverter: fixed dumpConverter
-+
+        problems
-+
-+
+-07-27 15:05  gezelter
-+
-+
+        * src/applications/utilities/dumpConverter: added dumpConverter
-+
-+
+-07-26 17:45  gezelter
-+
-+
+        * make/Makefile.in: removed shapes sample
-+
-+
+-07-26 17:45  gezelter
-+
-+
+        * src/applications/utilities/affineScale.in: fixed a spelling bug
-+
-+
+-07-26 17:01  gezelter
-+
-+
+        * configure: added perl interpreter to affineScale script
-+
-+
+-07-26 17:01  gezelter
-+
-+
+        * ac-tools/configure.in: added perl substitution for affineScale
-+
+        script
-+
-+
+-07-26 17:00  gezelter
-+
-+
+        * make/Makefile.in: added install target for scripts
-+
-+
+-07-26 17:00  gezelter
-+
-+
+        * src/applications/utilities/: Makefile, affineScale.in: Adding a
-+
+        directory for scripts Adding affineScale script
-+
-+
+-07-24 10:51  xsun
-+
-+
+        * src/UseTheForce/DarkSide/gb.F90: fixed a getSigma bug
-+
-+
+-07-19 08:46  chrisfen
-+
-+
+        * samples/: thermoIntegration/liquid/water.md,
-+
+        thermoIntegration/solid/water.md, water/dimer/water.md,
-+
+        water/spce/water.md, water/ssd/water.md, water/ssd-ion/water.md,
-+
+        water/ssde/water.md, water/ssdrf/water.md, water/tap/water.md,
-+
+        water/tip3p_ice/water.md, water/tip4p/water.md: Added tred to
-+
+        sample water.md files
-+
-+
+-07-19 08:35  chrisfen
-+
-+
+        * src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp,
-+
+        RigidBodyVisitor.cpp, RigidBodyVisitor.hpp: Added TRED water
-+
+        visitor for Dump2XYZ visualization
-+
-+
+-07-19 08:33  chrisfen
-+
-+
+        * forceFields/DUFF2.frc: Added TRED parameters to forcefield
-+
-+
+-07-17 14:13  xsun
-+
-+
+        * src/UseTheForce/DarkSide/gb.F90: fixed d / sigma0 confusion
-+
-+
+-07-15 22:48  gezelter
-+
-+
+        * src/io/ForceFieldOptions.cpp: testing commit logger
-+
-+
+-07-15 22:46  gezelter
-+
-+
+        * src/io/ForceFieldOptions.cpp: removed printing of GBN and GBM
-+
+        from previous debugging
-+
-+
+-07-14 10:47  xsun
-+
-+
+        * configure, ac-tools/OOPSE.m4: Fixed a bug in the fftw part of the
-+
+        configure script.
-+
-+
+-07-07 15:44  gezelter
-+
-+
+        * configure, ac-tools/configure.in, samples/gbljtest/2gb.md,
-+
+        src/UseTheForce/DarkSide/gb.F90: removed icc from C++ search lines,
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+        did some formatting work on GB module, mucked around with a GB
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+        example
-+
-+
+-07-07 10:18  chuckv
-+
-+
+        * src/applications/staticProps/: BondOrderParameter.cpp,
-+
+        BondOrderParameter.hpp: Adding more changes to orientational bond
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+        order parameter.
-+
-+
+-07-03 15:40  chuckv
-+
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+        * src/math/Wigner3jm.F90: Added utility function to winger3jm from
-+
+        slatac.
-+
-+
+-07-03 10:06  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/mpole.F90: Added the multipole
-+
+        interaction routine.  It doesn't work yet, so it's not included in
-+
+        the build.
