--- trunk/OOPSE-4/ChangeLog 2005/04/14 21:41:56 2199 +++ trunk/OOPSE-4/ChangeLog 2005/09/28 18:46:04 2337 @@ -1,3 +1,1030 @@ +2005-09-28 11:55 tim + + * src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid + divergence in rotation matrix to quaternion transformation + +2005-09-28 11:32 gezelter + + * src/primitives/RigidBody.cpp: Rotation matrix multiplication + order error + +2005-09-28 11:32 gezelter + + * src/io/DumpReader.cpp: tracking down quaternion bug + +2005-09-28 11:32 gezelter + + * forceFields/DUFF2.frc: Added DIP atom types for 2-point water + model + +2005-09-27 15:02 tim + + * src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix + to quaternion + +2005-09-26 13:38 chuckv + + * src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc + 7 so derfc is external. Other compilers should treat erfc as + intrinsic. + +2005-09-26 12:07 chuckv + + * src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc + and declared it to be external to fix issure with ifc7. Hopefully + this will not cause a problem with other compilers where derfc is + an intrinsic function. + +2005-09-26 11:42 chuckv + + * src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype + in simulation module. We needed a seperate receive buffer. + +2005-09-26 10:58 chuckv + + * src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added + support for skinThickness keyword to Globals. + +2005-09-26 10:56 tim + + * src/io/DumpReader.cpp: fix a typo in DumpReader + +2005-09-26 09:27 chrisfen + + * samples/: minimizer/tip4p_two.md, + thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, + water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md, + water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md, + water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md, + water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, + water/tip4p/tp4.md: fixing up some samples + +2005-09-24 12:39 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now + roughly the same speed as the old version when using dipoles + + energies are now exactly the same between the old version of OOPSE + and this version + +2005-09-24 12:38 chrisfen + + * samples/water/ssdrf/ssdrf.md: turned rf on + +2005-09-23 15:31 chuckv + + * src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the + skin thickness and hardcode listSkin to be 1.0. We now get listskin + from skin. This will get fixed to where we can manually set skin + thickness. + +2005-09-22 13:50 gezelter + + * src/math/derfc.F90: added error function + +2005-09-21 19:08 chuckv + + * src/integrators/Velocitizer.cpp: Removed print statement for + angular momentum and inertia tensor from velocitizer. + +2005-09-21 19:04 chuckv + + * src/integrators/Velocitizer.cpp: Removed print statements for + remove angular momentum. + +2005-09-21 18:45 chuckv + + * src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ + (say we are using EAM), we probably shouldn't rebuild the LJ mixing + map. + +2005-09-21 15:59 tim + + * src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: + DumpReader using pure c++ io + +2005-09-21 12:20 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a + defaultCutoff bug (HEMES!) + +2005-09-20 17:13 gezelter + + * make/Makefile.in: libz additions + +2005-09-20 17:03 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + src/config.h.in: added check for zlib in configure + +2005-09-20 16:22 tim + + * src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, + gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter + +2005-09-20 11:22 tim + + * test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding + testcase for zipstream + +2005-09-20 10:41 tim + + * src/io/zipstream.hpp: adding zipstream.hpp + +2005-09-20 10:34 chrisfen + + * samples/: dipole/splitInWater.md, dipole/split_SSD.md, + dipole/twoSplitDipole.md, minimizer/ssdEM.md, + minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, + zcons/zconsMoving.md: fixed up some sample md files + +2005-09-19 18:21 chrisfen + + * ChangeLog, samples/water/ssdrf/ssdrf.md, + src/UseTheForce/doForces.F90, + src/UseTheForce/DarkSide/electrostatic.F90, + src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp, + src/brains/fSimulation.h: Fixed bugs in reaction field, now it + appears as though it really is working... + +2005-09-18 15:45 chrisfen + + * ChangeLog, samples/water/ssdrf/ssdrf.md, + src/UseTheForce/doForces.F90, + src/UseTheForce/doForces_interface.F90, + src/UseTheForce/doForces_interface.h, + src/UseTheForce/DarkSide/electrostatic.F90, + src/UseTheForce/DarkSide/electrostatic_interface.h, + src/brains/SimInfo.cpp: reaction field seems to work now, still + need to do some testing... + +2005-09-16 18:04 chuckv + + * src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed + dump files. + +2005-09-16 16:07 chrisfen + + * src/: