--- trunk/OOPSE-4/ChangeLog 2006/05/19 20:45:55 2761 +++ trunk/OOPSE-4/ChangeLog 2006/05/19 21:26:41 2762 @@ -1,5 +1,171 @@ -2006-05-17 14:54 gezelter +2006-05-19 16:45 tim + * src/io/DumpWriter.cpp: Fix a bug of printing empty line in + DumpWriter + +2006-05-19 11:11 tim + + * make/Makefile.in: change the order of include path and library + path + +2006-05-17 17:51 tim + + * ChangeLog, samples/water/ssd/ssd.md, src/config.h.in, + src/UseTheForce/EAM_FF.cpp, src/UseTheForce/EAM_FF.hpp, + src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, + src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, + src/UseTheForce/doForces_interface.h, + src/UseTheForce/fForceOptions.h, + src/UseTheForce/DarkSide/eam_interface.h, + src/UseTheForce/DarkSide/electrostatic_interface.h, + src/UseTheForce/DarkSide/gb_interface.h, + src/UseTheForce/DarkSide/lj_interface.h, + src/UseTheForce/DarkSide/shapes_interface.h, + src/UseTheForce/DarkSide/simulation_interface.h, + src/UseTheForce/DarkSide/sticky_interface.h, + src/UseTheForce/DarkSide/suttonchen_interface.h, + src/applications/dynamicProps/CrossTimeCorrFunc.cpp, + src/applications/dynamicProps/CrossTimeCorrFunc.hpp, + src/applications/dynamicProps/DipoleCorrFunc.cpp, + src/applications/dynamicProps/DipoleCorrFunc.hpp, + src/applications/dynamicProps/LegendreCorrFunc.cpp, + src/applications/dynamicProps/LegendreCorrFunc.hpp, + src/applications/dynamicProps/ParticleTimeCorrFunc.cpp, + src/applications/dynamicProps/ParticleTimeCorrFunc.hpp, + src/applications/dynamicProps/RCorrFunc.cpp, + src/applications/dynamicProps/RCorrFunc.hpp, + src/applications/dynamicProps/TimeCorrFunc.hpp, + src/applications/dynamicProps/VCorrFunc.cpp, + src/applications/dynamicProps/VCorrFunc.hpp, + src/applications/hydrodynamics/Makefile, + src/applications/nanoRodBuilder/GeometryBuilder.cpp, + src/applications/nanoRodBuilder/GeometryBuilder.hpp, + src/applications/nanoRodBuilder/nanorodBuilder.cpp, + src/applications/randomBuilder/randomBuilder.cpp, + src/applications/simpleBuilder/randomBuilder.cpp, + src/applications/staticProps/DensityPlot.cpp, + src/applications/staticProps/DensityPlot.hpp, + src/applications/staticProps/GofAngle2.cpp, + src/applications/staticProps/GofAngle2.hpp, + src/applications/staticProps/GofR.cpp, + src/applications/staticProps/GofR.hpp, + src/applications/staticProps/GofRAngle.cpp, + src/applications/staticProps/GofRAngle.hpp, + src/applications/staticProps/GofXyz.cpp, + src/applications/staticProps/GofXyz.hpp, + src/applications/staticProps/Hxy.cpp, + src/applications/staticProps/Hxy.hpp, + src/applications/staticProps/P2OrderParameter.cpp, + src/applications/staticProps/P2OrderParameter.hpp, + src/applications/staticProps/RhoZ.cpp, + src/applications/staticProps/RhoZ.hpp, + src/applications/staticProps/SCDOrderParameter.cpp, + src/applications/staticProps/SCDOrderParameter.hpp, + src/applications/staticProps/StaticProps.cpp, + src/brains/BlockSnapshotManager.cpp, src/brains/DataStorage.cpp, + src/brains/DataStorage.hpp, src/brains/ForceManager.cpp, + src/brains/SimCreator.cpp, src/brains/SimInfo.cpp, + src/brains/SimInfo.hpp, src/brains/Snapshot.cpp, + src/brains/Snapshot.hpp, src/brains/Stats.hpp, + src/brains/Thermo.cpp, src/brains/Thermo.hpp, + src/brains/fSimulation.h, src/constraints/ConstraintElem.hpp, + src/constraints/ConstraintPair.hpp, src/constraints/Rattle.cpp, + src/constraints/Rattle.hpp, src/constraints/ZconsStruct.hpp, + src/constraints/ZconstraintForceManager.cpp, + src/constraints/ZconstraintForceManager.hpp, + src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp, + src/hydrodynamics/Shape.hpp, src/hydrodynamics/Sphere.cpp, + src/hydrodynamics/Sphere.hpp, src/integrators/DLM.cpp, + src/integrators/DLM.hpp, src/integrators/Integrator.hpp, + src/integrators/LDForceManager.cpp, + src/integrators/LDForceManager.hpp, + src/integrators/LangevinDynamics.cpp, + src/integrators/LangevinDynamics.hpp, src/integrators/NPAT.cpp, + src/integrators/NPAT.hpp, 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/NPrT.cpp, + src/integrators/NPrT.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/BendTypesSectionParser.cpp, + src/io/BondTypesSectionParser.cpp, + src/io/ChargeAtomTypesSectionParser.cpp, + src/io/DirectionalAtomTypesSectionParser.cpp, + src/io/DumpReader.cpp, src/io/DumpWriter.cpp, + src/io/EAMAtomTypesSectionParser.cpp, + src/io/EAMAtomTypesSectionParser.hpp, src/io/ForceFieldOptions.hpp, + src/io/Globals.hpp, src/io/MultipoleAtomTypesSectionParser.cpp, + src/io/RestReader.cpp, src/io/RestReader.hpp, + src/io/RestWriter.cpp, src/io/TorsionTypesSectionParser.cpp, + src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, + src/lattice/CubicLattice.cpp, src/lattice/CubicLattice.hpp, + src/lattice/FCCLattice.cpp, src/lattice/Lattice.cpp, + src/lattice/Lattice.hpp, src/lattice/shapedLattice.cpp, + src/lattice/shapedLattice.hpp, src/math/ChebyshevPolynomials.hpp, + src/math/CholeskyDecomposition.hpp, + src/math/LegendrePolynomial.cpp, src/math/LegendrePolynomial.hpp, + src/math/MatVec3.c, src/math/MatVec3.h, + src/math/MersenneTwister.hpp, src/math/Polynomial.hpp, + src/math/Quaternion.hpp, src/math/RandNumGen.hpp, + src/math/RealSphericalHarmonic.cpp, + src/math/RealSphericalHarmonic.hpp, src/math/SquareMatrix.hpp, + src/math/SquareMatrix3.hpp, src/math/Vector.hpp, + src/math/Vector3.hpp, src/mdParser/MDTreeParser.cpp, + src/mdParser/MDTreeParser.g, src/mdParser/MDTreeParser.hpp, + src/minimizers/CGFamilyMinimizer.cpp, + src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Minimizer.cpp, + src/minimizers/Minimizer.hpp, + src/minimizers/MinimizerParameterSet.hpp, src/minimizers/PRCG.cpp, + src/minimizers/SDMinimizer.cpp, src/minimizers/SDMinimizer.hpp, + src/primitives/Atom.cpp, src/primitives/Atom.hpp, + src/primitives/Bend.cpp, src/primitives/Bend.hpp, + src/primitives/Bond.hpp, src/primitives/CutoffGroup.hpp, + src/primitives/DirectionalAtom.cpp, + src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, + src/primitives/GhostBend.hpp, src/primitives/GhostTorsion.cpp, + src/primitives/GhostTorsion.hpp, src/primitives/Molecule.cpp, + src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, + src/primitives/RigidBody.hpp, src/primitives/StuntDouble.hpp, + src/primitives/Torsion.cpp, src/primitives/Torsion.hpp, + src/primitives/UreyBradleyBend.cpp, + src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, + src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, + src/restraints/ThermoIntegrationForceManager.hpp, + src/selection/DistanceFinder.cpp, src/selection/DistanceFinder.hpp, + src/selection/SelectionEvaluator.cpp, + src/selection/SelectionEvaluator.hpp, src/types/AtomStamp.cpp, + src/types/AtomStamp.hpp, src/types/AtomType.cpp, + src/types/AtomType.hpp, src/types/AtomTypeProperties.h, + src/types/BendType.hpp, src/types/BondType.hpp, + src/types/CharmmTorsionType.hpp, src/types/CubicBendType.hpp, + src/types/CubicBondType.hpp, src/types/CubicTorsionType.hpp, + src/types/DirectionalAtomType.cpp, + src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, + src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.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/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, + src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, + src/types/ZconsStamp.hpp, src/utils/Algorithm.hpp, + src/utils/GenericData.hpp, src/utils/MoLocator.cpp, + src/utils/MoLocator.hpp, src/utils/NumericConstant.hpp, + src/utils/OOPSEConstant.hpp, src/utils/ParameterManager.hpp, + src/utils/StringTokenizer.cpp, src/utils/StringTokenizer.hpp, + src/utils/Utility.hpp, src/utils/physmem.c, src/utils/physmem.h, + src/utils/residentMem.c, src/utils/residentMem.h, + src/visitors/ZconsVisitor.cpp, src/visitors/ZconsVisitor.hpp: + Adding single precision capabilities to c++ side + +2006-05-17 15:54 gezelter + * configure, ac-tools/configure.in, make/Makefile.in, src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/neighborLists.F90, @@ -9,12 +175,12 @@ src/utils/definitions.F90: Adding single precision capabilities to the fortran side -2006-05-17 11:10 gezelter +2006-05-17 12:10 gezelter * configure, ac-tools/configure.in, src/config.h.in: adding --enable-single to configure script -2006-05-17 10:37 gezelter +2006-05-17 11:37 gezelter * ac-tools/aclocal.m4, src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, @@ -30,17 +196,17 @@ src/math/erfc.F90, src/utils/interpolation.F90: Getting fortran side prepped for single precision... -2006-05-17 09:03 chrisfen +2006-05-17 10:03 chrisfen * samples/water/ssd-ion/ssdCl.md, src/UseTheForce/DarkSide/electrostatic.F90: electrostatic refinement -2006-05-16 22:03 gezelter +2006-05-16 23:03 gezelter * configure, ac-tools/OOPSE.m4, make/Makefile.in: zlib fixes -2006-05-16 15:38 gezelter +2006-05-16 16:38 gezelter * configure, ac-tools/OOPSE.m4, ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in, ac-tools/install-sh, @@ -50,7 +216,7 @@ src/applications/staticProps/StaticProps.cpp: Autoconf fixes for FFTW. Multiple FFTW version support. -2006-05-15 21:06 gezelter +2006-05-15 22:06 gezelter * README, configure, ac-tools/aclocal.m4, ac-tools/configure.in, make/Makefile.in, src/config.h.in, @@ -66,13 +232,13 @@ src/integrators/LDForceManager.hpp, src/math/SquareMatrix.hpp, src/utils/HydroProps.hpp: [no log message] -2006-05-12 16:34 xsun +2006-05-12 17:34 xsun * src/applications/staticProps/: Hxy.cpp, Hxy.hpp, Makefile, StaticProps.cpp, StaticPropsCmd.c, StaticPropsCmd.h: Changes to calculate undulation spectrum -2006-05-09 20:44 tim +2006-05-09 21:44 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/dump2Xyz/Dump2XYZ.ggo, @@ -82,48 +248,48 @@ visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: adding a gay-berne switch to Dump2XYZ -2006-05-05 12:58 gezelter +2006-05-05 13:58 gezelter * src/UseTheForce/DarkSide/qpole.F90: Adding qpole -2006-05-05 09:34 tim +2006-05-05 10:34 tim * ac-tools/aclocal.m4: finding ifort arguments that won't die under two different versions of the intel fortran compiler -2006-05-03 08:15 chrisfen +2006-05-03 09:15 chrisfen * src/applications/randomBuilder/Makefile: missing makefile was hanging up 'make clean' -2006-04-25 17:59 chuckv +2006-04-25 18:59 chuckv * src/applications/randomBuilder/: randomBuilder.cpp, randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added random builder to cvs. -2006-04-25 17:54 chuckv +2006-04-25 18:54 chuckv * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: Change in siminfo used in nanoparticleBuilder. -2006-04-25 17:30 chuckv +2006-04-25 18:30 chuckv * make/Makefile.in: Added random builder -2006-04-25 17:29 chuckv +2006-04-25 18:29 chuckv * src/applications/simpleBuilder/: Makefile, randomBuilder.cpp, randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added a random builder to oopse. -2006-04-25 08:35 gezelter +2006-04-25 09:35 gezelter * src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, ShapeBuilder.cpp, ShapeBuilder.hpp: Using OpenBabel element table to pick vdw radii for hydrodynamics if the LJ sigma can't be found. -2006-04-24 21:09 gezelter +2006-04-24 22:09 gezelter * configure, ac-tools/aclocal.m4, src/UseTheForce/DarkSide/LJ.F90, src/applications/hydrodynamics/Hydro.cpp, src/brains/Register.cpp, @@ -135,17 +301,17 @@ src/io/Globals.hpp, src/primitives/StuntDouble.hpp: Adding spherical boundary conditions to LD integrator -2006-04-24 21:06 gezelter +2006-04-24 22:06 gezelter * src/applications/hydrodynamics/: BeadModel.cpp, ShapeBuilder.cpp: Added EAM atom types to Hydro models -2006-04-21 15:02 chrisfen +2006-04-21 16:02 chrisfen * src/UseTheForce/DarkSide/eam.F90: put spline subroutines in the EAM module -2006-04-21 14:32 chrisfen +2006-04-21 15:32 chrisfen * ChangeLog, samples/shape/5CB.shape, samples/shape/8CB.shape, samples/shape/C60.shape, samples/shape/C70.shape, @@ -164,17 +330,17 @@ water samples to use shifted_force. Probably should set the defaults to use the damped version now that we sped it up. -2006-04-20 22:19 chrisfen +2006-04-20 23:19 chrisfen * samples/water/spce/spce.md, src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added... -2006-04-20 16:02 chrisfen +2006-04-20 17:02 chrisfen * samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90, src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky -2006-04-20 13:24 gezelter +2006-04-20 14:24 gezelter * samples/metals/EAM/Au_bulk_voter.md, samples/metals/Sutton-Chen/Au_bulk_SC.md, @@ -189,7 +355,7 @@ src/utils/interpolation.F90: Complete rewrite of spline code and everything that uses it. -2006-04-17 16:49 gezelter +2006-04-17 17:49 gezelter * configure, ac-tools/aclocal.m4, samples/argon/500.md, samples/metals/EAM/Au_bulk_voter.md, @@ -207,7 +373,7 @@ src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp, src/utils/interpolation.F90: Many performance improvements -2006-04-15 21:51 chrisfen +2006-04-15 22:51 chrisfen * configure, samples/argon/500.md, src/UseTheForce/doForces.F90, src/UseTheForce/fSwitchingFunction.h, @@ -215,48 +381,48 @@ src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to switcheroo -2006-04-15 16:58 chrisfen +2006-04-15 17:58 chrisfen * src/utils/Makefile.in: Since status.F90 is used by interpolation.F90, the former needs to be listed above the later in the Makefile. -2006-04-14 16:59 gezelter +2006-04-14 17:59 gezelter * src/utils/interpolation.F90: changed the interface a bit -2006-04-14 16:49 gezelter +2006-04-14 17:49 gezelter * src/utils/interpolation.F90: added some logical flags -2006-04-14 16:06 chrisfen +2006-04-14 17:06 chrisfen * src/utils/interpolation.F90: Wiped the spline with derivatives and corrected a boundary comparision error by eliminating the check. This algorithm REQUIRES known first derivatives at the endpoints. -2006-04-14 15:04 gezelter +2006-04-14 16:04 gezelter * src/utils/: Makefile.in, interpolation.F90: bug fixes for interpolation module -2006-04-14 14:57 gezelter +2006-04-14 15:57 gezelter * src/utils/interpolation.F90: Heavily modified interpolation module, also moved to "utils" -2006-04-12 16:15 chuckv +2006-04-12 17:15 chuckv * src/UseTheForce/DarkSide/interpolation.F90: Added interpolation module. -2006-04-11 10:33 gezelter +2006-04-11 11:33 gezelter * src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: [no log message] -2006-04-03 10:37 chuckv +2006-04-03 11:37 chuckv * configure, ac-tools/aclocal.m4, make/Makefile.in, src/UseTheForce/DarkSide/simParallel.F90: Added status module to @@ -1407,6 +1573,8 @@ * make/Makefile.in, src/applications/atom2mdin/Makefile, src/applications/atom2mdin/atom2mdin.cpp, + src/applications/mdinConverter/Makefile, + src/applications/mdinConverter/mdinConverter.cpp, src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp: rename mdinConverter to atom2mdin @@ -1471,6 +1639,11 @@ UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField optional parameters.... +2005-11-16 16:24 tim + + * src/applications/mdinConverter/: Makefile, mdinConverter.cpp: + adding mdinConverter + 2005-11-16 16:22 tim * src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp, @@ -1725,35 +1898,35 @@ * src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In process of adding sutton-chen forcefield. -2005-10-26 18:32 chrisfen +2005-10-26 19:32 chrisfen * src/brains/SimInfo.cpp: changed the default switching radius to 85% of rcut -2005-10-26 18:31 chrisfen +2005-10-26 19:31 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks to be working now - for charges and dipoles alike -2005-10-26 18:31 chrisfen +2005-10-26 19:31 chrisfen * src/UseTheForce/doForces.F90: reaction field looks to be working now -2005-10-26 18:30 chrisfen +2005-10-26 19:30 chrisfen * samples/water/ssdrf/water.md: added a test molecule -2005-10-26 18:30 chrisfen +2005-10-26 19:30 chrisfen * forceFields/DUFF2.frc: added a test atom type -2005-10-24 09:06 chrisfen +2005-10-24 10:06 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole reaction field - don't know if it works... -2005-10-23 16:08 chrisfen +2005-10-23 17:08 chrisfen * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp: @@ -1761,21 +1934,21 @@ added reaction field for charges - still need to do charge-dipole RF -2005-10-23 16:07 chrisfen +2005-10-23 17:07 chrisfen * samples/water/ssdrf/ssdrf.md: minor changes when testing reaction field -2005-10-23 16:06 chrisfen +2005-10-23 17:06 chrisfen * samples/water/spce/spce.md: reaction field now works for charges -2005-10-20 15:27 tim +2005-10-20 16:27 tim * src/primitives/Torsion.cpp: Fix the other branch of force calculation in Torision.cpp -2005-10-19 14:24 chrisfen +2005-10-19 15:24 chrisfen * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/electrostatic.F90, @@ -1783,47 +1956,47 @@ brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals toUpper problems - these changes should fix those... -2005-10-19 14:23 chrisfen +2005-10-19 15:23 chrisfen * samples/water/ssdrf/ssdrf.md: nothing -2005-10-19 12:03 gezelter +2005-10-19 13:03 gezelter * src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in GayBerne -2005-10-19 11:49 tim +2005-10-19 12:49 tim * src/: UseTheForce/DarkSide/fInteractionMap.h, brains/ForceManager.cpp: fix an index mismathcing between c and fortran -2005-10-18 18:03 gezelter +2005-10-18 19:03 gezelter * samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added samples for the cutoff methods that Yang Zheng has been working on -2005-10-18 16:13 gezelter +2005-10-18 17:13 gezelter * src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques and a rotation matrix bug -2005-10-18 16:13 gezelter +2005-10-18 17:13 gezelter * samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md, gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: added a few GB test cases -2005-10-18 16:13 gezelter +2005-10-18 17:13 gezelter * forceFields/DUFF2.frc: Fixing GB parameters -2005-10-18 13:36 kdaily +2005-10-18 14:36 kdaily * forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne type -2005-10-18 10:01 chrisfen +2005-10-18 11:01 chrisfen * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, UseTheForce/DarkSide/Makefile, @@ -1833,32 +2006,32 @@ UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged reaction field with electrostatics.F90 -2005-10-17 18:13 tim +2005-10-17 19:13 tim * src/: brains/ForceManager.cpp, brains/Stats.cpp, brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp, io/StatWriter.hpp: Customized StatWriter is working -2005-10-17 17:42 kdaily +2005-10-17 18:42 kdaily * src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver paper -2005-10-17 16:47 gezelter +2005-10-17 17:47 gezelter * src/UseTheForce/DarkSide/gb.F90: bugtracking gb -2005-10-17 14:24 tim +2005-10-17 15:24 tim * src/io/ParamConstraint.hpp: Another bug fix -2005-10-17 14:22 tim +2005-10-17 15:22 tim * src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace issues in Globals -2005-10-17 14:12 gezelter +2005-10-17 15:12 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90, UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90, @@ -1868,43 +2041,43 @@ types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: changing GB architecture -2005-10-17 14:12 gezelter +2005-10-17 15:12 gezelter * samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in, gbRotRoundZ.in: Adding samples for gb tests -2005-10-16 22:06 tim +2005-10-16 23:06 tim * src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy a string to event's err_msg, there are still tons of memory leaking problem in Globals -2005-10-16 19:51 tim +2005-10-16 20:51 tim * src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change error message in Globals -2005-10-14 16:43 tim +2005-10-14 17:43 tim * src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for parameters are working now -2005-10-14 11:43 gezelter +2005-10-14 12:43 gezelter * samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests -2005-10-14 11:05 gezelter +2005-10-14 12:05 gezelter * samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md, gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: Adding some Gay Berne tests -2005-10-14 11:05 gezelter +2005-10-14 12:05 gezelter * samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some cutoff tests -2005-10-14 10:44 kdaily +2005-10-14 11:44 kdaily * forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90, @@ -1912,18 +2085,18 @@ src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne LJ -2005-10-14 09:48 tim +2005-10-14 10:48 tim * src/io/ParamConstraint.hpp: Adding Parameter Constraint class -2005-10-14 09:18 chrisfen +2005-10-14 10:18 chrisfen * samples/thermoIntegration/liquid/ssde.md, samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp, src/restraints/Restraints.cpp: added default restraint spring constants into Globals -2005-10-13 17:26 tim +2005-10-13 18:26 tim * src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp, brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp, @@ -1935,49 +2108,49 @@ restraints/ThermoIntegrationForceManager.cpp, visitors/ZconsVisitor.cpp: rewrite Globals -2005-10-12 16:57 chuckv +2005-10-12 17:57 chuckv * src/brains/ForceManager.cpp: Fix to forceManager to pass potential array to fortran. -2005-10-12 16:00 gezelter +2005-10-12 17:00 gezelter * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't remember what we did -2005-10-12 16:00 gezelter +2005-10-12 17:00 gezelter * src/UseTheForce/: doForces.F90, doForces_interface.F90, DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h, DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: simplifying long range potential array -2005-10-12 16:00 gezelter +2005-10-12 17:00 gezelter * samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new cutoff methods -2005-10-12 16:00 gezelter +2005-10-12 17:00 gezelter * forceFields/DUFF2.frc: Messing with 2-point water models -2005-10-12 15:22 chuckv +2005-10-12 16:22 chuckv * src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran interface now expects an array for pot. -2005-10-12 15:18 chuckv +2005-10-12 16:18 chuckv * src/UseTheForce/: doForces.F90, DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for calculation of potential. -2005-10-12 14:55 chuckv +2005-10-12 15:55 chuckv * src/UseTheForce/doForces.F90: More changes to MPI potential calculations. -2005-10-12 13:59 chuckv +2005-10-12 14:59 chuckv * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/electrostatic.F90, @@ -1985,18 +2158,18 @@ DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky Breaky: Add Support for seperating potential contributions. -2005-10-11 17:00 chuckv +2005-10-11 18:00 chuckv * src/UseTheForce/doForces.F90: Free some variables that weren't freed before. -2005-10-11 16:59 chuckv +2005-10-11 17:59 chuckv * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod builder --twinned. -2005-10-11 16:57 chuckv +2005-10-11 17:57 chuckv * src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, @@ -2004,142 +2177,142 @@ sphericalNanoparticle.hpp: Added code for nanoparticle builder to cvs. -2005-10-10 16:34 chuckv +2005-10-10 17:34 chuckv * src/UseTheForce/doForces.F90: Bug fix, undeclared local variable in MPI. -2005-10-10 16:20 chuckv +2005-10-10 17:20 chuckv * src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column indexing of groupToGtype. We now have two seperate maps groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer that is set to groupToGtypeRow in the single processor version. -2005-10-06 13:44 chrisfen +2005-10-06 14:44 chrisfen * samples/water/: dimer/water.md, spce/water.md, ssd/water.md, ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md, tip3p_ice/water.md, tip4p/water.md: fixing up the samples -2005-10-05 16:12 tim +2005-10-05 17:12 tim * src/primitives/RigidBody.cpp: There is still something wrong with inertia tensor projection -2005-10-05 14:35 tim +2005-10-05 15:35 tim * src/primitives/RigidBody.cpp: erase output of inertia tensor. There is still something wrong with current implementation. -2005-10-05 14:34 tim +2005-10-05 15:34 tim * src/brains/MoleculeCreator.cpp: fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array -2005-10-05 14:12 tim +2005-10-05 15:12 tim * src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array -2005-10-04 14:34 chrisfen +2005-10-04 15:34 chrisfen * src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying mass ratio bug that results in simulation failure with massless particles -2005-10-04 14:33 chrisfen +2005-10-04 15:33 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on wolf -2005-10-04 14:32 chrisfen +2005-10-04 15:32 chrisfen * samples/water/dimer/two.md, samples/water/dimer/water.md, samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md, samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some random changes when testing -2005-10-03 10:54 tim +2005-10-03 11:54 tim * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame (previous commit is wrong) -2005-10-03 09:31 tim +2005-10-03 10:31 tim * src/primitives/RigidBody.cpp: fix a bug in projecting the inertia tensor of directional atom in rigibody into rigidbody's body frame -2005-09-28 13:47 chrisfen +2005-09-28 14:47 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: working on wolf -2005-09-28 13:46 chrisfen +2005-09-28 14:46 chrisfen * samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md, dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md, ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md, tip4p/tp4.md: fixed some samples -2005-09-28 13:46 chrisfen +2005-09-28 14:46 chrisfen * ChangeLog: updated -2005-09-28 11:55 tim +2005-09-28 12:55 tim * src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid divergence in rotation matrix to quaternion transformation -2005-09-28 11:32 gezelter +2005-09-28 12:32 gezelter * src/primitives/RigidBody.cpp: Rotation matrix multiplication order error -2005-09-28 11:32 gezelter +2005-09-28 12:32 gezelter * src/io/DumpReader.cpp: tracking down quaternion bug -2005-09-28 11:32 gezelter +2005-09-28 12:32 gezelter * forceFields/DUFF2.frc: Added DIP atom types for 2-point water model -2005-09-27 15:02 tim +2005-09-27 16:02 tim * src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix to quaternion -2005-09-26 13:38 chuckv +2005-09-26 14:38 chuckv * src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc 7 so derfc is external. Other compilers should treat erfc as intrinsic. -2005-09-26 12:07 chuckv +2005-09-26 13:07 chuckv * src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc and declared it to be external to fix issure with ifc7. Hopefully this will not cause a problem with other compilers where derfc is an intrinsic function. -2005-09-26 11:42 chuckv +2005-09-26 12:42 chuckv * src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype in simulation module. We needed a seperate receive buffer. -2005-09-26 10:58 chuckv +2005-09-26 11:58 chuckv * src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added support for skinThickness keyword to Globals. -2005-09-26 10:56 tim +2005-09-26 11:56 tim * src/io/DumpReader.cpp: fix a typo in DumpReader -2005-09-26 09:27 chrisfen +2005-09-26 10:27 chrisfen * samples/: minimizer/tip4p_two.md, thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, @@ -2149,7 +2322,7 @@ water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, water/tip4p/tp4.md: fixing up some samples -2005-09-24 12:39 chrisfen +2005-09-24 13:39 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now roughly the same speed as the old version when using dipoles @@ -2157,78 +2330,78 @@ energies are now exactly the same between the old version of OOPSE and this version -2005-09-24 12:38 chrisfen +2005-09-24 13:38 chrisfen * samples/water/ssdrf/ssdrf.md: turned rf on -2005-09-23 15:31 chuckv +2005-09-23 16:31 chuckv * src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the skin thickness and hardcode listSkin to be 1.0. We now get listskin from skin. This will get fixed to where we can manually set skin thickness. -2005-09-22 13:50 gezelter +2005-09-22 14:50 gezelter * src/math/derfc.F90: added error function -2005-09-21 19:08 chuckv +2005-09-21 20:08 chuckv * src/integrators/Velocitizer.cpp: Removed print statement for angular momentum and inertia tensor from velocitizer. -2005-09-21 19:04 chuckv +2005-09-21 20:04 chuckv * src/integrators/Velocitizer.cpp: Removed print statements for remove angular momentum. -2005-09-21 18:45 chuckv +2005-09-21 19:45 chuckv * src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ (say we are using EAM), we probably shouldn't rebuild the LJ mixing map. -2005-09-21 15:59 tim +2005-09-21 16:59 tim * src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: DumpReader using pure c++ io -2005-09-21 12:20 chrisfen +2005-09-21 13:20 chrisfen * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a defaultCutoff bug (HEMES!) -2005-09-20 17:13 gezelter +2005-09-20 18:13 gezelter * make/Makefile.in: libz additions -2005-09-20 17:03 gezelter +2005-09-20 18:03 gezelter * configure, ac-tools/aclocal.m4, ac-tools/configure.in, src/config.h.in: added check for zlib in configure -2005-09-20 16:22 tim +2005-09-20 17:22 tim * src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter -2005-09-20 11:22 tim +2005-09-20 12:22 tim * test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding testcase for zipstream -2005-09-20 10:41 tim +2005-09-20 11:41 tim * src/io/zipstream.hpp: adding zipstream.hpp -2005-09-20 10:34 chrisfen +2005-09-20 11:34 chrisfen * samples/: dipole/splitInWater.md, dipole/split_SSD.md, dipole/twoSplitDipole.md, minimizer/ssdEM.md, minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, zcons/zconsMoving.md: fixed up some sample md files -2005-09-19 18:21 chrisfen +2005-09-19 19:21 chrisfen * ChangeLog, samples/water/ssdrf/ssdrf.md, src/UseTheForce/doForces.F90, @@ -2237,7 +2410,7 @@ src/brains/fSimulation.h: Fixed bugs in reaction field, now it appears as though it really is working... -2005-09-18 15:45 chrisfen +2005-09-18 16:45 chrisfen * ChangeLog, samples/water/ssdrf/ssdrf.md, src/UseTheForce/doForces.F90, @@ -2248,126 +2421,126 @@ src/brains/SimInfo.cpp: reaction field seems to work now, still need to do some testing... -2005-09-16 18:04 chuckv +2005-09-16 19:04 chuckv * src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed dump files. -2005-09-16 16:07 chrisfen +2005-09-16 17:07 chrisfen * src/: UseTheForce/doForces_interface.F90, UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a bug that ifc missed... -2005-09-16 15:36 chrisfen +2005-09-16 16:36 chrisfen * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: fixing some summation method issues -2005-09-16 14:35 chrisfen +2005-09-16 15:35 chrisfen * src/brains/SimInfo.cpp: fixed a capitalization error -2005-09-16 14:34 chrisfen +2005-09-16 15:34 chrisfen * src/UseTheForce/: fElectrostaticSummationMethod.h, DarkSide/fElectrostaticSummationMethod.h: moved a header file around -2005-09-16 14:00 chrisfen +2005-09-16 15:00 chrisfen * src/: UseTheForce/DarkSide/electrostatic_interface.F90, brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there are known issues - particularly with reaction field... -2005-09-16 11:07 chrisfen +2005-09-16 12:07 chrisfen * src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking (cutting out the old way to do reaction field) -2005-09-15 17:05 gezelter +2005-09-15 18:05 gezelter * src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, DarkSide/electrostatic_interface.F90, DarkSide/electrostatic_interface.h: Working on adding WOLF -2005-09-15 14:17 tim +2005-09-15 15:17 tim * src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame is called without calling getNFrames -2005-09-15 08:47 chrisfen +2005-09-15 09:47 chrisfen * src/UseTheForce/fCoulombicCorrection.h: forgot to add a header -2005-09-14 21:48 chuckv +2005-09-14 22:48 chuckv * src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was not initialized after creation. When maxval(gtypeMaxCutoff) was called, the largest random garbage value was returned from the array. -2005-09-14 19:14 chrisfen +2005-09-14 20:14 chrisfen * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, io/Globals.hpp: changes to include the coulombicCorrection selector -2005-09-14 19:13 chrisfen +2005-09-14 20:13 chrisfen * src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, reactionField.F90: added in the undamped wolf, in the process of doing the damped wolf -2005-09-14 19:13 chrisfen +2005-09-14 20:13 chrisfen * src/UseTheForce/: doForces.F90, doForces_interface.F90, doForces_interface.h, notifyCutoffs.F90: some changes to activate the coulombicCorrection selector -2005-09-14 19:11 chrisfen +2005-09-14 20:11 chrisfen * samples/water/dimer/: cl.in, cl.md, water.md: just some testing -2005-09-14 19:11 chrisfen +2005-09-14 20:11 chrisfen * samples/argon/: 500.in, 500.md: Equilibrated the sample -2005-09-14 19:10 chrisfen +2005-09-14 20:10 chrisfen * forceFields/DUFF2.frc: re-added Cl- and Na+ -2005-09-14 15:31 chuckv +2005-09-14 16:31 chuckv * src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup eamAtypes instead of assuming a 1-1 correspondence to atypes. -2005-09-14 15:28 gezelter +2005-09-14 16:28 gezelter * src/UseTheForce/doForces.F90: fix to put back calculation of r in do_prepair -2005-09-14 14:02 gezelter +2005-09-14 15:02 gezelter * src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the createMixingMap routine. It should now set doShift correctly -2005-09-07 17:44 chuckv +2005-09-07 18:44 chuckv * src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. -2005-09-07 17:23 chuckv +2005-09-07 18:23 chuckv * src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi logical variables -2005-09-07 17:08 gezelter +2005-09-07 18:08 gezelter * src/UseTheForce/doForces.F90: bugfix on the grouptype finding algorithm -2005-09-07 15:46 gezelter +2005-09-07 16:46 gezelter * src/: UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, @@ -2376,30 +2549,30 @@ io/Globals.cpp, io/Globals.hpp: adding c-side interface to change cutoff Policy -2005-09-07 14:18 gezelter +2005-09-07 15:18 gezelter * src/UseTheForce/doForces.F90: Some bug hunting -2005-09-07 14:18 gezelter +2005-09-07 15:18 gezelter * samples/argon/argonNVT.md: Just a longer test -2005-09-06 12:32 chuckv +2005-09-06 13:32 chuckv * src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap etc.. -2005-09-01 17:56 gezelter +2005-09-01 18:56 gezelter * src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to zero -2005-09-01 15:17 gezelter +2005-09-01 16:17 gezelter * src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote createGtypeCutoffMap -2005-08-30 13:23 chrisfen +2005-08-30 14:23 chrisfen * src/: UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, @@ -2409,79 +2582,79 @@ brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some changes for implementing the wolf potential -2005-08-26 17:39 chrisfen +2005-08-26 18:39 chrisfen * src/UseTheForce/DarkSide/eam.F90: updated getEAMCut -2005-08-26 16:30 chrisfen +2005-08-26 17:30 chrisfen * src/UseTheForce/: doForces.F90, DarkSide/eam.F90, DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added some probably nonfunctional get*cut routines -2005-08-26 15:34 chuckv +2005-08-26 16:34 chuckv * src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. -2005-08-26 11:36 gezelter +2005-08-26 12:36 gezelter * src/UseTheForce/doForces.F90: fixing some of the problems in the interactionHash and gtypeCutoff routines -2005-08-17 10:26 gezelter +2005-08-17 11:26 gezelter * src/UseTheForce/: doForces.F90, fCutoffPolicy.h, DarkSide/simulation.F90: added fCutoffPolicy.h -2005-08-11 16:04 gezelter +2005-08-11 17:04 gezelter * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in progress -2005-08-10 14:17 gezelter +2005-08-10 15:17 gezelter * src/primitives/StuntDouble.hpp: putting spaceballs back where they belong -2005-08-09 17:33 gezelter +2005-08-09 18:33 gezelter * src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard Jones module -2005-08-09 17:33 gezelter +2005-08-09 18:33 gezelter * src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky -2005-08-09 14:40 chuckv +2005-08-09 15:40 chuckv * src/UseTheForce/doForces.F90: In process of re-write for group based cutoff.... -2005-07-29 14:38 gezelter +2005-07-29 15:38 gezelter * src/UseTheForce/doForces.F90: fixes in progress -2005-07-29 12:34 tim +2005-07-29 13:34 tim * src/UseTheForce/doForces.F90: fix a bug which does not update me_i and me_j correctly -2005-07-28 17:12 chuckv +2005-07-28 18:12 chuckv * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed cutoffs... Segfaults nicely now... -2005-07-20 12:04 gezelter +2005-07-20 13:04 gezelter * configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text error messages from pathscale compiler -2005-07-13 11:48 tim +2005-07-13 12:48 tim * src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in -2005-07-13 10:54 tim +2005-07-13 11:54 tim * src/: UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, @@ -2493,7 +2666,7 @@ utils/simError.c, utils/simError.h: replace c++ style comment in c files -2005-07-03 15:53 chuckv +2005-07-03 16:53 chuckv * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added @@ -2501,29 +2674,29 @@ simulation.F90 to determine if a particular atype is present in a simulation. -2005-06-28 08:58 gezelter +2005-06-28 09:58 gezelter * src/UseTheForce/doForces.F90: [no log message] -2005-06-27 17:21 chuckv +2005-06-27 18:21 chuckv * src/UseTheForce/doForces.F90: More breaking and destruction of force code. Does not build at this point... -2005-06-27 16:01 gezelter +2005-06-27 17:01 gezelter * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, UseTheForce/DarkSide/fInteractionMap.h, UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: Breaky breaky! -2005-06-20 11:03 gezelter +2005-06-20 12:03 gezelter * samples/water/ssd/ssd.md, src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a simulation -2005-06-13 13:25 tim +2005-06-13 14:25 tim * src/: applications/staticProps/DensityPlot.cpp, applications/staticProps/DensityPlot.hpp, @@ -2531,17 +2704,17 @@ applications/staticProps/StaticProps.cpp, io/AtomTypesSectionParser.cpp: working version of DensityPlot -2005-05-31 17:31 chuckv +2005-05-31 18:31 chuckv * src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to remove angular momentum. -2005-05-31 12:34 chuckv +2005-05-31 13:34 chuckv * src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in typo in nanorodBuilder. -2005-05-30 09:01 chuckv +2005-05-30 10:01 chuckv * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, @@ -2550,50 +2723,50 @@ momentum to velocitizer and added method to calculate system angular momentum to siminfo. -2005-05-29 16:16 chrisfen +2005-05-29 17:16 chrisfen * src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed balance from the Darkside (files) -2005-05-29 16:15 chrisfen +2005-05-29 17:15 chrisfen * src/UseTheForce/doForces.F90: Removed balance from doForces -2005-05-29 16:15 chrisfen +2005-05-29 17:15 chrisfen * samples/water/tap/: tap.in, tap.md: Updated tap sample -2005-05-29 16:15 chrisfen +2005-05-29 17:15 chrisfen * samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap dimer for testing purposes -2005-05-29 16:14 chrisfen +2005-05-29 17:14 chrisfen * forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It was apparently wiped earlier this month... -2005-05-29 16:13 chrisfen +2005-05-29 17:13 chrisfen * ChangeLog: ran make cvslog -2005-05-28 19:16 tim +2005-05-28 20:16 tim * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding AtomNameVisitor -2005-05-28 19:09 tim +2005-05-28 20:09 tim * src/integrators/Integrator.cpp: dding resetIntegrator -2005-05-28 19:06 tim +2005-05-28 20:06 tim * src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding resetIntegrator -2005-05-27 16:11 tim +2005-05-27 17:11 tim * src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, @@ -2601,7 +2774,7 @@ StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into StaticProps -2005-05-26 23:41 tim +2005-05-27 00:41 tim * src/: applications/staticProps/Makefile, applications/staticProps/P2OrderParameter.cpp, @@ -2612,7 +2785,7 @@ applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps -2005-05-26 17:45 tim +2005-05-26 18:45 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/dump2Xyz/Dump2XYZCmd.c, @@ -2632,7 +2805,7 @@ wrappingvisitor now wrap back to the center of the mass; adding P2OrderParameter into StaticProps -2005-05-22 16:36 chuckv +2005-05-22 17:36 chuckv * src/: applications/nanoRodBuilder/Geometry.cpp, applications/nanoRodBuilder/GeometryBuilder.cpp, @@ -2642,56 +2815,56 @@ integrators/VelocityVerletIntegrator.cpp: Fix to print pressure tensor. -2005-05-22 16:05 tim +2005-05-22 17:05 tim * src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, io/Globals.hpp, io/SectionParserManager.cpp: adding keyword printPressureTensor -2005-05-20 14:27 tim +2005-05-20 15:27 tim * src/integrators/NPrT.cpp: NPrT in progress -2005-05-20 11:01 tim +2005-05-20 12:01 tim * src/: integrators/NPrT.cpp, io/Globals.cpp, utils/OOPSEConstant.hpp: NPrT in progress -2005-05-19 16:31 tim +2005-05-19 17:31 tim * src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, io/Globals.hpp: NPAT is working -2005-05-19 10:49 tim +2005-05-19 11:49 tim * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT -2005-05-18 23:28 tim +2005-05-19 00:28 tim * src/: brains/Register.cpp, integrators/NPAT.cpp, integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators -2005-05-18 14:06 chrisfen +2005-05-18 15:06 chrisfen * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just some tap changes -2005-05-18 13:31 chrisfen +2005-05-18 14:31 chrisfen * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, DarkSide/sticky.F90: Modifications to temper the dipolar strength in the first solvation shell for tap -2005-05-18 07:35 chrisfen +2005-05-18 08:35 chrisfen * samples/water/tap/: tap.in, tap.md, water.md: added a tap example for testing purposes -2005-05-17 17:35 chrisfen +2005-05-17 18:35 chrisfen * ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, @@ -2701,29 +2874,29 @@ src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also correcting changes to the previous merge that were not caught -2005-05-16 23:20 chuckv +2005-05-17 00:20 chuckv * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: Fixed merge issues between Kyle and Chris so OOPSE will actually build. -2005-05-16 22:46 kdaily +2005-05-16 23:46 kdaily * src/io/: GayBerneAtomTypesSectionParser.cpp, GayBerneAtomTypesSectionParser.hpp, Makefile: help -2005-05-16 21:08 kdaily +2005-05-16 22:08 kdaily * forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, src/types/DirectionalAtomType.cpp, src/types/DirectionalAtomType.hpp: added gb -2005-05-13 15:36 chrisfen +2005-05-13 16:36 chrisfen * forceFields/DUFF2.frc: Better tap -2005-05-12 14:43 chrisfen +2005-05-12 15:43 chrisfen * forceFields/DUFF2.frc, samples/water/dimer/ssd.in, samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, @@ -2731,23 +2904,23 @@ src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. Need to parametrize. -2005-05-11 18:15 chuckv +2005-05-11 19:15 chuckv * src/: io/ShapeAtomTypesSectionParser.cpp, math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed build issues under ifc7. -2005-05-09 17:07 chuckv +2005-05-09 18:07 chuckv * src/applications/nanoRodBuilder/Geometry.hpp: More geometry builder changes. -2005-05-05 10:06 chrisfen +2005-05-05 11:06 chrisfen * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED to TAP -2005-05-05 09:47 chrisfen +2005-05-05 10:47 chrisfen * forceFields/DUFF2.frc, samples/water/ssde/ssde.md, samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, @@ -2765,23 +2938,23 @@ src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it... -2005-05-03 17:55 chuckv +2005-05-03 18:55 chuckv * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: Adding support for generic geometry to nanorodbuilder. -2005-05-03 12:55 chuckv +2005-05-03 13:55 chuckv * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, nanorodBuilderCmd.h: More changes to nanoRodBuilder.... -2005-04-29 14:16 gezelter +2005-04-29 15:16 gezelter * make/Makefile.in: [no log message] -2005-04-29 11:26 chrisfen +2005-04-29 12:26 chrisfen * forceFields/DUFF2.frc, samples/water/spce/water.md, samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, @@ -2789,14 +2962,14 @@ samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, samples/water/tip4p/water.md: Added TIP4P-Ew -2005-04-27 19:24 chuckv +2005-04-27 20:24 chuckv * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with nanoRodBuilder.... -2005-04-27 15:13 chrisfen +2005-04-27 16:13 chrisfen * samples/shape/Shapes.frc, samples/shape/linear.shape, src/UseTheForce/DarkSide/atype.F90, @@ -2805,17 +2978,17 @@ src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of write statements and am closer to a working shapes -2005-04-22 16:57 chuckv +2005-04-22 17:57 chuckv * src/utils/Predicate.hpp: Fixed gcc4 bug... -2005-04-22 16:52 tim +2005-04-22 17:52 tim * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, Trim.hpp: adding CharClassificationFunctor to fix the locale problem of c++ -2005-04-21 09:12 chrisfen +2005-04-21 10:12 chrisfen * samples/shape/Shapes.frc, samples/shape/linear.in, samples/shape/linear.md, src/UseTheForce/ForceField.hpp, @@ -2835,12 +3008,12 @@ bounds overwrite (I think...). At least the parser loads the forcefield fine... -2005-04-18 10:44 chrisfen +2005-04-18 11:44 chrisfen * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on Mac (capitalization confusion of filenames) -2005-04-17 22:50 chrisfen +2005-04-17 23:50 chrisfen * src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, UseTheForce/Shapes_FF.cpp, @@ -2848,25 +3021,25 @@ io/ShapeAtomTypesSectionParser.cpp, io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... -2005-04-15 17:43 gezelter +2005-04-15 18:43 gezelter * README: gmake in case people forget -2005-04-15 17:40 gezelter +2005-04-15 18:40 gezelter * src/applications/oopse/oopse.cpp: fixed the spacing on the banner. Vanity. -2005-04-15 17:22 gezelter +2005-04-15 18:22 gezelter * src/: config.h.in, applications/oopse/oopse.cpp: Version string in banner (and version numbers in config.h) -2005-04-15 17:22 gezelter +2005-04-15 18:22 gezelter * ChangeLog, LICENSE, README: Documentation changes -2005-04-15 17:03 gezelter +2005-04-15 18:03 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, @@ -3087,70 +3260,70 @@ visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has been drafted to perform our indentation services -2005-04-15 17:03 gezelter +2005-04-15 18:03 gezelter * configure, ac-tools/configure.in: Jedi mind-trick warning messages have been added to make users ignore CGAL. -2005-04-15 13:41 tim +2005-04-15 14:41 tim * make/Makefile.in: fix make install -2005-04-15 13:41 tim +2005-04-15 14:41 tim * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: add Makefile of samples -2005-04-15 13:33 tim +2005-04-15 14:33 tim * samples/: lipid/Makefile, water/dimer/Makefile, water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not installed correctly -2005-04-14 16:41 gezelter +2005-04-14 17:41 gezelter * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, scripts/filepp, scripts/filepp.in: configure now searches for perl to use with filepp -2005-04-14 16:20 gezelter +2005-04-14 17:20 gezelter * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of MoLocator -2005-04-14 14:12 gezelter +2005-04-14 15:12 gezelter * LICENSE: [no log message] -2005-04-14 11:10 chuckv +2005-04-14 12:10 chuckv * src/applications/nanoRodBuilder/nanorodBuilder.cpp: nanorodbuilder now exit's when libCGAL is not present. -2005-04-14 10:20 tim +2005-04-14 11:20 tim * src/io/make_nodes.h: fix one more warning message in make_nodes -2005-04-13 18:36 chuckv +2005-04-13 19:36 chuckv * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed interface name for SGI Compiler -2005-04-13 18:29 chrisfen +2005-04-13 19:29 chrisfen * samples/water/ssde/ssde.md: oops... bad sample -2005-04-13 18:00 chuckv +2005-04-13 19:00 chuckv * src/config.h.in: Change typo in CGAL. -2005-04-13 17:43 tim +2005-04-13 18:43 tim * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, selection/SelectionCompiler.hpp: fix some warning messages -2005-04-13 17:30 gezelter +2005-04-13 18:30 gezelter * configure, ac-tools/aclocal.m4, ac-tools/configure.in, make/Makefile.in, src/config.h.in, @@ -3159,7 +3332,7 @@ src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL checks -2005-04-13 15:36 chuckv +2005-04-13 16:36 chuckv * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, DarkSide/LJ.F90, DarkSide/electrostatic.F90, @@ -3169,12 +3342,12 @@ DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added destroy methods for Fortran modules. -2005-04-13 15:17 chuckv +2005-04-13 16:17 chuckv * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, shapes_interface.h: Added destroy method to clean up memory -2005-04-13 13:41 tim +2005-04-13 14:41 tim * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -3183,31 +3356,31 @@ types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are fixed -2005-04-12 17:44 chuckv +2005-04-12 18:44 chuckv * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed for nanoRodBuilder. -2005-04-12 17:42 tim +2005-04-12 18:42 tim * src/applications/: nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder and simpleBuilder(forget to delete lattice) -2005-04-12 17:33 tim +2005-04-12 18:33 tim * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: refactory lattice -2005-04-12 17:07 tim +2005-04-12 18:07 tim * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory LatticeFactory and LatticeCreator -2005-04-12 16:58 tim +2005-04-12 17:58 tim * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, @@ -3216,21 +3389,21 @@ lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, lattice/Makefile: refactory LatticeFactory and LatticeCreator -2005-04-12 16:28 gezelter +2005-04-12 17:28 gezelter * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, vector_class.F90: cleaned up vector_class memory leak fix by deallocating in reverse order of how we allocated. Also migrated MoLocator into utils directory -2005-04-12 16:27 gezelter +2005-04-12 17:27 gezelter * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice directory -2005-04-12 16:27 gezelter +2005-04-12 17:27 gezelter * src/applications/: nanoRodBuilder/BaseLattice.cpp, nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, @@ -3248,72 +3421,72 @@ simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of these files are now redundant -2005-04-12 16:27 gezelter +2005-04-12 17:27 gezelter * src/UseTheForce/DarkSide/: atype_interface.F90, atype_interface.h: cleaned up memory leak fix -2005-04-12 16:26 gezelter +2005-04-12 17:26 gezelter * make/Makefile.in: added lattice subdirectory -2005-04-12 15:57 chrisfen +2005-04-12 16:57 chrisfen * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added a space by accident -2005-04-12 15:56 chrisfen +2005-04-12 16:56 chrisfen * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added quadrupole sample -2005-04-12 15:56 chrisfen +2005-04-12 16:56 chrisfen * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating samples -2005-04-12 13:30 tim +2005-04-12 14:30 tim * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom type in fortran side -2005-04-12 12:45 chuckv +2005-04-12 13:45 chuckv * src/utils/vector_class.F90: Further changes to vector_class destroy function. -2005-04-12 12:39 chuckv +2005-04-12 13:39 chuckv * src/utils/vector_class.F90: Fixed pointer memory leak in vector_class. -2005-04-12 12:12 chuckv +2005-04-12 13:12 chuckv * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, DarkSide/atype_interface.F90, DarkSide/atype_interface.h, DarkSide/eam.F90, DarkSide/eam_interface.F90, DarkSide/eam_interface.h: Updates to deallocate object in fortran. -2005-04-12 09:24 chrisfen +2005-04-12 10:24 chrisfen * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI output -2005-04-11 19:29 chuckv +2005-04-11 20:29 chuckv * src/: UseTheForce/DarkSide/atype.F90, applications/nanoRodBuilder/Makefile: Changes to delete atypes... -2005-04-11 19:28 chuckv +2005-04-11 20:28 chuckv * src/utils/vector_class.F90: Added code to delete vector. -2005-04-11 16:58 tim +2005-04-11 17:58 tim * src/io/basic_ifstrstream.hpp: avoid multiple inherit in basic_ifstrstream -2005-04-11 16:37 chuckv +2005-04-11 17:37 chuckv * make/Makefile.in, src/applications/nanoRodBuilder/BaseLattice.cpp, @@ -3337,74 +3510,74 @@ nanoRodBuilder application (may not work yet). ((Doesn't work yet.)) (((May never work....))) -2005-04-11 15:54 tim +2005-04-11 16:54 tim * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete prepareVisitor in Dump2XYZ -2005-04-11 15:19 chrisfen +2005-04-11 16:19 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the quadrupoles. look! it's divide by 3 like stone says! -2005-04-11 15:18 chrisfen +2005-04-11 16:18 chrisfen * forceFields/DUFF2.frc: fixing of the quadrupoles -2005-04-11 15:16 tim +2005-04-11 16:16 tim * src/selection/Token.hpp: change the parameter name in constructors -2005-04-11 14:49 gezelter +2005-04-11 15:49 gezelter * make/Makefile.in: One more bug fix for GNU make versions < 3.80 -2005-04-11 14:06 gezelter +2005-04-11 15:06 gezelter * make/Makefile.in: Fixed the uc and lc functions for GNU make versions < 3.80 -2005-04-11 11:13 gezelter +2005-04-11 12:13 gezelter * make/Makefile.in, src/UseTheForce/Makefile, src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added some stuff to clean out module files during "make clean" -2005-04-08 17:13 chrisfen +2005-04-08 18:13 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole interactions should be working with a remaining question of interaction magnitude -2005-04-08 17:12 chrisfen +2005-04-08 18:12 chrisfen * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with samples -2005-04-08 13:48 chrisfen +2005-04-08 14:48 chrisfen * samples/water/ssd/ssd.md: oops... messed up a sample -2005-04-08 09:43 chrisfen +2005-04-08 10:43 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix charge-dipole interactions -2005-04-08 09:42 chrisfen +2005-04-08 10:42 chrisfen * samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole -2005-04-08 09:41 chrisfen +2005-04-08 10:41 chrisfen * forceFields/DUFF2.frc: added Cl- and Na+ -2005-04-06 18:59 tim +2005-04-06 19:59 tim * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser -2005-04-05 18:09 tim +2005-04-05 19:09 tim * src/selection/: NameFinder.cpp, SelectionCompiler.cpp, SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' @@ -7309,43 +7482,43 @@ DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: these core classes get compiled -2004-10-29 17:37 tim +2004-10-29 18:37 tim * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule class -2004-10-29 17:28 chrisfen +2004-10-29 18:28 chrisfen * src/: UseTheForce/DarkSide/atype.F90, UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, types/ShapeAtomType.cpp: still debugging -2004-10-29 17:28 chrisfen +2004-10-29 18:28 chrisfen * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: shapes rcut calculator added -2004-10-29 17:27 chrisfen +2004-10-29 18:27 chrisfen * samples/shape/linear.md: shorter run -2004-10-29 15:54 tim +2004-10-29 16:54 tim * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. -2004-10-29 11:22 tim +2004-10-29 12:22 tim * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove some deprecated files -2004-10-29 11:20 tim +2004-10-29 12:20 tim * test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: More painful reconstruction is coming !!! -2004-10-28 17:34 tim +2004-10-28 18:34 tim * src/brains/DataStorage.hpp, src/utils/next_combination.hpp, test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, @@ -7353,7 +7526,7 @@ test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, DirectionalAtom and RigidBody -2004-10-28 17:26 tim +2004-10-28 18:26 tim * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, src/applications/simpleBuilder/MoLocator.cpp, @@ -7361,36 +7534,36 @@ src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: remove old Vector3d.hpp from application/simpleBuilder -2004-10-28 16:42 tim +2004-10-28 17:42 tim * src/utils/next_combination.hpp: Minor change in next_combination -2004-10-28 16:28 tim +2004-10-28 17:28 tim * src/utils/next_combination.hpp, test/utils/NextCombinationTestCase.cpp, test/utils/ReplaceWildCardTestCase.cpp: Done with combination -2004-10-28 16:11 tim +2004-10-28 17:11 tim * src/utils/next_combination.hpp: change documentation of next_combination.hpp -2004-10-28 15:41 tim +2004-10-28 16:41 tim * ChangeLog, src/utils/next_combination.hpp, test/utils/NextCombinationTestCase.cpp, test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working -2004-10-28 15:01 tim +2004-10-28 16:01 tim * src/utils/next_combination.hpp: adding replace wildcard function -2004-10-28 14:33 tim +2004-10-28 15:33 tim * src/utils/next_combination.hpp: Minor change -2004-10-28 14:06 tim +2004-10-28 15:06 tim * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, src/applications/simpleBuilder/simpleBuilder.cpp, @@ -7400,122 +7573,122 @@ test/utils/next_combination.hpp: STL next_permutation like next_combination is working -2004-10-28 12:22 chrisfen +2004-10-28 13:22 chrisfen * src/UseTheForce/WATER.cpp: fix of setDipoles -2004-10-28 12:20 gezelter +2004-10-28 13:20 gezelter * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the shapeFile -2004-10-28 12:20 gezelter +2004-10-28 13:20 gezelter * samples/shape/linear.md: forgot the orientation line -2004-10-28 11:56 gezelter +2004-10-28 12:56 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 -2004-10-28 11:55 gezelter +2004-10-28 12:55 gezelter * samples/lipid/5x5.md: uncommented .in line -2004-10-28 10:42 tim +2004-10-28 11:42 tim * test/utils/: Makefile, NextCombinationTestCase.cpp, NextCombinationTestCase.hpp, next_combination.hpp: next_combination in progress -2004-10-28 10:15 tim +2004-10-28 11:15 tim * test/utils/: NextCombinationTestCase.cpp, NextCombinationTestCase.hpp: adding next_combination test case -2004-10-28 10:02 tim +2004-10-28 11:02 tim * test/utils/next_combination.hpp: STL Compatible combination sequence generator -2004-10-28 01:23 tim +2004-10-28 02:23 tim * test/utils/: GenerateCombination.hpp, ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp -2004-10-28 01:16 tim +2004-10-28 02:16 tim * test/utils/GenerateCombination.hpp: a STL next_permutaion like next_combination function. -2004-10-27 22:27 tim +2004-10-27 23:27 tim * test/utils/ReplaceWildCard.hpp: no message -2004-10-27 22:14 tim +2004-10-27 23:14 tim * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: ReplaceWildCard(recursive version) is working, need refactoring. An iterative version is on the way -2004-10-27 21:28 tim +2004-10-27 22:28 tim * test/utils/: Makefile, ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress -2004-10-27 21:08 tim +2004-10-27 22:08 tim * test/utils/: ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard -2004-10-27 18:17 tim +2004-10-27 19:17 tim * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need test -2004-10-27 01:25 tim +2004-10-27 02:25 tim * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild char matching is on the way -2004-10-27 01:07 tim +2004-10-27 02:07 tim * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 -2004-10-26 22:00 gezelter +2004-10-26 23:00 gezelter * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix -2004-10-26 21:20 gezelter +2004-10-26 22:20 gezelter * src/UseTheForce/ForceFields.hpp: subclass foo -2004-10-26 21:16 gezelter +2004-10-26 22:16 gezelter * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> string conversion -2004-10-26 19:01 gezelter +2004-10-26 20:01 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, brains/SimSetup.hpp: char* -> string -2004-10-26 17:25 gezelter +2004-10-26 18:25 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 -2004-10-26 17:25 gezelter +2004-10-26 18:25 gezelter * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: define name collision -2004-10-26 17:24 gezelter +2004-10-26 18:24 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, @@ -7524,14 +7697,14 @@ UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: forcefield refactoring for shapes -2004-10-26 17:24 gezelter +2004-10-26 18:24 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 -2004-10-26 17:19 tim +2004-10-26 18:19 tim * ChangeLog, src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, @@ -7539,22 +7712,22 @@ test/brains/DataStorageTestCase.hpp, test/brains/Makefile: DataStorage passes unit test -2004-10-26 13:03 chrisfen +2004-10-26 14:03 chrisfen * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: Changes to help advance shapes -2004-10-26 13:02 chrisfen +2004-10-26 14:02 chrisfen * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to Shapes force field reader -2004-10-26 12:28 tim +2004-10-26 13:28 tim * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and SnapshotTestCase in progress -2004-10-25 17:46 tim +2004-10-25 18:46 tim * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, src/math/Vector.hpp, @@ -7563,7 +7736,7 @@ test/math/VectorTestCase.cpp: add getArray function to RectMatrix and Vector classes -2004-10-25 12:03 tim +2004-10-25 13:03 tim * ChangeLog, src/utils/GenericFactory.hpp, test/utils/GenericFactoryTestCase.cpp, @@ -7571,41 +7744,41 @@ GenericFactory Test Case. GenericFactory now can bed used to creat ForcefieldFactory and IntegratorFactory etc. -2004-10-24 23:08 tim +2004-10-25 