-+
-+
+-07-03 09:18  chrisfen
-+
-+
+        * src/: UseTheForce/doForces.F90,
-+
+        UseTheForce/doForces_interface.F90,
-+
+        UseTheForce/doForces_interface.h,
-+
+        UseTheForce/DarkSide/electrostatic.F90,
-+
+        UseTheForce/DarkSide/simulation.F90, brains/ForceManager.cpp,
-+
+        brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp,
-+
+        brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp,
-+
+        brains/fSimulation.h, integrators/VelocityVerletIntegrator.cpp,
-+
+        io/Globals.cpp, io/Globals.hpp,
-+
+        restraints/ThermoIntegrationForceManager.cpp: Added simulation box
-+
+        dipole moment accumulation for the purposes of calculating
-+
+        dielectric constants
-+
-+
+-07-01 18:27  kdaily
-+
-+
+        * src/UseTheForce/DarkSide/gb.F90: fixed forces and torques for GB
-+
-+
+-06-28 10:35  chrisfen
-+
-+
+        * src/io/: DumpReader.cpp, RestReader.cpp, RestReader.hpp: more
-+
+        efficient file reading for thermodynamic integration, and fixed
-+
+        some formatting
-+
-+
+-06-27 12:36  chuckv
-+
-+
+        * src/applications/staticProps/: BondOrderParameter.cpp,
-+
+        BondOrderParameter.hpp: Beginnings of a order parameter.
-+
-+
+-06-27 12:19  chuckv
-+
-+
+        * src/applications/staticProps/: BondOrderParameter.cpp,
-+
+        BondOrderParameter.hpp: Adding code for bond orientational
-+
+        parameters.
-+
-+
+-06-22 11:21  chrisfen
-+
-+
+        * src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp,
-+
+        integrators/VelocityVerletIntegrator.cpp, io/RestWriter.cpp,
-+
+        io/RestWriter.hpp, restraints/ThermoIntegrationForceManager.cpp:
-+
+        MPI thermodynamic integration works now.
-+
-+
+-06-21 14:28  chrisfen
-+
-+
+        * src/visitors/AtomVisitor.cpp: fixed a build problem...
-+
+        GB_12b_ratio no longer exists (replaced with BG_l).
-+
-+
+-06-19 13:55  chuckv
-+
-+
+        * src/math/: Makefile, Wigner3jm.F90, Wigner3jm_interface.h: Added
-+
+        support for Winger3jm coefficients.
-+
-+
+-06-18 21:36  chrisfen
-+
-+
+        * src/: io/RestReader.cpp, io/RestWriter.cpp,
-+
+        restraints/ThermoIntegrationForceManager.cpp: fixes for mpi
-+
+        thermodynamic integration, close to fully working...
-+
-+
+-06-17 13:02  tim
-+
-+
+        * src/visitors/AtomVisitor.cpp: output the principle axis of GB
-+
-+
+-06-15 14:38  gezelter
-+
-+
+        * configure, ac-tools/OOPSE.m4, ac-tools/configure.in,
-+
+        samples/water/tip4p/tp4.md: added mpi compilers, demoted pg
-+
+        compilers after pathscale
-+
-+
+-06-09 14:26  chrisfen
-+
-+
+        * src/UseTheForce/DarkSide/electrostatic.F90: reformulated some of
-+
+        the electrostatics
-+
-+
+-06-07 18:49  chrisfen
-+
-+
+        * samples/water/ssd/ssd.md,
-+
+        src/UseTheForce/DarkSide/electrostatic.F90: damping now works for
-+
+        charge-quadrupole and dipole-dipole
-+
-+
+-06-07 14:05  chrisfen
-+
-+
+        * src/: UseTheForce/DarkSide/simParallel.F90, io/RestReader.cpp:
-+
+        Fixed a spelling error and a bug in MPI Thermodynamic Integration
-+
+        on file read-in
-+
-+
+-06-06 14:26  chrisfen
-+
-+
+        * src/io/: DumpReader.cpp, MultipoleAtomTypesSectionParser.cpp:
-+
+        fixed some typos
-+
-+
+-06-06 13:43  gezelter
-+
-+
+        * forceFields/DUFF2.frc, samples/gbljtest/2gb.in,
-+
+        samples/gbljtest/2gb.md, samples/gbljtest/gb.md,
-+
+        samples/gbljtest/gb2lj1.in, samples/gbljtest/gb2lj1.md,
-+
+        samples/gbljtest/gbRotRoundX.in, samples/gbljtest/gbRotRoundX.md,
-+
+        samples/gbljtest/gbRotRoundY.in, samples/gbljtest/gbRotRoundY.md,
-+
