--- trunk/OOPSE-4/ChangeLog 2007/05/01 17:59:04 3130 +++ trunk/OOPSE-4/ChangeLog 2007/05/02 00:18:08 3131 @@ -1,10 +1,457 @@ -2006-10-10 10:08 chrisfen +2007-05-01 10:59 chuckv + * samples/bond-order/: Readme.txt, surface_icosahedron.md: Added md + file for half of a icosahedron. + +2007-04-20 11:15 chrisfen + + * src/: UseTheForce/doForces.F90, + UseTheForce/doForces_interface.F90, + UseTheForce/doForces_interface.h, UseTheForce/DarkSide/LJ.F90, + brains/SimInfo.cpp, brains/SimInfo.hpp, + hydrodynamics/Ellipsoid.cpp, integrators/LDForceManager.cpp, + restraints/Restraints.cpp, types/TorsionStamp.hpp: SF Lennard-Jones + was added for everyones' enjoyment. The behavior is tethered to + the electrostaticSummationMethod keyword. + +2007-04-11 16:27 chuckv + + * src/applications/staticProps/: BOPofR.cpp, BOPofR.hpp, Makefile, + StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, + StaticPropsCmd.h: Added Bond Order Parameter as a function of + radius. + +2007-04-09 11:24 gezelter + + * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: more changes for + atomic virials and Lennard-Jones force switching + +2007-04-06 14:53 gezelter + + * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/LJ.F90, + UseTheForce/DarkSide/simulation.F90, brains/ForceManager.cpp, + brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, + brains/fSimulation.h, integrators/LDForceManager.cpp, + integrators/LDForceManager.hpp, + integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, + io/Globals.hpp, primitives/RigidBody.cpp, primitives/RigidBody.hpp: + Massive update to do virials (both atomic and cutoff-group) + correctly. The rigid body constraint contributions had been + missing and this was masked by the use of cutoff groups... + +2007-03-07 15:07 gezelter + + * samples/water/ice_surfaces/secondary_prism.md: Adding a starter + file for the secondary prism {1,1,-2,0} face. + +2007-03-07 11:29 gezelter + + * samples/water/ice_surfaces/: basal.md, prism2.md, water.md: + adding new ice surface files + +2007-03-05 16:01 chrisfen + + * src/applications/utilities/waterBoxer: forgot a tolerance for + simple cubic lattice magic number determination + +2007-02-27 16:53 chuckv + + * src/UseTheForce/DarkSide/electrostatic.F90: Fixed conversion bug + in self_self, when adding self energy to mypot, energy needs to be + converted by pre11. + +2007-02-25 20:45 chuckv + + * src/: UseTheForce/DarkSide/neighborLists_interface.h, + brains/SimInfo.cpp: Fixed a bug in NeighborListNeighbors. + +2007-02-02 10:55 chuckv + + * src/integrators/LDForceManager.cpp: Spherical boundary + conditions. + +2007-01-22 14:27 gezelter + + * src/applications/utilities/: md-solvator, waterBoxer: fixed a bug + in waterBoxer + +2007-01-16 14:18 chuckv + + * src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: Support for + printPosOnly in Dump2XYZ. + +2007-01-16 14:17 chuckv + + * src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, + Dump2XYZCmd.c, Dump2XYZCmd.h: Added printPosOnly to Dump2XYZ as a + userbase(BETH) request. + +2007-01-11 13:46 gezelter + + * src/applications/utilities/md-solvator: adding md-solvator + +2007-01-08 19:42 gezelter + + * src/applications/utilities/waterBoxer: Added the ability of + waterBoxer to deal with non-cubical boxes. + +2007-01-08 13:32 chuckv + + * src/applications/dynamicProps/: ThetaCorrFunc.cpp, + ThetaCorrFunc.hpp: Added thetacorr functions to dynamic props. + +2007-01-08 13:29 chuckv + + * src/UseTheForce/DarkSide/simParallel.F90: Added more error + reporting to simParallel. + +2007-01-03 12:46 chuckv + + * src/: applications/dynamicProps/DynamicProps.cpp, + applications/dynamicProps/DynamicProps.ggo, + applications/dynamicProps/DynamicPropsCmd.c, + applications/dynamicProps/DynamicPropsCmd.h, + applications/dynamicProps/Makefile, + applications/dynamicProps/RadialRCorrFunc.cpp, + applications/dynamicProps/RadialRCorrFunc.hpp, brains/Snapshot.cpp, + brains/Snapshot.hpp, io/DumpReader.cpp, primitives/StuntDouble.hpp: + Changes to add thetacorr to dynamic props and fixes to radial + rcorr. + +2007-01-02 20:40 chuckv + + * src/applications/dynamicProps/Makefile: Remove snapshotcentroid + from makefile. + +2007-01-02 20:40 chuckv + + * src/applications/dynamicProps/: RadialRCorrFunc.cpp, + RadialRCorrFunc.hpp, SnapshotCentroid.cpp, SnapshotCentroid.hpp: + Removeing snapshot centroid and adding support for COM calculaton + from snapshot. + +2007-01-02 12:42 chuckv + + * src/applications/utilities/mdSplit: More changes to mdsplit. + +2007-01-02 12:30 chuckv + + * src/applications/utilities/mdSplit: Breaking more mdsplit + stuff.... + +2007-01-02 12:12 chuckv + + * src/applications/utilities/mdSplit: Changed how mdsplit gets file + names. Full path is now removed from name. + +2006-12-29 13:57 gezelter + + * src/brains/: BlockSnapshotManager.cpp, BlockSnapshotManager.hpp: + Fixing an implementation problem + +2006-12-29 13:51 gezelter + + * src/brains/BlockSnapshotManager.hpp: BSM has to talk to reader + about center of mass properties + +2006-12-29 13:43 gezelter + + * src/: applications/dynamicProps/TimeCorrFunc.hpp, + brains/DataStorage.cpp, brains/DataStorage.hpp, + brains/Snapshot.cpp, brains/Snapshot.hpp, io/DumpReader.cpp, + io/DumpReader.hpp: Adding the ability to compute Center of Mass + properties on reading in a dump file. DumpReader must be told if + it needs to do this, however. + +2006-12-29 12:21 chuckv + + * src/brains/: SimInfo.cpp, SimInfo.hpp: Added function to + calculate volume based on ellipsoid definded by radius of gyration. + +2006-12-21 12:50 gezelter + + * samples/bond-order/: Readme.txt, bcc.md, icosahedron.md, sc.md, + tet.md: new ideal structures + +2006-12-20 18:20 gezelter + + * samples/bond-order/: Ag_Cu_bulkslab_lattice.md, Readme.txt, + bcc.md, fcc.md, hcp.md, icosahedron.md, metals.md, tet.md: Added a + bunch of bond order parameter test cases. + +2006-12-20 13:03 gezelter + + * src/applications/staticProps/BondOrderParameter.cpp: bug fixing + Wigner 3-j import to C++ + +2006-12-19 07:45 gezelter + + * configure, ac-tools/configure.in, src/math/Makefile, + src/math/Makefile.in: fixed a configuration error + +2006-12-14 11:38 chuckv + + * src/applications/dynamicProps/: DynamicProps.cpp, + DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, + RadialRCorrFunc.hpp: Code to run radial rcorr. + +2006-12-14 11:32 chuckv + + * src/math/: ConvexHull.cpp, ConvexHull.hpp, Makefile: Added + preliminary support for CGAL and computation of convex hull. + +2006-12-05 17:05 chuckv + + * src/applications/dynamicProps/: Makefile, RadialRCorrFunc.cpp, + RadialRCorrFunc.hpp, SnapshotCentroid.cpp, SnapshotCentroid.hpp: + Adding support for radial rcorr. + +2006-12-04 16:17 chuckv + + * src/: UseTheForce/DarkSide/Makefile, + UseTheForce/DarkSide/neighborLists.F90, + UseTheForce/DarkSide/neighborLists_interface.F90, + UseTheForce/DarkSide/neighborLists_interface.h, brains/SimInfo.cpp, + io/Globals.cpp, io/Globals.hpp: Added interface to change number of + neighbors in calculating neighbor list. + +2006-11-21 12:44 gezelter + + * src/applications/staticProps/BondOrderParameter.cpp: fixes for + BOP + +2006-11-20 15:12 chuckv + + * src/applications/staticProps/Makefile: Fix to makefile. + +2006-11-17 11:45 chuckv + + * src/applications/staticProps/RhoR.cpp: Histogram bin change. + +2006-11-10 10:45 chuckv + + * src/applications/staticProps/: Makefile, RhoR.cpp, RhoR.hpp, + StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, + StaticPropsCmd.h: Added support for nanoparticle density profile. + +2006-11-03 14:02 gezelter + + * src/applications/staticProps/BondOrderParameter.cpp: possible fix + for unnormalized BO + +2006-11-01 14:22 chrisfen + + * src/brains/SimInfo.cpp: user selected dampingAlpha now gets set + +2006-10-29 14:41 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: returned to half + self-term values + +2006-10-23 13:27 chuckv + + * src/applications/nanoRodBuilder/GeometryBuilder.hpp: Support for + OOPSE RealType. + +2006-10-23 11:21 gezelter + + * make/Makefile.in: fixes for CGAL + +2006-10-23 11:11 chuckv + + * configure, ac-tools/configure.in, + src/applications/nanoRodBuilder/nanorodBuilder.cpp: Changes to + nanorod builder for new dump format. Changes to configure to test + for new version of cgal. + +2006-10-20 08:40 gezelter + + * src/: brains/Register.cpp, openbabel/amberformat.hpp, + openbabel/fingerprintformat.hpp, openbabel/gromos96format.hpp, + openbabel/pdbformat.hpp, openbabel/povrayformat.hpp, + openbabel/smilesformat.hpp, openbabel/tinkerformat.hpp, + openbabel/xyzformat.hpp: fixes for open babel + +2006-10-20 07:59 gezelter + + * make/Makefile.in, samples/builders/runMe, + src/applications/thermalizer/Makefile, + src/applications/thermalizer/thermalizer.cpp, + src/applications/thermalizer/thermalizer.ggo, + src/applications/thermalizer/thermalizerCmd.c, + src/applications/thermalizer/thermalizerCmd.h, + src/applications/velocitizer/Makefile, + src/applications/velocitizer/velocitizer.cpp, + src/applications/velocitizer/velocitizer.ggo, + src/applications/velocitizer/velocitizerCmd.c, + src/applications/velocitizer/velocitizerCmd.h: more openbabel + updates, also changing velocitizer to thermalizer to avoid a + filename collision on case-insensitve file systems + +2006-10-19 13:50 gezelter + + * src/openbabel/: amberformat.hpp, fingerprintformat.hpp, + gromos96format.hpp, pdbformat.hpp, povrayformat.hpp, + smilesformat.hpp, tinkerformat.hpp, xyzformat.hpp: Updating + OpenBabel to version 2.0.2. These files aren't used anymore + +2006-10-19 13:49 gezelter + + * forceFields/SMARTS_InteLigand.txt, + forceFields/SMARTS_InteLigand_051110.txt, forceFields/atomtyp.txt, + forceFields/extable.txt, forceFields/phmodel.txt, + forceFields/resdata.txt, forceFields/types.txt, src/config.h.in, + src/openbabel/amberformat.cpp, src/openbabel/chains.cpp, + src/openbabel/chains.hpp, src/openbabel/data.cpp, + src/openbabel/dlhandler.hpp, src/openbabel/fingerprint.cpp, + src/openbabel/fingerprint.hpp, src/openbabel/fingerprintformat.cpp, + src/openbabel/gromos96format.cpp, src/openbabel/kekulize.cpp, + src/openbabel/matrix3x3.cpp, src/openbabel/matrix3x3.hpp, + src/openbabel/mol.cpp, src/openbabel/mol.hpp, + src/openbabel/obconversion.cpp, src/openbabel/obconversion.hpp, + src/openbabel/oberror.cpp, src/openbabel/obiter.cpp, + src/openbabel/obutil.cpp, src/openbabel/obutil.hpp, + src/openbabel/parsmart.cpp, src/openbabel/parsmart.hpp, + src/openbabel/patty.cpp, src/openbabel/pdbformat.cpp, + src/openbabel/phmodel.cpp, src/openbabel/povrayformat.cpp, + src/openbabel/rotor.cpp, src/openbabel/smilesformat.cpp, + src/openbabel/tinkerformat.cpp, src/openbabel/typer.cpp, + src/openbabel/vector3.cpp, src/openbabel/vector3.hpp, + src/openbabel/xyzformat.cpp, src/openbabel/zipstream.hpp, + src/openbabel/zipstreamimpl.hpp: updated OpenBabel to version 2.0.2 + +2006-10-19 12:51 gezelter + + * src/openbabel/oopseformat.cpp: Slight changes to oopseformat to + allow importing of openbabel's perceived atom types into OOPSE md + files + +2006-10-19 08:57 gezelter + + * make/Makefile.in, samples/builders/Makefile, + samples/builders/runMe, src/Makefile, src/applications/Makefile, + src/applications/velocitizer/Makefile, + src/applications/velocitizer/velocitizer.cpp, + src/applications/velocitizer/velocitizer.ggo, + src/applications/velocitizer/velocitizerCmd.c, + src/applications/velocitizer/velocitizerCmd.h, + src/integrators/Velocitizer.cpp: Added velocitizer utility program, + added samples of its use to the builder samples. + +2006-10-18 14:58 gezelter + + * src/: applications/staticProps/BondOrderParameter.cpp, + applications/staticProps/DensityPlot.cpp, + applications/staticProps/GofAngle2.cpp, + applications/staticProps/GofR.cpp, + applications/staticProps/GofRAngle.cpp, + applications/staticProps/GofXyz.cpp, + applications/staticProps/Hxy.cpp, + applications/staticProps/P2OrderParameter.cpp, + applications/staticProps/RhoZ.cpp, + applications/staticProps/SCDOrderParameter.cpp, + applications/staticProps/SCDOrderParameter.hpp, + applications/staticProps/StaticAnalyser.hpp, brains/SimInfo.cpp, + io/Globals.cpp, io/Globals.hpp: fixing a wrapVector problem in + staticProps, also making Shifted force and electrostatic damping + the default behavior + +2006-10-18 12:35 gezelter + + * src/applications/: nanoparticleBuilder/nanoparticleBuilder.cpp, + nanoparticleBuilder/nanoparticleBuilder.ggo, + nanoparticleBuilder/nanoparticleBuilderCmd.c, + nanoparticleBuilder/nanoparticleBuilderCmd.h, + randomBuilder/randomBuilder.cpp: bug fixes for vacancies + +2006-10-18 12:34 gezelter + + * samples/builders/: bimetallic.md, gold.md, metals.md, runMe: + Adding samples for builders + +2006-10-17 10:51 gezelter + + * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: bug + fixes + +2006-10-17 08:24 gezelter + + * src/: + applications/nanoparticleBuilder/shapedLatticeSpherical.cpp, + lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: bugfixing + shapedLattice to have crystal origin at one of the occupied lattice + sites + +2006-10-15 11:02 chuckv + + * src/applications/utilities/mdSplit: More typos... + +2006-10-15 10:59 chuckv + + * src/applications/utilities/mdSplit: Typo in mdSplit. + +2006-10-15 10:02 chuckv + + * src/applications/utilities/mdSplit: Fixed printing of OOPSE + version at header and trailer. + +2006-10-14 13:21 gezelter + + * samples/argon/500.md, + src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp, + src/applications/nanoparticleBuilder/shapedLatticeSpherical.cpp, + src/applications/nanoparticleBuilder/shapedLatticeSpherical.hpp, + src/lattice/shapedLattice.cpp, src/lattice/shapedLattice.hpp: fixed + a few bugs + +2006-10-13 13:16 chuckv + + * src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, + nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, + nanoparticleBuilderCmd.h: Changed nanoparticle builder for new dump + syntax. + +2006-10-11 12:24 chrisfen + + * src/applications/utilities/solvator: now the -n command works + +2006-10-10 11:34 gezelter + + * samples/builders/one_component.md, samples/builders/runMe, + src/applications/randomBuilder/randomBuilder.cpp, + src/applications/randomBuilder/randomBuilder.ggo, + src/applications/randomBuilder/randomBuilderCmd.c, + src/applications/randomBuilder/randomBuilderCmd.h, + src/applications/simpleBuilder/simpleBuilder.cpp, + src/applications/simpleBuilder/simpleBuilder.ggo, + src/applications/simpleBuilder/simpleBuilderCmd.c, + src/applications/simpleBuilder/simpleBuilderCmd.h: fixing missing + lattice arguments, adding a builder sample + +2006-10-10 08:55 gezelter + + * make/Makefile.in, samples/builders/Makefile, + samples/builders/lj.md, samples/builders/runMe, + samples/builders/three_component.md: adding builder samples + +2006-10-10 07:52 gezelter + + * src/applications/randomBuilder/randomBuilder.cpp: nearly complete + rewrite of randomBuilder + +2006-10-10 07:36 chrisfen + + * ChangeLog, configure, ac-tools/configure.in, + src/applications/utilities/affineScale: oops with the affineScale + +2006-10-10 07:08 chrisfen + * src/applications/utilities/: affineScale, affineScale.in, solvator, solvator.in, waterBoxer, waterBoxer.in: who needs .in files for perl? using env -2006-10-09 22:44 gezelter +2006-10-09 19:44 gezelter * src/: applications/randomBuilder/randomBuilder.cpp, applications/randomBuilder/randomBuilder.ggo, @@ -12,7 +459,7 @@ applications/randomBuilder/randomBuilderCmd.h, utils/MoLocator.cpp: fixing bugs in randomBuilder -2006-10-09 18:16 gezelter +2006-10-09 15:16 gezelter * samples/argon/lj.md, src/applications/randomBuilder/randomBuilder.cpp, @@ -23,183 +470,183 @@ src/applications/simpleBuilder/randomBuilderCmd.h: Fixing the builders to prepare for OOPSE-4 release -2006-10-06 17:29 chuckv +2006-10-06 14:29 chuckv * src/applications/utilities/mdSplit: Added utility to split dump file frames into md files. -2006-10-03 18:39 chrisfen +2006-10-03 15:39 chrisfen * src/applications/utilities/Makefile: forgot to adjust the makefile -2006-10-03 18:38 chrisfen +2006-10-03 15:38 chrisfen * src/applications/utilities/: solvator.in, waterBoxer.in: added solvator and adjusted waterBoxer -2006-10-02 19:54 chrisfen +2006-10-02 16:54 chrisfen * src/applications/utilities/waterBoxer.in: improvements to waterBoxer -2006-10-02 19:27 chrisfen +2006-10-02 16:27 chrisfen * src/applications/utilities/waterBoxer.in: fixed a bug in waterBoxer for invalid water names -2006-09-26 17:55 gezelter +2006-09-26 14:55 gezelter * AUTHORS, README: Starting cleanup for 4.0 release -2006-09-26 12:08 gezelter +2006-09-26 09:08 gezelter * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp: Cleaned up the code for BondOrderParameter and added a bunch of comments. Fixed a memory leak or ten. -2006-09-26 10:33 gezelter +2006-09-26 07:33 gezelter * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp: Some efficiency fixes (now computes Wigner 3-j coefficients only once in the constructor). -2006-09-25 21:30 gezelter +2006-09-25 18:30 gezelter * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: Mostly done with BondOrderParameter. Only a few performance tweaks remain -2006-09-25 18:08 gezelter +2006-09-25 15:08 gezelter * src/: applications/staticProps/BondOrderParameter.cpp, applications/staticProps/BondOrderParameter.hpp, applications/staticProps/StaticProps.cpp, brains/SimCreator.cpp, math/SphericalHarmonic.cpp: fixing bond order parameter code -2006-09-22 18:19 chrisfen +2006-09-22 15:19 chrisfen * src/: UseTheForce/DarkSide/simulation.F90, brains/SimInfo.cpp, brains/fSimulation.h, io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp, io/Globals.cpp, io/Globals.hpp: refined the reaction field dielectric passing -2006-09-21 21:41 gezelter +2006-09-21 18:41 gezelter * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp: bug fixes (still broken, however) -2006-09-21 21:36 gezelter +2006-09-21 18:36 gezelter * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp: Following Rein ten Wolde article -2006-09-21 17:47 gezelter +2006-09-21 14:47 gezelter * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp: more bug fixes -2006-09-21 16:43 gezelter +2006-09-21 13:43 gezelter * src/applications/staticProps/BondOrderParameter.cpp: more changes to BOP and SH -2006-09-21 14:25 chrisfen +2006-09-21 11:25 chrisfen * src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, io/Globals.cpp: fixed the half self term for wolf electrostatics and OOPSE now chooses a cutoff radius dependent alpha for damped electrostatics -2006-09-21 14:04 gezelter +2006-09-21 11:04 gezelter * src/applications/staticProps/BondOrderParameter.cpp: Fixed a bug in Wl code in BondOrderParameter -2006-09-21 10:45 gezelter +2006-09-21 07:45 gezelter * src/: applications/staticProps/BondOrderParameter.cpp, math/SphericalHarmonic.cpp, math/SphericalHarmonic.hpp: Bugfixes in BondOrderParameter and SphericalHarmonic -2006-09-20 18:16 gezelter +2006-09-20 15:16 gezelter * src/: applications/staticProps/BondOrderParameter.cpp, math/Makefile, math/SphericalHarmonic.cpp, math/SphericalHarmonic.hpp: added SphericalHarmonics, fixed a few problems with BondOrderParameter -2006-09-20 16:13 gezelter +2006-09-20 13:13 gezelter * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp, GofAngle2.cpp, StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: fixed bugs (mostly in BondOrderParameter) -2006-09-19 17:20 gezelter +2006-09-19 14:20 gezelter * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp: Adding BondOrderParameter to StaticProps -2006-09-19 17:14 gezelter +2006-09-19 14:14 gezelter * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp, Makefile, StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: Working on BondOrderParameter -2006-09-18 17:31 chuckv +2006-09-18 14:31 chuckv * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp: Latest Version -2006-09-08 12:13 gezelter +2006-09-08 09:13 gezelter * src/: brains/BlockSnapshotManager.cpp, io/DumpReader.cpp, utils/residentMem.c: fixed a DumpReader bug, took out extra printing statements in residentMem and BlockSnapshotManager -2006-09-04 09:37 gezelter +2006-09-04 06:37 gezelter * configure, ac-tools/configure.in, src/applications/utilities/Makefile: changing configure script to process the new utilities -2006-09-01 18:58 chrisfen +2006-09-01 15:58 chrisfen * src/applications/utilities/waterBoxer.in: added some features to waterBoxer -2006-09-01 17:08 chrisfen +2006-09-01 14:08 chrisfen * src/applications/utilities/: Makefile, affineScale.in, waterBoxer.in: added the waterBoxer script -2006-09-01 15:22 chrisfen +2006-09-01 12:22 chrisfen * src/applications/utilities/affineScale.in: added comment info -2006-09-01 15:16 gezelter +2006-09-01 12:16 gezelter * src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, brains/Register.cpp, integrators/Makefile, integrators/NgammaT.cpp, integrators/NgammaT.hpp, io/Globals.cpp: adding NgammaT integrator -2006-09-01 14:29 chrisfen +2006-09-01 11:29 chrisfen * src/applications/utilities/affineScale.in: modified affineScale to work with the new OOPSE files -2006-09-01 10:15 chrisfen +2006-09-01 07:15 chrisfen * src/io/: RestReader.cpp, RestWriter.cpp: fixed TI MPI bug -2006-08-31 18:34 chrisfen +2006-08-31 15:34 chrisfen * src/: integrators/VelocityVerletIntegrator.cpp, restraints/ThermoIntegrationForceManager.cpp: fixes to zang writing -2006-08-31 16:12 chrisfen +2006-08-31 13:12 chrisfen * samples/alkane/butane.in, samples/alkane/butane.md, samples/argon/500.in, samples/argon/500.md, samples/argon/ar864.in, @@ -256,12 +703,12 @@ Fixed an MPI bug in thermodynamic integration -2006-08-30 17:13 gezelter +2006-08-30 14:13 gezelter * src/applications/hydrodynamics/Hydro.cpp: removed extra file in Hydro.cpp -2006-08-30 17:04 gezelter +2006-08-30 14:04 gezelter * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/dynamicProps/DynamicProps.cpp, @@ -269,13 +716,13 @@ applications/utilities/dumpConverter, openbabel/oopseformat.cpp: Changing utility programs to use the new file format -2006-08-30 16:33 gezelter +2006-08-30 13:33 gezelter * src/: brains/SimCreator.cpp, io/DumpReader.cpp, io/DumpWriter.cpp: fixed some bugs in DumpWriter, eliminated some extra printing of debugging information -2006-08-30 14:42 tim +2006-08-30 11:42 tim * configure, ac-tools/OOPSE.m4, forceFields/Au.u3.funcfl, forceFields/Ni.u3.funcfl, samples/argon/lj.md, @@ -292,17 +739,17 @@ .dump, .eor) now contains meta-data information along with the configuration information. -2006-08-24 13:42 xsun +2006-08-24 10:42 xsun * src/io/Globals.cpp: change the globals.cpp to make sure we can set targetPressure and surfaceTension to be negative. -2006-08-14 16:32 chrisfen +2006-08-14 13:32 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: fixed an ordering issue in quadrupole-charge interactions -2006-08-02 15:40 gezelter +2006-08-02 12:40 gezelter * make/Makefile.in, samples/water/ssde/ssde.md, src/config.h.in, src/antlr/Makefile, src/applications/atom2md/atom2md.cpp, @@ -310,56 +757,56 @@ src/openbabel/Makefile, src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp: starting change of file formats -2006-08-02 14:06 gezelter +2006-08-02 11:06 gezelter * src/applications/: atom2md/Makefile, atom2md/atom2md.cpp, atom2mdin/Makefile, atom2mdin/atom2mdin.cpp: Changing atom2mdin into atom2md to reflect new unified file format -2006-07-27 17:02 chrisfen +2006-07-27 14:02 chrisfen * src/applications/utilities/dumpConverter: fixed a pvf bug -2006-07-27 16:36 tim +2006-07-27 13:36 tim * src/applications/utilities/dumpConverter: fixed dumpConverter problems -2006-07-27 15:05 gezelter +2006-07-27 12:05 gezelter * src/applications/utilities/dumpConverter: added dumpConverter -2006-07-26 17:45 gezelter +2006-07-26 14:45 gezelter * make/Makefile.in: removed shapes sample -2006-07-26 17:45 gezelter +2006-07-26 14:45 gezelter * src/applications/utilities/affineScale.in: fixed a spelling bug -2006-07-26 17:01 gezelter +2006-07-26 14:01 gezelter * configure: added perl interpreter to affineScale script -2006-07-26 17:01 gezelter +2006-07-26 14:01 gezelter * ac-tools/configure.in: added perl substitution for affineScale script -2006-07-26 17:00 gezelter +2006-07-26 14:00 gezelter * make/Makefile.in: added install target for scripts -2006-07-26 17:00 gezelter +2006-07-26 14:00 gezelter * src/applications/utilities/: Makefile, affineScale.in: Adding a directory for scripts Adding affineScale script -2006-07-24 10:51 xsun +2006-07-24 07:51 xsun * src/UseTheForce/DarkSide/gb.F90: fixed a getSigma bug -2006-07-19 08:46 chrisfen +2006-07-19 05:46 chrisfen * samples/: thermoIntegration/liquid/water.md, thermoIntegration/solid/water.md, water/dimer/water.md, @@ -368,59 +815,59 @@ water/tip3p_ice/water.md, water/tip4p/water.md: Added tred to sample water.md files -2006-07-19 08:35 chrisfen +2006-07-19 05:35 chrisfen * src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp, RigidBodyVisitor.cpp, RigidBodyVisitor.hpp: Added TRED water visitor for Dump2XYZ visualization -2006-07-19 08:33 chrisfen +2006-07-19 05:33 chrisfen * forceFields/DUFF2.frc: Added TRED parameters to forcefield -2006-07-17 14:13 xsun +2006-07-17 11:13 xsun * src/UseTheForce/DarkSide/gb.F90: fixed d / sigma0 confusion -2006-07-15 22:48 gezelter +2006-07-15 19:48 gezelter * src/io/ForceFieldOptions.cpp: testing commit logger -2006-07-15 22:46 gezelter +2006-07-15 19:46 gezelter * src/io/ForceFieldOptions.cpp: removed printing of GBN and GBM from previous debugging -2006-07-14 10:47 xsun +2006-07-14 07:47 xsun * configure, ac-tools/OOPSE.m4: Fixed a bug in the fftw part of the configure script. -2006-07-07 15:44 gezelter +2006-07-07 12:44 gezelter * configure, ac-tools/configure.in, samples/gbljtest/2gb.md, src/UseTheForce/DarkSide/gb.F90: removed icc from C++ search lines, did some formatting work on GB module, mucked around with a GB example -2006-07-07 10:18 chuckv +2006-07-07 07:18 chuckv * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp: Adding more changes to orientational bond order parameter. -2006-07-03 15:40 chuckv +2006-07-03 12:40 chuckv * src/math/Wigner3jm.F90: Added utility function to winger3jm from slatac. -2006-07-03 10:06 chrisfen +2006-07-03 07:06 chrisfen * src/UseTheForce/DarkSide/mpole.F90: Added the multipole interaction routine. It doesn't work yet, so it's not included in the build. -2006-07-03 09:18 chrisfen +2006-07-03 06:18 chrisfen * src/: UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, @@ -435,83 +882,83 @@ dipole moment accumulation for the purposes of calculating dielectric constants -2006-07-01 18:27 kdaily +2006-07-01 15:27 kdaily * src/UseTheForce/DarkSide/gb.F90: fixed forces and torques for GB -2006-06-28 10:35 chrisfen +2006-06-28 07:35 chrisfen * src/io/: DumpReader.cpp, RestReader.cpp, RestReader.hpp: more efficient file reading for thermodynamic integration, and fixed some formatting -2006-06-27 12:36 chuckv +2006-06-27 09:36 chuckv * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp: Beginnings of a order parameter. -2006-06-27 12:19 chuckv +2006-06-27 09:19 chuckv * src/applications/staticProps/: BondOrderParameter.cpp, BondOrderParameter.hpp: Adding code for bond orientational parameters. -2006-06-22 11:21 chrisfen +2006-06-22 08:21 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. -2006-06-21 14:28 chrisfen +2006-06-21 11:28 chrisfen * src/visitors/AtomVisitor.cpp: fixed a build problem... GB_12b_ratio no longer exists (replaced with BG_l). -2006-06-19 13:55 chuckv +2006-06-19 10:55 chuckv * src/math/: Makefile, Wigner3jm.F90, Wigner3jm_interface.h: Added support for Winger3jm coefficients. -2006-06-18 21:36 chrisfen +2006-06-18 18:36 chrisfen * src/: io/RestReader.cpp, io/RestWriter.cpp, restraints/ThermoIntegrationForceManager.cpp: fixes for mpi thermodynamic integration, close to fully working... -2006-06-17 13:02 tim +2006-06-17 10:02 tim * src/visitors/AtomVisitor.cpp: output the principle axis of GB -2006-06-15 14:38 