UseTheForce/doForces_interface.F90, + UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a + bug that ifc missed... + +2005-09-16 15:36 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: + fixing some summation method issues + +2005-09-16 14:35 chrisfen + + * src/brains/SimInfo.cpp: fixed a capitalization error + +2005-09-16 14:34 chrisfen + + * src/UseTheForce/: fElectrostaticSummationMethod.h, + DarkSide/fElectrostaticSummationMethod.h: moved a header file + around + +2005-09-16 14:00 chrisfen + + * src/: UseTheForce/DarkSide/electrostatic_interface.F90, + brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there + are known issues - particularly with reaction field... + +2005-09-16 11:07 chrisfen + + * src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, + io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking + (cutting out the old way to do reaction field) + +2005-09-15 17:05 gezelter + + * src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, + fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, + DarkSide/electrostatic_interface.F90, + DarkSide/electrostatic_interface.h: Working on adding WOLF + +2005-09-15 14:17 tim + + * src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame + is called without calling getNFrames + +2005-09-15 08:47 chrisfen + + * src/UseTheForce/fCoulombicCorrection.h: forgot to add a header + +2005-09-14 21:48 chuckv + + * src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was + not initialized after creation. When maxval(gtypeMaxCutoff) was + called, the largest random garbage value was returned from the + array. + +2005-09-14 19:14 chrisfen + + * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, + io/Globals.hpp: changes to include the coulombicCorrection selector + +2005-09-14 19:13 chrisfen + + * src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, + reactionField.F90: added in the undamped wolf, in the process of + doing the damped wolf + +2005-09-14 19:13 chrisfen + + * src/UseTheForce/: doForces.F90, doForces_interface.F90, + doForces_interface.h, notifyCutoffs.F90: some changes to activate + the coulombicCorrection selector + +2005-09-14 19:11 chrisfen + + * samples/water/dimer/: cl.in, cl.md, water.md: just some testing + +2005-09-14 19:11 chrisfen + + * samples/argon/: 500.in, 500.md: Equilibrated the sample + +2005-09-14 19:10 chrisfen + + * forceFields/DUFF2.frc: re-added Cl- and Na+ + +2005-09-14 15:31 chuckv + + * src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup + eamAtypes instead of assuming a 1-1 correspondence to atypes. + +2005-09-14 15:28 gezelter + + * src/UseTheForce/doForces.F90: fix to put back calculation of r in + do_prepair + +2005-09-14 14:02 gezelter + + * src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the + createMixingMap routine. It should now set doShift correctly + +2005-09-07 17:44 chuckv + + * src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. + +2005-09-07 17:23 chuckv + + * src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi + logical variables + +2005-09-07 17:08 gezelter + + * src/UseTheForce/doForces.F90: bugfix on the grouptype finding + algorithm + +2005-09-07 15:46 gezelter + + * src/: UseTheForce/doForces.F90, + UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, + UseTheForce/notifyCutoffs_interface.F90, + UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, + io/Globals.cpp, io/Globals.hpp: adding c-side interface to change + cutoff Policy + +2005-09-07 14:18 gezelter + + * src/UseTheForce/doForces.F90: Some bug hunting + +2005-09-07 14:18 gezelter + + * samples/argon/argonNVT.md: Just a longer test + +2005-09-06 12:32 chuckv + + * src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap + etc.. + +2005-09-01 17:56 gezelter + + * src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to + zero + +2005-09-01 15:17 gezelter + + * src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote + createGtypeCutoffMap + +2005-08-30 13:23 chrisfen + + * src/: UseTheForce/doForces.F90, + UseTheForce/doForces_interface.F90, + UseTheForce/doForces_interface.h, + UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, + brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some + changes for implementing the wolf potential + +2005-08-26 17:39 chrisfen + + * src/UseTheForce/DarkSide/eam.F90: updated getEAMCut + +2005-08-26 16:30 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/eam.F90, + DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added + some probably nonfunctional get*cut routines + +2005-08-26 15:34 chuckv + + * src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. + +2005-08-26 11:36 gezelter + + * src/UseTheForce/doForces.F90: fixing some of the problems in the + interactionHash and gtypeCutoff routines + +2005-08-17 10:26 gezelter + + * src/UseTheForce/: doForces.F90, fCutoffPolicy.h, + DarkSide/simulation.F90: added