+        samples/gbljtest/gbRotRoundZ.in, samples/gbljtest/gbRotRoundZ.md,
-+
+        src/UseTheForce/DarkSide/gb.F90,
-+
+        src/integrators/LDForceManager.cpp,
-+
+        src/integrators/LDForceManager.hpp, src/io/ForceFieldOptions.cpp,
-+
+        src/utils/interpolation.F90, src/visitors/AtomVisitor.hpp: testing
-+
+        GB, removing CM drift in Langevin Dynamics, fixing a memory leak,
-+
+        adding a visitor
-+
-+
+-06-05 14:44  gezelter
-+
-+
+        * src/UseTheForce/DarkSide/: fForceOptions.F90, gb.F90: Added
-+
+        methods to access GB_mu and GB_nu from the force field options
-+
-+
+-06-05 14:24  gezelter
-+
-+
+        * forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp,
-+
+        src/UseTheForce/doForces.F90, src/UseTheForce/fForceOptions.h,
-+
+        src/UseTheForce/DarkSide/gb.F90,
-+
+        src/UseTheForce/DarkSide/gb_interface.F90,
-+
+        src/UseTheForce/DarkSide/gb_interface.h,
-+
+        src/applications/hydrodynamics/AnalyticalModel.cpp,
-+
+        src/applications/hydrodynamics/ApproximationModel.cpp,
-+
+        src/applications/hydrodynamics/ApproximationModel.hpp,
-+
+        src/applications/hydrodynamics/CompositeShape.cpp,
-+
+        src/applications/hydrodynamics/CompositeShape.hpp,
-+
+        src/applications/hydrodynamics/HydrodynamicsModel.cpp,
-+
+        src/applications/hydrodynamics/HydrodynamicsModel.hpp,
-+
+        src/applications/hydrodynamics/ShapeBuilder.cpp,
-+
+        src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp,
-+
+        src/hydrodynamics/HydroProp.cpp, src/hydrodynamics/HydroProp.hpp,
-+
+        src/hydrodynamics/Makefile, src/hydrodynamics/Shape.hpp,
-+
+        src/hydrodynamics/Sphere.cpp, src/hydrodynamics/Sphere.hpp,
-+
+        src/integrators/LDForceManager.cpp,
-+
+        src/integrators/LDForceManager.hpp, src/io/ForceFieldOptions.cpp,
-+
+        src/io/ForceFieldOptions.hpp,
-+
+        src/io/GayBerneAtomTypesSectionParser.cpp,
-+
+        src/io/GayBerneAtomTypesSectionParser.hpp,
-+
+        src/types/DirectionalAtomType.cpp,
-+
+        src/types/DirectionalAtomType.hpp, src/utils/HydroProps.hpp:
-+
+        Massive changes for GB code with multiple ellipsoid types (a la
-+
+        Cleaver's paper).
-+
-+
+        Also, changes in hydrodynamics code to make HydroProp a somewhat
-+
+        smarter class (rather than just a struct).
-+
-+
+-06-01 14:06  xsun
-+
-+
+        * src/applications/staticProps/: Makefile, RippleOP.cpp,
-+
+        RippleOP.hpp, StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c,
-+
+        StaticPropsCmd.h: Add the RippleOP to calculate the orderparameter
-+
+        of the ripples.
-+
-+
+-05-25 17:40  chrisfen
-+
-+
+        * forceFields/DUFF2.frc, samples/thermoIntegration/liquid/water.md,
-+
+        samples/thermoIntegration/solid/water.md,
-+
+        samples/water/dimer/water.md, samples/water/spce/water.md,
-+
+        samples/water/ssd/water.md, samples/water/ssd-ion/water.md,
-+
+        samples/water/ssde/water.md, samples/water/ssdrf/water.md,
-+
+        samples/water/tap/water.md, samples/water/tip3p_ice/water.md,
-+
+        samples/water/tip4p/water.md, src/io/Globals.cpp: Added TIP5P-E and
-+
+        fixed a bug for Thermodynamic integration (you can now have a
-+
+        lambda of 0)
-+
-+
+-05-25 13:02  tim
-+
-+
+        * src/applications/hydrodynamics/ApproximationModel.cpp: Fix a type
-+
+        promotion problem
-+
-+
+-05-25 12:27  tim
-+
-+
+        * src/applications/hydrodynamics/: AnalyticalModel.hpp,
-+
+        ApproximationModel.cpp, Hydro.cpp, HydrodynamicsModel.hpp: replace
-+
+        double with RealType
-+
-+
+-05-25 11:27  gezelter
-+
-+
+        * configure: What?