gezelter +2006-06-15 11:38 gezelter * configure, ac-tools/OOPSE.m4, ac-tools/configure.in, samples/water/tip4p/tp4.md: added mpi compilers, demoted pg compilers after pathscale -2006-06-09 14:26 chrisfen +2006-06-09 11:26 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: reformulated some of the electrostatics -2006-06-07 18:49 chrisfen +2006-06-07 15:49 chrisfen * samples/water/ssd/ssd.md, src/UseTheForce/DarkSide/electrostatic.F90: damping now works for charge-quadrupole and dipole-dipole -2006-06-07 14:05 chrisfen +2006-06-07 11:05 chrisfen * src/: UseTheForce/DarkSide/simParallel.F90, io/RestReader.cpp: Fixed a spelling error and a bug in MPI Thermodynamic Integration on file read-in -2006-06-06 14:26 chrisfen +2006-06-06 11:26 chrisfen * src/io/: DumpReader.cpp, MultipoleAtomTypesSectionParser.cpp: fixed some typos -2006-06-06 13:43 gezelter +2006-06-06 10:43 gezelter * forceFields/DUFF2.frc, samples/gbljtest/2gb.in, samples/gbljtest/2gb.md, samples/gbljtest/gb.md, @@ -526,12 +973,12 @@ GB, removing CM drift in Langevin Dynamics, fixing a memory leak, adding a visitor -2006-06-05 14:44 gezelter +2006-06-05 11:44 gezelter * src/UseTheForce/DarkSide/: fForceOptions.F90, gb.F90: Added methods to access GB_mu and GB_nu from the force field options -2006-06-05 14:24 gezelter +2006-06-05 11:24 gezelter * forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, src/UseTheForce/doForces.F90, src/UseTheForce/fForceOptions.h, @@ -563,14 +1010,14 @@ Also, changes in hydrodynamics code to make HydroProp a somewhat smarter class (rather than just a struct). -2006-06-01 14:06 xsun +2006-06-01 11:06 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. -2006-05-25 17:40 chrisfen +2006-05-25 14:40 chrisfen * forceFields/DUFF2.frc, samples/thermoIntegration/liquid/water.md, samples/thermoIntegration/solid/water.md, @@ -582,35 +1029,35 @@ fixed a bug for Thermodynamic integration (you can now have a lambda of 0) -2006-05-25 13:02 tim +2006-05-25 10:02 tim * src/applications/hydrodynamics/ApproximationModel.cpp: Fix a type promotion problem -2006-05-25 12:27 tim +2006-05-25 09:27 tim * src/applications/hydrodynamics/: AnalyticalModel.hpp, ApproximationModel.cpp, Hydro.cpp, HydrodynamicsModel.hpp: replace double with RealType -2006-05-25 11:27 gezelter +2006-05-25 08:27 gezelter * configure: What? -2006-05-25 11:24 gezelter +2006-05-25 08:24 gezelter * ac-tools/OOPSE.m4: more changes -2006-05-25 11:19 gezelter +2006-05-25 08:19 gezelter * configure, ac-tools/OOPSE.m4: more changes for MPICH with profiling libraries required -2006-05-25 10:54 gezelter +2006-05-25 07:54 gezelter * configure, ac-tools/OOPSE.m4: MPI stuff -2006-05-24 14:31 gezelter +2006-05-24 11:31 gezelter * configure, ac-tools/OOPSE.m4, src/config.h.in, src/applications/hydrodynamics/AnalyticalModel.cpp, @@ -632,47 +1079,47 @@ src/applications/hydrodynamics/Spheric.cpp, src/applications/hydrodynamics/Spheric.hpp: fixes for Hydrodynamics -2006-05-24 12:18 tim +2006-05-24 09:18 tim * src/integrators/LDForceManager.cpp: fix a bug in parsing HydroProp file -2006-05-24 11:24 gezelter +2006-05-24 08:24 gezelter * src/integrators/LDForceManager.cpp: Fixed a bug when spherical boundary conditions were off. -2006-05-23 17:12 xsun +2006-05-23 14:12 xsun * src/applications/staticProps/Hxy.cpp: fixed an initialization bug of Hxy.cpp. -2006-05-23 14:46 tim +2006-05-23 11:46 tim * src/applications/dump2Xyz/Dump2XYZ.cpp: wrapping back to PBC by molecule instead of by individual atom -2006-05-22 11:30 xsun +2006-05-22 08:30 xsun * src/applications/staticProps/: Hxy.cpp, Hxy.hpp, StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: fixed the bugs of Hxy.cpp. -2006-05-19 17:26 chrisfen +2006-05-19 14:26 chrisfen * ChangeLog, src/io/DumpWriter.cpp: Last bug showed up in 2 places, fixed the other one. -2006-05-19 16:45 tim +2006-05-19 13:45 tim * src/io/DumpWriter.cpp: Fix a bug of printing empty line in DumpWriter -2006-05-19 11:11 tim +2006-05-19 08:11 tim * make/Makefile.in: change the order of include path and library path -2006-05-17 17:51 tim +2006-05-17 14:51 tim * ChangeLog, samples/water/ssd/ssd.md, src/config.h.in, src/UseTheForce/EAM_FF.cpp, src/UseTheForce/EAM_FF.hpp, @@ -828,7 +1275,7 @@ src/visitors/ZconsVisitor.cpp, src/visitors/ZconsVisitor.hpp: Adding single precision capabilities to c++ side -2006-05-17 15:54 gezelter +2006-05-17 12:54 gezelter * configure, ac-tools/configure.in, make/Makefile.in, src/UseTheForce/doForces.F90, @@ -839,12 +1286,12 @@ src/utils/definitions.F90: Adding single precision capabilities to the fortran side -2006-05-17 12:10 gezelter +2006-05-17 09:10 gezelter * configure, ac-tools/configure.in, src/config.h.in: adding --enable-single to configure script -2006-05-17 11:37 gezelter +2006-05-17 08:37 gezelter * ac-tools/aclocal.m4, src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, @@ -860,17 +1307,17 @@ src/math/erfc.F90, src/utils/interpolation.F90: Getting fortran side prepped for single precision... -2006-05-17 10:03 chrisfen +2006-05-17 07:03 chrisfen * samples/water/ssd-ion/ssdCl.md, src/UseTheForce/DarkSide/electrostatic.F90: electrostatic refinement -2006-05-16 23:03 gezelter +2006-05-16 20:03 gezelter * configure, ac-tools/OOPSE.m4, make/Makefile.in: zlib fixes -2006-05-16 16:38 gezelter +2006-05-16 13:38 gezelter * configure, ac-tools/OOPSE.m4, ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in, ac-tools/install-sh, @@ -880,7 +1327,7 @@ src/applications/staticProps/StaticProps.cpp: Autoconf fixes for FFTW. Multiple FFTW version support. -2006-05-15 22:06 gezelter +2006-05-15 19:06 gezelter * README, configure, ac-tools/aclocal.m4, ac-tools/configure.in, make/Makefile.in, src/config.h.in, @@ -896,13 +1343,13 @@ src/integrators/LDForceManager.hpp, src/math/SquareMatrix.hpp, src/utils/HydroProps.hpp: [no log message] -2006-05-12 17:34 xsun +2006-05-12 14:34 xsun * src/applications/staticProps/: Hxy.cpp, Hxy.hpp, Makefile, StaticProps.cpp, StaticPropsCmd.c, StaticPropsCmd.h: Changes to calculate undulation spectrum -2006-05-09 21:44 tim +2006-05-09 18:44 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/dump2Xyz/Dump2XYZ.ggo, @@ -912,48 +1359,48 @@ visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: adding a gay-berne switch to Dump2XYZ -2006-05-05 13:58 gezelter +2006-05-05 10:58 gezelter * src/UseTheForce/DarkSide/qpole.F90: Adding qpole -2006-05-05 10:34 tim +2006-05-05 07:34 tim * ac-tools/aclocal.m4: finding ifort arguments that won't die under two different versions of the intel fortran compiler -2006-05-03 09:15 chrisfen +2006-05-03 06:15 chrisfen * src/applications/randomBuilder/Makefile: missing makefile was hanging up 'make clean' -2006-04-25 18:59 chuckv +2006-04-25 15:59 chuckv * src/applications/randomBuilder/: randomBuilder.cpp, randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added random builder to cvs. -2006-04-25 18:54 chuckv +2006-04-25 15:54 chuckv * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: Change in siminfo used in nanoparticleBuilder. -2006-04-25 18:30 chuckv +2006-04-25 15:30 chuckv * make/Makefile.in: Added random builder -2006-04-25 18:29 chuckv +2006-04-25 15:29 chuckv * src/applications/simpleBuilder/: Makefile, randomBuilder.cpp, randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added a random builder to oopse. -2006-04-25 09:35 gezelter +2006-04-25 06:35 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 22:09 gezelter +2006-04-24 19:09 gezelter * configure, ac-tools/aclocal.m4, src/UseTheForce/DarkSide/LJ.F90, src/applications/hydrodynamics/Hydro.cpp, src/brains/Register.cpp, @@ -965,17 +1412,17 @@ src/io/Globals.hpp, src/primitives/StuntDouble.hpp: Adding spherical boundary conditions to LD integrator -2006-04-24 22:06 gezelter +2006-04-24 19:06 gezelter * src/applications/hydrodynamics/: BeadModel.cpp, ShapeBuilder.cpp: Added EAM atom types to Hydro models -2006-04-21 16:02 chrisfen +2006-04-21 13:02 chrisfen * src/UseTheForce/DarkSide/eam.F90: put spline subroutines in the EAM module -2006-04-21 15:32 chrisfen +2006-04-21 12:32 chrisfen * ChangeLog, samples/shape/5CB.shape, samples/shape/8CB.shape, samples/shape/C60.shape, samples/shape/C70.shape, @@ -994,17 +1441,17 @@ 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 23:19 chrisfen +2006-04-20 20:19 chrisfen * samples/water/spce/spce.md, src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added... -2006-04-20 17:02 chrisfen +2006-04-20 14:02 chrisfen * samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90, src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky -2006-04-20 14:24 gezelter +2006-04-20 11:24 gezelter * samples/metals/EAM/Au_bulk_voter.md, samples/metals/Sutton-Chen/Au_bulk_SC.md, @@ -1019,7 +1466,7 @@ src/utils/interpolation.F90: Complete rewrite of spline code and everything that uses it. -2006-04-17 17:49 gezelter +2006-04-17 14:49 gezelter * configure, ac-tools/aclocal.m4, samples/argon/500.md, samples/metals/EAM/Au_bulk_voter.md, @@ -1037,7 +1484,7 @@ src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp, src/utils/interpolation.F90: Many performance improvements -2006-04-15 22:51 chrisfen +2006-04-15 19:51 chrisfen * configure, samples/argon/500.md, src/UseTheForce/doForces.F90, src/UseTheForce/fSwitchingFunction.h, @@ -1045,85 +1492,85 @@ src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to switcheroo -2006-04-15 17:58 chrisfen +2006-04-15 14:58 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 17:59 gezelter +2006-04-14 14:59 gezelter * src/utils/interpolation.F90: changed the interface a bit -2006-04-14 17:49 gezelter +2006-04-14 14:49 gezelter * src/utils/interpolation.F90: added some logical flags -2006-04-14 17:06 chrisfen +2006-04-14 14:06 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 16:04 gezelter +2006-04-14 13:04 gezelter * src/utils/: Makefile.in, interpolation.F90: bug fixes for interpolation module -2006-04-14 15:57 gezelter +2006-04-14 12:57 gezelter * src/utils/interpolation.F90: Heavily modified interpolation module, also moved to "utils" -2006-04-12 17:15 chuckv +2006-04-12 14:15 chuckv * src/UseTheForce/DarkSide/interpolation.F90: Added interpolation module. -2006-04-11 11:33 gezelter +2006-04-11 08:33 gezelter * src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: [no log message] -2006-04-03 11:37 chuckv +2006-04-03 08:37 chuckv * configure, ac-tools/aclocal.m4, make/Makefile.in, src/UseTheForce/DarkSide/simParallel.F90: Added status module to simParallel for error reporting. -2006-03-31 13:09 tim +2006-03-31 10:09 tim * src/: integrators/NPrT.cpp, io/Globals.cpp: NPrT might work now -2006-03-30 16:08 chuckv +2006-03-30 13:08 chuckv * src/UseTheForce/DarkSide/suttonchen.F90: Fixed memory leak bug where SCList capacity was not reset to zero on destruction. -2006-03-30 14:37 chuckv +2006-03-30 11:37 chuckv * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: More testing of nanoparticleBuilder. -2006-03-29 17:24 chuckv +2006-03-29 14:24 chuckv * src/mdParser/SimplePreprocessor.hpp: Added check to make sure md file exists. -2006-03-29 14:17 chuckv +2006-03-29 11:17 chuckv * src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: Fixed latticeOrt in shapedlatice and latticebuilder. -2006-03-29 13:11 tim +2006-03-29 10:11 tim * src/applications/dynamicProps/: DipoleCorrFunc.cpp, LegendreCorrFunc.cpp, VCorrFunc.cpp: Fix the normalization problem in calculating correlation functions -2006-03-29 13:09 tim +2006-03-29 10:09 tim * src/applications/hydrodynamics/: ApproximationModel.cpp, ApproximationModel.hpp, CompositeShape.cpp, Hydro.cpp, Hydro.ggo, @@ -1131,29 +1578,29 @@ RoughShell Model is working; (20)Adding a new option into Hydro which allows user to generate the beads only -2006-03-27 11:21 chuckv +2006-03-27 08:21 chuckv * src/applications/nanoparticleBuilder/Makefile: Makefile for nanoparticle builder. -2006-03-27 11:03 chuckv +2006-03-27 08:03 chuckv * make/Makefile.in, src/lattice/shapedLattice.cpp, src/lattice/shapedLattice.hpp: Added nanoparticle builder to makefile -2006-03-24 15:46 chuckv +2006-03-24 12:46 chuckv * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: Debugging changes to nanoparticle builder. -2006-03-24 12:29 tim +2006-03-24 09:29 tim * src/applications/dynamicProps/: DynamicProps.cpp, DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: back to previous DynamicProps -2006-03-24 11:49 tim +2006-03-24 08:49 tim * src/applications/dynamicProps/: DynamicProps.cpp, DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, @@ -1162,39 +1609,39 @@ --rcorr is for position correlation and --rmsd is for mean square displacement. -2006-03-23 10:03 tim +2006-03-23 07:03 tim * src/applications/hydrodynamics/: AnalyticalModel.cpp, AnalyticalModel.hpp, ApproximationModel.cpp, ApproximationModel.hpp, HydrodynamicsModel.hpp: update writeBeads method -2006-03-23 10:02 tim +2006-03-23 07:02 tim * src/io/Globals.hpp: remove a unknown method -2006-03-23 10:00 tim +2006-03-23 07:00 tim * src/math/CholeskyDecomposition.hpp: The off diagnal is not set -2006-03-23 09:59 tim +2006-03-23 06:59 tim * src/mdParser/SimplePreprocessor.hpp: Throw exception if the file can not be opened for preprocessing -2006-03-22 15:57 chuckv +2006-03-22 12:57 chuckv * src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, shapedLatticeSpherical.cpp, shapedLatticeSpherical.hpp: Added shaped lattice. -2006-03-21 10:33 tim +2006-03-21 07:33 tim * src/applications/hydrodynamics/ApproximationModel.cpp: fix a bug in calculating hydrodynamics tensor when the radius of beads are not the same -2006-03-20 19:26 tim +2006-03-20 16:26 tim * src/: applications/hydrodynamics/AnalyticalModel.cpp, applications/hydrodynamics/BeadModel.cpp, @@ -1202,7 +1649,7 @@ integrators/LDForceManager.cpp: Fix a bug in friction calculation for ellipsoid -2006-03-20 14:12 tim +2006-03-20 11:12 tim * src/: applications/hydrodynamics/AnalyticalModel.cpp, applications/hydrodynamics/Ellipsoid.cpp, @@ -1211,12 +1658,12 @@ integrators/LDForceManager.cpp: Verify the correctness of Ellipsoid's hydrodynamics properties -2006-03-17 18:51 tim +2006-03-17 15:51 tim * src/applications/hydrodynamics/: Hydro.cpp, ShapeBuilder.cpp: New version of Hydro is working now. -2006-03-17 18:20 tim +2006-03-17 15:20 tim * src/: applications/hydrodynamics/AnalyticalModel.cpp, applications/hydrodynamics/AnalyticalModel.hpp, @@ -1250,59 +1697,59 @@ io/Globals.cpp, io/Globals.hpp, math/SquareMatrix.hpp, utils/HydroProps.hpp: refactor Hydrodynamics module. -2006-03-17 11:10 chuckv +2006-03-17 08:10 chuckv * src/lattice/: shapedLattice.cpp, shapedLattice.hpp, Makefile: Generic Shaped Lattice for oopse. Can overload to get spherical or nanorod. -2006-03-16 17:50 tim +2006-03-16 14:50 tim * src/: applications/hydrodynamics/HydrodynamicsModel.cpp, integrators/LDForceManager.cpp, math/MersenneTwister.hpp: LagevinDynamics is working? -2006-03-16 16:52 gezelter +2006-03-16 13:52 gezelter * src/applications/hydrodynamics/RoughShell.hpp: fixed a const problem -2006-03-15 17:08 tim +2006-03-15 14:08 tim * src/applications/hydrodynamics/HydrodynamicsModel.cpp: unit conversion for diffusion tensor is wrong -2006-03-15 16:28 tim +2006-03-15 13:28 tim * src/: applications/hydrodynamics/HydrodynamicsModel.cpp, utils/NumericConstant.hpp: change the epsilon of numeric_limit -2006-03-15 15:58 tim +2006-03-15 12:58 tim * src/applications/hydrodynamics/HydrodynamicsModel.cpp: correcting the unit in HydrodynamicsModel -2006-03-15 12:35 tim +2006-03-15 09:35 tim * src/primitives/RigidBody.cpp: using setFrc in RigidBody::calcForcesAndTorques will discard if there are force and torque applied in rigid body itself. use addFrc instead. -2006-03-15 10:51 tim +2006-03-15 07:51 tim * src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, RoughShell.cpp, RoughShell.hpp: Adding RoughShell and BeadModel -2006-03-15 10:50 tim +2006-03-15 07:50 tim * make/Makefile.in, src/applications/hydrodynamics/Makefile: adding hydrodynamics module into build system -2006-03-14 18:46 tim +2006-03-14 15:46 tim * src/math/CholeskyDecomposition.hpp: adding Cholesky Decomposition -2006-03-13 17:42 tim +2006-03-13 14:42 tim * src/: applications/hydrodynamics/HydrodynamicsModel.cpp, applications/hydrodynamics/HydrodynamicsModel.hpp, @@ -1315,18 +1762,18 @@ math/RandNumGen.hpp, math/SquareMatrix3.hpp: LangevinDynamics in progress -2006-03-07 11:43 gezelter +2006-03-07 08:43 gezelter * src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Fixed a double/int bug. Surprised no one ever noticed before... -2006-02-24 16:17 tim +2006-02-24 13:17 tim * src/applications/hydrodynamics/HydrodynamicsModel.cpp: fix bugs in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out product of Rij -2006-02-23 18:16 tim +2006-02-23 15:16 tim * src/applications/hydrodynamics/: Hydro.cpp, Hydro.ggo, HydroCmd.c, HydroCmd.h, HydrodynamicsModel.cpp, @@ -1335,7 +1782,7 @@ MoleculeShape.cpp, MoleculeShape.hpp, StuntDoubleShape.cpp, StuntDoubleShape.hpp: Bead Model is working -2006-02-22 15:35 tim +2006-02-22 12:35 tim * src/: applications/hydrodynamics/Hydro.cpp, applications/hydrodynamics/Hydro.ggo, @@ -1352,11 +1799,11 @@ math/RectMatrix.hpp, math/SquareMatrix3.hpp: Adding Hydrodynamics Module -2006-02-16 17:05 gezelter +2006-02-16 14:05 gezelter * src/brains/Snapshot.cpp: fixed a spelling error -2006-02-16 16:40 gezelter +2006-02-16 13:40 gezelter * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/simulation.F90, math/Makefile, @@ -1364,70 +1811,70 @@ larger than 1/2 the length of the shortest box dimension. added a few fortran utility routines -2006-02-15 15:46 chuckv +2006-02-15 12:46 chuckv * src/applications/nanoparticleBuilder/: sphericalNanoparticle.cpp, sphericalNanoparticle.hpp: Changed Names of class files. -2006-02-10 10:45 kdaily +2006-02-10 07:45 kdaily * src/applications/dynamicProps/LegendreCorrFunc.cpp: [no log message] -2006-02-10 10:12 tim +2006-02-10 07:12 tim * src/math/: LegendrePolynomial.cpp, Vector.hpp: fix a bug in converting integer to double -2006-02-08 13:21 chrisfen +2006-02-08 10:21 chrisfen * forceFields/DUFF2.frc: added DPD molecule type parameters -2006-02-07 11:39 tim +2006-02-07 08:39 tim * src/applications/dynamicProps/: DipoleCorrFunc.cpp, LegendreCorrFunc.cpp: Fixing a bug which reads the wrong frame of trajectory file during analysis -2006-02-02 12:14 tim +2006-02-02 09:14 tim * src/: math/Polynomial.hpp, math/SquareMatrix3.hpp, types/AtomStamp.cpp: adding transpose into SquareMatrix3; fix a bug in AtomStamp where orientation is not set correctly. -2006-02-02 11:49 gezelter +2006-02-02 08:49 gezelter * src/primitives/RigidBody.cpp: fixed a bug in rigid bodies that contain directional atoms -2006-02-02 10:49 xsun +2006-02-02 07:49 xsun * src/: applications/dump2Xyz/Dump2XYZ.cpp, visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Adding visitor for GBlipid atom type -2006-02-01 21:57 gezelter +2006-02-01 18:57 gezelter * make/Makefile.in: added CXXFLAGS to the LinkOptions to allow compilation with icc9 (skipping the gcc-4 std c++ libraries). -2006-02-01 16:06 chrisfen +2006-02-01 13:06 chrisfen * src/brains/SimInfo.cpp: Missing brace caused the last commit not to build -2006-02-01 15:54 chrisfen +2006-02-01 12:54 chrisfen * samples/water/spce/spce.md, src/brains/SimInfo.cpp: Changes to cutoff radius setting to a more logical procedure - still may change... -2006-02-01 12:26 gezelter +2006-02-01 09:26 gezelter * src/: math/Polynomial.hpp, utils/GenericData.hpp, utils/any.hpp: Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X -2006-01-30 17:25 tim +2006-01-30 14:25 tim * src/: applications/dynamicProps/DipoleCorrFunc.cpp, applications/dynamicProps/DynamicProps.cpp, @@ -1440,68 +1887,68 @@ math/LegendrePolynomial.hpp, math/Makefile, math/Polynomial.hpp: Adding :LegendrePolynomial -2006-01-19 17:54 chuckv +2006-01-19 14:54 chuckv * src/applications/nanoparticleBuilder/: Makefile, nanoparticleBuilder.cpp, sphericalNanoparticle.hpp: Changes to nanoparticle builder -2006-01-18 16:08 chuckv +2006-01-18 13:08 chuckv * src/applications/nanoparticleBuilder/Makefile: Added Makefile for nanoparticle builder. -2006-01-17 11:16 gezelter +2006-01-17 08:16 gezelter * AUTHORS, README: Cleaning up for 3.0.1 release -2006-01-17 10:50 gezelter +2006-01-17 07:50 gezelter * ChangeLog: Prepping 3.0.1 release -2006-01-17 10:32 gezelter +2006-01-17 07:32 gezelter * src/config.h.in: new version number -2006-01-17 10:32 gezelter +2006-01-17 07:32 gezelter * doc/: OOPSE.pdf, SelectionExpression.html, cppstyle.html, definition.jpg, gofr.jpg, gofrtheta.jpg, heirarchy.png, oopseManual.pdf: Updated Documentation -2006-01-16 18:10 gezelter +2006-01-16 15:10 gezelter * ChangeLog, README: Getting ready for release! -2006-01-16 10:26 gezelter +2006-01-16 07:26 gezelter * configure: Testing commit -2006-01-13 16:57 chuckv +2006-01-13 13:57 chuckv * src/: UseTheForce/SC_FF.cpp, applications/nanoparticleBuilder/sphericalNanoparticle.cpp, io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals. Handled by forceField now. -2006-01-13 14:17 chuckv +2006-01-13 11:17 chuckv * src/io/Globals.cpp: Added NPAT to Globals integrators. -2006-01-13 11:33 gezelter +2006-01-13 08:33 gezelter * Makefile: [no log message] -2006-01-13 11:26 gezelter +2006-01-13 08:26 gezelter * Makefile: testing to make sure GNU make is the make that was used to build OOPSE -2006-01-13 10:48 gezelter +2006-01-13 07:48 gezelter * configure, ac-tools/configure.in: changed compiler search order -2006-01-12 19:09 chuckv +2006-01-12 16:09 chuckv * forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc, samples/metals/Sutton-Chen/Au_bulk.in, @@ -1509,46 +1956,46 @@ samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen units -2006-01-12 16:16 gezelter +2006-01-12 13:16 gezelter * LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some version info and the copyright date -2006-01-12 15:52 gezelter +2006-01-12 12:52 gezelter * src/config.h.in: added some missing checks for header files (particularly zlib.h), used autoheader to help generate config.h.in -2006-01-12 15:51 gezelter +2006-01-12 12:51 gezelter * configure, ac-tools/configure.in: added some missing checks for header files (particularly zlib.h) -2006-01-12 15:19 gezelter +2006-01-12 12:19 gezelter * make/Makefile.in: fixed a dependency problem for the Executable builds -2006-01-12 15:02 gezelter +2006-01-12 12:02 gezelter * samples/gbljtest/Makefile: Missing Makefile in this sample directory -2006-01-12 15:01 gezelter +2006-01-12 12:01 gezelter * make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile: Old makefile.in no longer required -2006-01-12 15:01 gezelter +2006-01-12 12:01 gezelter * forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff needs to be installed -2006-01-12 14:56 chuckv +2006-01-12 11:56 chuckv * src/io/DumpWriter.cpp: Changed formating. -2006-01-12 11:47 chrisfen +2006-01-12 08:47 chrisfen * samples/water/tip4p/tp4.md, src/UseTheForce/DarkSide/electrostatic.F90, @@ -1556,30 +2003,30 @@ src/UseTheForce/DarkSide/electrostatic_interface.h, src/brains/SimInfo.cpp: unifying function name in electrostatics -2006-01-12 11:04 tim +2006-01-12 08:04 tim * samples/metals/: EAM/nanoparticle/Makefile, EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile, Sutton-Chen/Makefile: fix make install problem for metals samples -2006-01-12 10:22 tim +2006-01-12 07:22 tim * make/Makefile.in: remove samples/metals from install list. -2006-01-12 09:31 tim +2006-01-12 06:31 tim * src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not handle multiple line macro, just convert multiple line macro into single line macro. -2006-01-11 23:13 chrisfen +2006-01-11 20:13 chrisfen * src/: UseTheForce/DarkSide/electrostatic.F90, UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some changes to electrostatics for shifted-potential and shifted-force with mono and multipoles -2006-01-11 18:04 gezelter +2006-01-11 15:04 gezelter * src/config.h.in, src/UseTheForce/doForces_interface.h, src/UseTheForce/DarkSide/atype_interface.h, @@ -1598,17 +2045,17 @@ src/utils/fError.c, configure, make/Makefile.in: autoconf modernization and cruft removal -2006-01-11 18:04 gezelter +2006-01-11 15:04 gezelter * ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf modernization and cruft-removal -2006-01-11 17:50 tim +2006-01-11 14:50 tim * src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix some error messages -2006-01-11 14:01 tim +2006-01-11 11:01 tim * src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp, io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp, @@ -1617,32 +2064,32 @@ utils/StringUtils.hpp: instead of printing to std::cout, throwing an exception when error is found. -2006-01-11 13:41 gezelter +2006-01-11 10:41 gezelter * src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling error -2006-01-10 17:55 chuckv +2006-01-10 14:55 chuckv * forceFields/SuttonChen.frc: Changed conversion factor. -2006-01-10 16:14 chuckv +2006-01-10 13:14 chuckv * samples/metals/Sutton-Chen/Au_bulk_SC.md, src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be working now. -2006-01-09 17:22 chuckv +2006-01-09 14:22 chuckv * src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC -2006-01-09 17:14 tim +2006-01-09 14:14 tim * src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp, StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: fixing RhoZ -2006-01-09 14:26 chuckv +2006-01-09 11:26 chuckv * forceFields/SuttonChen.frc, samples/metals/Sutton-Chen/Au_bulk_SC.md, @@ -1650,27 +2097,27 @@ src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to section parsers. -2006-01-09 14:11 tim +2006-01-09 11:11 tim * src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp, utils/StringUtils.hpp: replace isType with isInteger -2006-01-06 16:15 tim +2006-01-06 13:15 tim * src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra forceFieldOptions from SC_FF -2006-01-06 15:27 chuckv +2006-01-06 12:27 chuckv * forceFields/SuttonChen.frc: Add force file. -2005-12-31 17:42 chuckv +2005-12-31 14:42 chuckv * src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer segfaults or produces 0 potential, but rather produces Inf for the potential. Progress.... -2005-12-30 18:15 chuckv +2005-12-30 15:15 chuckv * samples/metals/Sutton-Chen/Au_bulk_SC.md, src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, @@ -1678,88 +2125,88 @@ src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More Sutton-Chen bug fixes. -2005-12-30 16:25 tim +2005-12-30 13:25 tim * src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range potential return from fortran is already accumulated, it should not be accumulated again; nGroupTypesCol is not initialized; GroupMaxCutoffCol is not allocated; -2005-12-30 10:32 tim +2005-12-30 07:32 tim * make/Makefile.in, src/brains/SimCreator.cpp: In order to compile MPI version, we need to cast const char* to void* for stringstream.str(); Previous Makefile use bjects of single version to make the MPI library; -2005-12-29 19:18 chuckv +2005-12-29 16:18 chuckv * make/Makefile.in, samples/metals/Makefile, src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes. Almost there... -2005-12-29 15:19 chuckv +2005-12-29 12:19 chuckv * forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in forcefield. -2005-12-29 15:07 chuckv +2005-12-29 12:07 chuckv * samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile, metals.md: added files for sutton-chen -2005-12-29 11:37 chuckv +2005-12-29 08:37 chuckv * samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile, metals.md: More cvs changing. -2005-12-29 11:34 chuckv +2005-12-29 08:34 chuckv * samples/metals/Au_nanoparticle.in: More moving... -2005-12-29 11:33 chuckv +2005-12-29 08:33 chuckv * samples/metals/EAM/nanoparticle/: Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md, Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More changes to directory structure. -2005-12-29 11:21 chuckv +2005-12-29 08:21 chuckv * samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md, Au_bulk_voter.md, Makefile, metals.md: More Directory changes... -2005-12-29 11:17 chuckv +2005-12-29 08:17 chuckv * samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md, Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of directory structure -2005-12-29 11:03 chuckv +2005-12-29 08:03 chuckv * src/: UseTheForce/DarkSide/fForceOptions_interface.F90, brains/SimCreator.cpp: Fixed issue with symbol naming and added call to set force options in SimCreator. -2005-12-28 16:44 chuckv +2005-12-28 13:44 chuckv * src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More changes to forcefield options. -2005-12-28 16:42 chuckv +2005-12-28 13:42 chuckv * src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options passed to fortran. -2005-12-23 18:04 chuckv +2005-12-23 15:04 chuckv * src/: UseTheForce/DarkSide/fForceOptions_interface.h, io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option changes. -2005-12-16 16:52 tim +2005-12-16 13:52 tim * configure, ac-tools/aclocal.m4, ac-tools/configure.in, src/config.h.in, src/UseTheForce/DarkSide/gb.F90, @@ -1782,16 +2229,16 @@ autoconf test to check for __func__ usability. Changed some default compile flags for the Sun architecture -2005-12-16 14:01 gezelter +2005-12-16 11:01 gezelter * ac-tools/AC_CXX_HAVE_STL.m4: added the STL check -2005-12-16 13:55 tim +2005-12-16 10:55 tim * src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor change to build oopse under solaris -2005-12-16 13:26 tim +2005-12-16 10:26 tim * src/: brains/SimCreator.cpp, io/Globals.cpp, types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library @@ -1799,43 +2246,43 @@ define a macro to handle it. Adding exception handling to SimCreator. -2005-12-16 10:53 gezelter +2005-12-16 07:53 gezelter * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom which was living inside the GB particle. No alien-like ripping out of the stomach was required. -2005-12-15 21:57 tim +2005-12-15 18:57 tim * src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: replace grammar for numerical parsing -2005-12-15 16:43 gezelter +2005-12-15 13:43 gezelter * src/UseTheForce/doForces.F90: fixed a cutoff bug -2005-12-15 09:48 gezelter +2005-12-15 06:48 gezelter * src/antlr/: CharScanner.hpp, config.hpp: Removing compiler dependencies and replacing them with real autoconf checks -2005-12-15 09:47 gezelter +2005-12-15 06:47 gezelter * configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4, ac-tools/configure.in, src/config.h.in: Adding checks for various features used by ANTLR -2005-12-14 13:02 tim +2005-12-14 10:02 tim * src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a nasty negative integer parsing problem by refining the grammar -2005-12-12 14:32 gezelter +2005-12-12 11:32 gezelter * src/: UseTheForce/doForces_interface.F90, UseTheForce/doForces_interface.h, @@ -1847,33 +2294,33 @@ some minor changes to allow compilation with the portland group compilers -2005-12-10 11:54 tim +2005-12-10 08:54 tim * src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation problem for icc7 -2005-12-09 16:18 gezelter +2005-12-09 13:18 gezelter * src/utils/CaseConversion.hpp: added missing include -2005-12-09 12:11 gezelter +2005-12-09 09:11 gezelter * configure, ac-tools/aclocal.m4: added some checks for pathscale compiler -2005-12-08 17:05 gezelter +2005-12-08 14:05 gezelter * src/io/ForceFieldOptions.cpp: added copyright -2005-12-08 17:04 gezelter +2005-12-08 14:04 gezelter * src/UseTheForce/doForces.F90: added info printout -2005-12-08 17:04 gezelter +2005-12-08 14:04 gezelter * configure, ac-tools/configure.in: added pathscale -2005-12-08 10:38 chuckv +2005-12-08 07:38 chuckv * src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp, @@ -1899,23 +2346,23 @@ Wow thats alot o' files. Now passing forceFieldOptions to all of the parsers. -2005-12-07 18:10 chuckv +2005-12-07 15:10 chuckv * src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp, SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things.... Started adding support for ForceOptions to section parsers. -2005-12-07 18:01 gezelter +2005-12-07 15:01 gezelter * src/UseTheForce/DarkSide/gb_interface.h: [no log message] -2005-12-07 18:00 chuckv +2005-12-07 15:00 chuckv * src/io/: LennardJonesAtomTypesSectionParser.cpp, LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to section parser -2005-12-07 14:58 chuckv +2005-12-07 11:58 chuckv * src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90, lj_interface.h, suttonchen.F90, suttonchen_interface.F90, @@ -1923,41 +2370,41 @@ individual modules and now use force options to detemine what the deal is. -2005-12-07 14:46 chuckv +2005-12-07 11:46 chuckv * src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90: Further fixes for compiler issues. -2005-12-07 14:44 chuckv +2005-12-07 11:44 chuckv * src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue. -2005-12-07 14:38 chuckv +2005-12-07 11:38 chuckv * src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90, fForceOptions_interface.F90, fForceOptions_interface.h: Added support for fortran force options. -2005-12-06 16:01 tim +2005-12-06 13:01 tim * src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion -2005-12-06 14:26 chuckv +2005-12-06 11:26 chuckv * src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC. -2005-12-06 12:53 chuckv +2005-12-06 09:53 chuckv * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned crystal -2005-12-06 12:52 chuckv +2005-12-06 09:52 chuckv * src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for dumpwriter. -2005-12-06 11:49 tim +2005-12-06 08:49 tim * samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md, argon/ar864.md, argon/argonNVT.md, argon/lj.md, @@ -1984,103 +2431,103 @@ zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated keywords from samples -2005-12-05 18:37 tim +2005-12-05 15:37 tim * src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp, Globals.cpp, Makefile: Fix parsing error in OptionSectionParser -2005-12-05 17:23 gezelter +2005-12-05 14:23 gezelter * src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp, UseTheForce/Makefile, brains/Register.cpp, io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding handler for CLAY force field -2005-12-05 16:45 chuckv +2005-12-05 13:45 chuckv * src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug in openbabel. -2005-12-05 14:10 tim +2005-12-05 11:10 tim * src/types/MoleculeStamp.cpp: reformat error message -2005-12-05 14:07 gezelter +2005-12-05 11:07 gezelter * forceFields/CLAYFF.frc: Adding .frc file for CLAYFF -2005-12-05 13:23 tim +2005-12-05 10:23 tim * src/: types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.hpp, types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp: adding more checking for topology -2005-12-02 17:37 gezelter +2005-12-02 14:37 gezelter * src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon removal -2005-12-02 17:37 gezelter +2005-12-02 14:37 gezelter * src/config.h.in: We've made big changes. This isn't 2.0 anymore. -2005-12-02 17:37 gezelter +2005-12-02 14:37 gezelter * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md, traditional.md: removing deprecated nAtoms and nComponents lines -2005-12-02 15:34 tim +2005-12-02 12:34 tim * src/selection/SelectionToken.cpp: adding SelectionToken.cpp -2005-12-02 15:18 tim +2005-12-02 12:18 tim * src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding FragmentStamp -2005-12-02 15:11 gezelter +2005-12-02 12:11 gezelter * src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no longer thrown with consts (fixes compilation bug on the Mac). -2005-12-02 15:10 gezelter +2005-12-02 12:10 gezelter * src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious printing out of timestep -2005-12-02 15:10 gezelter +2005-12-02 12:10 gezelter * src/brains/ForceManager.cpp: Got rid of spurious printing out of junk -2005-12-02 15:10 gezelter +2005-12-02 12:10 gezelter * make/Makefile.in: Change build process for libOOPSE.a so that the libraries aren't unpacked. libOOPSE.a is now made directly from the object files -2005-12-02 15:09 gezelter +2005-12-02 12:09 gezelter * configure, ac-tools/configure.in: added check for egrep (grep -E) needed for new build of libOOPSE.a -2005-12-02 13:43 tim +2005-12-02 10:43 tim * src/types/DataHolder.hpp: adding DataHolder -2005-12-02 12:01 gezelter +2005-12-02 09:01 gezelter * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test case for the cutoff policies -2005-12-02 10:38 tim +2005-12-02 07:38 tim * make/Makefile.in: update Makefile -2005-12-02 10:38 tim +2005-12-02 07:38 tim * src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp, antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp, @@ -2167,40 +2614,40 @@ Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser -2005-11-30 16:00 chuckv +2005-11-30 13:00 chuckv * src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to calculate rho(Z) to calculate density profiles for water slabs. -2005-11-29 17:54 chuckv +2005-11-29 14:54 chuckv * configure, ac-tools/configure.in: added checks for some functions to configure script -2005-11-22 20:05 chuckv +2005-11-22 17:05 chuckv * src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp, obbond.cpp: Changed file names that conflict w/ oopse file name object files. -2005-11-21 17:59 gezelter +2005-11-21 14:59 gezelter * src/utils/residentMem.c: compilation bug -2005-11-21 17:59 gezelter +2005-11-21 14:59 gezelter * src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp -2005-11-21 17:59 gezelter +2005-11-21 14:59 gezelter * src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes -2005-11-21 17:59 gezelter +2005-11-21 14:59 gezelter * src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation issue -2005-11-21 17:58 gezelter +2005-11-21 14:58 gezelter * src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90, doForces_interface.F90, doForces_interface.h, fForceOptions.h, @@ -2209,31 +2656,31 @@ DarkSide/electrostatic.F90, DarkSide/gb.F90, DarkSide/suttonchen.F90: Cutoff mixing fixes have been made. -2005-11-21 11:22 tim +2005-11-21 08:22 tim * src/io/ParamConstraint.cpp: Adding ParamConstraint.cpp -2005-11-21 09:59 tim +2005-11-21 06:59 tim * forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt, atomtyp.txt, bondtyp.txt, element.txt, extable.txt, isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt, resdata.txt, torlib.txt, types.txt: adding openbabel data files -2005-11-18 15:17 tim +2005-11-18 12:17 tim * src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp: adding support for soft linking -2005-11-18 15:17 tim +2005-11-18 12:17 tim * make/Makefile.in: Adding support for soft linking -2005-11-18 12:50 gezelter +2005-11-18 09:50 gezelter * make/Makefile.in: Adding linking stuff -2005-11-18 11:38 tim +2005-11-18 08:38 tim * make/Makefile.in, src/applications/atom2mdin/Makefile, src/applications/atom2mdin/atom2mdin.cpp, @@ -2242,24 +2689,24 @@ src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp: rename mdinConverter to atom2mdin -2005-11-17 15:44 gezelter +2005-11-17 12:44 gezelter * src/openbabel/obconversion.cpp: fixed a bug -2005-11-17 15:39 gezelter +2005-11-17 12:39 gezelter * configure: Adding some config checks for OpenBabel codes we are using -2005-11-17 15:39 gezelter +2005-11-17 12:39 gezelter * ac-tools/configure.in: Adding some checks for OpenBabel code -2005-11-17 15:39 gezelter +2005-11-17 12:39 gezelter * src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel -2005-11-17 15:38 gezelter +2005-11-17 12:38 gezelter * src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp, bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp, @@ -2271,11 +2718,11 @@ find our default (and environment variable) Force Field directories. -2005-11-17 13:35 tim +2005-11-17 10:35 tim * src/io/ForceFieldOptions.hpp: adding ForceFieldOptions -2005-11-16 18:10 tim +2005-11-16 15:10 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp, @@ -2296,19 +2743,19 @@ types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser get compiled -2005-11-16 16:37 chuckv +2005-11-16 13:37 chuckv * src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp, io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp, UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField optional parameters.... -2005-11-16 16:24 tim +2005-11-16 13:24 tim * src/applications/mdinConverter/: Makefile, mdinConverter.cpp: adding mdinConverter -2005-11-16 16:22 tim +2005-11-16 13:22 tim * src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp, fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp, @@ -2318,25 +2765,25 @@ tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp: adding more readers/writers -2005-11-16 16:20 tim +2005-11-16 13:20 tim * make/Makefile.in: adding openbabel -2005-11-16 16:20 tim +2005-11-16 13:20 tim * src/brains/: Register.cpp, Register.hpp: register openbabel readers/writers -2005-11-16 14:57 chrisfen +2005-11-16 11:57 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: included shifted potential self term -2005-11-16 14:57 chrisfen +2005-11-16 11:57 chrisfen * samples/water/spce/spce.md: just some parameters -2005-11-16 14:42 tim +2005-11-16 11:42 tim * src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp, babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp, @@ -2357,65 +2804,65 @@ types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp, zipstreamimpl.hpp: adding openbabel -2005-11-15 14:42 chrisfen +2005-11-15 11:42 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary commented code -2005-11-15 14:04 chrisfen +2005-11-15 11:04 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the charge-charge interactions a bit... -2005-11-15 14:03 chrisfen +2005-11-15 11:03 chrisfen * samples/water/spce/: spce.md, water.md: just playing -2005-11-15 11:38 chrisfen +2005-11-15 08:38 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the shifted_potential case -2005-11-15 11:37 chrisfen +2005-11-15 08:37 chrisfen * samples/: argon/500.md, water/spce/spce.md, water/spce/water.md: just playing around - we need to refresh all the samples sometime soon... -2005-11-15 11:18 chuckv +2005-11-15 08:18 chuckv * src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made preforce calc public in suttonchen. -2005-11-15 11:05 chuckv +2005-11-15 08:05 chuckv * src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to SimInfo -2005-11-15 11:01 chuckv +2005-11-15 08:01 chuckv * src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h, DarkSide/simulation.F90: Added Sutton-Chen to force loop... -2005-11-15 10:34 chuckv +2005-11-15 07:34 chuckv * forceFields/Makefile: Added sutton-chen to makefile. -2005-11-14 17:20 chuckv +2005-11-14 14:20 chuckv * src/UseTheForce/DarkSide/: suttonchen.F90, suttonchen_interface.h: Build Fixes for sutton-chen. -2005-11-14 17:03 chuckv +2005-11-14 14:03 chuckv * src/io/Makefile: Missed makefile for sutton-chen. -2005-11-14 17:03 chuckv +2005-11-14 14:03 chuckv * src/UseTheForce/: Makefile, DarkSide/Makefile, DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff -2005-11-14 16:29 chuckv +2005-11-14 13:29 chuckv * src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp, io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, @@ -2426,96 +2873,96 @@ types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to fix do_forces to use Sutton-Chen. -2005-11-11 12:21 chrisfen +2005-11-11 09:21 chrisfen * src/UseTheForce/DarkSide/: fSwitchingFunctionType.h, switcheroo_interface.F90, switcheroo_interface.h: Forgot to add some files -2005-11-11 10:22 chrisfen +2005-11-11 07:22 chrisfen * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp, io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial switching function option -2005-11-11 10:21 chrisfen +2005-11-11 07:21 chrisfen * src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a 5th order polynomial switching function -2005-11-11 10:21 chrisfen +2005-11-11 07:21 chrisfen * samples/water/ssd/ssd.md: playing with switching functions again -2005-11-11 10:21 chrisfen +2005-11-11 07:21 chrisfen * samples/argon/500.md: playing with switching functions -2005-11-08 19:11 chuckv +2005-11-08 16:11 chuckv * forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force files for Sutton-Chen and Quantum Sutton-Chen -2005-11-08 08:32 chrisfen +2005-11-08 05:32 chrisfen * src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp, DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and ability to output forces and torques -2005-11-08 08:32 chrisfen +2005-11-08 05:32 chrisfen * src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for output of forces and torques -2005-11-08 08:31 chrisfen +2005-11-08 05:31 chrisfen * src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90: Working on shifted_force... -2005-11-08 08:31 chrisfen +2005-11-08 05:31 chrisfen * samples/water/: spce/spce.md, ssde/ssde.md: Just testing... -2005-11-03 18:22 chrisfen +2005-11-03 15:22 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly commented section -2005-11-03 18:12 chrisfen +2005-11-03 15:12 chrisfen * src/: UseTheForce/DarkSide/electrostatic.F90, UseTheForce/DarkSide/fElectrostaticScreeningMethod.h, UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: improvements in shifted-force -2005-11-03 18:11 chrisfen +2005-11-03 15:11 chrisfen * samples/water/spce/spce.md: mmm... damped shifted force... -2005-11-03 18:06 chuckv +2005-11-03 15:06 chuckv * src/UseTheForce/DarkSide/suttonchen.F90: More work on SC. -2005-11-02 18:50 chuckv +2005-11-02 15:50 chuckv * src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen. -2005-11-02 16:01 chrisfen +2005-11-02 13:01 chrisfen * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: removed some test code -2005-11-02 15:45 chrisfen +2005-11-02 12:45 chrisfen * src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the screening method header -2005-11-02 15:36 chrisfen +2005-11-02 12:36 chrisfen * src/brains/SimInfo.cpp: again, changing how we deal with summation and screening methods -2005-11-02 15:36 chrisfen +2005-11-02 12:36 chrisfen * src/: UseTheForce/DarkSide/electrostatic.F90, UseTheForce/DarkSide/electrostatic_interface.F90, @@ -2524,11 +2971,11 @@ io/Globals.cpp, io/Globals.hpp: changing how we deal with summation and screening methods -2005-11-02 15:35 chrisfen +2005-11-02 12:35 chrisfen * src/UseTheForce/doForces.F90: debug stuff for rf removed -2005-11-01 18:32 chuckv +2005-11-01 15:32 chuckv * src/: UseTheForce/DarkSide/atype.F90, UseTheForce/DarkSide/atype_interface.F90, @@ -2536,61 +2983,61 @@ types/AtomTypeProperties.h: Added suppport to atypes for MEAM and sutton-chen -2005-11-01 14:24 chrisfen +2005-11-01 11:24 chrisfen * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: removed some testing code... -2005-11-01 14:14 chrisfen +2005-11-01 11:14 chrisfen * src/: brains/Register.cpp, brains/SimInfo.cpp, brains/fSimulation.h, integrators/IntegratorFactory.hpp, io/Globals.cpp: fixed a capitalization problem with NPT integrator initialization -2005-11-01 14:13 chrisfen +2005-11-01 11:13 chrisfen * src/applications/oopse/oopse.cpp: nothing -2005-11-01 14:09 chrisfen +2005-11-01 11:09 chrisfen * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, DarkSide/simulation.F90: still fixing up wolf... -2005-11-01 13:29 chuckv +2005-11-01 10:29 chuckv * src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In process of adding sutton-chen forcefield. -2005-10-26 19:32 chrisfen +2005-10-26 16:32 chrisfen * src/brains/SimInfo.cpp: changed the default switching radius to 85% of rcut -2005-10-26 19:31 chrisfen +2005-10-26 16:31 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks to be working now - for charges and dipoles alike -2005-10-26 19:31 chrisfen +2005-10-26 16:31 chrisfen * src/UseTheForce/doForces.F90: reaction field looks to be working now -2005-10-26 19:30 chrisfen +2005-10-26 16:30 chrisfen * samples/water/ssdrf/water.md: added a test molecule -2005-10-26 19:30 chrisfen +2005-10-26 16:30 chrisfen * forceFields/DUFF2.frc: added a test atom type -2005-10-24 10:06 chrisfen +2005-10-24 07:06 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole reaction field - don't know if it works... -2005-10-23 17:08 chrisfen +2005-10-23 14:08 chrisfen * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp: @@ -2598,21 +3045,21 @@ added reaction field for charges - still need to do charge-dipole RF -2005-10-23 17:07 chrisfen +2005-10-23 14:07 chrisfen * samples/water/ssdrf/ssdrf.md: minor changes when testing reaction field -2005-10-23 17:06 chrisfen +2005-10-23 14:06 chrisfen * samples/water/spce/spce.md: reaction field now works for charges -2005-10-20 16:27 tim +2005-10-20 13:27 tim * src/primitives/Torsion.cpp: Fix the other branch of force calculation in Torision.cpp -2005-10-19 15:24 chrisfen +2005-10-19 12:24 chrisfen * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/electrostatic.F90, @@ -2620,47 +3067,47 @@ brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals toUpper problems - these changes should fix those... -2005-10-19 15:23 chrisfen +2005-10-19 12:23 chrisfen * samples/water/ssdrf/ssdrf.md: nothing -2005-10-19 13:03 gezelter +2005-10-19 10:03 gezelter * src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in GayBerne -2005-10-19 12:49 tim +2005-10-19 09:49 tim * src/: UseTheForce/DarkSide/fInteractionMap.h, brains/ForceManager.cpp: fix an index mismathcing between c and fortran -2005-10-18 19:03 gezelter +2005-10-18 16:03 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 17:13 gezelter +2005-10-18 14:13 gezelter * src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques and a rotation matrix bug -2005-10-18 17:13 gezelter +2005-10-18 14:13 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 17:13 gezelter +2005-10-18 14:13 gezelter * forceFields/DUFF2.frc: Fixing GB parameters -2005-10-18 14:36 kdaily +2005-10-18 11:36 kdaily * forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne type -2005-10-18 11:01 chrisfen +2005-10-18 08:01 chrisfen * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, UseTheForce/DarkSide/Makefile, @@ -2670,32 +3117,32 @@ UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged reaction field with electrostatics.F90 -2005-10-17 19:13 tim +2005-10-17 16:13 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 18:42 kdaily +2005-10-17 15:42 kdaily * src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver paper -2005-10-17 17:47 gezelter +2005-10-17 14:47 gezelter * src/UseTheForce/DarkSide/gb.F90: bugtracking gb -2005-10-17 15:24 tim +2005-10-17 12:24 tim * src/io/ParamConstraint.hpp: Another bug fix -2005-10-17 15:22 tim +2005-10-17 12:22 tim * src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace issues in Globals -2005-10-17 15:12 gezelter +2005-10-17 12:12 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90, UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90, @@ -2705,43 +3152,43 @@ types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: changing GB architecture -2005-10-17 15:12 gezelter +2005-10-17 12:12 gezelter * samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in, gbRotRoundZ.in: Adding samples for gb tests -2005-10-16 23:06 tim +2005-10-16 20:06 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 20:51 tim +2005-10-16 17:51 tim * src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change error message in Globals -2005-10-14 17:43 tim +2005-10-14 14:43 tim * src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for parameters are working now -2005-10-14 12:43 gezelter +2005-10-14 09:43 gezelter * samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests -2005-10-14 12:05 gezelter +2005-10-14 09:05 gezelter * samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md, gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: Adding some Gay Berne tests -2005-10-14 12:05 gezelter +2005-10-14 09:05 gezelter * samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some cutoff tests -2005-10-14 11:44 kdaily +2005-10-14 08:44 kdaily * forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90, @@ -2749,18 +3196,18 @@ src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne LJ -2005-10-14 10:48 tim +2005-10-14 07:48 tim * src/io/ParamConstraint.hpp: Adding Parameter Constraint class -2005-10-14 10:18 chrisfen +2005-10-14 07:18 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 18:26 tim +2005-10-13 15:26 tim * src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp, brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp, @@ -2772,49 +3219,49 @@ restraints/ThermoIntegrationForceManager.cpp, visitors/ZconsVisitor.cpp: rewrite Globals -2005-10-12 17:57 chuckv +2005-10-12 14:57 chuckv * src/brains/ForceManager.cpp: Fix to forceManager to pass potential array to fortran. -2005-10-12 17:00 gezelter +2005-10-12 14:00 gezelter * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't remember what we did -2005-10-12 17:00 gezelter +2005-10-12 14:00 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 17:00 gezelter +2005-10-12 14:00 gezelter * samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new cutoff methods -2005-10-12 17:00 gezelter +2005-10-12 14:00 gezelter * forceFields/DUFF2.frc: Messing with 2-point water models -2005-10-12 16:22 chuckv +2005-10-12 13:22 chuckv * src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran interface now expects an array for pot. -2005-10-12 16:18 chuckv +2005-10-12 13:18 chuckv * src/UseTheForce/: doForces.F90, DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for calculation of potential. -2005-10-12 15:55 chuckv +2005-10-12 12:55 chuckv * src/UseTheForce/doForces.F90: More changes to MPI potential calculations. -2005-10-12 14:59 chuckv +2005-10-12 11:59 chuckv * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/electrostatic.F90, @@ -2822,18 +3269,18 @@ DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky Breaky: Add Support for seperating potential contributions. -2005-10-11 18:00 chuckv +2005-10-11 15:00 chuckv * src/UseTheForce/doForces.F90: Free some variables that weren't freed before. -2005-10-11 17:59 chuckv +2005-10-11 14:59 chuckv * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod builder --twinned. -2005-10-11 17:57 chuckv +2005-10-11 14:57 chuckv * src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, @@ -2841,142 +3288,142 @@ sphericalNanoparticle.hpp: Added code for nanoparticle builder to cvs. -2005-10-10 17:34 chuckv +2005-10-10 14:34 chuckv * src/UseTheForce/doForces.F90: Bug fix, undeclared local variable in MPI. -2005-10-10 17:20 chuckv +2005-10-10 14:20 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 14:44 chrisfen +2005-10-06 11:44 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 17:12 tim +2005-10-05 14:12 tim * src/primitives/RigidBody.cpp: There is still something wrong with inertia tensor projection -2005-10-05 15:35 tim +2005-10-05 12:35 tim * src/primitives/RigidBody.cpp: erase output of inertia tensor. There is still something wrong with current implementation. -2005-10-05 15:34 tim +2005-10-05 12:34 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 15:12 tim +2005-10-05 12:12 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 15:34 chrisfen +2005-10-04 12:34 chrisfen * src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying mass ratio bug that results in simulation failure with massless particles -2005-10-04 15:33 chrisfen +2005-10-04 12:33 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on wolf -2005-10-04 15:32 chrisfen +2005-10-04 12:32 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 11:54 tim +2005-10-03 08:54 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 10:31 tim +2005-10-03 07:31 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 14:47 chrisfen +2005-09-28 11:47 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: working on wolf -2005-09-28 14:46 chrisfen +2005-09-28 11:46 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 14:46 chrisfen +2005-09-28 11:46 chrisfen * ChangeLog: updated -2005-09-28 12:55 tim +2005-09-28 09:55 tim * src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid divergence in rotation matrix to quaternion transformation -2005-09-28 12:32 gezelter +2005-09-28 09:32 gezelter * src/primitives/RigidBody.cpp: Rotation matrix multiplication order error -2005-09-28 12:32 gezelter +2005-09-28 09:32 gezelter * src/io/DumpReader.cpp: tracking down quaternion bug -2005-09-28 12:32 gezelter +2005-09-28 09:32 gezelter * forceFields/DUFF2.frc: Added DIP atom types for 2-point water model -2005-09-27 16:02 tim +2005-09-27 13:02 tim * src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix to quaternion -2005-09-26 14:38 chuckv +2005-09-26 11:38 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 13:07 chuckv +2005-09-26 10:07 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 12:42 chuckv +2005-09-26 09:42 chuckv * src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype in simulation module. We needed a seperate receive buffer. -2005-09-26 11:58 chuckv +2005-09-26 08:58 chuckv * src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added support for skinThickness keyword to Globals. -2005-09-26 11:56 tim +2005-09-26 08:56 tim * src/io/DumpReader.cpp: fix a typo in DumpReader -2005-09-26 10:27 chrisfen +2005-09-26 07:27 chrisfen * samples/: minimizer/tip4p_two.md, thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, @@ -2986,7 +3433,7 @@ water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, water/tip4p/tp4.md: fixing up some samples -2005-09-24 13:39 chrisfen +2005-09-24 10:39 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now roughly the same speed as the old version when using dipoles @@ -2994,78 +3441,78 @@ energies are now exactly the same between the old version of OOPSE and this version -2005-09-24 13:38 chrisfen +2005-09-24 10:38 chrisfen * samples/water/ssdrf/ssdrf.md: turned rf on -2005-09-23 16:31 chuckv +2005-09-23 13:31 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 14:50 gezelter +2005-09-22 11:50 gezelter * src/math/derfc.F90: added error function -2005-09-21 20:08 chuckv +2005-09-21 17:08 chuckv * src/integrators/Velocitizer.cpp: Removed print statement for angular momentum and inertia tensor from velocitizer. -2005-09-21 20:04 chuckv +2005-09-21 17:04 chuckv * src/integrators/Velocitizer.cpp: Removed print statements for remove angular momentum. -2005-09-21 19:45 chuckv +2005-09-21 16:45 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 16:59 tim +2005-09-21 13:59 tim * src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: DumpReader using pure c++ io -2005-09-21 13:20 chrisfen +2005-09-21 10:20 chrisfen * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a defaultCutoff bug (HEMES!) -2005-09-20 18:13 gezelter +2005-09-20 15:13 gezelter * make/Makefile.in: libz additions -2005-09-20 18:03 gezelter +2005-09-20 15:03 gezelter * configure, ac-tools/aclocal.m4, ac-tools/configure.in, src/config.h.in: added check for zlib in configure -2005-09-20 17:22 tim +2005-09-20 14:22 tim * src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter -2005-09-20 12:22 tim +2005-09-20 09:22 tim * test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding testcase for zipstream -2005-09-20 11:41 tim +2005-09-20 08:41 tim * src/io/zipstream.hpp: adding zipstream.hpp -2005-09-20 11:34 chrisfen +2005-09-20 08:34 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 19:21 chrisfen +2005-09-19 16:21 chrisfen * ChangeLog, samples/water/ssdrf/ssdrf.md, src/UseTheForce/doForces.F90, @@ -3074,7 +3521,7 @@ src/brains/fSimulation.h: Fixed bugs in reaction field, now it appears as though it really is working... -2005-09-18 16:45 chrisfen +2005-09-18 13:45 chrisfen * ChangeLog, samples/water/ssdrf/ssdrf.md, src/UseTheForce/doForces.F90, @@ -3085,126 +3532,126 @@ src/brains/SimInfo.cpp: reaction field seems to work now, still need to do some testing... -2005-09-16 19:04 chuckv +2005-09-16 16:04 chuckv * src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed dump files. -2005-09-16 17:07 chrisfen +2005-09-16 14:07 chrisfen * src/: UseTheForce/doForces_interface.F90, UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a bug that ifc missed... -2005-09-16 16:36 chrisfen +2005-09-16 13:36 chrisfen * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: fixing some summation method issues -2005-09-16 15:35 chrisfen +2005-09-16 12:35 chrisfen * src/brains/SimInfo.cpp: fixed a capitalization error -2005-09-16 15:34 chrisfen +2005-09-16 12:34 chrisfen * src/UseTheForce/: fElectrostaticSummationMethod.h, DarkSide/fElectrostaticSummationMethod.h: moved a header file around -2005-09-16 15:00 chrisfen +2005-09-16 12:00 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 12:07 chrisfen +2005-09-16 09:07 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 18:05 gezelter +2005-09-15 15:05 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 15:17 tim +2005-09-15 12:17 tim * src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame is called without calling getNFrames -2005-09-15 09:47 chrisfen +2005-09-15 06:47 chrisfen * src/UseTheForce/fCoulombicCorrection.h: forgot to add a header -2005-09-14 22:48 chuckv +2005-09-14 19:48 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 20:14 chrisfen +2005-09-14 17:14 chrisfen * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, io/Globals.hpp: changes to include the coulombicCorrection selector -2005-09-14 20:13 chrisfen +2005-09-14 17:13 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 20:13 chrisfen +2005-09-14 17:13 chrisfen * src/UseTheForce/: doForces.F90, doForces_interface.F90, doForces_interface.h, notifyCutoffs.F90: some changes to activate the coulombicCorrection selector -2005-09-14 20:11 chrisfen +2005-09-14 17:11 chrisfen * samples/water/dimer/: cl.in, cl.md, water.md: just some testing -2005-09-14 20:11 chrisfen +2005-09-14 17:11 chrisfen * samples/argon/: 500.in, 500.md: Equilibrated the sample -2005-09-14 20:10 chrisfen +2005-09-14 17:10 chrisfen * forceFields/DUFF2.frc: re-added Cl- and Na+ -2005-09-14 16:31 chuckv +2005-09-14 13:31 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 16:28 gezelter +2005-09-14 13:28 gezelter * src/UseTheForce/doForces.F90: fix to put back calculation of r in do_prepair -2005-09-14 15:02 gezelter +2005-09-14 12:02 gezelter * src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the createMixingMap routine. It should now set doShift correctly -2005-09-07 18:44 chuckv +2005-09-07 15:44 chuckv * src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. -2005-09-07 18:23 chuckv +2005-09-07 15:23 chuckv * src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi logical variables -2005-09-07 18:08 gezelter +2005-09-07 15:08 gezelter * src/UseTheForce/doForces.F90: bugfix on the grouptype finding algorithm -2005-09-07 16:46 gezelter +2005-09-07 13:46 gezelter * src/: UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, @@ -3213,30 +3660,30 @@ io/Globals.cpp, io/Globals.hpp: adding c-side interface to change cutoff Policy -2005-09-07 15:18 gezelter +2005-09-07 12:18 gezelter * src/UseTheForce/doForces.F90: Some bug hunting -2005-09-07 15:18 gezelter +2005-09-07 12:18 gezelter * samples/argon/argonNVT.md: Just a longer test -2005-09-06 13:32 chuckv +2005-09-06 10:32 chuckv * src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap etc.. -2005-09-01 18:56 gezelter +2005-09-01 15:56 gezelter * src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to zero -2005-09-01 16:17 gezelter +2005-09-01 13:17 gezelter * src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote createGtypeCutoffMap -2005-08-30 14:23 chrisfen +2005-08-30 11:23 chrisfen * src/: UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, @@ -3246,79 +3693,79 @@ brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some changes for implementing the wolf potential -2005-08-26 18:39 chrisfen +2005-08-26 15:39 chrisfen * src/UseTheForce/DarkSide/eam.F90: updated getEAMCut -2005-08-26 17:30 chrisfen +2005-08-26 14:30 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 16:34 chuckv +2005-08-26 13:34 chuckv * src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. -2005-08-26 12:36 gezelter +2005-08-26 09:36 gezelter * src/UseTheForce/doForces.F90: fixing some of the problems in the interactionHash and gtypeCutoff routines -2005-08-17 11:26 gezelter +2005-08-17 08:26 gezelter * src/UseTheForce/: doForces.F90, fCutoffPolicy.h, DarkSide/simulation.F90: added fCutoffPolicy.h -2005-08-11 17:04 gezelter +2005-08-11 14:04 gezelter * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in progress -2005-08-10 15:17 gezelter +2005-08-10 12:17 gezelter * src/primitives/StuntDouble.hpp: putting spaceballs back where they belong -2005-08-09 18:33 gezelter +2005-08-09 15:33 gezelter * src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard Jones module -2005-08-09 18:33 gezelter +2005-08-09 15:33 gezelter * src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky -2005-08-09 15:40 chuckv +2005-08-09 12:40 chuckv * src/UseTheForce/doForces.F90: In process of re-write for group based cutoff.... -2005-07-29 15:38 gezelter +2005-07-29 12:38 gezelter * src/UseTheForce/doForces.F90: fixes in progress -2005-07-29 13:34 tim +2005-07-29 10:34 tim * src/UseTheForce/doForces.F90: fix a bug which does not update me_i and me_j correctly -2005-07-28 18:12 chuckv +2005-07-28 15:12 chuckv * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed cutoffs... Segfaults nicely now... -2005-07-20 13:04 gezelter +2005-07-20 10:04 gezelter * configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text error messages from pathscale compiler -2005-07-13 12:48 tim +2005-07-13 09:48 tim * src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in -2005-07-13 11:54 tim +2005-07-13 08:54 tim * src/: UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, @@ -3330,7 +3777,7 @@ utils/simError.c, utils/simError.h: replace c++ style comment in c files -2005-07-03 16:53 chuckv +2005-07-03 13:53 chuckv * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added @@ -3338,29 +3785,29 @@ simulation.F90 to determine if a particular atype is present in a simulation. -2005-06-28 09:58 gezelter +2005-06-28 06:58 gezelter * src/UseTheForce/doForces.F90: [no log message] -2005-06-27 18:21 chuckv +2005-06-27 15:21 chuckv * src/UseTheForce/doForces.F90: More breaking and destruction of force code. Does not build at this point... -2005-06-27 17:01 gezelter +2005-06-27 14:01 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 12:03 gezelter +2005-06-20 09:03 gezelter * samples/water/ssd/ssd.md, src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a simulation -2005-06-13 14:25 tim +2005-06-13 11:25 tim * src/: applications/staticProps/DensityPlot.cpp, applications/staticProps/DensityPlot.hpp, @@ -3368,17 +3815,17 @@ applications/staticProps/StaticProps.cpp, io/AtomTypesSectionParser.cpp: working version of DensityPlot -2005-05-31 18:31 chuckv +2005-05-31 15:31 chuckv * src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to remove angular momentum. -2005-05-31 13:34 chuckv +2005-05-31 10:34 chuckv * src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in typo in nanorodBuilder. -2005-05-30 10:01 chuckv +2005-05-30 07:01 chuckv * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, @@ -3387,50 +3834,50 @@ momentum to velocitizer and added method to calculate system angular momentum to siminfo. -2005-05-29 17:16 chrisfen +2005-05-29 14:16 chrisfen * src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed balance from the Darkside (files) -2005-05-29 17:15 chrisfen +2005-05-29 14:15 chrisfen * src/UseTheForce/doForces.F90: Removed balance from doForces -2005-05-29 17:15 chrisfen +2005-05-29 14:15 chrisfen * samples/water/tap/: tap.in, tap.md: Updated tap sample -2005-05-29 17:15 chrisfen +2005-05-29 14:15 chrisfen * samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap dimer for testing purposes -2005-05-29 17:14 chrisfen +2005-05-29 14:14 chrisfen * forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It was apparently wiped earlier this month... -2005-05-29 17:13 chrisfen +2005-05-29 14:13 chrisfen * ChangeLog: ran make cvslog -2005-05-28 20:16 tim +2005-05-28 17:16 tim * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding AtomNameVisitor -2005-05-28 20:09 tim +2005-05-28 17:09 tim * src/integrators/Integrator.cpp: dding resetIntegrator -2005-05-28 20:06 tim +2005-05-28 17:06 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 17:11 tim +2005-05-27 14:11 tim * src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, @@ -3438,7 +3885,7 @@ StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into StaticProps -2005-05-27 00:41 tim +2005-05-26 21:41 tim * src/: applications/staticProps/Makefile, applications/staticProps/P2OrderParameter.cpp, @@ -3449,7 +3896,7 @@ applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps -2005-05-26 18:45 tim +2005-05-26 15:45 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/dump2Xyz/Dump2XYZCmd.c, @@ -3469,7 +3916,7 @@ wrappingvisitor now wrap back to the center of the mass; adding P2OrderParameter into StaticProps -2005-05-22 17:36 chuckv +2005-05-22 14:36 chuckv * src/: applications/nanoRodBuilder/Geometry.cpp, applications/nanoRodBuilder/GeometryBuilder.cpp, @@ -3479,56 +3926,56 @@ integrators/VelocityVerletIntegrator.cpp: Fix to print pressure tensor. -2005-05-22 17:05 tim +2005-05-22 14:05 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 15:27 tim +2005-05-20 12:27 tim * src/integrators/NPrT.cpp: NPrT in progress -2005-05-20 12:01 tim +2005-05-20 09:01 tim * src/: integrators/NPrT.cpp, io/Globals.cpp, utils/OOPSEConstant.hpp: NPrT in progress -2005-05-19 17:31 tim +2005-05-19 14:31 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 11:49 tim +2005-05-19 08:49 tim * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT -2005-05-19 00:28 tim +2005-05-18 21:28 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 15:06 chrisfen +2005-05-18 12:06 chrisfen * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just some tap changes -2005-05-18 14:31 chrisfen +2005-05-18 11:31 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 08:35 chrisfen +2005-05-18 05:35 chrisfen * samples/water/tap/: tap.in, tap.md, water.md: added a tap example for testing purposes -2005-05-17 18:35 chrisfen +2005-05-17 15:35 chrisfen * ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, @@ -3538,29 +3985,29 @@ src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also correcting changes to the previous merge that were not caught -2005-05-17 00:20 chuckv +2005-05-16 21:20 chuckv * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: Fixed merge issues between Kyle and Chris so OOPSE will actually build. -2005-05-16 23:46 kdaily +2005-05-16 20:46 kdaily * src/io/: GayBerneAtomTypesSectionParser.cpp, GayBerneAtomTypesSectionParser.hpp, Makefile: help -2005-05-16 22:08 kdaily +2005-05-16 19:08 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 16:36 chrisfen +2005-05-13 13:36 chrisfen * forceFields/DUFF2.frc: Better tap -2005-05-12 15:43 chrisfen +2005-05-12 12:43 chrisfen * forceFields/DUFF2.frc, samples/water/dimer/ssd.in, samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, @@ -3568,23 +4015,23 @@ src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. Need to parametrize. -2005-05-11 19:15 chuckv +2005-05-11 16:15 chuckv * src/: io/ShapeAtomTypesSectionParser.cpp, math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed build issues under ifc7. -2005-05-09 18:07 chuckv +2005-05-09 15:07 chuckv * src/applications/nanoRodBuilder/Geometry.hpp: More geometry builder changes. -2005-05-05 11:06 chrisfen +2005-05-05 08:06 chrisfen * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED to TAP -2005-05-05 10:47 chrisfen +2005-05-05 07:47 chrisfen * forceFields/DUFF2.frc, samples/water/ssde/ssde.md, samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, @@ -3602,23 +4049,23 @@ src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's not parametrized, but OOPSE will now let me run it... -2005-05-03 18:55 chuckv +2005-05-03 15:55 chuckv * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: Adding support for generic geometry to nanorodbuilder. -2005-05-03 13:55 chuckv +2005-05-03 10:55 chuckv * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, nanorodBuilderCmd.h: More changes to nanoRodBuilder.... -2005-04-29 15:16 gezelter +2005-04-29 12:16 gezelter * make/Makefile.in: [no log message] -2005-04-29 12:26 chrisfen +2005-04-29 09:26 chrisfen * forceFields/DUFF2.frc, samples/water/spce/water.md, samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, @@ -3626,14 +4073,14 @@ samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, samples/water/tip4p/water.md: Added TIP4P-Ew -2005-04-27 20:24 chuckv +2005-04-27 17:24 chuckv * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with nanoRodBuilder.... -2005-04-27 16:13 chrisfen +2005-04-27 13:13 chrisfen * samples/shape/Shapes.frc, samples/shape/linear.shape, src/UseTheForce/DarkSide/atype.F90, @@ -3642,17 +4089,17 @@ src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of write statements and am closer to a working shapes -2005-04-22 17:57 chuckv +2005-04-22 14:57 chuckv * src/utils/Predicate.hpp: Fixed gcc4 bug... -2005-04-22 17:52 tim +2005-04-22 14:52 tim * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, Trim.hpp: adding CharClassificationFunctor to fix the locale problem of c++ -2005-04-21 10:12 chrisfen +2005-04-21 07:12 chrisfen * samples/shape/Shapes.frc, samples/shape/linear.in, samples/shape/linear.md, src/UseTheForce/ForceField.hpp, @@ -3672,12 +4119,12 @@ bounds overwrite (I think...). At least the parser loads the forcefield fine... -2005-04-18 11:44 chrisfen +2005-04-18 08:44 chrisfen * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on Mac (capitalization confusion of filenames) -2005-04-17 23:50 chrisfen +2005-04-17 20:50 chrisfen * src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, UseTheForce/Shapes_FF.cpp, @@ -3685,25 +4132,25 @@ io/ShapeAtomTypesSectionParser.cpp, io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... -2005-04-15 18:43 gezelter +2005-04-15 15:43 gezelter * README: gmake in case people forget -2005-04-15 18:40 gezelter +2005-04-15 15:40 gezelter * src/applications/oopse/oopse.cpp: fixed the spacing on the banner. Vanity. -2005-04-15 18:22 gezelter +2005-04-15 15:22 gezelter * src/: config.h.in, applications/oopse/oopse.cpp: Version string in banner (and version numbers in config.h) -2005-04-15 18:22 gezelter +2005-04-15 15:22 gezelter * ChangeLog, LICENSE, README: Documentation changes -2005-04-15 18:03 gezelter +2005-04-15 15:03 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, @@ -3924,70 +4371,70 @@ visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has been drafted to perform our indentation services -2005-04-15 18:03 gezelter +2005-04-15 15:03 gezelter * configure, ac-tools/configure.in: Jedi mind-trick warning messages have been added to make users ignore CGAL. -2005-04-15 14:41 tim +2005-04-15 11:41 tim * make/Makefile.in: fix make install -2005-04-15 14:41 tim +2005-04-15 11:41 tim * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: add Makefile of samples -2005-04-15 14:33 tim +2005-04-15 11:33 tim * samples/: lipid/Makefile, water/dimer/Makefile, water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not installed correctly -2005-04-14 17:41 gezelter +2005-04-14 14:41 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 17:20 gezelter +2005-04-14 14:20 gezelter * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of MoLocator -2005-04-14 15:12 gezelter +2005-04-14 12:12 gezelter * LICENSE: [no log message] -2005-04-14 12:10 chuckv +2005-04-14 09:10 chuckv * src/applications/nanoRodBuilder/nanorodBuilder.cpp: nanorodbuilder now exit's when libCGAL is not present. -2005-04-14 11:20 tim +2005-04-14 08:20 tim * src/io/make_nodes.h: fix one more warning message in make_nodes -2005-04-13 19:36 chuckv +2005-04-13 16:36 chuckv * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed interface name for SGI Compiler -2005-04-13 19:29 chrisfen +2005-04-13 16:29 chrisfen * samples/water/ssde/ssde.md: oops... bad sample -2005-04-13 19:00 chuckv +2005-04-13 16:00 chuckv * src/config.h.in: Change typo in CGAL. -2005-04-13 18:43 tim +2005-04-13 15:43 tim * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, selection/SelectionCompiler.hpp: fix some warning messages -2005-04-13 18:30 gezelter +2005-04-13 15:30 gezelter * configure, ac-tools/aclocal.m4, ac-tools/configure.in, make/Makefile.in, src/config.h.in, @@ -3996,7 +4443,7 @@ src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL checks -2005-04-13 16:36 chuckv +2005-04-13 13:36 chuckv * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, DarkSide/LJ.F90, DarkSide/electrostatic.F90, @@ -4006,12 +4453,12 @@ DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added destroy methods for Fortran modules. -2005-04-13 16:17 chuckv +2005-04-13 13:17 chuckv * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, shapes_interface.h: Added destroy method to clean up memory -2005-04-13 14:41 tim +2005-04-13 11:41 tim * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -4020,31 +4467,31 @@ types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are fixed -2005-04-12 18:44 chuckv +2005-04-12 15:44 chuckv * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed for nanoRodBuilder. -2005-04-12 18:42 tim +2005-04-12 15:42 tim * src/applications/: nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder and simpleBuilder(forget to delete lattice) -2005-04-12 18:33 tim +2005-04-12 15:33 tim * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: refactory lattice -2005-04-12 18:07 tim +2005-04-12 15:07 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 17:58 tim +2005-04-12 14:58 tim * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, @@ -4053,21 +4500,21 @@ lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, lattice/Makefile: refactory LatticeFactory and LatticeCreator -2005-04-12 17:28 gezelter +2005-04-12 14:28 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 17:27 gezelter +2005-04-12 14:27 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 17:27 gezelter +2005-04-12 14:27 gezelter * src/applications/: nanoRodBuilder/BaseLattice.cpp, nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, @@ -4085,72 +4532,72 @@ simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of these files are now redundant -2005-04-12 17:27 gezelter +2005-04-12 14:27 gezelter * src/UseTheForce/DarkSide/: atype_interface.F90, atype_interface.h: cleaned up memory leak fix -2005-04-12 17:26 gezelter +2005-04-12 14:26 gezelter * make/Makefile.in: added lattice subdirectory -2005-04-12 16:57 chrisfen +2005-04-12 13:57 chrisfen * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added a space by accident -2005-04-12 16:56 chrisfen +2005-04-12 13:56 chrisfen * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added quadrupole sample -2005-04-12 16:56 chrisfen +2005-04-12 13:56 chrisfen * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating samples -2005-04-12 14:30 tim +2005-04-12 11:30 tim * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom type in fortran side -2005-04-12 13:45 chuckv +2005-04-12 10:45 chuckv * src/utils/vector_class.F90: Further changes to vector_class destroy function. -2005-04-12 13:39 chuckv +2005-04-12 10:39 chuckv * src/utils/vector_class.F90: Fixed pointer memory leak in vector_class. -2005-04-12 13:12 chuckv +2005-04-12 10:12 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 10:24 chrisfen +2005-04-12 07:24 chrisfen * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI output -2005-04-11 20:29 chuckv +2005-04-11 17:29 chuckv * src/: UseTheForce/DarkSide/atype.F90, applications/nanoRodBuilder/Makefile: Changes to delete atypes... -2005-04-11 20:28 chuckv +2005-04-11 17:28 chuckv * src/utils/vector_class.F90: Added code to delete vector. -2005-04-11 17:58 tim +2005-04-11 14:58 tim * src/io/basic_ifstrstream.hpp: avoid multiple inherit in basic_ifstrstream -2005-04-11 17:37 chuckv +2005-04-11 14:37 chuckv * make/Makefile.in, src/applications/nanoRodBuilder/BaseLattice.cpp, @@ -4174,99 +4621,99 @@ nanoRodBuilder application (may not work yet). ((Doesn't work yet.)) (((May never work....))) -2005-04-11 16:54 tim +2005-04-11 13:54 tim * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete prepareVisitor in Dump2XYZ -2005-04-11 16:19 chrisfen +2005-04-11 13:19 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the quadrupoles. look! it's divide by 3 like stone says! -2005-04-11 16:18 chrisfen +2005-04-11 13:18 chrisfen * forceFields/DUFF2.frc: fixing of the quadrupoles -2005-04-11 16:16 tim +2005-04-11 13:16 tim * src/selection/Token.hpp: change the parameter name in constructors -2005-04-11 15:49 gezelter +2005-04-11 12:49 gezelter * make/Makefile.in: One more bug fix for GNU make versions < 3.80 -2005-04-11 15:06 gezelter +2005-04-11 12:06 gezelter * make/Makefile.in: Fixed the uc and lc functions for GNU make versions < 3.80 -2005-04-11 12:13 gezelter +2005-04-11 09:13 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 18:13 chrisfen +2005-04-08 15:13 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole interactions should be working with a remaining question of interaction magnitude -2005-04-08 18:12 chrisfen +2005-04-08 15:12 chrisfen * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with samples -2005-04-08 14:48 chrisfen +2005-04-08 11:48 chrisfen * samples/water/ssd/ssd.md: oops... messed up a sample -2005-04-08 10:43 chrisfen +2005-04-08 07:43 chrisfen * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix charge-dipole interactions -2005-04-08 10:42 chrisfen +2005-04-08 07:42 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 10:41 chrisfen +2005-04-08 07:41 chrisfen * forceFields/DUFF2.frc: added Cl- and Na+ -2005-04-06 19:59 tim +2005-04-06 16:59 tim * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser -2005-04-05 19:09 tim +2005-04-05 16:09 tim * src/selection/: NameFinder.cpp, SelectionCompiler.cpp, SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' in atom type name;clean the code a little bit -2005-03-29 16:00 tim +2005-03-29 13:00 tim * src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug in converting rotation matrix to quaternion -2005-03-28 17:41 tim +2005-03-28 14:41 tim * src/visitors/LipidTransVisitor.cpp: fixed the wrapping -2005-03-28 17:30 tim +2005-03-28 14:30 tim * src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do the wrapping -2005-03-28 10:54 tim +2005-03-28 07:54 tim * src/applications/staticProps/GofXyz.cpp: fix a bug in getting the dimension of histogram -2005-03-22 11:38 tim +2005-03-22 08:38 tim * make/Makefile.in, src/applications/dump2Xyz/Makefile, src/applications/dynamicProps/Makefile, @@ -4276,52 +4723,52 @@ executable for dump2XYZ, simpleBuilder, staticProps and dynamicProps -2005-03-21 17:34 chrisfen +2005-03-21 14:34 chrisfen * forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the forcefield files -2005-03-21 15:51 chrisfen +2005-03-21 12:51 chrisfen * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, DarkSide/reactionField.F90: Make sure electrostatic_module provides data for reaction_field -2005-03-21 15:50 chrisfen +2005-03-21 12:50 chrisfen * forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE WILL CHANGE THIS BACK, RIGHT? -2005-03-21 14:23 gezelter +2005-03-21 11:23 gezelter * src/UseTheForce/DarkSide/electrostatic.F90: constant back to correct value -2005-03-21 14:22 gezelter +2005-03-21 11:22 gezelter * make/Makefile.in: fixed an install-related bug. $(InstallCommand) had been set to $(InstallData) -2005-03-15 09:21 gezelter +2005-03-15 06:21 gezelter * src/integrators/Integrator.cpp: VelocityVerletIntegrator already deletes and Nullifies restWriter, so Integrator shouldn't do it. -2005-03-15 09:20 gezelter +2005-03-15 06:20 gezelter * src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos -2005-03-13 