fCutoffPolicy.h + +2005-08-11 16:04 gezelter + + * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in + progress + +2005-08-10 14:17 gezelter + + * src/primitives/StuntDouble.hpp: putting spaceballs back where + they belong + +2005-08-09 17:33 gezelter + + * src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard + Jones module + +2005-08-09 17:33 gezelter + + * src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky + +2005-08-09 14:40 chuckv + + * src/UseTheForce/doForces.F90: In process of re-write for group + based cutoff.... + +2005-07-29 14:38 gezelter + + * src/UseTheForce/doForces.F90: fixes in progress + +2005-07-29 12:34 tim + + * src/UseTheForce/doForces.F90: fix a bug which does not update + me_i and me_j correctly + +2005-07-28 17:12 chuckv + + * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed + cutoffs... Segfaults nicely now... + +2005-07-20 12:04 gezelter + + * configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text + error messages from pathscale compiler + +2005-07-13 11:48 tim + + * src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in + + +2005-07-13 10:54 tim + + * src/: UseTheForce/fSwitchingFunction.h, + UseTheForce/mpiComponentPlan.h, + UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, + io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, + io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, + io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, + io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, + utils/simError.c, utils/simError.h: replace c++ style comment in c + files + +2005-07-03 15:53 chuckv + + * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, + UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added + subroutine to set cuttoff for Interaction map and function in + simulation.F90 to determine if a particular atype is present in a + simulation. + +2005-06-28 08:58 gezelter + + * src/UseTheForce/doForces.F90: [no log message] + +2005-06-27 17:21 chuckv + + * src/UseTheForce/doForces.F90: More breaking and destruction of + force code. Does not build at this point... + +2005-06-27 16:01 gezelter + + * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/fInteractionMap.h, + UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: + Breaky breaky! + +2005-06-20 11:03 gezelter + + * samples/water/ssd/ssd.md, + src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a + simulation + +2005-06-13 13:25 tim + + * src/: applications/staticProps/DensityPlot.cpp, + applications/staticProps/DensityPlot.hpp, + applications/staticProps/SCDOrderParameter.cpp, + applications/staticProps/StaticProps.cpp, + io/AtomTypesSectionParser.cpp: working version of DensityPlot + +2005-05-31 17:31 chuckv + + * src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to + remove angular momentum. + +2005-05-31 12:34 chuckv + + * src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in + typo in nanorodBuilder. + +2005-05-30 09:01 chuckv + + * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, + brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, + brains/Stats.hpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp: Added method to remove system angular + momentum to velocitizer and added method to calculate system + angular momentum to siminfo. + +2005-05-29 16:16 chrisfen + + * src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed + balance from the Darkside (files) + +2005-05-29 16:15 chrisfen + + * src/UseTheForce/doForces.F90: Removed balance from doForces + +2005-05-29 16:15 chrisfen + + * samples/water/tap/: tap.in, tap.md: Updated tap sample + +2005-05-29 16:15 chrisfen + + * samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap + dimer for testing purposes + +2005-05-29 16:14 chrisfen + + * forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It + was apparently wiped earlier this month... + +2005-05-29 16:13 chrisfen + + * ChangeLog: ran make cvslog + +2005-05-28 19:16 tim + + * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding + AtomNameVisitor + +2005-05-28 19:09 tim + + * src/integrators/Integrator.cpp: dding resetIntegrator + +2005-05-28 19:06 tim + + * src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, + NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, + VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding + resetIntegrator + +2005-05-27 16:11 tim + + * src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, + Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, + SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, + StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into + StaticProps + +2005-05-26 23:41 tim + + * src/: applications/staticProps/Makefile, + applications/staticProps/P2OrderParameter.cpp, + applications/staticProps/P2OrderParameter.