-+
-+
+-05-25 11:24  gezelter
-+
-+
+        * ac-tools/OOPSE.m4: more changes
-+
-+
+-05-25 11:19  gezelter
-+
-+
+        * configure, ac-tools/OOPSE.m4: more changes for MPICH with
-+
+        profiling libraries required
-+
-+
+-05-25 10:54  gezelter
-+
-+
+        * configure, ac-tools/OOPSE.m4: MPI stuff
-+
-+
+-05-24 14:31  gezelter
-+
-+
+        * configure, ac-tools/OOPSE.m4, src/config.h.in,
-+
+        src/applications/hydrodynamics/AnalyticalModel.cpp,
-+
+        src/applications/hydrodynamics/AnalyticalModel.hpp,
-+
+        src/applications/hydrodynamics/ApproximationModel.cpp,
-+
+        src/applications/hydrodynamics/ApproximationModel.hpp,
-+
+        src/applications/hydrodynamics/CompositeShape.cpp,
-+
+        src/applications/hydrodynamics/CompositeShape.hpp,
-+
+        src/applications/hydrodynamics/Ellipsoid.cpp,
-+
+        src/applications/hydrodynamics/Ellipsoid.hpp,
-+
+        src/applications/hydrodynamics/Hydro.cpp,
-+
+        src/applications/hydrodynamics/HydrodynamicsModel.cpp,
-+
+        src/applications/hydrodynamics/HydrodynamicsModel.hpp,
-+
+        src/applications/hydrodynamics/RoughShell.cpp,
-+
+        src/applications/hydrodynamics/RoughShell.hpp,
-+
+        src/applications/hydrodynamics/Shape.hpp,
-+
+        src/applications/hydrodynamics/ShapeBuilder.cpp,
-+
+        src/applications/hydrodynamics/ShapeBuilder.hpp,
-+
+        src/applications/hydrodynamics/Spheric.cpp,
-+
+        src/applications/hydrodynamics/Spheric.hpp: fixes for Hydrodynamics
-+
-+
+-05-24 12:18  tim
-+
-+
+        * src/integrators/LDForceManager.cpp: fix a bug in parsing
-+
+        HydroProp file
-+
-+
+-05-24 11:24  gezelter
-+
-+
+        * src/integrators/LDForceManager.cpp: Fixed a bug when spherical
-+
+        boundary conditions were off.
-+
-+
+-05-23 17:12  xsun
-+
-+
+        * src/applications/staticProps/Hxy.cpp: fixed an initialization bug
-+
+        of Hxy.cpp.
-+
-+
+-05-23 14:46  tim
-+
-+
+        * src/applications/dump2Xyz/Dump2XYZ.cpp: wrapping back to PBC by
-+
+        molecule instead of by individual atom
-+
-+
+-05-22 11:30  xsun
-+
-+
+        * src/applications/staticProps/: Hxy.cpp, Hxy.hpp, StaticProps.ggo,
-+
+        StaticPropsCmd.c, StaticPropsCmd.h: fixed the bugs of Hxy.cpp.
-+
-+
+-05-19 17:26  chrisfen
-+
-+
+        * ChangeLog, src/io/DumpWriter.cpp: Last bug showed up in 2 places,
-+
+        fixed the other one.
-+
+-05-19 16:45  tim
+        * src/io/DumpWriter.cpp: Fix a bug of printing empty line in

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Comparing trunk/OOPSE-4/ChangeLog (file contents): Revision 2762 by chrisfen, Fri May 19 21:26:41 2006 UTC vs. Revision 3038 by chrisfen, Tue Oct 10 14:36:02 2006 UTC

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Comparing trunk/OOPSE-4/ChangeLog (file contents):
Revision 2762 by chrisfen, Fri May 19 21:26:41 2006 UTC vs.
Revision 3038 by chrisfen, Tue Oct 10 14:36:02 2006 UTC