02:39 gezelter +2005-03-12 23:39 gezelter * src/UseTheForce/DarkSide/electrostatic.F90: first run at charge-quadrupole interactions -2005-03-12 14:12 chrisfen +2005-03-12 11:12 chrisfen * samples/: Makefile.in, thermoIntegration/liquid/Makefile, thermoIntegration/solid/Makefile: forgot a couple of makefiles -2005-03-12 14:05 chrisfen +2005-03-12 11:05 chrisfen * samples/thermoIntegration/liquid/ssde.in, samples/thermoIntegration/liquid/ssde.md, @@ -4336,27 +4783,27 @@ src/restraints/ThermoIntegrationForceManager.cpp: added some samples -2005-03-11 12:50 tim +2005-03-11 09:50 tim * src/: brains/SimCreator.cpp, io/MultipoleAtomTypesSectionParser.cpp: fix a typo in MultipoleAtomTypesSectionParser -2005-03-11 10:55 tim +2005-03-11 07:55 tim * src/brains/SimInfo.cpp: pairs inside cutoff group should not be excluded -2005-03-11 10:53 gezelter +2005-03-11 07:53 gezelter * src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for quadrupoles -2005-03-11 10:52 gezelter +2005-03-11 07:52 gezelter * forceFields/DUFF2.frc: quadrupoles for SSD models -2005-03-11 10:00 tim +2005-03-11 07:00 tim * ChangeLog, doc/SelectionExpression.html, doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, @@ -4366,85 +4813,85 @@ src/selection/TokenMap.cpp: clean up SimInfo; modify the images of SelectionExpression.html -2005-03-10 19:43 chrisfen +2005-03-10 16:43 chrisfen * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, src/restraints/Restraints.cpp, src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in MPI restraints -2005-03-10 18:56 tim +2005-03-10 15:56 tim * doc/SelectionExpression.html, src/brains/SimInfo.cpp, src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody and cutoff group -2005-03-10 17:06 gezelter +2005-03-10 14:06 gezelter * src/types/MorseBondType.hpp: fixed a doxygen problem -2005-03-10 16:51 gezelter +2005-03-10 13:51 gezelter * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with the split dipole test cases -2005-03-10 16:51 gezelter +2005-03-10 13:51 gezelter * doc/SelectionExpression.html: updated some documentation -2005-03-10 15:40 gezelter +2005-03-10 12:40 gezelter * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, Makefile: LinkedList removal project starts now -2005-03-10 15:28 tim +2005-03-10 12:28 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: using map to replace link list -2005-03-10 14:11 tim +2005-03-10 11:11 tim * samples/dipole/: splitInWater.in, splitInWater.md: adding test case of split dipole -2005-03-10 14:10 chrisfen +2005-03-10 11:10 chrisfen * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, src/io/RestWriter.cpp, src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now builds... -2005-03-10 13:44 tim +2005-03-10 10:44 tim * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: adding test case for split dipole -2005-03-10 12:54 gezelter +2005-03-10 09:54 gezelter * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side support for split dipoles -2005-03-10 11:27 chrisfen +2005-03-10 08:27 chrisfen * samples/water/tip3p_ice/tp3.md, src/restraints/ThermoIntegrationForceManager.cpp: fixes to restraints -2005-03-10 11:15 chrisfen +2005-03-10 08:15 chrisfen * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints -2005-03-10 11:14 tim +2005-03-10 08:14 tim * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, src/io/MultipoleAtomTypesSectionParser.cpp, src/selection/SelectionEvaluator.cpp: minor change -2005-03-10 10:10 chrisfen +2005-03-10 07:10 chrisfen * make/Makefile.in, samples/water/tip3p_ice/tp3.md, src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, @@ -4461,12 +4908,12 @@ src/restraints/ThermoIntegrationForceManager.hpp: First commit of the new restraints code -2005-03-09 13:48 tim +2005-03-09 10:48 tim * src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding IndexFinder -2005-03-09 13:46 tim +2005-03-09 10:46 tim * src/: applications/dump2Xyz/Dump2XYZ.ggo, applications/dump2Xyz/Dump2XYZCmd.c, @@ -4474,7 +4921,7 @@ selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: fix compilation issue -2005-03-09 12:58 tim +2005-03-09 09:58 tim * forceFields/DUFF2.frc, scripts/filepp, src/UseTheForce/EAM_FF.cpp, @@ -4482,7 +4929,7 @@ src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug in SectionParser (lineNo is not updated) -2005-03-09 12:30 tim +2005-03-09 09:30 tim * src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, applications/dump2Xyz/Dump2XYZ.ggo, @@ -4504,58 +4951,58 @@ MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ; -2005-03-09 12:28 tim +2005-03-09 09:28 tim * forceFields/DUFF2.frc: change the format of DUFF2 -2005-03-09 10:44 gezelter +2005-03-09 07:44 gezelter * src/UseTheForce/DarkSide/: electrostatic.F90, electrostatic_interface.F90, electrostatic_interface.h: new electrostatic module -2005-03-09 09:26 gezelter +2005-03-09 06:26 gezelter * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole and fixed quadrupole stuff -2005-03-09 09:25 gezelter +2005-03-09 06:25 gezelter * src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines for outdated charge and dipole interfaces -2005-03-08 16:08 gezelter +2005-03-08 13:08 gezelter * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun charge-dipole test cases -2005-03-08 16:07 gezelter +2005-03-08 13:07 gezelter * src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a strange icc8 bug (we think). -2005-03-08 16:07 gezelter +2005-03-08 13:07 gezelter * src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! -2005-03-08 16:07 gezelter +2005-03-08 13:07 gezelter * src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic Unification Project -2005-03-08 16:07 gezelter +2005-03-08 13:07 gezelter * src/io/Globals.cpp: Dunno -2005-03-08 16:06 gezelter +2005-03-08 13:06 gezelter * src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using OOPSE_itoa and checking a NULL left over from the LinkedList days -2005-03-08 16:06 gezelter +2005-03-08 13:06 gezelter * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, atype_interface.F90, atype_interface.h, charge.F90, @@ -4563,52 +5010,52 @@ dipole_interface.F90, dipole_interface.h: electrostatic unification project fixed an uninitialized variable in Lennard Jones mixing map -2005-03-08 16:05 gezelter +2005-03-08 13:05 gezelter * src/UseTheForce/doForces.F90: electrostatic unification project -2005-03-08 16:05 gezelter +2005-03-08 13:05 gezelter * samples/water/dimer/: two.md, water.md: making some cool test cases -2005-03-08 16:05 gezelter +2005-03-08 13:05 gezelter * forceFields/DUFF2.frc: Added a charge for Chlorine -2005-03-07 17:39 tim +2005-03-07 14:39 tim * src/: brains/SimInfo.cpp, io/DumpReader.cpp, math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: Fixing a bug in BitSet.cpp -2005-03-04 10:28 gezelter +2005-03-04 07:28 gezelter * src/config.h.in: Cleaning up config.h.in by adding comments -2005-03-04 10:28 gezelter +2005-03-04 07:28 gezelter * configure, ac-tools/configure.in, make/Makefile.in, src/brains/SimCreator.cpp: SPRNG eradication project -2005-03-03 09:40 tim +2005-03-03 06:40 tim * src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the missing atom type problem) -2005-03-02 11:29 tim +2005-03-02 08:29 tim * src/math/RandNumGen.hpp: adding base class of Random Number generator -2005-03-02 11:28 tim +2005-03-02 08:28 tim * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in Velocitizer is not initialized which causes a seg fault -2005-03-02 10:36 tim +2005-03-02 07:36 tim * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, math/Makefile, @@ -4618,23 +5065,23 @@ MersenneTwister.hpp which causes all kinds of trouble. Refactory random number generator -2005-03-02 02:32 tim +2005-03-01 23:32 tim * test/math/testRandNumGen.cpp: Adding unit test for random number generator -2005-03-01 18:17 tim +2005-03-01 15:17 tim * src/brains/Thermo.hpp: fixed a file inclusion problem -2005-03-01 18:17 tim +2005-03-01 15:17 tim * test/math/: Makefile, OOPSERandNumGenTestCase.cpp, OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, RandNumGenTestCase.hpp: fixed compilation problem -2005-03-01 18:02 tim +2005-03-01 15:02 tim * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, math/Makefile, @@ -4642,18 +5089,18 @@ math/ParallelRandNumGen.hpp, math/mt19937ar.c, math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand -2005-03-01 18:00 tim +2005-03-01 15:00 tim * test/math/: Makefile, ParallelandNumGenTestCase.cpp, ParallelandNumGenTestCase.hpp: Change the name of test case -2005-03-01 16:00 tim +2005-03-01 13:00 tim * test/math/: Makefile, OOPSERandNumGenTestCase.cpp, OOPSERandNumGenTestCase.hpp: adding testcase for random number generator -2005-03-01 15:10 tim +2005-03-01 12:10 tim * src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, @@ -4664,42 +5111,42 @@ utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 -2005-03-01 14:11 tim +2005-03-01 11:11 tim * src/: brains/SimCreator.cpp, brains/SimInfo.hpp, integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding OOPSERandNumGen -2005-03-01 10:44 gezelter +2005-03-01 07:44 gezelter * make/Makefile.in: Fixed the damned build problem with the libraries not being removed in make clean and make distclean (at least we think it is fixed). -2005-03-01 10:26 gezelter +2005-03-01 07:26 gezelter * src/math/MersenneTwister.hpp: Making small modifications to allow for use on MPI machines -2005-03-01 09:45 tim +2005-03-01 06:45 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, integrators/Velocitizer.cpp, io/DumpReader.cpp, math/MersenneTwister.hpp: adding MersenneTwister random number generator -2005-02-28 22:55 tim +2005-02-28 19:55 tim * src/math/MersenneTwister.hpp: Adding a modified version of MersenneTwister.hpp -2005-02-28 12:24 tim +2005-02-28 09:24 tim * doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, definition.jpg: selection expression -2005-02-25 16:22 tim +2005-02-25 13:22 tim * src/: UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.F90, @@ -4707,12 +5154,12 @@ io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, types/AtomType.hpp: adding soft potential to LJ Module -2005-02-25 11:38 tim +2005-02-25 08:38 tim * doc/SelectionExpression.html: adding documentation for selection expression -2005-02-24 15:55 tim +2005-02-24 12:55 tim * src/: applications/simpleBuilder/simpleBuilder.cpp, integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, @@ -4720,35 +5167,35 @@ adding basic_teebuf which can operate on multiple stream simutaneously. -2005-02-22 14:26 chrisfen +2005-02-22 11:26 chrisfen * samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf sample -2005-02-22 13:56 tim +2005-02-22 10:56 tim * src/: UseTheForce/DarkSide/reactionField.F90, primitives/RigidBody.cpp: reactionfield get fixed -2005-02-21 11:57 tim +2005-02-21 08:57 tim * src/: applications/staticProps/GofRAngle.cpp, visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix a bug in GofRAngle -2005-02-21 10:28 tim +2005-02-21 07:28 tim * src/primitives/Molecule.cpp: Fix for compilation on the Sun -2005-02-21 10:22 tim +2005-02-21 07:22 tim * src/utils/next_combination.hpp: fix for compilation on the Sun -2005-02-21 10:21 tim +2005-02-21 07:21 tim * src/utils/GenericData.hpp: fix problem in sun -2005-02-18 18:07 tim +2005-02-18 15:07 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/dump2Xyz/Dump2XYZ.ggo, @@ -4765,76 +5212,76 @@ visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, visitors/Makefile: adding LipidTransVisitor, GofXyz is working now -2005-02-18 10:58 gezelter +2005-02-18 07:58 gezelter * src/brains/Register.cpp: Corrected filename collision for EAM on Mac OS X -2005-02-18 10:58 gezelter +2005-02-18 07:58 gezelter * src/applications/oopse/oopse.cpp: Updated copyright information -2005-02-18 10:58 gezelter +2005-02-18 07:58 gezelter * src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, Makefile: corrected filename collision for EAM on operating systems which are not case sensitive (aka Mac OS X) -2005-02-17 15:15 tim +2005-02-17 12:15 tim * src/applications/staticProps/GofXyz.cpp: more bug get fixed -2005-02-17 14:50 tim +2005-02-17 11:50 tim * src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug in GofXyz -2005-02-17 14:09 tim +2005-02-17 11:09 tim * src/applications/staticProps/RadialDistrFunc.hpp: make processHistogram non-abstrct function -2005-02-17 13:41 tim +2005-02-17 10:41 tim * src/applications/staticProps/GofXyz.cpp: [no log message] -2005-02-17 13:30 tim +2005-02-17 10:30 tim * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: finish GofXyz -2005-02-17 11:21 tim +2005-02-17 08:21 tim * src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial distribution function -2005-02-17 10:23 tim +2005-02-17 07:23 tim * src/utils/BitSet.hpp: forget the const correctness for BitSet -2005-02-17 10:18 tim +2005-02-17 07:18 tim * src/: brains/BlockSnapshotManager.cpp, selection/DistanceFinder.cpp: The change of interface of BitSet cause a bug in SelectionEvaluation -2005-02-16 16:13 tim +2005-02-16 13:13 tim * src/utils/residentMem.c: return residentMem in byte -2005-02-16 16:00 tim +2005-02-16 13:00 tim * src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix a bug in writing out the value of cosang -2005-02-16 15:43 tim +2005-02-16 12:43 tim * src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to estimate avaliable memory -2005-02-16 15:30 tim +2005-02-16 12:30 tim * src/: applications/staticProps/GofAngle2.cpp, applications/staticProps/GofAngle2.hpp, @@ -4850,7 +5297,7 @@ applications/staticProps/StaticPropsCmd.h, brains/BlockSnapshotManager.cpp: change the default bin number -2005-02-16 14:36 tim +2005-02-16 11:36 tim * src/: applications/dynamicProps/DipoleCorrFunc.cpp, applications/dynamicProps/RCorrFunc.cpp, @@ -4867,12 +5314,12 @@ utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output files;fix the problem of counting in staticProps -2005-02-15 14:39 tim +2005-02-15 11:39 tim * src/brains/BlockSnapshotManager.cpp: fix a bug in BlockSnapshotManager -2005-02-15 14:36 tim +2005-02-15 11:36 tim * src/: applications/dynamicProps/TimeCorrFunc.cpp, applications/staticProps/RadialDistrFunc.cpp, @@ -4880,24 +5327,24 @@ selection/SelectionEvaluator.cpp: BlockSnapshotManager is using reference counting now -2005-02-15 12:49 tim +2005-02-15 09:49 tim * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: replace std::make_pair by VariablesType::value_type to make Sun Compiler happy -2005-02-15 12:35 tim +2005-02-15 09:35 tim * src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to TokenMap, using TokenMapType::value_type instead of std::make_pair to make Sun compiler happy -2005-02-15 12:24 tim +2005-02-15 09:24 tim * src/applications/staticProps/: GofRAngle.cpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps -2005-02-15 12:11 tim +2005-02-15 09:11 tim * src/: applications/staticProps/GofR.cpp, applications/staticProps/RadialDistrFunc.cpp, @@ -4906,35 +5353,35 @@ #ifdef __RWSTD to make sun compiler happy (2) fix pair density calculation problem when two selections intersect with each other -2005-02-15 10:24 gezelter +2005-02-15 07:24 gezelter * src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy xlc++ -2005-02-15 10:17 gezelter +2005-02-15 07:17 gezelter * configure, ac-tools/configure.in, src/config.h.in, src/utils/residentMem.c: [no log message] -2005-02-15 01:17 gezelter +2005-02-14 22:17 gezelter * src/utils/residentMem.c: bug fix for null termination -2005-02-15 01:11 gezelter +2005-02-14 22:11 gezelter * configure, ac-tools/configure.in, src/utils/residentMem.c: bugfixing residentMem -2005-02-15 00:59 gezelter +2005-02-14 21:59 gezelter * configure, ac-tools/configure.in, src/config.h.in, src/utils/residentMem.c: bugfixes for residentMem on LINUX -2005-02-15 00:08 gezelter +2005-02-14 21:08 gezelter * src/utils/Makefile.in: added residentMem -2005-02-15 00:05 gezelter +2005-02-14 21:05 gezelter * configure, ac-tools/configure.in, make/Makefile.in, src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, @@ -4942,38 +5389,38 @@ other processes autoconf fixes ps syntax checking config.h file cleaning -2005-02-14 18:26 gezelter +2005-02-14 15:26 gezelter * configure, ac-tools/configure.in, make/Makefile.in: ps niceness -2005-02-14 18:16 gezelter +2005-02-14 15:16 gezelter * configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps strangeness -2005-02-14 14:42 tim +2005-02-14 11:42 tim * src/brains/BlockSnapshotManager.cpp: fix a bug in BlockSnapshotManager.hpp -2005-02-14 13:51 tim +2005-02-14 10:51 tim * src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c: default length for staticProps is 1/2 smallest length of first frame -2005-02-14 13:12 tim +2005-02-14 10:12 tim * src/integrators/VelocityVerletIntegrator.cpp: fix a bug in VelocityVerletIntegrator : last frame is written twice -2005-02-14 12:57 tim +2005-02-14 09:57 tim * src/: applications/dynamicProps/TimeCorrFunc.cpp, brains/SimInfo.cpp, primitives/RigidBody.cpp, primitives/StuntDouble.hpp: begin bug fix -2005-02-14 12:35 tim +2005-02-14 09:35 tim * src/applications/dynamicProps/: CorrelationFunction.cpp, CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, @@ -4983,37 +5430,37 @@ RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, VCorrFunc.hpp: refactory CorrelationFunction -2005-02-14 10:18 gezelter +2005-02-14 07:18 gezelter * src/applications/dynamicProps/CorrelationFunction.cpp: bug fix and start of switch for type of correlation function -2005-02-13 16:18 tim +2005-02-13 13:18 tim * src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in calculating bytes per stuntdouble -2005-02-13 16:03 tim +2005-02-13 13:03 tim * src/applications/dynamicProps/CorrelationFunction.cpp: more fix -2005-02-13 15:57 tim +2005-02-13 12:57 tim * src/applications/dynamicProps/CorrelationFunction.cpp: fixed a bug in CorrelationFunction -2005-02-13 15:36 tim +2005-02-13 12:36 tim * src/: applications/staticProps/GofR.cpp, applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a bug in SimInfo::getCutoff() -2005-02-13 15:08 tim +2005-02-13 12:08 tim * make/Makefile.in: adding staticProps and dynamicProps into Makefile.in -2005-02-13 15:05 tim +2005-02-13 12:05 tim * src/: applications/dynamicProps/CorrelationFunction.cpp, applications/dynamicProps/CorrelationFunction.hpp, @@ -5024,11 +5471,11 @@ brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length defaults to the cutoff radius -2005-02-13 14:14 tim +2005-02-13 11:14 tim * src/utils/Algorithm.hpp: adding Algorithm.hpp -2005-02-13 14:10 tim +2005-02-13 11:10 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/dynamicProps/CorrelationFunction.cpp, @@ -5042,14 +5489,14 @@ utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, visitors/OtherVisitor.cpp: dynamicProps get built -2005-02-13 10:56 tim +2005-02-13 07:56 tim * src/: applications/dynamicProps/CorrelationFunction.cpp, brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in progress -2005-02-13 03:04 tim +2005-02-13 00:04 tim * src/: applications/dynamicProps/CorrelationFunction.hpp, brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, @@ -5057,22 +5504,22 @@ brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more work in dynamicProps -2005-02-13 02:25 tim +2005-02-12 23:25 tim * src/applications/dynamicProps/DynamicProps.cpp: adding dynamicProps -2005-02-13 02:14 tim +2005-02-12 23:14 tim * src/applications/dynamicProps/: DynamicPropsCmd.c, DynamicPropsCmd.h: adding command line option to DynamicProps -2005-02-13 02:13 tim +2005-02-12 23:13 tim * src/applications/dynamicProps/: DynamicProps.ggo, Makefile: adding command line option for DynamicProps -2005-02-13 01:57 tim +2005-02-12 22:57 tim * src/: applications/dynamicProps/CorrelationFunction.cpp, applications/dynamicProps/CorrelationFunction.hpp, @@ -5089,35 +5536,35 @@ primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding dynamicProps -2005-02-12 15:09 tim +2005-02-12 12:09 tim * src/selection/SelectionManager.cpp: adding SelectionManager.cpp -2005-02-11 17:41 tim +2005-02-11 14:41 tim * src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one more constructor to Snapshot to create customized DataStorage -2005-02-11 17:39 tim +2005-02-11 14:39 tim * src/selection/: DistanceFinder.hpp, Makefile, SelectionManager.hpp: adding beginSelected, nextSelected method to SelectionManager -2005-02-11 17:36 tim +2005-02-11 14:36 tim * src/config.h.in, configure: adding support for physmem -2005-02-11 17:35 tim +2005-02-11 14:35 tim * ac-tools/configure.in: adding supprot for physmem -2005-02-11 17:35 tim +2005-02-11 14:35 tim * src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding physmem -2005-02-10 17:37 tim +2005-02-10 14:37 tim * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, @@ -5125,7 +5572,7 @@ StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: more work in StaticProps -2005-02-10 13:14 tim +2005-02-10 10:14 tim * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, @@ -5134,115 +5581,115 @@ StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, StaticPropsCmd.h: change the filenames -2005-02-10 09:15 tim +2005-02-10 06:15 tim * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofRAngle -2005-02-09 13:21 tim +2005-02-09 10:21 tim * src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some useless files -2005-02-09 13:12 tim +2005-02-09 10:12 tim * src/applications/staticProps/: GofR.cpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress -2005-02-09 12:08 tim +2005-02-09 09:08 tim * src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR -2005-02-07 17:39 tim +2005-02-07 14:39 tim * src/primitives/Molecule.hpp: add getRigidBodyAt function into Molecule class -2005-02-07 17:38 tim +2005-02-07 14:38 tim * src/applications/dump2Xyz/Dump2XYZCmd.c: update help info -2005-02-07 17:36 tim +2005-02-07 14:36 tim * src/selection/: NameFinder.cpp, NameFinder.hpp, SelectionCompiler.cpp: support select internal index selection, for example, select DMPC.3 -2005-02-07 16:11 tim +2005-02-07 13:11 tim * src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update help info for Dump2XYZ -2005-02-07 15:39 chrisfen +2005-02-07 12:39 chrisfen * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: selection librarys added -2005-02-07 15:31 tim +2005-02-07 12:31 tim * src/selection/Makefile, make/Makefile.in: adding Makefile -2005-02-07 15:20 chrisfen +2005-02-07 12:20 chrisfen * src/utils/wildcards.hpp: issue commented out in wildcards -2005-02-07 15:06 tim +2005-02-07 12:06 tim * src/selection/SelectionEvaluator.cpp: forget to reset the pc which cause reevaluate return NULL -2005-02-07 14:14 tim +2005-02-07 11:14 tim * src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, SimSnapshotManager.hpp: fix a bug in determing the global index for rigidbodies -2005-02-07 14:13 tim +2005-02-07 11:13 tim * src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change in Bitset -2005-02-07 14:13 tim +2005-02-07 11:13 tim * src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, SelectionCompiler.cpp, SelectionCompiler.hpp, SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, TokenMap.cpp: selection library is working -2005-02-04 17:46 tim +2005-02-04 14:46 tim * src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor -2005-02-04 17:45 tim +2005-02-04 14:45 tim * src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor and XYZVisitor now use selection library -2005-02-04 17:44 tim +2005-02-04 14:44 tim * src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: adding SelectionManager into SimInfo -2005-02-04 17:43 tim +2005-02-04 14:43 tim * src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of selection library -2005-02-04 17:42 tim +2005-02-04 14:42 tim * src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change in BitSet -2005-02-04 17:41 tim +2005-02-04 14:41 tim * src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing implementation -2005-02-04 17:39 tim +2005-02-04 14:39 tim * src/selection/: NameFinder.cpp, NameFinder.hpp, SelectionCompiler.cpp, SelectionCompiler.hpp, @@ -5250,27 +5697,27 @@ SelectionManager.hpp, Token.hpp: half of the selection utility is working need to debug within keyword and atomproperty keyword -2005-02-04 00:42 tim +2005-02-03 21:42 tim * src/selection/: NameFinder.cpp, NameFinder.hpp: selection library get built -2005-02-04 00:42 tim +2005-02-03 21:42 tim * src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet -2005-02-04 00:26 tim +2005-02-03 21:26 tim * src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: remove some useless files -2005-02-03 23:57 tim +2005-02-03 20:57 tim * src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: adding wildcard class; NameFinder is finished -2005-02-03 18:14 tim +2005-02-03 15:14 tim * src/selection/: NameFinder.cpp, NameFinder.hpp, SelectionCompiler.cpp, SelectionCompiler.hpp, @@ -5278,59 +5725,59 @@ SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in selection library -2005-02-03 09:04 tim +2005-02-03 06:04 tim * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: selection in progress -2005-02-02 18:13 tim +2005-02-02 15:13 tim * src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in progress, except SelectionEvaluator, other files are compiled -2005-02-02 18:12 tim +2005-02-02 15:12 tim * src/utils/: Makefile.in, any.hpp: adding boost::any -2005-02-02 07:51 tim +2005-02-02 04:51 tim * src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp -2005-02-01 17:49 tim +2005-02-01 14:49 tim * src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, selection/Token.hpp: Selection in progress -2005-02-01 01:55 tim +2005-01-31 22:55 tim * src/: selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, selection/Token.hpp, utils/BitSet.cpp, utils/BitSet.hpp: adding selection library -2005-01-26 10:26 tim +2005-01-26 07:26 tim * src/integrators/: Integrator.cpp, Integrator.hpp, VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget to add eorWriter -2005-01-26 10:15 tim +2005-01-26 07:15 tim * src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: (1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the wrong column of electroframe -2005-01-25 16:59 tim +2005-01-25 13:59 tim * src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in SimInfo, use number of cutoff stamp as counter to loop over rigidbody stamp -2005-01-25 12:45 tim +2005-01-25 09:45 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/MoleculeCreator.cpp, brains/SimCreator.cpp, @@ -5350,28 +5797,28 @@ inertial tensor from the directional atoms before calculate rigidbody's inertial tensor -2005-01-17 17:17 tim +2005-01-17 14:17 tim * forceFields/DUFF2.frc: forget to set dipole for lipid head group -2005-01-17 11:58 tim +2005-01-17 08:58 tim * src/integrators/NVT.cpp: fix a bug in loading initial extended system parameters -2005-01-17 11:05 tim +2005-01-17 08:05 tim * src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT -2005-01-14 17:02 tim +2005-01-14 14:02 tim * src/UseTheForce/WATER.cpp: remove WATER.cpp -2005-01-14 16:37 tim +2005-01-14 13:37 tim * forceFields/Makefile: sync Makefile -2005-01-14 16:13 gezelter +2005-01-14 13:13 gezelter * make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, @@ -5385,18 +5832,18 @@ src/visitors/Makefile: moved Package variable into subdirectory makefiles to speed up the building process -2005-01-14 15:48 gezelter +2005-01-14 12:48 gezelter * src/applications/oopse/oopse.cpp: Fixed publication details in banner -2005-01-14 15:48 gezelter +2005-01-14 12:48 gezelter * src/UseTheForce/DarkSide/: simParallel_interface.F90, simParallel_interface.h: added dummy subroutine to avoid empty unit, synchronized this dummy routine between C and fortran -2005-01-14 15:31 gezelter +2005-01-14 12:31 gezelter * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, @@ -5412,53 +5859,53 @@ DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating modules and C/Fortran interface subroutines -2005-01-14 15:15 gezelter +2005-01-14 12:15 gezelter * configure, ac-tools/aclocal.m4: more fixes for gnugetopt -2005-01-14 