00:08 tim * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes get reconstructed -2004-10-24 02:55 tim +2004-10-24 03:55 tim * src/utils/GenericFactory.hpp: GenericFactory pass unit test -2004-10-23 18:09 tim +2004-10-23 19:09 tim * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, RigidBody.cpp: Refactoring in progress -2004-10-22 18:09 tim +2004-10-22 19:09 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 -2004-10-22 17:59 chrisfen +2004-10-22 18:59 chrisfen * src/: UseTheForce/LJFF.cpp, UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear god! It runs and conserves energy! -2004-10-22 17:54 chrisfen +2004-10-22 18:54 chrisfen * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY -2004-10-22 17:53 chrisfen +2004-10-22 18:53 chrisfen * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, @@ -7613,35 +7786,35 @@ brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey breakey -2004-10-22 17:53 chrisfen +2004-10-22 18:53 chrisfen * make/Makefile.in: compiler flags -2004-10-22 16:20 gezelter +2004-10-22 17:20 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 -2004-10-22 15:22 gezelter +2004-10-22 16:22 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 -2004-10-22 15:21 gezelter +2004-10-22 16:21 gezelter * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, DirectionalAtomType.hpp, Makefile: More on AtomType and DirectionalAtomType -2004-10-22 09:47 gezelter +2004-10-22 10:47 gezelter * src/types/AtomType.hpp: Adding AtomType -2004-10-21 16:31 tim +2004-10-21 17:31 tim * ChangeLog, src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, @@ -7650,14 +7823,14 @@ test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: Snapshot and SnapshotManager in progress -2004-10-21 16:30 tim +2004-10-21 17:30 tim * test/brains/: BrainsTest.cpp, Makefile, SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for Snapshot and snapshotManager. -2004-10-21 15:15 gezelter +2004-10-21 16:15 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, @@ -7668,16 +7841,16 @@ brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. Fixey Fixey. -2004-10-21 11:32 tim +2004-10-21 12:32 tim * src/utils/GenericData.cpp, src/utils/Makefile, test/utils/Makefile, test/utils/UtilTest: remove some junk files -2004-10-21 11:24 tim +2004-10-21 12:24 tim * test/utils/GenericData.hpp: remove backup of GenericData.hpp -2004-10-21 11:22 tim +2004-10-21 12:22 tim * ChangeLog, src/brains/SimSetup.cpp, src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, @@ -7695,17 +7868,17 @@ src/visitors/ZconsVisitor.hpp: replace old GebericData with new GenericData -2004-10-21 10:25 chuckv +2004-10-21 11:25 chuckv * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj module. -2004-10-21 10:24 chuckv +2004-10-21 11:24 chuckv * src/UseTheForce/DarkSide/lj_interface.h: Added interface for fortran lj module. -2004-10-20 17:54 tim +2004-10-20 18:54 tim * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, test/utils/GenericDataTestCase.cpp, test/utils/Makefile, @@ -7713,18 +7886,18 @@ test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: GenericData and PropertyMap pass unit test. -2004-10-20 16:52 gezelter +2004-10-20 17:52 gezelter * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, DarkSide/sticky_interface.h: fixed a fortran name problem -2004-10-20 16:38 tim +2004-10-20 17:38 tim * test/utils/: GenericData.hpp, GenericDataTestCase.cpp, GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, UtilTest, UtilTest.cpp: adding generic data test case -2004-10-20 16:16 chuckv +2004-10-20 17:16 chuckv * configure, ac-tools/aclocal.m4, src/UseTheForce/DarkSide/Makefile, @@ -7736,13 +7909,13 @@ Fortran/C++ interface de-obfuscation project appears to be complete! Woo hoo! -2004-10-20 15:47 chuckv +2004-10-20 16:47 chuckv * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project continues -2004-10-20 15:46 chuckv +2004-10-20 16:46 chuckv * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, @@ -7759,50 +7932,50 @@ brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface de-obfuscation project (It is a very long story) -2004-10-20 13:07 tim +2004-10-20 14:07 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 -2004-10-20 00:52 tim +2004-10-20 01:52 tim * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and SnapshotManager in design phase -2004-10-19 23:54 gezelter +2004-10-20 00:54 gezelter * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace problem prevented linking -2004-10-19 23:54 gezelter +2004-10-20 00:54 gezelter * src/UseTheForce/Shapes_FF.cpp: fixed include -2004-10-19 23:26 gezelter +2004-10-20 00:26 gezelter * src/utils/: Makefile, definitions.F90, definitions_module.F90, oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: more fortran name mangling -2004-10-19 23:23 gezelter +2004-10-20 00:23 gezelter * src/profiling/timing.F90: yet more fortran renaming -2004-10-19 23:19 gezelter +2004-10-20 00:19 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 -2004-10-19 23:12 gezelter +2004-10-20 00:12 gezelter * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some broken fortran stuff -2004-10-19 23:02 gezelter +2004-10-20 00:02 gezelter * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, atype_interface.h, atype_module.F90, atype_module_interface.h, @@ -7819,23 +7992,23 @@ sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: name sanity on the fortran side -2004-10-19 19:18 tim +2004-10-19 20:18 tim * test/math/SquareMatrix3TestCase.hpp: [no log message] -2004-10-19 18:01 tim +2004-10-19 19:01 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 -2004-10-19 17:43 chuckv +2004-10-19 18:43 chuckv * src/UseTheForce/do_Forces.h: Added correct prototypes for C-fortran interface functions. -2004-10-19 17:37 chuckv +2004-10-19 18:37 chuckv * src/UseTheForce/DarkSide/: atype_module_interface.h, eam_module_inteface.h, gb_module_interface.h, @@ -7843,7 +8016,7 @@ sticky_pair_module_interface.h: Added correct prototypes for C-fortran interface functions. -2004-10-19 16:28 tim +2004-10-19 17:28 tim * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, src/math/Vector.hpp, @@ -7853,7 +8026,7 @@ test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more bugs get fixed at math library -2004-10-19 15:43 chuckv +2004-10-19 16:43 chuckv * src/UseTheForce/: DarkSide/atype_module_interface.h, DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, @@ -7867,43 +8040,43 @@ notifycutoffs_module_interface.h: Added new files for fortran interface. -2004-10-19 15:43 gezelter +2004-10-19 16:43 gezelter * src/UseTheForce/Makefile: regressing -2004-10-19 15:40 gezelter +2004-10-19 16:40 gezelter * src/: UseTheForce/DarkSide/calc_shapes.F90, UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: working on shapes for portability -2004-10-19 15:40 gezelter +2004-10-19 16:40 gezelter * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes -2004-10-19 13:21 chrisfen +2004-10-19 14:21 chrisfen * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around findBegin -2004-10-18 23:34 tim +2004-10-19 00:34 tim * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs are fixed in Vector class -2004-10-18 23:28 tim +2004-10-19 00:28 tim * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix some bugs in RectMatrixTestCase -2004-10-18 23:21 tim +2004-10-19 00:21 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 -2004-10-18 18:13 tim +2004-10-18 19:13 tim * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, @@ -7912,7 +8085,7 @@ test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more tests on math library -2004-10-18 16:03 tim +2004-10-18 17:03 tim * test/math/: Makefile, QuaternionTestCase.cpp, QuaternionTestCase.hpp, RectMatrixTestCase.cpp, @@ -7920,236 +8093,236 @@ Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding more testing units -2004-10-18 12:07 tim +2004-10-18 13:07 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 -2004-10-18 11:30 gezelter +2004-10-18 12:30 gezelter * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: Your basic run of the mill real-valued versions of Y_l^m(\theta, \phi) -2004-10-18 11:29 gezelter +2004-10-18 12:29 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 -2004-10-18 10:21 gezelter +2004-10-18 11:21 gezelter * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType -2004-10-18 00:23 tim +2004-10-18 01:23 tim * test/math/VectorTestCase.hpp: adding vector test case -2004-10-18 00:23 tim +2004-10-18 01:23 tim * src/utils/GenericFactory.hpp: adding generic factory and vector test case -2004-10-16 20:19 tim +2004-10-16 21:19 tim * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in progress -2004-10-15 20:31 tim +2004-10-15 21:31 tim * src/math/Quaternion.hpp: add quaternion class -2004-10-15 16:11 tim +2004-10-15 17:11 tim * test/io/: DUFF.frc, IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: adding test file -2004-10-15 16:10 tim +2004-10-15 17:10 tim * src/io/basic_ifstrstream.hpp: fix a bunch of bugs -2004-10-15 15:42 tim +2004-10-15 16:42 tim * src/io/basic_ifstrstream.hpp: change const_cast to statc_const -2004-10-15 15:35 tim +2004-10-15 16:35 tim * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp -2004-10-15 15:34 tim +2004-10-15 16:34 tim * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use namespace oopse -2004-10-15 14:38 chuckv +2004-10-15 15:38 chuckv * configure, ac-tools/aclocal.m4: Changed optimization flags for XLF and XLC. -2004-10-15 13:28 tim +2004-10-15 14:28 tim * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: adding ifstrstream test case -2004-10-15 13:20 tim +2004-10-15 14:20 tim * src/io/basic_ifstrstream.hpp: fix include -2004-10-15 13:18 tim +2004-10-15 14:18 tim * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi -2004-10-15 13:17 tim +2004-10-15 14:17 tim * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile -2004-10-15 13:16 tim +2004-10-15 14:16 tim * test/io/: Makefile, ifstrstreamTestCase.cpp, ifstrstreamTestCase.hpp: adding test case for ifstrstream -2004-10-15 10:37 tim +2004-10-15 11:37 tim * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, ifstrstreamTestCase.hpp: add ifstrstreamTestCase -2004-10-15 10:20 tim +2004-10-15 11:20 tim * src/io/basic_ifstrstream.hpp: add checkFilename Option -2004-10-15 10:19 tim +2004-10-15 11:19 tim * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add SquareMatrixTestCase class -2004-10-15 02:52 tim +2004-10-15 03:52 tim * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream -2004-10-14 18:28 tim +2004-10-14 19:28 tim * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp: math library in progress -2004-10-14 18:27 tim +2004-10-14 19:27 tim * src/io/FileReader.hpp: FileReader in progress -2004-10-13 18:53 tim +2004-10-13 19:53 tim * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, test in isOrthogonal of SquareMatrix is failed by some reasons -2004-10-13 17:28 tim +2004-10-13 18:28 tim * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap class -2004-10-13 17:27 tim +2004-10-13 18:27 tim * test/math/: MainTest.cpp, RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: adding testing unit -2004-10-13 17:24 tim +2004-10-13 18:24 tim * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix -2004-10-13 01:51 tim +2004-10-13 02:51 tim * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: refactory vector and matrix classes -2004-10-13 01:50 tim +2004-10-13 02:50 tim * src/math/Vector3d.hpp: Remove some Makefile.in -2004-10-12 18:57 tim +2004-10-12 19:57 tim * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and Matrix3x3d.hpp -2004-10-12 14:08 tim +2004-10-12 15:08 tim * doc/: cppstyle.html, style.css: adding c++ coding style -2004-10-11 17:15 tim +2004-10-11 18:15 tim * src/: constraints/AbstractClasses.hpp, integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: change #include "mpi.h" to #include in AbstractClasses.hpp -2004-10-11 16:54 tim +2004-10-11 17:54 tim * scripts/filepp: fix a bug in filepp -2004-10-11 16:13 tim +2004-10-11 17:13 tim * make/Makefile.in: using filepp to generate dependencies instead of compilers -2004-10-11 16:10 tim +2004-10-11 17:10 tim * scripts/filepp: filepp can be used to generate dependencies for c/c++ now -2004-10-11 13:40 tim +2004-10-11 14:40 tim * make/Makefile.in: remove -module from F90Options -2004-10-11 13:01 tim +2004-10-11 14:01 tim * make/Makefile.in: adding rules to move fortran 90 module to target directory -2004-10-11 10:43 gezelter +2004-10-11 11:43 gezelter * make/Makefile.in: fixed makefile.in -2004-10-11 09:51 tim +2004-10-11 10:51 tim * scripts/filepp: remove "use bytes" which causes problem in sgi machine -2004-10-11 09:26 tim +2004-10-11 10:26 tim * forceFields/Makefile: add Makefile -2004-10-11 09:23 tim +2004-10-11 10:23 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 -2004-10-11 09:23 tim +2004-10-11 10:23 tim * samples/argon/Makefile: remove argon.dump and argon.eor from Makefile -2004-10-09 01:01 tim +2004-10-09 02:01 tim * samples/: alkane/Makefile.in, argon/Makefile.in, lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in -2004-10-08 18:15 tim +2004-10-08 19:15 tim * make/Makefile.in: [no log message] -2004-10-08 17:51 tim +2004-10-08 18:51 tim * make/Makefile.in: fix make install -2004-10-08 17:10 tim +2004-10-08 18:10 tim * make/Makefile.in: adding make install -2004-10-08 17:04 tim +2004-10-08 18:04 tim * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, metals/Makefile, minimizer/Makefile, water/Makefile.in, @@ -8160,70 +8333,70 @@ water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, zcons/Makefile.in: add Makefile to sample directory -2004-10-06 18:03 gezelter +2004-10-06 19:03 gezelter * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt stuff -2004-10-06 18:03 gezelter +2004-10-06 19:03 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 -2004-10-06 17:20 tim +2004-10-06 18:20 tim * make/: Doxyfile, Makefile.in: adding doxygen configuration file -2004-10-06 17:19 tim +2004-10-06 18:19 tim * scripts/filepp: filepp can handle different fortran module case and suffix -2004-10-06 16:27 gezelter +2004-10-06 17:27 gezelter * src/restraints/Restraints.cpp: Chris doesn't know about the OOPSE-2.0 directory structure yet -2004-10-06 16:27 gezelter +2004-10-06 17:27 gezelter * ChangeLog: Yeah yeah, we'lll get around to it later -2004-10-06 16:22 gezelter +2004-10-06 17:22 gezelter * configure, ac-tools/configure.in, ac-tools/fortran90.m4, make/Makefile.in: cleaning up build process -2004-10-06 15:01 chrisfen +2004-10-06 16:01 chrisfen * src/restraints/Restraints.cpp: made the file reading in restraints more intelligent - no longer gives uninformative seg faults -2004-10-06 14:55 gezelter +2004-10-06 15:55 gezelter * src/applications/simpleBuilder/Make.ftemp.old: cleaning up -2004-10-06 14:51 gezelter +2004-10-06 15:51 gezelter * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit -2004-10-06 13:53 tim +2004-10-06 14:53 tim * make/: Makefile, Makefile.in: fix make statistics -2004-10-06 13:18 tim +2004-10-06 14:18 tim * make/: Makefile, Makefile.in: adding GNU make functions to combine all of the static libraries to a big library -2004-10-05 17:57 tim +2004-10-05 18:57 tim * make/: Makefile, Makefile.in: adding shared library flag -2004-10-05 14:37 tim +2004-10-05 15:37 tim * src/: Makefile, UseTheForce/Makefile, UseTheForce/mpiSimulation_module.F90, @@ -8231,62 +8404,62 @@ UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move mpiSimulation_module to DarkSide -2004-10-05 14:35 tim +2004-10-05 15:35 tim * make/: Makefile, Makefile.in: building MPI version;using static library instead of shared library -2004-10-05 09:14 tim +2004-10-05 10:14 tim * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 to filepp -2004-10-04 15:56 tim +2004-10-04 16:56 tim * make/: Makefile, Makefile.in: add make cvslog -2004-10-04 11:24 gezelter +2004-10-04 12:24 gezelter * make/: Makefile, Makefile.in: more work on the parallel build -2004-10-04 11:06 gezelter +2004-10-04 12:06 gezelter * make/: Makefile, Makefile.in: changes to backport declare flags -2004-10-04 10:27 gezelter +2004-10-04 11:27 gezelter * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging shapes -2004-10-01 23:40 tim +2004-10-02 00:40 tim * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree -2004-10-01 23:22 tim +2004-10-02 00:22 tim * make/: Makefile, Makefile.in: add oopse_ as library prefix -2004-10-01 16:59 tim +2004-10-01 17:59 tim * make/: Makefile, Makefile.in: fix a space trimming bug in filepp -2004-10-01 16:22 gezelter +2004-10-01 17:22 gezelter * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A few minor build changes -2004-10-01 16:11 tim +2004-10-01 17:11 tim * scripts/filepp: adding fortran90 make dependency tool -2004-09-30 10:41 tim +2004-09-30 11:41 tim * make/: Makefile, Makefile.in: make clean is smart enough to only remove object files belong to current package. turn off silent mode -2004-09-29 16:55 tim +2004-09-29 17:55 tim * src/: Makefile, UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, @@ -8297,45 +8470,45 @@ restraints/Makefile, types/Makefile, utils/Makefile, visitors/Makefile: define DEV_ROOT as relative path -2004-09-29 16:54 tim +2004-09-29 17:54 tim * make/: Makefile, Makefile.in: get the relative path by shell script -2004-09-29 16:32 tim +2004-09-29 17:32 tim * make/Makefile: eliminate DEV_ROOT by relative path -2004-09-29 13:37 tim +2004-09-29 14:37 tim * make/Makefile.in: add PackageLibs; fix dependency rule -2004-09-29 12:57 gezelter +2004-09-29 13:57 gezelter * configure, ac-tools/configure.in: updates -2004-09-29 12:56 gezelter +2004-09-29 13:56 gezelter * make/: Make.conf.in, Makefile.in, _files/style.css: Working on make stuff -2004-09-29 12:46 tim +2004-09-29 13:46 tim * Makefile: If makefile does not exist, print error message -2004-09-29 12:12 tim +2004-09-29 13:12 tim * make/: Make.conf.in, Makefile: fix dependencies rule -2004-09-29 10:58 gezelter +2004-09-29 11:58 gezelter * Makefile, make/Makefile: still working on build process -2004-09-29 10:00 tim +2004-09-29 11:00 tim * make/Makefile: add print statment to rules -2004-09-29 09:59 tim +2004-09-29 10:59 tim * src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, applications/oopse/Makefile, @@ -8345,12 +8518,12 @@ profiling/Makefile, restraints/Makefile, types/Makefile, utils/Makefile, visitors/Makefile: change Makefile to relative path -2004-09-28 21:55 tim +2004-09-28 22:55 tim * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c which cause headache in bulding libutils -2004-09-28 18:24 tim +2004-09-28 19:24 tim * src/applications/: BaseLattice.cpp, BaseLattice.hpp, Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, @@ -8373,16 +8546,16 @@ change directory structure of application. Every executable file is replaced in seperate directory -2004-09-28 17:15 gezelter +2004-09-28 18:15 gezelter * lib/dummy: Keep that lib around, please. -2004-09-28 17:14 gezelter +2004-09-28 18:14 gezelter * Makefile, configure, ac-tools/configure.in, make/Make.conf.in: starting a configure version -2004-09-28 16:08 tim +2004-09-28 17:08 tim * src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, UseTheForce/DarkSide/Makefile, @@ -8391,7 +8564,7 @@ brains/Makefile, brains/simulation_module.F90: move fortran files around to solve dependency problem -2004-09-28 15:43 tim +2004-09-28 16:43 tim * Makefile, src/UseTheForce/ForceFields.hpp, src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, @@ -8401,25 +8574,25 @@ src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, src/utils/Makefile: [no log message] -2004-09-28 15:41 tim +2004-09-28 16:41 tim * make/Makefile, scripts/sfmakedepend: fix fortran dependency problem -2004-09-28 11:13 tim +2004-09-28 12:13 tim * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, src/io/Makefile: add yacc and lex rules -2004-09-27 15:24 tim +2004-09-27 16:24 tim * make/Makefile: adding include path to F90Options -2004-09-27 15:13 tim +2004-09-27 16:13 tim * make/Makefile: change suffix from .cc to .cpp -2004-09-24 11:27 tim +2004-09-24 12:27 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, @@ -8486,7 +8659,7 @@ visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: change the #include in source files -2004-09-23 23:16 gezelter +2004-09-24 00:16 gezelter * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, @@ -8662,7 +8835,7 @@ forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 -2004-09-23 23:16 gezelter +2004-09-24 00:16 gezelter * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,