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticProps.ggo, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, + utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps + +2005-05-26 17:45 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, + applications/staticProps/Makefile, + applications/staticProps/P2OrderParameter.cpp, + applications/staticProps/P2OrderParameter.hpp, + applications/staticProps/RadialDistrFunc.cpp, + applications/staticProps/RadialDistrFunc.hpp, + applications/staticProps/StaticAnalyser.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticProps.ggo, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, visitors/Makefile, + visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding + AtomNameVisitor to convert atom name to its base name; + wrappingvisitor now wrap back to the center of the mass; adding + P2OrderParameter into StaticProps + +2005-05-22 16:36 chuckv + + * samples/metals/nanorod/Au_nanoparticle_FCC.md, + src/applications/nanoRodBuilder/Geometry.cpp, + src/applications/nanoRodBuilder/GeometryBuilder.cpp, + src/applications/nanoRodBuilder/GeometryFactory.cpp, + src/applications/nanoRodBuilder/GeometryFactory.hpp, + src/applications/nanoRodBuilder/nanorodBuilder.cpp, + src/integrators/VelocityVerletIntegrator.cpp: Fix to print pressure + tensor. + +2005-05-22 16:05 tim + + * src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, + integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, + io/Globals.hpp, io/SectionParserManager.cpp: adding keyword + printPressureTensor + +2005-05-20 14:27 tim + + * src/integrators/NPrT.cpp: NPrT in progress + +2005-05-20 11:01 tim + + * src/: integrators/NPrT.cpp, io/Globals.cpp, + utils/OOPSEConstant.hpp: NPrT in progress + +2005-05-19 16:31 tim + + * src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, + integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, + io/Globals.hpp: NPAT is working + +2005-05-19 10:49 tim + + * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, + integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT + +2005-05-18 23:28 tim + + * src/: brains/Register.cpp, integrators/NPAT.cpp, + integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, + io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators + +2005-05-18 14:06 chrisfen + + * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just + some tap changes + +2005-05-18 13:31 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, + DarkSide/sticky.F90: Modifications to temper the dipolar strength + in the first solvation shell for tap + +2005-05-18 07:35 chrisfen + + * samples/water/tap/: tap.in, tap.md, water.md: added a tap example + for testing purposes + +2005-05-17 17:35 chrisfen + + * ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, + samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, + src/UseTheForce/doForces.F90, + src/UseTheForce/DarkSide/electrostatic.F90, + src/UseTheForce/DarkSide/electrostatic_interface.F90, + src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also + correcting changes to the previous merge that were not caught + +2005-05-16 23:20 chuckv + + * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: + Fixed merge issues between Kyle and Chris so OOPSE will actually + build. + +2005-05-16 22:46 kdaily + + * src/io/: GayBerneAtomTypesSectionParser.cpp, + GayBerneAtomTypesSectionParser.hpp, Makefile: help + +2005-05-16 21:08 kdaily + + * forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, + src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, + src/types/DirectionalAtomType.cpp, + src/types/DirectionalAtomType.hpp: added gb + +2005-05-13 15:36 chrisfen + + * forceFields/DUFF2.frc: Better tap + +2005-05-12 14:43 chrisfen + + * forceFields/DUFF2.frc, samples/water/dimer/ssd.in, + samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, + src/applications/dump2Xyz/Dump2XYZ.cpp, + src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. + Need to parametrize. + +2005-05-11 18:15 chuckv + + * src/: io/ShapeAtomTypesSectionParser.cpp, + math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed + build issues under ifc7. + +2005-05-09 17:07 chuckv + + * src/applications/nanoRodBuilder/Geometry.hpp: More geometry + builder changes. + +2005-05-05 10:06 chrisfen + + * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED + to TAP + +2005-05-05 09:47 chrisfen + + * forceFields/DUFF2.frc, samples/water/ssde/ssde.md, + samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, + src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, + src/UseTheForce/DarkSide/atype.F90, + src/UseTheForce/DarkSide/atype_interface.F90, + src/UseTheForce/DarkSide/simulation.F90, + src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, + src/brains/fSimulation.h, src/io/Makefile, + src/io/StickyAtomTypesSectionParser.cpp, + src/io/StickyPowerAtomTypesSectionParser.cpp, + src/io/StickyPowerAtomTypesSectionParser.hpp, + src/types/AtomType.cpp, src/types/AtomType.hpp, + src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, + src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's + not parametrized, but OOPSE will now let me run it... + +2005-05-03 17:55 chuckv + + * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, + GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: + Adding support for generic geometry to nanorodbuilder. + +2005-05-03 12:55 chuckv + + * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, + nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, + nanorodBuilderCmd.h: More changes to nanoRodBuilder.... + +2005-04-29 14:16 gezelter + + * make/Makefile.in: [no log message] + +2005-04-29 11:26 chrisfen + + * forceFields/DUFF2.frc, samples/water/spce/water.md, + samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, + samples/water/ssd-ion/water.md, samples/water/ssde/water.md, + samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, + samples/water/tip4p/water.md: Added TIP4P-Ew + +2005-04-27 19:24 chuckv + + * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, + GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, + nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with + nanoRodBuilder.... + +2005-04-27 15:13 chrisfen + + * samples/shape/Shapes.frc, samples/shape/linear.shape, + src/UseTheForce/DarkSide/atype.F90, + src/UseTheForce/DarkSide/shapes.F90, + src/UseTheForce/DarkSide/shapes_interface.F90, + src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of + write statements and am closer to a working shapes + +2005-04-22 16:57 chuckv + + * src/utils/Predicate.hpp: Fixed gcc4 bug... + +2005-04-22 16:52 tim + + * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, + Trim.hpp: adding CharClassificationFunctor to fix the locale + problem of c++ + +2005-04-21 09:12 chrisfen + + * samples/shape/Shapes.frc, samples/shape/linear.in, + samples/shape/linear.md, src/UseTheForce/ForceField.hpp, + src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, + src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, + src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, + src/UseTheForce/DarkSide/shapes.F90, + src/UseTheForce/DarkSide/shapes_interface.F90, + src/UseTheForce/DarkSide/shapes_interface.h, + src/brains/Register.cpp, src/brains/SimCreator.cpp, + src/io/Makefile, src/io/SectionParser.cpp, + src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, + src/io/ShapeAtomTypesSectionParser.cpp, + src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, + src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, + src/types/ShapeAtomType.hpp: Shapes is limping along with a array + bounds overwrite (I think...). At least the parser loads the + forcefield fine... + +2005-04-18 10:44 chrisfen + + * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on + Mac (capitalization confusion of filenames) + +2005-04-17 22:50 chrisfen + + * src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, + UseTheForce/Shapes_FF.cpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/ShapeAtomTypesSectionParser.cpp, + io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... + +2005-04-15 17:43 gezelter + + * README: gmake in case people forget + +2005-04-15 17:40 gezelter + + * src/applications/oopse/oopse.cpp: fixed the spacing on the + banner. Vanity. + +2005-04-15 17:22 gezelter + + * src/: config.h.in, applications/oopse/oopse.cpp: Version string + in banner (and version numbers in config.h) + +2005-04-15 17:22 gezelter + + * ChangeLog, LICENSE, README: Documentation changes + +2005-04-15 17:03 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, + UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + UseTheForce/ForceFieldCreator.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, + UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, + UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, + UseTheForce/notifyCutoffs.F90, + UseTheForce/notifyCutoffs_interface.F90, + UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, + UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/atype_interface.F90, + UseTheForce/DarkSide/eam.F90, + UseTheForce/DarkSide/eam_interface.F90, + UseTheForce/DarkSide/eam_interface.h, + UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/electrostatic_interface.F90, + UseTheForce/DarkSide/electrostatic_interface.h, + UseTheForce/DarkSide/force_globals.F90, + UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, + UseTheForce/DarkSide/lj_interface.F90, + UseTheForce/DarkSide/lj_interface.h, + UseTheForce/DarkSide/neighborLists.F90, + UseTheForce/DarkSide/reactionField.F90, + UseTheForce/DarkSide/shapes.F90, + UseTheForce/DarkSide/shapes_interface.F90, + UseTheForce/DarkSide/shapes_interface.h, + UseTheForce/DarkSide/simParallel.F90, + UseTheForce/DarkSide/simParallel_interface.F90, + UseTheForce/DarkSide/simParallel_interface