15:09 gezelter +2005-01-14 12:09 gezelter * configure, ac-tools/configure.in, src/config.h.in, src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt -2005-01-14 11:49 tim +2005-01-14 08:49 tim * src/: io/EAMAtomTypesSectionParser.cpp, utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, utils/StringUtils.hpp: using c library to do conversion instead of using iostream due to a bug in libstdc++(GCC 3.2) -2005-01-13 21:40 tim +2005-01-13 18:40 tim * src/brains/SimSetup.cpp: no message -2005-01-13 20:56 tim +2005-01-13 17:56 tim * src/primitives/Molecule.hpp: fix a bug in global index -2005-01-13 20:04 tim +2005-01-13 17:04 tim * src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include Integrator.hpp in Minimizer -2005-01-13 17:14 gezelter +2005-01-13 14:14 gezelter * src/utils/Makefile: compile getopt and getopt1 if we need to -2005-01-13 16:56 gezelter +2005-01-13 13:56 gezelter * make/Makefile.in: template flags -2005-01-13 16:48 gezelter +2005-01-13 13:48 gezelter * src/applications/oopse/Makefile: formatting -2005-01-13 16:48 gezelter +2005-01-13 13:48 gezelter * make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir target -2005-01-13 14:40 tim +2005-01-13 11:40 tim * src/: UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, @@ -5466,29 +5913,29 @@ primitives/RigidBody.cpp, types/AtomTypeProperties.h, types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform -2005-01-13 13:26 tim +2005-01-13 10:26 tim * make/Makefile.in: change the order of linking (object file comes first and then follow by user built library) -2005-01-12 18:24 tim +2005-01-12 15:24 tim * src/io/DumpWriter.cpp: remove useless debug info -2005-01-12 18:21 tim +2005-01-12 15:21 tim * src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix -2005-01-12 18:17 tim +2005-01-12 15:17 tim * make/: Makefile.in, Makefile.in: missing tab -2005-01-12 18:15 tim +2005-01-12 15:15 tim * src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor get fixed -2005-01-12 17:40 gezelter +2005-01-12 14:40 gezelter * make/Makefile.in, src/UseTheForce/DUFF.cpp, src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, @@ -5698,18 +6145,18 @@ src/visitors/ZconsVisitor.hpp: merging new_design branch into OOPSE-2.0 -2005-01-12 13:13 tim +2005-01-12 10:13 tim * src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, utils/TypeContainer.hpp: forget to include -2005-01-12 12:25 tim +2005-01-12 09:25 tim * forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force fields -2005-01-12 12:14 tim +2005-01-12 09:14 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, @@ -5871,12 +6318,12 @@ visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: change license -2005-01-12 12:14 tim +2005-01-12 09:14 tim * src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on branch new_design. -2005-01-11 16:03 tim +2005-01-11 13:03 tim * src/: constraints/ZconstraintForceManager.cpp, constraints/ZconstraintForceManager.hpp, @@ -5884,73 +6331,73 @@ minimizers/MinimizerParameterSet.hpp: change const static double data member to const double -2005-01-11 15:50 tim +2005-01-11 12:50 tim * src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: -2005-01-11 15:39 tim +2005-01-11 12:39 tim * src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: change data type from logical to integer in AtomTypeProperties.h -2005-01-11 11:36 tim +2005-01-11 08:36 tim * forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding new format of EAM force field -2005-01-11 11:24 tim +2005-01-11 08:24 tim * src/UseTheForce/DUFF.cpp: change default name of DUFF force field to DUFF2.frc -2005-01-11 11:23 tim +2005-01-11 08:23 tim * forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to DUFF2.frc -2005-01-11 11:09 tim +2005-01-11 08:09 tim * make/Makefile.in: adding constraints and minimizers into Makefile.in -2005-01-11 11:03 tim +2005-01-11 08:03 tim * src/io/: ChargeAtomTypesSectionParser.cpp, ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless files -2005-01-11 10:59 tim +2005-01-11 07:59 tim * src/io/ZConsWriter.cpp: [no log message] -2005-01-11 10:53 tim +2005-01-11 07:53 tim * src/UseTheForce/EAM.cpp: minor fix -2005-01-11 10:52 tim +2005-01-11 07:52 tim * src/constraints/Rattle.hpp: file Rattle.hpp was initially added on branch new_design. -2005-01-11 10:52 tim +2005-01-11 07:52 tim * src/constraints/Rattle.cpp: file Rattle.cpp was initially added on branch new_design. -2005-01-11 10:52 tim +2005-01-11 07:52 tim * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm -2005-01-11 10:47 tim +2005-01-11 07:47 tim * make/Makefile.in: forget a '$' sign -2005-01-11 10:46 tim +2005-01-11 07:46 tim * make/Makefile.in: missing tab in rules -2005-01-10 17:04 tim +2005-01-10 14:04 tim * src/: UseTheForce/ForceFieldCreator.cpp, UseTheForce/ForceFieldCreator.hpp, @@ -5969,17 +6416,17 @@ minimizers/MinimizerFactory.hpp: create a register module to register force fields, integrators and minimizers -2005-01-10 17:04 tim +2005-01-10 14:04 tim * src/brains/Register.cpp: file Register.cpp was initially added on branch new_design. -2005-01-10 17:04 tim +2005-01-10 14:04 tim * src/brains/Register.hpp: file Register.hpp was initially added on branch new_design. -2005-01-10 15:52 tim +2005-01-10 12:52 tim * src/: UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, brains/ForceManager.hpp, @@ -5991,7 +6438,7 @@ visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint method is working now -2005-01-10 13:05 tim +2005-01-10 10:05 tim * src/: constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, @@ -6001,24 +6448,24 @@ visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in zconstraint -2005-01-10 13:05 tim +2005-01-10 10:05 tim * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was initially added on branch new_design. -2005-01-07 16:50 tim +2005-01-07 13:50 tim * src/constraints/ZconstraintForceManager.cpp: file ZconstraintForceManager.cpp was initially added on branch new_design. -2005-01-07 16:50 tim +2005-01-07 13:50 tim * src/constraints/ZconstraintForceManager.hpp: file ZconstraintForceManager.hpp was initially added on branch new_design. -2005-01-07 16:50 tim +2005-01-07 13:50 tim * src/: applications/simpleBuilder/BaseLattice.hpp, applications/simpleBuilder/Lattice.hpp, @@ -6032,12 +6479,12 @@ integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, utils/NumericConstant.hpp: ZConstraintForceManager in progress -2005-01-07 16:50 tim +2005-01-07 13:50 tim * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was initially added on branch new_design. -2005-01-06 17:31 tim +2005-01-06 14:31 tim * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -6046,12 +6493,12 @@ io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: constraint is almost working -2005-01-05 19:36 tim +2005-01-05 16:36 tim * src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is working -2005-01-05 19:16 tim +2005-01-05 16:16 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, @@ -6066,17 +6513,17 @@ minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder in progress -2005-01-05 12:35 tim +2005-01-05 09:35 tim * src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp was initially added on branch new_design. -2005-01-05 12:35 tim +2005-01-05 09:35 tim * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially added on branch new_design. -2005-01-05 12:35 tim +2005-01-05 09:35 tim * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, @@ -6084,27 +6531,27 @@ OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, SDMinimizer.hpp: minimizer in progress -2005-01-05 12:35 tim +2005-01-05 09:35 tim * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp was initially added on branch new_design. -2005-01-05 12:35 tim +2005-01-05 09:35 tim * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp was initially added on branch new_design. -2005-01-05 12:35 tim +2005-01-05 09:35 tim * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp was initially added on branch new_design. -2005-01-05 12:35 tim +2005-01-05 09:35 tim * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially added on branch new_design. -2005-01-04 17:18 tim +2005-01-04 14:18 tim * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, @@ -6115,74 +6562,74 @@ primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in progress -2005-01-04 17:18 tim +2005-01-04 14:18 tim * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was initially added on branch new_design. -2005-01-04 17:18 tim +2005-01-04 14:18 tim * src/minimizers/MinimizerParameterSet.cpp: file MinimizerParameterSet.cpp was initially added on branch new_design. -2005-01-04 17:18 tim +2005-01-04 14:18 tim * src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was initially added on branch new_design. -2005-01-04 17:18 tim +2005-01-04 14:18 tim * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp was initially added on branch new_design. -2005-01-04 17:18 tim +2005-01-04 14:18 tim * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress -2005-01-04 17:18 tim +2005-01-04 14:18 tim * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on branch new_design. -2004-12-20 15:50 chuckv +2004-12-20 12:50 chuckv * make/Makefile.in: Fixed Makefile test bug under OSX and possibly other BSD's, replaced test -f *.mod with ls function since BSD test apparently doesn't support wildcards. -2004-12-20 15:36 tim +2004-12-20 12:36 tim * make/Makefile.in: fix a test command incompatiable problem -2004-12-20 14:49 tim +2004-12-20 11:49 tim * src/integrators/NPTi.cpp: NPT is working now -2004-12-16 14:20 tim +2004-12-16 11:20 tim * src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the invalid stamp id -2004-12-16 14:00 tim +2004-12-16 11:00 tim * forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: adding new EAM force field files -2004-12-16 13:55 tim +2004-12-16 10:55 tim * src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays in EAM parameter file is incorrect -2004-12-16 12:27 tim +2004-12-16 09:27 tim * src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM -2004-12-15 17:34 tim +2004-12-15 14:34 tim * src/: applications/simpleBuilder/BaseLattice.cpp, applications/simpleBuilder/BaseLattice.hpp, @@ -6195,33 +6642,33 @@ applications/simpleBuilder/simpleBuilder.cpp, io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream -2004-12-15 16:07 tim +2004-12-15 13:07 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: add EAM Force Field -2004-12-15 14:40 tim +2004-12-15 11:40 tim * src/applications/oopse/oopse.cpp: add more force fields -2004-12-15 11:44 tim +2004-12-15 08:44 tim * src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget to call All_reduce in MPI version) -2004-12-15 11:13 tim +2004-12-15 08:13 tim * src/: brains/SimCreator.cpp, brains/SimInfo.cpp, io/DumpReader.cpp: MPI in NVE is working -2004-12-14 16:57 tim +2004-12-14 13:57 tim * src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. Master nodes does not brocast the total number of frames -2004-12-14 14:08 tim +2004-12-14 11:08 tim * src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, @@ -6230,7 +6677,7 @@ minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, minimizers/SDMinimizer.cpp: more fix in MPI version -2004-12-13 17:30 tim +2004-12-13 14:30 tim * src/: UseTheForce/DarkSide/simParallel.F90, applications/oopse/oopse.cpp, brains/SimCreator.cpp, @@ -6248,62 +6695,62 @@ utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version is built -2004-12-10 13:41 tim +2004-12-10 10:41 tim * src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp -2004-12-10 11:14 tim +2004-12-10 08:14 tim * src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: forget to zero out the torque. Sticky and Dipole is working now -2004-12-09 18:15 tim +2004-12-09 15:15 tim * src/: UseTheForce/DarkSide/dipole.F90, UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: fix an index problem in eFrame matrix -2004-12-09 18:09 tim +2004-12-09 15:09 tim * src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when initializing the new Charge AtomType -2004-12-09 16:15 tim +2004-12-09 13:15 tim * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, types/DirectionalAtomType.cpp: sticky module get compiled -2004-12-09 15:43 gezelter +2004-12-09 12:43 gezelter * src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for GB -2004-12-09 15:42 gezelter +2004-12-09 12:42 gezelter * src/UseTheForce/doForces.F90: u_l -> eFrame -2004-12-09 15:27 gezelter +2004-12-09 12:27 gezelter * src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky module now has the option for multiple sticky types -2004-12-09 15:27 gezelter +2004-12-09 12:27 gezelter * src/UseTheForce/doForces.F90: sticky -2004-12-09 11:22 tim +2004-12-09 08:22 tim * src/integrators/: NPT.cpp, NVT.cpp: fix an interface inconsistency in lab2Bidy -2004-12-09 10:45 tim +2004-12-09 07:45 tim * src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug in calculating torque in rigid body -2004-12-08 15:37 tim +2004-12-08 12:37 tim * src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, brains/SnapShot.cpp, brains/Snapshot.hpp, @@ -6311,45 +6758,45 @@ io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: fix a parsing bug in ElectroStaticAtomTypesSectionParser -2004-12-08 12:03 tim +2004-12-08 09:03 tim * src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane in NVT is working -2004-12-07 18:08 tim +2004-12-07 15:08 tim * src/: UseTheForce/Makefile, brains/SimInfo.hpp, integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, io/DumpWriter.cpp: NPT in progress -2004-12-07 09:43 tim +2004-12-07 06:43 tim * test/utils/: Makefile, NextCombinationTestCase.hpp: [no log message] -2004-12-07 00:12 tim +2004-12-06 21:12 tim * src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in UseInitXSstate -2004-12-07 00:00 tim +2004-12-06 21:00 tim * src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message -2004-12-06 23:47 tim +2004-12-06 20:47 tim * src/types/DirectionalAtomType.cpp: [no log message] -2004-12-06 21:18 tim +2004-12-06 18:18 tim * forceFields/newDUFF.frc: merge WATER force field into DUFF -2004-12-06 20:33 tim +2004-12-06 17:33 tim * forceFields/newDUFF.frc: change the force constant of bonds -2004-12-06 18:29 tim +2004-12-06 15:29 tim * src/: UseTheForce/DarkSide/charge.F90, UseTheForce/DarkSide/charge_interface.h, @@ -6357,18 +6804,18 @@ UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: fix atom type ident in Charge and Dipole Module -2004-12-06 17:56 tim +2004-12-06 14:56 tim * src/primitives/Torsion.cpp: butane is working now -2004-12-06 15:15 tim +2004-12-06 12:15 tim * src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, primitives/Bond.hpp, primitives/Torsion.cpp: short range interaction for butane is correct.Still something wrong with long range one -2004-12-05 23:49 tim +2004-12-05 20:49 tim * src/: brains/Exclude.cpp, brains/Exclude.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -6376,44 +6823,44 @@ primitives/Atom.hpp, utils/NumericConstant.hpp, utils/TypeContainer.hpp: fix a bug in Exclude List -2004-12-05 17:21 tim +2004-12-05 14:21 tim * forceFields/newDUFF.frc: minor fix in DUFF -2004-12-05 17:02 tim +2004-12-05 14:02 tim * src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: fix a bug in filling MolMembership -2004-12-05 12:12 tim +2004-12-05 09:12 tim * forceFields/newDUFF.frc: minor fix in force field file -2004-12-05 12:09 tim +2004-12-05 09:09 tim * src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp -2004-12-04 15:09 tim +2004-12-04 12:09 tim * src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, math/Vector3.hpp: NVE is working now, get the same result as OOPSE-1.0 -2004-12-04 14:29 tim +2004-12-04 11:29 tim * src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy -2004-12-04 14:24 gezelter +2004-12-04 11:24 gezelter * src/primitives/: Bend.cpp, Torsion.cpp: What? -2004-12-04 14:24 gezelter +2004-12-04 11:24 gezelter * src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion -2004-12-04 00:24 tim +2004-12-03 21:24 tim * src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, integrators/Integrator.hpp, @@ -6424,7 +6871,7 @@ dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step 4 EAM Step 5 Shape Step 6 Constraint & Restraint -2004-12-03 19:01 tim +2004-12-03 16:01 tim * src/: UseTheForce/DarkSide/LJ.F90, applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, @@ -6433,12 +6880,12 @@ io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, energy of NVE is not conserved -2004-12-03 17:36 tim +2004-12-03 14:36 tim * src/: brains/DataStorage.hpp, brains/Snapshot.hpp, primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running -2004-12-03 16:30 tim +2004-12-03 13:30 tim * src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, @@ -6446,12 +6893,12 @@ primitives/Molecule.hpp, primitives/StuntDouble.hpp, primitives/Torsion.hpp: more missing function get implemented -2004-12-03 15:30 tim +2004-12-03 12:30 tim * src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo -2004-12-03 12:59 tim +2004-12-03 09:59 tim * src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -6460,12 +6907,12 @@ io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, utils/TypeContainer.hpp: begin to fix bugs -2004-12-02 19:26 tim +2004-12-02 16:26 tim * src/utils/Trim.cpp: file Trim.cpp was initially added on branch new_design. -2004-12-02 19:26 tim +2004-12-02 16:26 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/ForceFieldCreator.cpp, @@ -6476,15 +6923,15 @@ utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a bug in countTokens in StringTokenizer -2004-12-02 19:06 tim +2004-12-02 16:06 tim * forceFields/newDUFF.frc: minor fix -2004-12-02 18:15 tim +2004-12-02 15:15 tim * forceFields/newDUFF.frc: new ForceField format -2004-12-02 17:15 tim +2004-12-02 14:15 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/ForceFieldCreator.cpp, @@ -6503,32 +6950,32 @@ types/Makefile: refine factory pattern to make it initialized correctly -2004-12-02 17:15 tim +2004-12-02 14:15 tim * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp was initially added on branch new_design. -2004-12-02 17:15 tim +2004-12-02 14:15 tim * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp was initially added on branch new_design. -2004-12-02 17:15 tim +2004-12-02 14:15 tim * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp was initially added on branch new_design. -2004-12-02 17:15 tim +2004-12-02 14:15 tim * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp was initially added on branch new_design. -2004-12-02 11:53 tim +2004-12-02 08:53 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, types/DirectionalAtomType.cpp, types/Makefile: oopse get built -2004-12-02 11:04 tim +2004-12-02 08:04 tim * src/: applications/simpleBuilder/LatticeCreator.cpp, applications/simpleBuilder/LatticeCreator.hpp, @@ -6552,7 +6999,7 @@ visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still have two linking problem -2004-12-02 00:17 tim +2004-12-01 21:17 tim * src/: applications/dump2Xyz/Dump2XYZ.cpp, applications/simpleBuilder/Lattice.cpp, @@ -6564,7 +7011,7 @@ visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, visitors/ZconsVisitor.cpp: change endl to std::endl -2004-12-02 00:14 tim +2004-12-01 21:14 tim * src/: UseTheForce/Shapes_FF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, @@ -6580,12 +7027,12 @@ visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp: minor fix -2004-12-02 00:09 tim +2004-12-01 21:09 tim * src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: remove StreamTokenizer -2004-12-02 00:06 tim +2004-12-01 21:06 tim * src/: UseTheForce/Shapes_FF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, @@ -6594,7 +7041,7 @@ restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using namespace std in .cpp file -2004-12-02 00:04 tim +2004-12-01 21:04 tim * src/: UseTheForce/Shapes_FF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, @@ -6618,7 +7065,7 @@ visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding qulified name prefix std -2004-12-01 23:55 tim +2004-12-01 20:55 tim * src/: UseTheForce/Shapes_FF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, @@ -6634,7 +7081,7 @@ visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp: replace string by std::string -2004-12-01 22:12 tim +2004-12-01 19:12 tim * make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, src/applications/simpleBuilder/BaseLattice.hpp, @@ -6655,14 +7102,14 @@ test/brains/RigidBody.cpp: replace misuse of using namespace std in header files -2004-12-01 21:23 tim +2004-12-01 18:23 tim * src/: primitives/Atom.hpp, primitives/RigidBody.hpp, primitives/StuntDouble.hpp, utils/TypeContainer.hpp, utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: begin to fix linking problem -2004-12-01 21:08 tim +2004-12-01 18:08 tim * src/: applications/oopse/oopse.cpp, brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, @@ -6674,22 +7121,22 @@ utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, still has some linking problem -2004-12-01 19:26 tim +2004-12-01 16:26 tim * src/: integrators/NVT.cpp, integrators/NVT.hpp, utils/OOPSEConstant.hpp: NVT get built -2004-12-01 19:09 tim +2004-12-01 16:09 tim * src/integrators/DLM.cpp: file DLM.cpp was initially added on branch new_design. -2004-12-01 19:09 tim +2004-12-01 16:09 tim * src/integrators/DLM.hpp: file DLM.hpp was initially added on branch new_design. -2004-12-01 19:09 tim +2004-12-01 16:09 tim * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, @@ -6701,12 +7148,12 @@ integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE get built -2004-12-01 19:09 tim +2004-12-01 16:09 tim * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp was initially added on branch new_design. -2004-12-01 17:45 tim +2004-12-01 14:45 tim * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, integrators/IntegratorFactory.cpp, @@ -6717,12 +7164,12 @@ io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, io/StatWriter.hpp: rename DumpWrite to DumpWriter -2004-12-01 17:45 tim +2004-12-01 14:45 tim * src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on branch new_design. -2004-12-01 15:05 tim +2004-12-01 12:05 tim * src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, @@ -6731,11 +7178,11 @@ visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: visitors get built -2004-12-01 14:32 chrisfen +2004-12-01 11:32 chrisfen * samples/water/tip3p_ice/tp3.md: fixed a sample -2004-12-01 14:10 tim +2004-12-01 11:10 tim * src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, @@ -6744,7 +7191,7 @@ src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: spell check -2004-12-01 13:42 tim +2004-12-01 10:42 tim * src/: UseTheForce/DarkSide/atype.F90, io/ElectrostaticAtomTypesSectionParser.cpp, @@ -6753,7 +7200,7 @@ primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator and constraint, other directories get built -2004-12-01 12:38 tim +2004-12-01 09:38 tim * src/: brains/DataStorage.cpp, brains/DataStorage.hpp, brains/ForceManager.cpp, brains/MoleculeCreator.cpp, @@ -6766,28 +7213,28 @@ types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: refactory AtomType -2004-11-30 22:11 tim +2004-11-30 19:11 tim * src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change -2004-11-30 21:30 tim +2004-11-30 18:30 tim * src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change NumericConstant -2004-11-30 21:24 tim +2004-11-30 18:24 tim * src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, primitives/RigidBody.cpp: minor fix -2004-11-30 18:14 tim +2004-11-30 15:14 tim * src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io get built, next is integrator -2004-11-30 17:43 tim +2004-11-30 14:43 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/ForceField.hpp, brains/SimCreator.cpp, @@ -6795,14 +7242,14 @@ io/BASS_interface.cpp, primitives/StuntDouble.hpp, utils/StringUtils.hpp: brains get built -2004-11-30 15:50 tim +2004-11-30 12:50 tim * src/: brains/ForceManager.cpp, brains/Makefile, brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, primitives/RigidBody.cpp, primitives/RigidBody.hpp, utils/StringUtils.hpp: brains get built, io is next -2004-11-30 14:58 tim +2004-11-30 11:58 tim * src/: brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp, brains/ForceManager.hpp, @@ -6813,28 +7260,28 @@ brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo -2004-11-30 14:58 tim +2004-11-30 11:58 tim * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially added on branch new_design. -2004-11-30 12:54 tim +2004-11-30 09:54 tim * src/: primitives/Bend.hpp, primitives/Bond.hpp, primitives/StuntDouble.hpp, primitives/Torsion.hpp, utils/LocalIndexManager.hpp: more get fixed -2004-11-30 00:03 tim +2004-11-29 21:03 tim * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was initially added on branch new_design. -2004-11-30 00:03 tim +2004-11-29 21:03 tim * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename LocalndexManager.hpp to LocalIndexManager.hpp -2004-11-29 23:43 tim +2004-11-29 20:43 tim * src/: io/BendTypesSectionParser.cpp, io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, @@ -6843,7 +7290,7 @@ types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp: Section Parsers get compiled -2004-11-29 23:14 tim +2004-11-29 20:14 tim * src/: io/BendTypesSectionParser.cpp, io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, @@ -6851,7 +7298,7 @@ types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor fixed -2004-11-29 22:49 tim +2004-11-29 19:49 tim * src/: io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, @@ -6859,70 +7306,70 @@ types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp: minor fixed -2004-11-29 22:32 tim +2004-11-29 19:32 tim * src/: io/TorsionTypesSectionParser.cpp, types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp: #inlcude statement can not be embedded -2004-11-29 16:42 tim +2004-11-29 13:42 tim * test/math/: Makefile, PolynomialTestCase.cpp, PolynomialTestCase.hpp: add PolynomialTestCase -2004-11-29 16:42 tim +2004-11-29 13:42 tim * src/math/Polynomial.hpp: Polynomial passes unit test -2004-11-29 15:03 tim +2004-11-29 12:03 tim * src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename QuarticTorsion.hpp to QuarticTorsionType.hpp -2004-11-29 15:03 tim +2004-11-29 12:03 tim * src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was initially added on branch new_design. -2004-11-29 14:56 tim +2004-11-29 11:56 tim * src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was initially added on branch new_design. -2004-11-29 14:56 tim +2004-11-29 11:56 tim * src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add CubicTorsionType and QuarticTorsionType -2004-11-29 14:56 tim +2004-11-29 11:56 tim * src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was initially added on branch new_design. -2004-11-29 13:00 tim +2004-11-29 10:00 tim * src/: brains/DataStorage.hpp, brains/Snapshot.hpp, types/CubicBendType.hpp, types/CubicBondType.hpp, types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get fixed -2004-11-29 12:59 tim +2004-11-29 09:59 tim * src/utils/Trim.hpp: file Trim.hpp was initially added on branch new_design. -2004-11-29 12:59 tim +2004-11-29 09:59 tim * src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim Algorithm for std::string -2004-11-29 10:52 tim +2004-11-29 07:52 tim * src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove some useless files -2004-11-29 10:50 tim +2004-11-29 07:50 tim * src/io/: BondTypesSectionParser.cpp, ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, @@ -6933,7 +7380,7 @@ SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, StickyAtomTypesSectionParser.hpp: more files get fixed -2004-11-29 10:27 tim +2004-11-29 07:27 tim * src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, DirectionalAtomTypesSectionParser.cpp, @@ -6942,28 +7389,28 @@ SectionParserManager.cpp, SectionParserManager.hpp: part of io get built -2004-11-29 09:49 tim +2004-11-29 06:49 tim * src/types/UreyBradleyBendType.hpp: types get built -2004-11-29 09:40 tim +2004-11-29 06:40 tim * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: types get built -2004-11-25 21:13 tim +2004-11-25 18:13 tim * src/: UseTheForce/ForceField.hpp, io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some files -2004-11-25 15:18 tim +2004-11-25 12:18 tim * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was initially added on branch new_design. -2004-11-25 15:18 tim +2004-11-25 12:18 tim * src/: io/AtomTypesSectionParser.cpp, io/BondTypesSectionParser.cpp, @@ -6972,12 +7419,12 @@ types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some files -2004-11-25 15:18 tim +2004-11-25 12:18 tim * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was initially added on branch new_design. -2004-11-24 17:12 tim +2004-11-24 14:12 tim * src/: io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, @@ -7000,13 +7447,13 @@ io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built -2004-11-24 16:33 tim +2004-11-24 13:33 tim * src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, LJFF.cpp, Makefile: UseTheForce get built -2004-11-24 15:55 tim +2004-11-24 12:55 tim * src/: math/RectMatrix.hpp, primitives/Bend.cpp, primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, @@ -7016,37 +7463,37 @@ primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp: types and primitives get built -2004-11-24 14:49 tim +2004-11-24 11:49 tim * test/utils/: Makefile, NextCombinationTestCase.cpp, StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint StringTokenizerTestCase -2004-11-24 14:49 tim +2004-11-24 11:49 tim * src/utils/: GenericData.hpp, StringTokenizer.cpp, StringTokenizer.hpp: StringTokenizer passes unit test -2004-11-24 13:20 tim +2004-11-24 10:20 tim * ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: change Makefile -2004-11-24 13:06 chrisfen +2004-11-24 10:06 chrisfen * src/io/RestraintReader.cpp: improved restraints - mpi should work fine -2004-11-24 13:06 chrisfen +2004-11-24 10:06 chrisfen * src/integrators/Integrator.cpp: improved restraints -2004-11-24 13:05 chrisfen +2004-11-24 10:05 chrisfen * samples/water/tip3p_ice/tp3.md: oops... -2004-11-24 12:42 tim +2004-11-24 09:42 tim * src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, brains/DataStorage.hpp, brains/SimCreator.cpp, @@ -7055,7 +7502,7 @@ primitives/DirectionalAtom.cpp: add SetForceManager method to integrator -2004-11-23 18:12 tim +2004-11-23 15:12 tim * src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, @@ -7067,12 +7514,12 @@ integrators/VelocityVerletIntegrator.hpp, types/UreyBradleyBendType.hpp: refactory NPT integrator -2004-11-23 17:50 chrisfen +2004-11-23 14:50 chrisfen * samples/water/tip3p_ice/tp3.md: Back to normal... Oh... Restraints should work in parallel now -2004-11-23 17:48 chrisfen +2004-11-23 14:48 chrisfen * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, @@ -7082,12 +7529,12 @@ restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements to restraints -2004-11-23 17:47 chrisfen +2004-11-23 14:47 chrisfen * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll return to the original on next commit -2004-11-23 12:53 tim +2004-11-23 09:53 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, @@ -7100,73 +7547,73 @@ io/SectionParser.hpp, types/DirectionalAtomType.cpp, utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser -2004-11-23 12:53 tim +2004-11-23 09:53 tim * src/io/ElectrostaticAtomTypesSectionParser.hpp: file ElectrostaticAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-23 12:53 tim +2004-11-23 09:53 tim * src/io/ElectrostaticAtomTypesSectionParser.cpp: file ElectrostaticAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-23 01:03 tim +2004-11-22 22:03 tim * src/: io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, types/AtomType.hpp, types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: add EAM AtomType Section Parser -2004-11-23 01:03 tim +2004-11-22 22:03 tim * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp was initially added on branch new_design. -2004-11-23 01:03 tim +2004-11-22 22:03 tim * src/io/EAMAtomTypesSectionParser.hpp: file EAMAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-23 01:03 tim +2004-11-22 22:03 tim * src/io/EAMAtomTypesSectionParser.cpp: file EAMAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 23:35 tim +2004-11-22 20:35 tim * src/io/TorsionTypesSectionParser.hpp: file TorsionTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 23:35 tim +2004-11-22 20:35 tim * src/io/BendTypesSectionParser.hpp: file BendTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 23:35 tim +2004-11-22 20:35 tim * src/io/BondTypesSectionParser.hpp: file BondTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 23:35 tim +2004-11-22 20:35 tim * src/io/BondTypesSectionParser.cpp: file BondTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 23:35 tim +2004-11-22 20:35 tim * src/io/TorsionTypesSectionParser.cpp: file TorsionTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 23:35 tim +2004-11-22 20:35 tim * src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, @@ -7174,117 +7621,117 @@ BondTypesSectionParser, BendTypesSectionParser and TorsionTypeSectionParser -2004-11-22 23:35 tim +2004-11-22 20:35 tim * src/io/BendTypesSectionParser.cpp: file BendTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 18:04 tim +2004-11-22 15:04 tim * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in DUFF and EAM -2004-11-22 18:02 tim +2004-11-22 15:02 tim * src/io/: DirectionalAtomTypesParser.hpp, DirectionalAtomTypesSectionParser.hpp: adding section parsers -2004-11-22 18:02 tim +2004-11-22 15:02 tim * src/io/DirectionalAtomTypesSectionParser.hpp: file DirectionalAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/DipoleAtomTypesSectionParser.hpp: file DipoleAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/AtomTypesSectionParser.hpp: file AtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/HarmonicBondTypesSectionParser.hpp: file HarmonicBondTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/StickyAtomTypesSectionParser.cpp: file StickyAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/LennardJonesAtomTypesSectionParser.hpp: file LennardJonesAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/HarmonicBondTypesSectionParser.cpp: file HarmonicBondTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/DirectionalAtomTypesSectionParser.cpp: file DirectionalAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/SectionParserManager.cpp: file SectionParserManager.cpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/AtomTypesSectionParser.cpp: file AtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/ChargeAtomTypesSectionParser.cpp: file ChargeAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/DipoleAtomTypesSectionParser.cpp: file DipoleAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/LennardJonesAtomTypesSectionParser.cpp: file LennardJonesAtomTypesSectionParser.cpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/ChargeAtomTypesSectionParser.hpp: file ChargeAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/StickyAtomTypesSectionParser.hpp: file StickyAtomTypesSectionParser.hpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/SectionParser.hpp: file SectionParser.hpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, @@ -7306,112 +7753,112 @@ types/AtomType.hpp, types/DirectionalAtomType.hpp, utils/GenericData.hpp: adding section parsers -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/DirectionalAtomTypesParser.hpp: file DirectionalAtomTypesParser.hpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/SectionParserManager.hpp: file SectionParserManager.hpp was initially added on branch new_design. -2004-11-22 15:55 tim +2004-11-22 12:55 tim * src/io/SectionParser.cpp: file SectionParser.cpp was initially added on branch new_design. -2004-11-19 17:12 tim +2004-11-19 14:12 tim * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially added on branch new_design. -2004-11-19 17:12 tim +2004-11-19 14:12 tim * src/: brains/SimState.cpp, brains/SimState.hpp, io/InitializeFromFile.cpp, types/FixBondType.hpp, types/FixedBondType.hpp: remove more useless files -2004-11-19 16:47 tim +2004-11-19 13:47 tim * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, integrators/Integrator.cpp, applications/Makedepend: remove more useless files -2004-11-19 16:38 tim +2004-11-19 13:38 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, integrators/NVT.hpp: refactory integrator -2004-11-19 16:38 tim +2004-11-19 13:38 tim * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on branch new_design. -2004-11-19 16:38 tim +2004-11-19 13:38 tim * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on branch new_design. -2004-11-19 16:38 tim +2004-11-19 13:38 tim * src/integrators/NPT.hpp: file NPT.hpp was initially added on branch new_design. -2004-11-19 16:38 tim +2004-11-19 13:38 tim * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added on branch new_design. -2004-11-19 16:38 tim +2004-11-19 13:38 tim * src/integrators/NVT.hpp: file NVT.hpp was initially added on branch new_design. -2004-11-19 15:37 tim +2004-11-19 12:37 tim * forceFields/newDUFF.frc: new DUFF forcefield -2004-11-19 15:23 tim +2004-11-19 12:23 tim * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on branch new_design. -2004-11-19 15:23 tim +2004-11-19 12:23 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, utils/TypeContainer.hpp: add EAM -2004-11-19 15:23 tim +2004-11-19 12:23 tim * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on branch new_design. -2004-11-19 13:02 tim +2004-11-19 10:02 tim * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except error checking -2004-11-19 12:56 tim +2004-11-19 09:56 tim * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp was initially added on branch new_design. -2004-11-19 12:56 tim +2004-11-19 09:56 tim * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp was initially added on branch new_design. -2004-11-19 12:56 tim +2004-11-19 09:56 tim * src/types/FixBondType.hpp: file FixBondType.hpp was initially added on branch new_design. -2004-11-19 12:56 tim +2004-11-19 09:56 tim * src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, @@ -7422,16 +7869,16 @@ utils/StringTokenizer.cpp: DUFF is almost done except error checking -2004-11-18 19:11 tim +2004-11-18 16:11 tim * src/UseTheForce/DUFF.cpp: adding DUFF parser -2004-11-18 18:26 tim +2004-11-18 15:26 tim * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was initially added on branch new_design. -2004-11-18 18:26 tim +2004-11-18 15:26 tim * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, @@ -7443,37 +7890,37 @@ types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding DUFF parser -2004-11-18 16:42 tim +2004-11-18 13:42 tim * forceFields/newDUFF.frc: adding new format DUFF force field -2004-11-18 10:57 chrisfen +2004-11-18 07:57 chrisfen * src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that slowed down the force loop -2004-11-18 00:42 tim +2004-11-17 21:42 tim * src/utils/NumericConstant.cpp: file NumericConstant.cpp was initially added on branch new_design. -2004-11-18 00:42 tim +2004-11-17 21:42 tim * src/utils/NumericConstant.hpp: file NumericConstant.hpp was initially added on branch new_design. -2004-11-18 00:42 tim +2004-11-17 21:42 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, primitives/Bend.cpp, utils/NumericConstant.cpp, utils/NumericConstant.hpp: Adding NumericConstant class -2004-11-17 23:16 tim +2004-11-17 20:16 tim * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp: remove more junk files -2004-11-17 23:12 tim +2004-11-17 20:12 tim * src/: brains/ForceFields.cpp, brains/SimSetup.cpp, brains/SimSetup.hpp, constraints/AbstractClasses.hpp, @@ -7482,60 +7929,60 @@ primitives/BondExtensions.cpp, primitives/SRI.hpp, primitives/TorsionExtensions.cpp: remove some junk files -2004-11-17 23:07 tim +2004-11-17 20:07 tim * src/primitives/BendExtensions.cpp: remove some junk files -2004-11-17 23:04 tim +2004-11-17 20:04 tim * src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, QuadraticBondType.hpp: refine QudraticBond -2004-11-17 22:57 tim +2004-11-17 19:57 tim * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp -2004-11-17 22:57 tim +2004-11-17 19:57 tim * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was initially added on branch new_design. -2004-11-17 16:47 tim +2004-11-17 13:47 tim * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp was initially added on branch new_design. -2004-11-17 16:47 tim +2004-11-17 13:47 tim * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially added on branch new_design. -2004-11-17 16:47 tim +2004-11-17 13:47 tim * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially added on branch new_design. -2004-11-17 16:47 tim +2004-11-17 13:47 tim * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was initially added on branch new_design. -2004-11-17 16:47 tim +2004-11-17 13:47 tim * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was initially added on branch new_design. -2004-11-17 16:47 tim +2004-11-17 13:47 tim * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was initially added on branch new_design. -2004-11-17 16:47 tim +2004-11-17 13:47 tim * src/types/CubicBondType.hpp: file CubicBondType.hpp was initially added on branch new_design. -2004-11-17 16:47 tim +2004-11-17 13:47 tim * src/: math/ChebyshevPolynomials.cpp, math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, @@ -7547,17 +7994,17 @@ types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: UreyBradleyBend and GhostBend -2004-11-17 13:58 tim +2004-11-17 10:58 tim * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp was initially added on branch new_design. -2004-11-17 13:58 tim +2004-11-17 10:58 tim * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp was initially added on branch new_design. -2004-11-17 13:58 tim +2004-11-17 10:58 tim * src/: math/ChebyshevPolynomials.cpp, math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, @@ -7566,22 +8013,22 @@ types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types stuff and Chebyshev Polynomial -2004-11-17 13:58 tim +2004-11-17 10:58 tim * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was initially added on branch new_design. -2004-11-17 01:37 tim +2004-11-16 22:37 tim * src/types/PolynomialTorsionType.hpp: file PolynomialTorsionType.hpp was initially added on branch new_design. -2004-11-17 01:37 tim +2004-11-16 22:37 tim * src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was initially added on branch new_design. -2004-11-17 01:37 tim +2004-11-16 22:37 tim * src/: math/Polynomial.hpp, primitives/Bend.cpp, primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, @@ -7595,75 +8042,75 @@ CharmmTorsionType. Need to refine the design and add document for them -2004-11-17 01:37 tim +2004-11-16 22:37 tim * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was initially added on branch new_design. -2004-11-17 01:37 tim +2004-11-16 22:37 tim * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was initially added on branch new_design. -2004-11-17 01:37 tim +2004-11-16 22:37 tim * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was initially added on branch new_design. -2004-11-16 20:11 tim +2004-11-16 17:11 tim * src/types/: BendType.hpp, PolynomialBondType.hpp, TorsionType.hpp: add PolynomialBondType -2004-11-16 20:11 tim +2004-11-16 17:11 tim * src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was initially added on branch new_design. -2004-11-16 18:20 tim +2004-11-16 15:20 tim * src/math/Polynomial.hpp: file Polynomial.hpp was initially added on branch new_design. -2004-11-16 18:20 tim +2004-11-16 15:20 tim * src/math/Polynomial.hpp: Adding Polynomial class -2004-11-16 17:04 gezelter +2004-11-16 14:04 gezelter * src/types/MorseBondType.hpp: file MorseBondType.hpp was initially added on branch new_design. -2004-11-16 17:04 gezelter +2004-11-16 14:04 gezelter * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was initially added on branch new_design. -2004-11-16 17:04 gezelter +2004-11-16 14:04 gezelter * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, MorseBondType.hpp, TorsionType.hpp: added some new stuff -2004-11-16 15:36 tim +2004-11-16 12:36 tim * src/: primitives/Bend.cpp, primitives/Bend.hpp, primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and TorsionType -2004-11-15 21:07 tim +2004-11-15 18:07 tim * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on branch new_design. -2004-11-15 21:07 tim +2004-11-15 18:07 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, utils/StringTokenizer.cpp: adding DUFF class; adding checking statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer -2004-11-15 18:00 tim +2004-11-15 15:00 tim * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, @@ -7671,37 +8118,37 @@ UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, types/AtomType.hpp: adding ForceFieldFactory and LJFF classes -2004-11-15 18:00 tim +2004-11-15 15:00 tim * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp was initially added on branch new_design. -2004-11-15 18:00 tim +2004-11-15 15:00 tim * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp was initially added on branch new_design. -2004-11-15 18:00 tim +2004-11-15 15:00 tim * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on branch new_design. -2004-11-15 13:02 tim +2004-11-15 10:02 tim * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was initially added on branch new_design. -2004-11-15 13:02 tim +2004-11-15 10:02 tim * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on branch new_design. -2004-11-15 13:02 tim +2004-11-15 10:02 tim * src/io/DumpReader.hpp: file DumpReader.hpp was initially added on branch new_design. -2004-11-15 13:02 tim +2004-11-15 10:02 tim * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, @@ -7709,7 +8156,7 @@ io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, DumpWriter.Next Step is LJFF and integrators -2004-11-13 00:08 tim +2004-11-12 21:08 tim * src/: brains/ForceManager.cpp, brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, @@ -7717,34 +8164,34 @@ primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, refactory, refactory -2004-11-12 17:43 tim +2004-11-12 14:43 tim * src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, StringTokenizer.cpp: bug fix in hasMoreTokens -2004-11-12 17:28 tim +2004-11-12 14:28 tim * src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was initially added on branch new_design. -2004-11-12 17:28 tim +2004-11-12 14:28 tim * src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding StringUtils, a c-style strtok like class, need unit test -2004-11-12 12:40 tim +2004-11-12 09:40 tim * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test -2004-11-12 02:05 tim +2004-11-11 23:05 tim * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, primitives/CutoffGroup.hpp, primitives/Molecule.cpp: MoleculeCreator forget to create CutoffGroups for free atoms -2004-11-12 01:19 tim +2004-11-11 22:19 tim * src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -7752,30 +8199,30 @@ io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: OOPSE = Object-Obfuscated Parallel Simulation Engine -2004-11-11 16:48 chrisfen +2004-11-11 13:48 chrisfen * samples/water/tip3p_ice/tp3.md: working sample -2004-11-11 16:47 chrisfen +2004-11-11 13:47 chrisfen * src/restraints/Restraints.cpp: working towards parallel restraints -2004-11-11 16:47 chrisfen +2004-11-11 13:47 chrisfen * src/integrators/Integrator.cpp: Commented out some write statements -2004-11-11 16:46 chrisfen +2004-11-11 13:46 chrisfen * src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some write statements -2004-11-11 16:46 chrisfen +2004-11-11 13:46 chrisfen * samples/water/tip3p_ice/tp3.md: Fun with ice -2004-11-11 11:41 tim +2004-11-11 08:41 tim * src/: brains/Exclude.cpp, brains/Exclude.hpp, brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, @@ -7784,18 +8231,18 @@ io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove useless mpiSimulation -2004-11-11 11:41 tim +2004-11-11 08:41 tim * src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on branch new_design. -2004-11-10 17:50 tim +2004-11-10 14:50 tim * src/: brains/ForceManager.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo -2004-11-10 17:01 tim +2004-11-10 14:01 tim * src/: brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, @@ -7809,33 +8256,33 @@ BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint -2004-11-10 09:52 tim +2004-11-10 06:52 tim * src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a configurable StatWriter -2004-11-10 09:52 tim +2004-11-10 06:52 tim * src/io/StatWriter.hpp: file StatWriter.hpp was initially added on branch new_design. -2004-11-09 21:58 tim +2004-11-09 18:58 tim * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation in progress -2004-11-09 18:11 tim +2004-11-09 15:11 tim * src/brains/ForceManager.cpp: file ForceManager.cpp was initially added on branch new_design. -2004-11-09 18:11 tim +2004-11-09 15:11 tim * src/integrators/VelocityVerletIntegrator.cpp: file VelocityVerletIntegrator.cpp was initially added on branch new_design. -2004-11-09 18:11 tim +2004-11-09 15:11 tim * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, @@ -7844,57 +8291,57 @@ integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, integrators/VelocityVerletIntegrator.hpp: adding ForceManager -2004-11-09 18:11 tim +2004-11-09 15:11 tim * src/brains/ForceManager.hpp: file ForceManager.hpp was initially added on branch new_design. -2004-11-09 18:11 tim +2004-11-09 15:11 tim * src/integrators/NVE.cpp: file NVE.cpp was initially added on branch new_design. -2004-11-08 20:08 tim +2004-11-08 17:08 tim * src/integrators/VelocityVerletIntegrator.hpp: file VelocityVerletIntegrator.hpp was initially added on branch new_design. -2004-11-08 20:08 tim +2004-11-08 17:08 tim * src/integrators/NVE.hpp: file NVE.hpp was initially added on branch new_design. -2004-11-08 20:08 tim +2004-11-08 17:08 tim * src/: brains/Exclude.hpp, brains/Stats.hpp, integrators/Integrator.hpp, integrators/NVE.hpp, integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, utils/TypeContainer.hpp: More to break -2004-11-06 00:21 tim +2004-11-05 21:21 tim * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially added on branch new_design. -2004-11-06 00:21 tim +2004-11-05 21:21 tim * src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, utils/TypeContainer.hpp, utils/next_combination.hpp: adding ForceField and TypeContainer classes -2004-11-05 18:38 tim +2004-11-05 15:38 tim * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was initially added on branch new_design. -2004-11-05 18:38 tim +2004-11-05 15:38 tim * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was initially added on branch new_design. -2004-11-05 18:38 tim +2004-11-05 15:38 tim * src/: brains/Exclude.cpp, brains/Exclude.hpp, brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, @@ -7902,58 +8349,58 @@ brains/SimInfo.hpp, primitives/Molecule.hpp, utils/LocalndexManager.hpp: Fix Exclude class etc. -2004-11-05 16:45 chrisfen +2004-11-05 13:45 chrisfen * src/: applications/dump2Xyz/Dump2XYZ.cpp, visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the linear visitor -2004-11-05 16:04 chrisfen +2004-11-05 13:04 chrisfen * src/UseTheForce/DarkSide/shapes.F90: current status of the debugging process -2004-11-05 16:04 chrisfen +2004-11-05 13:04 chrisfen * make/Makefile.in: included visitors and minimizer -2004-11-05 16:03 chrisfen +2004-11-05 13:03 chrisfen * ChangeLog: new changes -2004-11-04 21:56 tim +2004-11-04 18:56 tim * src/: brains/SimCreator.cpp, brains/SimCreator.hpp, primitives/Molecule.hpp: Pain...... -2004-11-04 15:55 tim +2004-11-04 12:55 tim * ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, src/brains/Stats.hpp: time to break SimSetup -2004-11-04 15:51 gezelter +2004-11-04 12:51 gezelter * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new classes in progress -2004-11-04 14:48 tim +2004-11-04 11:48 tim * src/brains/Stats.cpp: file Stats.cpp was initially added on branch new_design. -2004-11-04 14:48 tim +2004-11-04 11:48 tim * src/brains/Stats.hpp: file Stats.hpp was initially added on branch new_design. -2004-11-04 14:48 tim +2004-11-04 11:48 tim * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats class -2004-11-04 11:22 gezelter +2004-11-04 08:22 gezelter * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and @@ -7962,45 +8409,45 @@ false and "-1" but there should be logic to figure them out in the other two classes -2004-11-04 11:20 gezelter +2004-11-04 08:20 gezelter * src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't remember what I did -2004-11-04 11:20 gezelter +2004-11-04 08:20 gezelter * src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky -2004-11-04 11:20 gezelter +2004-11-04 08:20 gezelter * src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX in the entry_plug so that it only is set if the atoms really are in the simulation -2004-11-04 11:20 gezelter +2004-11-04 08:20 gezelter * samples/water/ssd/ssd.md: testing force fields -2004-11-04 11:19 gezelter +2004-11-04 08:19 gezelter * samples/shape/linear.in: testing shapes -2004-11-03 14:56 tim +2004-11-03 11:56 tim * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator class(similar as SimSetup) -2004-11-03 14:56 tim +2004-11-03 11:56 tim * src/brains/SimCreator.hpp: file SimCreator.hpp was initially added on branch new_design. -2004-11-03 14:56 tim +2004-11-03 11:56 tim * src/brains/SimCreator.cpp: file SimCreator.cpp was initially added on branch new_design. -2004-11-03 13:00 tim +2004-11-03 10:00 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, @@ -8010,7 +8457,7 @@ visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get compiled. Still a long way to go ...... -2004-11-03 11:08 tim +2004-11-03 08:08 tim * ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, @@ -8025,55 +8472,55 @@ src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... -2004-11-02 17:41 tim +2004-11-02 14:41 tim * src/: brains/Migrator.hpp, brains/SimModel.cpp, utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. Need unit test -2004-11-02 17:41 tim +2004-11-02 14:41 tim * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was initially added on branch new_design. -2004-11-02 17:41 tim +2004-11-02 14:41 tim * src/brains/Migrator.hpp: file Migrator.hpp was initially added on branch new_design. -2004-11-02 11:59 tim +2004-11-02 08:59 tim * src/brains/SimModel.cpp: file SimModel.cpp was initially added on branch new_design. -2004-11-02 11:59 tim +2004-11-02 08:59 tim * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, SimSnapshotManager.hpp: SimModel in progress -2004-11-02 10:28 chrisfen +2004-11-02 07:28 chrisfen * src/: UseTheForce/DarkSide/shapes.F90, primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes looks like it's working -2004-11-02 10:27 tim +2004-11-02 07:27 tim * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some functions for dealing with memory issue -2004-11-02 10:27 tim +2004-11-02 07:27 tim * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially added on branch new_design. -2004-11-02 10:23 tim +2004-11-02 07:23 tim * src/: brains/SimModel.hpp, brains/Snapshot.hpp, brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding SimModel(something similar as SimInfo) -2004-11-01 17:52 tim +2004-11-01 14:52 tim * src/: applications/simpleBuilder/MoLocator.hpp, applications/simpleBuilder/simpleBuilder.cpp, @@ -8092,47 +8539,47 @@ visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, RigidBody and StuntDouble classes get compiled -2004-11-01 16:40 tim +2004-11-01 13:40 tim * src/primitives/Torsion.hpp: file Torsion.hpp was initially added on branch new_design. -2004-11-01 16:40 tim +2004-11-01 13:40 tim * src/primitives/Bend.hpp: file Bend.hpp was initially added on branch new_design. -2004-11-01 