.h, + UseTheForce/DarkSide/simulation.F90, + UseTheForce/DarkSide/simulation_interface.F90, + UseTheForce/DarkSide/simulation_interface.h, + UseTheForce/DarkSide/sticky.F90, + UseTheForce/DarkSide/sticky_interface.F90, + UseTheForce/DarkSide/sticky_interface.h, + UseTheForce/DarkSide/switcheroo.F90, + applications/dump2Xyz/Dump2XYZ.cpp, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, + applications/dynamicProps/CrossTimeCorrFunc.cpp, + applications/dynamicProps/CrossTimeCorrFunc.hpp, + applications/dynamicProps/DipoleCorrFunc.cpp, + applications/dynamicProps/DipoleCorrFunc.hpp, + applications/dynamicProps/DynamicProps.cpp, + applications/dynamicProps/DynamicPropsCmd.c, + applications/dynamicProps/DynamicPropsCmd.h, + applications/dynamicProps/FrameTimeCorrFunc.hpp, + applications/dynamicProps/ParticleTimeCorrFunc.cpp, + applications/dynamicProps/ParticleTimeCorrFunc.hpp, + applications/dynamicProps/RCorrFunc.cpp, + applications/dynamicProps/RCorrFunc.hpp, + applications/dynamicProps/TimeCorrFunc.cpp, + applications/dynamicProps/TimeCorrFunc.hpp, + applications/dynamicProps/VCorrFunc.cpp, + applications/dynamicProps/VCorrFunc.hpp, + applications/nanoRodBuilder/GeometryBuilder.cpp, + applications/nanoRodBuilder/GeometryBuilder.hpp, + applications/nanoRodBuilder/nanorodBuilder.cpp, + applications/nanoRodBuilder/nanorodBuilderCmd.c, + applications/nanoRodBuilder/nanorodBuilderCmd.h, + applications/oopse/oopse.cpp, + applications/simpleBuilder/simpleBuilder.cpp, + applications/simpleBuilder/simpleBuilderCmd.c, + applications/simpleBuilder/simpleBuilderCmd.h, + applications/staticProps/GofAngle2.cpp, + applications/staticProps/GofAngle2.hpp, + applications/staticProps/GofR.cpp, + applications/staticProps/GofR.hpp, + applications/staticProps/GofRAngle.cpp, + applications/staticProps/GofRAngle.hpp, + applications/staticProps/GofXyz.cpp, + applications/staticProps/GofXyz.hpp, + applications/staticProps/RadialDistrFunc.cpp, + applications/staticProps/RadialDistrFunc.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, + brains/Exclude.hpp, brains/ForceManager.cpp, + brains/ForceManager.hpp, brains/MoleculeCreator.cpp, + brains/MoleculeCreator.hpp, brains/Register.cpp, + brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, + brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, + brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, + brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, + brains/fSimulation.h, constraints/ConstraintElem.hpp, + constraints/ConstraintPair.hpp, constraints/Rattle.cpp, + constraints/Rattle.hpp, constraints/ZconsStruct.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, + integrators/DLM.hpp, integrators/Integrator.cpp, + integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/NPT.cpp, + integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, + integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, + integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, + integrators/NVT.cpp, integrators/NVT.hpp, + integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, + io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, + io/BASS_parse.h, io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, + io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, + io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, + io/Globals.cpp, io/Globals.hpp, + io/LennardJonesAtomTypesSectionParser.cpp, + io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, + io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, + io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, + io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, + io/SectionParser.cpp, io/SectionParser.hpp, + io/SectionParserManager.cpp, io/SectionParserManager.hpp, + io/StatWriter.cpp, io/StatWriter.hpp, + io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, + io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, + io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, + io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, + io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, + io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, + io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, + lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, + lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, + lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, + lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, + math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, + math/ParallelRandNumGen.hpp, math/Polynomial.hpp, + math/Quaternion.hpp, math/RandNumGen.hpp, + math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, + math/RectMatrix.hpp, math/SeqRandNumGen.cpp, + math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, + math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, + minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, + minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, + minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, + minimizers/MinimizerFactory.hpp, + minimizers/MinimizerParameterSet.cpp, + minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, + minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, + minimizers/SDMinimizer.hpp, primitives/Atom.cpp, + primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, + primitives/Bond.hpp, primitives/CutoffGroup.hpp, + primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, + primitives/GhostBend.cpp, primitives/GhostBend.hpp, + primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, + primitives/Molecule.cpp, primitives/Molecule.hpp, + primitives/RigidBody.cpp, primitives/RigidBody.hpp, + primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, + primitives/Torsion.cpp, primitives/Torsion.hpp, + primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, + profiling/mdProfile.cpp, profiling/mdProfile.hpp, + profiling/timing.F90, restraints/Restraints.cpp, + restraints/Restraints.hpp, + restraints/ThermoIntegrationForceManager.cpp, + restraints/ThermoIntegrationForceManager.hpp, + selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, + selection/IndexFinder.cpp, selection/IndexFinder.hpp, + selection/NameFinder.cpp, selection/NameFinder.hpp, + selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, + selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, + selection/SelectionManager.cpp, selection/SelectionManager.hpp, + selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, + selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, + types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, + types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, + types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, + types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, + types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, + types/CubicBondType.hpp, types/CubicTorsionType.hpp, + types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, + types/DirectionalAtomType.hpp, types/FixedBondType.hpp, + types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, + types/MakeStamps.cpp, types/MakeStamps.hpp, + types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, + types/MorseBondType.hpp, types/OplsTorsionType.hpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, + types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, + types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, + types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, + types/TorsionStamp.cpp, types/TorsionStamp.hpp, + types/TorsionType.hpp, types/UreyBradleyBendType.hpp, + types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, + utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, + utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, + utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, + utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, + utils/PropertyMap.cpp, utils/PropertyMap.hpp, + utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, + utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, + utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, + utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, + utils/any.hpp, utils/definitions.F90, utils/fError.c, + utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, + utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, + utils/residentMem.h, utils/simError.c, utils/simError.h, + utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, + visitors/AtomData.hpp, visitors/AtomVisitor.cpp, + visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, + visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, + visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, + visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, + visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, + visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has + been drafted to perform our indentation services + +2005-04-15 17:03 gezelter + + * configure, ac-tools/configure.in: Jedi mind-trick warning + messages have been added to make users ignore CGAL. + +2005-04-15 13:41 tim + + * make/Makefile.in: fix make install + +2005-04-15 13:41 tim + + * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: + add Makefile of samples + +2005-04-15 13:33 tim + + * samples/: lipid/Makefile, water/dimer/Makefile, + water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not + installed correctly + +2005-04-14 16:41 gezelter + + * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, + make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, + scripts/filepp, scripts/filepp.in: configure now searches for perl + to use with filepp + 2005-04-14 16:20 gezelter * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of