16:40 tim +2004-11-01 13:40 tim * src/primitives/Bond.hpp: file Bond.hpp was initially added on branch new_design. -2004-11-01 16:40 tim +2004-11-01 13:40 tim * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial version of Bond, Bend and Torsion. -2004-11-01 16:37 tim +2004-11-01 13:37 tim * src/types/BendType.hpp: file BendType.hpp was initially added on branch new_design. -2004-11-01 16:37 tim +2004-11-01 13:37 tim * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding BondType, BendType, TorsionType -2004-11-01 16:37 tim +2004-11-01 13:37 tim * src/types/TorsionType.hpp: file TorsionType.hpp was initially added on branch new_design. -2004-11-01 16:37 tim +2004-11-01 13:37 tim * src/types/BondType.hpp: file BondType.hpp was initially added on branch new_design. -2004-11-01 15:15 tim +2004-11-01 12:15 tim * src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, @@ -8140,49 +8587,49 @@ RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: break, break and break..... -2004-11-01 14:57 tim +2004-11-01 11:57 tim * test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: these core classes get compiled -2004-10-29 18:37 tim +2004-10-29 15:37 tim * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule class -2004-10-29 18:28 chrisfen +2004-10-29 15:28 chrisfen * src/: UseTheForce/DarkSide/atype.F90, UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, types/ShapeAtomType.cpp: still debugging -2004-10-29 18:28 chrisfen +2004-10-29 15:28 chrisfen * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: shapes rcut calculator added -2004-10-29 18:27 chrisfen +2004-10-29 15:27 chrisfen * samples/shape/linear.md: shorter run -2004-10-29 16:54 tim +2004-10-29 13:54 tim * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. -2004-10-29 12:22 tim +2004-10-29 09:22 tim * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove some deprecated files -2004-10-29 12:20 tim +2004-10-29 09:20 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 18:34 tim +2004-10-28 15:34 tim * src/brains/DataStorage.hpp, src/utils/next_combination.hpp, test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, @@ -8190,7 +8637,7 @@ test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, DirectionalAtom and RigidBody -2004-10-28 18:26 tim +2004-10-28 15:26 tim * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, src/applications/simpleBuilder/MoLocator.cpp, @@ -8198,36 +8645,36 @@ src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: remove old Vector3d.hpp from application/simpleBuilder -2004-10-28 17:42 tim +2004-10-28 14:42 tim * src/utils/next_combination.hpp: Minor change in next_combination -2004-10-28 17:28 tim +2004-10-28 14:28 tim * src/utils/next_combination.hpp, test/utils/NextCombinationTestCase.cpp, test/utils/ReplaceWildCardTestCase.cpp: Done with combination -2004-10-28 17:11 tim +2004-10-28 14:11 tim * src/utils/next_combination.hpp: change documentation of next_combination.hpp -2004-10-28 16:41 tim +2004-10-28 13:41 tim * ChangeLog, src/utils/next_combination.hpp, test/utils/NextCombinationTestCase.cpp, test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working -2004-10-28 16:01 tim +2004-10-28 13:01 tim * src/utils/next_combination.hpp: adding replace wildcard function -2004-10-28 15:33 tim +2004-10-28 12:33 tim * src/utils/next_combination.hpp: Minor change -2004-10-28 15:06 tim +2004-10-28 12:06 tim * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, src/applications/simpleBuilder/simpleBuilder.cpp, @@ -8237,122 +8684,122 @@ test/utils/next_combination.hpp: STL next_permutation like next_combination is working -2004-10-28 13:22 chrisfen +2004-10-28 10:22 chrisfen * src/UseTheForce/WATER.cpp: fix of setDipoles -2004-10-28 13:20 gezelter +2004-10-28 10:20 gezelter * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the shapeFile -2004-10-28 13:20 gezelter +2004-10-28 10:20 gezelter * samples/shape/linear.md: forgot the orientation line -2004-10-28 12:56 gezelter +2004-10-28 09:56 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 12:55 gezelter +2004-10-28 09:55 gezelter * samples/lipid/5x5.md: uncommented .in line -2004-10-28 11:42 tim +2004-10-28 08:42 tim * test/utils/: Makefile, NextCombinationTestCase.cpp, NextCombinationTestCase.hpp, next_combination.hpp: next_combination in progress -2004-10-28 11:15 tim +2004-10-28 08:15 tim * test/utils/: NextCombinationTestCase.cpp, NextCombinationTestCase.hpp: adding next_combination test case -2004-10-28 11:02 tim +2004-10-28 08:02 tim * test/utils/next_combination.hpp: STL Compatible combination sequence generator -2004-10-28 02:23 tim +2004-10-27 23:23 tim * test/utils/: GenerateCombination.hpp, ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp -2004-10-28 02:16 tim +2004-10-27 23:16 tim * test/utils/GenerateCombination.hpp: a STL next_permutaion like next_combination function. -2004-10-27 23:27 tim +2004-10-27 20:27 tim * test/utils/ReplaceWildCard.hpp: no message -2004-10-27 23:14 tim +2004-10-27 20:14 tim * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: ReplaceWildCard(recursive version) is working, need refactoring. An iterative version is on the way -2004-10-27 22:28 tim +2004-10-27 19:28 tim * test/utils/: Makefile, ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress -2004-10-27 22:08 tim +2004-10-27 19:08 tim * test/utils/: ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard -2004-10-27 19:17 tim +2004-10-27 16:17 tim * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need test -2004-10-27 02:25 tim +2004-10-26 23:25 tim * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild char matching is on the way -2004-10-27 02:07 tim +2004-10-26 23:07 tim * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 -2004-10-26 23:00 gezelter +2004-10-26 20:00 gezelter * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix -2004-10-26 22:20 gezelter +2004-10-26 19:20 gezelter * src/UseTheForce/ForceFields.hpp: subclass foo -2004-10-26 22:16 gezelter +2004-10-26 19:16 gezelter * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> string conversion -2004-10-26 20:01 gezelter +2004-10-26 17:01 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, brains/SimSetup.hpp: char* -> string -2004-10-26 18:25 gezelter +2004-10-26 15:25 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 18:25 gezelter +2004-10-26 15:25 gezelter * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: define name collision -2004-10-26 18:24 gezelter +2004-10-26 15:24 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, @@ -8361,14 +8808,14 @@ UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: forcefield refactoring for shapes -2004-10-26 18:24 gezelter +2004-10-26 15:24 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 18:19 tim +2004-10-26 15:19 tim * ChangeLog, src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, @@ -8376,22 +8823,22 @@ test/brains/DataStorageTestCase.hpp, test/brains/Makefile: DataStorage passes unit test -2004-10-26 14:03 chrisfen +2004-10-26 11:03 chrisfen * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: Changes to help advance shapes -2004-10-26 14:02 chrisfen +2004-10-26 11:02 chrisfen * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to Shapes force field reader -2004-10-26 13:28 tim +2004-10-26 10:28 tim * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and SnapshotTestCase in progress -2004-10-25 18:46 tim +2004-10-25 15:46 tim * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, src/math/Vector.hpp, @@ -8400,7 +8847,7 @@ test/math/VectorTestCase.cpp: add getArray function to RectMatrix and Vector classes -2004-10-25 13:03 tim +2004-10-25 10:03 tim * ChangeLog, src/utils/GenericFactory.hpp, test/utils/GenericFactoryTestCase.cpp, @@ -8408,41 +8855,41 @@ GenericFactory Test Case. GenericFactory now can bed used to creat ForcefieldFactory and IntegratorFactory etc. -2004-10-25 00:08 tim +2004-10-24 21:08 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 03:55 tim +2004-10-24 00:55 tim * src/utils/GenericFactory.hpp: GenericFactory pass unit test -2004-10-23 19:09 tim +2004-10-23 16:09 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 19:09 tim +2004-10-22 16:09 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 18:59 chrisfen +2004-10-22 15:59 chrisfen * src/: UseTheForce/LJFF.cpp, UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear god! It runs and conserves energy! -2004-10-22 18:54 chrisfen +2004-10-22 15:54 chrisfen * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY -2004-10-22 18:53 chrisfen +2004-10-22 15:53 chrisfen * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, @@ -8450,35 +8897,35 @@ brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey breakey -2004-10-22 18:53 chrisfen +2004-10-22 15:53 chrisfen * make/Makefile.in: compiler flags -2004-10-22 17:20 gezelter +2004-10-22 14:20 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 16:22 gezelter +2004-10-22 13:22 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 16:21 gezelter +2004-10-22 13:21 gezelter * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, DirectionalAtomType.hpp, Makefile: More on AtomType and DirectionalAtomType -2004-10-22 10:47 gezelter +2004-10-22 07:47 gezelter * src/types/AtomType.hpp: Adding AtomType -2004-10-21 17:31 tim +2004-10-21 14:31 tim * ChangeLog, src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, @@ -8487,14 +8934,14 @@ test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: Snapshot and SnapshotManager in progress -2004-10-21 17:30 tim +2004-10-21 14:30 tim * test/brains/: BrainsTest.cpp, Makefile, SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for Snapshot and snapshotManager. -2004-10-21 16:15 gezelter +2004-10-21 13:15 gezelter * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, @@ -8505,16 +8952,16 @@ brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. Fixey Fixey. -2004-10-21 12:32 tim +2004-10-21 09:32 tim * src/utils/GenericData.cpp, src/utils/Makefile, test/utils/Makefile, test/utils/UtilTest: remove some junk files -2004-10-21 12:24 tim +2004-10-21 09:24 tim * test/utils/GenericData.hpp: remove backup of GenericData.hpp -2004-10-21 12:22 tim +2004-10-21 09:22 tim * ChangeLog, src/brains/SimSetup.cpp, src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, @@ -8532,17 +8979,17 @@ src/visitors/ZconsVisitor.hpp: replace old GebericData with new GenericData -2004-10-21 11:25 chuckv +2004-10-21 08:25 chuckv * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj module. -2004-10-21 11:24 chuckv +2004-10-21 08:24 chuckv * src/UseTheForce/DarkSide/lj_interface.h: Added interface for fortran lj module. -2004-10-20 18:54 tim +2004-10-20 15:54 tim * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, test/utils/GenericDataTestCase.cpp, test/utils/Makefile, @@ -8550,18 +8997,18 @@ test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: GenericData and PropertyMap pass unit test. -2004-10-20 17:52 gezelter +2004-10-20 14:52 gezelter * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, DarkSide/sticky_interface.h: fixed a fortran name problem -2004-10-20 17:38 tim +2004-10-20 14:38 tim * test/utils/: GenericData.hpp, GenericDataTestCase.cpp, GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, UtilTest, UtilTest.cpp: adding generic data test case -2004-10-20 17:16 chuckv +2004-10-20 14:16 chuckv * configure, ac-tools/aclocal.m4, src/UseTheForce/DarkSide/Makefile, @@ -8573,13 +9020,13 @@ Fortran/C++ interface de-obfuscation project appears to be complete! Woo hoo! -2004-10-20 16:47 chuckv +2004-10-20 13:47 chuckv * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project continues -2004-10-20 16:46 chuckv +2004-10-20 13:46 chuckv * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, @@ -8596,50 +9043,50 @@ brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface de-obfuscation project (It is a very long story) -2004-10-20 14:07 tim +2004-10-20 11:07 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 01:52 tim +2004-10-19 22:52 tim * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and SnapshotManager in design phase -2004-10-20 00:54 gezelter +2004-10-19 21:54 gezelter * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace problem prevented linking -2004-10-20 00:54 gezelter +2004-10-19 21:54 gezelter * src/UseTheForce/Shapes_FF.cpp: fixed include -2004-10-20 00:26 gezelter +2004-10-19 21:26 gezelter * src/utils/: Makefile, definitions.F90, definitions_module.F90, oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: more fortran name mangling -2004-10-20 00:23 gezelter +2004-10-19 21:23 gezelter * src/profiling/timing.F90: yet more fortran renaming -2004-10-20 00:19 gezelter +2004-10-19 21:19 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 -2004-10-20 00:12 gezelter +2004-10-19 21:12 gezelter * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some broken fortran stuff -2004-10-20 00:02 gezelter +2004-10-19 21:02 gezelter * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, atype_interface.h, atype_module.F90, atype_module_interface.h, @@ -8656,23 +9103,23 @@ sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: name sanity on the fortran side -2004-10-19 20:18 tim +2004-10-19 17:18 tim * test/math/SquareMatrix3TestCase.hpp: [no log message] -2004-10-19 19:01 tim +2004-10-19 16:01 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 18:43 chuckv +2004-10-19 15:43 chuckv * src/UseTheForce/do_Forces.h: Added correct prototypes for C-fortran interface functions. -2004-10-19 18:37 chuckv +2004-10-19 15:37 chuckv * src/UseTheForce/DarkSide/: atype_module_interface.h, eam_module_inteface.h, gb_module_interface.h, @@ -8680,7 +9127,7 @@ sticky_pair_module_interface.h: Added correct prototypes for C-fortran interface functions. -2004-10-19 17:28 tim +2004-10-19 14:28 tim * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, src/math/Vector.hpp, @@ -8690,7 +9137,7 @@ test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more bugs get fixed at math library -2004-10-19 16:43 chuckv +2004-10-19 13:43 chuckv * src/UseTheForce/: DarkSide/atype_module_interface.h, DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, @@ -8704,43 +9151,43 @@ notifycutoffs_module_interface.h: Added new files for fortran interface. -2004-10-19 16:43 gezelter +2004-10-19 13:43 gezelter * src/UseTheForce/Makefile: regressing -2004-10-19 16:40 gezelter +2004-10-19 13:40 gezelter * src/: UseTheForce/DarkSide/calc_shapes.F90, UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: working on shapes for portability -2004-10-19 16:40 gezelter +2004-10-19 13:40 gezelter * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes -2004-10-19 14:21 chrisfen +2004-10-19 11:21 chrisfen * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around findBegin -2004-10-19 00:34 tim +2004-10-18 21:34 tim * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs are fixed in Vector class -2004-10-19 00:28 tim +2004-10-18 21:28 tim * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix some bugs in RectMatrixTestCase -2004-10-19 00:21 tim +2004-10-18 21:21 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 19:13 tim +2004-10-18 16:13 tim * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, @@ -8749,7 +9196,7 @@ test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more tests on math library -2004-10-18 17:03 tim +2004-10-18 14:03 tim * test/math/: Makefile, QuaternionTestCase.cpp, QuaternionTestCase.hpp, RectMatrixTestCase.cpp, @@ -8757,236 +9204,236 @@ Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding more testing units -2004-10-18 13:07 tim +2004-10-18 10:07 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 12:30 gezelter +2004-10-18 09:30 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 12:29 gezelter +2004-10-18 09:29 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 11:21 gezelter +2004-10-18 08:21 gezelter * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType -2004-10-18 01:23 tim +2004-10-17 22:23 tim * test/math/VectorTestCase.hpp: adding vector test case -2004-10-18 01:23 tim +2004-10-17 22:23 tim * src/utils/GenericFactory.hpp: adding generic factory and vector test case -2004-10-16 21:19 tim +2004-10-16 18:19 tim * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in progress -2004-10-15 21:31 tim +2004-10-15 18:31 tim * src/math/Quaternion.hpp: add quaternion class -2004-10-15 17:11 tim +2004-10-15 14:11 tim * test/io/: DUFF.frc, IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: adding test file -2004-10-15 17:10 tim +2004-10-15 14:10 tim * src/io/basic_ifstrstream.hpp: fix a bunch of bugs -2004-10-15 16:42 tim +2004-10-15 13:42 tim * src/io/basic_ifstrstream.hpp: change const_cast to statc_const -2004-10-15 16:35 tim +2004-10-15 13:35 tim * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp -2004-10-15 16:34 tim +2004-10-15 13:34 tim * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use namespace oopse -2004-10-15 15:38 chuckv +2004-10-15 12:38 chuckv * configure, ac-tools/aclocal.m4: Changed optimization flags for XLF and XLC. -2004-10-15 14:28 tim +2004-10-15 11:28 tim * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: adding ifstrstream test case -2004-10-15 14:20 tim +2004-10-15 11:20 tim * src/io/basic_ifstrstream.hpp: fix include -2004-10-15 14:18 tim +2004-10-15 11:18 tim * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi -2004-10-15 14:17 tim +2004-10-15 11:17 tim * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile -2004-10-15 14:16 tim +2004-10-15 11:16 tim * test/io/: Makefile, ifstrstreamTestCase.cpp, ifstrstreamTestCase.hpp: adding test case for ifstrstream -2004-10-15 11:37 tim +2004-10-15 08:37 tim * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, ifstrstreamTestCase.hpp: add ifstrstreamTestCase -2004-10-15 11:20 tim +2004-10-15 08:20 tim * src/io/basic_ifstrstream.hpp: add checkFilename Option -2004-10-15 11:19 tim +2004-10-15 08:19 tim * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add SquareMatrixTestCase class -2004-10-15 03:52 tim +2004-10-15 00:52 tim * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream -2004-10-14 19:28 tim +2004-10-14 16:28 tim * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp: math library in progress -2004-10-14 19:27 tim +2004-10-14 16:27 tim * src/io/FileReader.hpp: FileReader in progress -2004-10-13 19:53 tim +2004-10-13 16:53 tim * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, test in isOrthogonal of SquareMatrix is failed by some reasons -2004-10-13 18:28 tim +2004-10-13 15:28 tim * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap class -2004-10-13 18:27 tim +2004-10-13 15:27 tim * test/math/: MainTest.cpp, RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: adding testing unit -2004-10-13 18:24 tim +2004-10-13 15:24 tim * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix -2004-10-13 02:51 tim +2004-10-12 23:51 tim * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: refactory vector and matrix classes -2004-10-13 02:50 tim +2004-10-12 23:50 tim * src/math/Vector3d.hpp: Remove some Makefile.in -2004-10-12 19:57 tim +2004-10-12 16:57 tim * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and Matrix3x3d.hpp -2004-10-12 15:08 tim +2004-10-12 12:08 tim * doc/: cppstyle.html, style.css: adding c++ coding style -2004-10-11 18:15 tim +2004-10-11 15:15 tim * src/: constraints/AbstractClasses.hpp, integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: change #include "mpi.h" to #include in AbstractClasses.hpp -2004-10-11 17:54 tim +2004-10-11 14:54 tim * scripts/filepp: fix a bug in filepp -2004-10-11 17:13 tim +2004-10-11 14:13 tim * make/Makefile.in: using filepp to generate dependencies instead of compilers -2004-10-11 17:10 tim +2004-10-11 14:10 tim * scripts/filepp: filepp can be used to generate dependencies for c/c++ now -2004-10-11 14:40 tim +2004-10-11 11:40 tim * make/Makefile.in: remove -module from F90Options -2004-10-11 14:01 tim +2004-10-11 11:01 tim * make/Makefile.in: adding rules to move fortran 90 module to target directory -2004-10-11 11:43 gezelter +2004-10-11 08:43 gezelter * make/Makefile.in: fixed makefile.in -2004-10-11 10:51 tim +2004-10-11 07:51 tim * scripts/filepp: remove "use bytes" which causes problem in sgi machine -2004-10-11 10:26 tim +2004-10-11 07:26 tim * forceFields/Makefile: add Makefile -2004-10-11 10:23 tim +2004-10-11 07:23 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 10:23 tim +2004-10-11 07:23 tim * samples/argon/Makefile: remove argon.dump and argon.eor from Makefile -2004-10-09 02:01 tim +2004-10-08 23:01 tim * samples/: alkane/Makefile.in, argon/Makefile.in, lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: Remove some Makefile.in -2004-10-08 19:15 tim +2004-10-08 16:15 tim * make/Makefile.in: [no log message] -2004-10-08 18:51 tim +2004-10-08 15:51 tim * make/Makefile.in: fix make install -2004-10-08 18:10 tim +2004-10-08 15:10 tim * make/Makefile.in: adding make install -2004-10-08 18:04 tim +2004-10-08 15:04 tim * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, metals/Makefile, minimizer/Makefile, water/Makefile.in, @@ -8997,70 +9444,70 @@ water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, zcons/Makefile.in: add Makefile to sample directory -2004-10-06 19:03 gezelter +2004-10-06 16:03 gezelter * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt stuff -2004-10-06 19:03 gezelter +2004-10-06 16:03 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 18:20 tim +2004-10-06 15:20 tim * make/: Doxyfile, Makefile.in: adding doxygen configuration file -2004-10-06 18:19 tim +2004-10-06 15:19 tim * scripts/filepp: filepp can handle different fortran module case and suffix -2004-10-06 17:27 gezelter +2004-10-06 14:27 gezelter * src/restraints/Restraints.cpp: Chris doesn't know about the OOPSE-2.0 directory structure yet -2004-10-06 17:27 gezelter +2004-10-06 14:27 gezelter * ChangeLog: Yeah yeah, we'lll get around to it later -2004-10-06 17:22 gezelter +2004-10-06 14:22 gezelter * configure, ac-tools/configure.in, ac-tools/fortran90.m4, make/Makefile.in: cleaning up build process -2004-10-06 16:01 chrisfen +2004-10-06 13:01 chrisfen * src/restraints/Restraints.cpp: made the file reading in restraints more intelligent - no longer gives uninformative seg faults -2004-10-06 15:55 gezelter +2004-10-06 12:55 gezelter * src/applications/simpleBuilder/Make.ftemp.old: cleaning up -2004-10-06 15:51 gezelter +2004-10-06 12:51 gezelter * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit -2004-10-06 14:53 tim +2004-10-06 11:53 tim * make/: Makefile, Makefile.in: fix make statistics -2004-10-06 14:18 tim +2004-10-06 11:18 tim * make/: Makefile, Makefile.in: adding GNU make functions to combine all of the static libraries to a big library -2004-10-05 18:57 tim +2004-10-05 15:57 tim * make/: Makefile, Makefile.in: adding shared library flag -2004-10-05 15:37 tim +2004-10-05 12:37 tim * src/: Makefile, UseTheForce/Makefile, UseTheForce/mpiSimulation_module.F90, @@ -9068,62 +9515,62 @@ UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move mpiSimulation_module to DarkSide -2004-10-05 15:35 tim +2004-10-05 12:35 tim * make/: Makefile, Makefile.in: building MPI version;using static library instead of shared library -2004-10-05 10:14 tim +2004-10-05 07:14 tim * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 to filepp -2004-10-04 16:56 tim +2004-10-04 13:56 tim * make/: Makefile, Makefile.in: add make cvslog -2004-10-04 12:24 gezelter +2004-10-04 09:24 gezelter * make/: Makefile, Makefile.in: more work on the parallel build -2004-10-04 12:06 gezelter +2004-10-04 09:06 gezelter * make/: Makefile, Makefile.in: changes to backport declare flags -2004-10-04 11:27 gezelter +2004-10-04 08:27 gezelter * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging shapes -2004-10-02 00:40 tim +2004-10-01 21:40 tim * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree -2004-10-02 00:22 tim +2004-10-01 21:22 tim * make/: Makefile, Makefile.in: add oopse_ as library prefix -2004-10-01 17:59 tim +2004-10-01 14:59 tim * make/: Makefile, Makefile.in: fix a space trimming bug in filepp -2004-10-01 17:22 gezelter +2004-10-01 14:22 gezelter * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A few minor build changes -2004-10-01 17:11 tim +2004-10-01 14:11 tim * scripts/filepp: adding fortran90 make dependency tool -2004-09-30 11:41 tim +2004-09-30 08:41 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 17:55 tim +2004-09-29 14:55 tim * src/: Makefile, UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, @@ -9134,45 +9581,45 @@ restraints/Makefile, types/Makefile, utils/Makefile, visitors/Makefile: define DEV_ROOT as relative path -2004-09-29 17:54 tim +2004-09-29 14:54 tim * make/: Makefile, Makefile.in: get the relative path by shell script -2004-09-29 17:32 tim +2004-09-29 14:32 tim * make/Makefile: eliminate DEV_ROOT by relative path -2004-09-29 14:37 tim +2004-09-29 11:37 tim * make/Makefile.in: add PackageLibs; fix dependency rule -2004-09-29 13:57 gezelter +2004-09-29 10:57 gezelter * configure, ac-tools/configure.in: updates -2004-09-29 13:56 gezelter +2004-09-29 10:56 gezelter * make/: Make.conf.in, Makefile.in, _files/style.css: Working on make stuff -2004-09-29 13:46 tim +2004-09-29 10:46 tim * Makefile: If makefile does not exist, print error message -2004-09-29 13:12 tim +2004-09-29 10:12 tim * make/: Make.conf.in, Makefile: fix dependencies rule -2004-09-29 11:58 gezelter +2004-09-29 08:58 gezelter * Makefile, make/Makefile: still working on build process -2004-09-29 11:00 tim +2004-09-29 08:00 tim * make/Makefile: add print statment to rules -2004-09-29 10:59 tim +2004-09-29 07:59 tim * src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, applications/oopse/Makefile, @@ -9182,12 +9629,12 @@ profiling/Makefile, restraints/Makefile, types/Makefile, utils/Makefile, visitors/Makefile: change Makefile to relative path -2004-09-28 22:55 tim +2004-09-28 19:55 tim * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c which cause headache in bulding libutils -2004-09-28 19:24 tim +2004-09-28 16:24 tim * src/applications/: BaseLattice.cpp, BaseLattice.hpp, Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, @@ -9210,16 +9657,16 @@ change directory structure of application. Every executable file is replaced in seperate directory -2004-09-28 18:15 gezelter +2004-09-28 15:15 gezelter * lib/dummy: Keep that lib around, please. -2004-09-28 18:14 gezelter +2004-09-28 15:14 gezelter * Makefile, configure, ac-tools/configure.in, make/Make.conf.in: starting a configure version -2004-09-28 17:08 tim +2004-09-28 14:08 tim * src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, UseTheForce/DarkSide/Makefile, @@ -9228,7 +9675,7 @@ brains/Makefile, brains/simulation_module.F90: move fortran files around to solve dependency problem -2004-09-28 16:43 tim +2004-09-28 13:43 tim * Makefile, src/UseTheForce/ForceFields.hpp, src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, @@ -9238,25 +9685,25 @@ src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, src/utils/Makefile: [no log message] -2004-09-28 16:41 tim +2004-09-28 13:41 tim * make/Makefile, scripts/sfmakedepend: fix fortran dependency problem -2004-09-28 12:13 tim +2004-09-28 09:13 tim * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, src/io/Makefile: add yacc and lex rules -2004-09-27 16:24 tim +2004-09-27 13:24 tim * make/Makefile: adding include path to F90Options -2004-09-27 16:13 tim +2004-09-27 13:13 tim * make/Makefile: change suffix from .cc to .cpp -2004-09-24 12:27 tim +2004-09-24 09:27 tim * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, @@ -9323,7 +9770,7 @@ visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: change the #include in source files -2004-09-24 00:16 gezelter +2004-09-23 21:16 gezelter * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, @@ -9499,7 +9946,7 @@ forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 -2004-09-24 00:16 gezelter +2004-09-23 21:16 gezelter * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,