--- trunk/OOPSE/ChangeLog 2003/08/20 19:41:04 705 +++ trunk/OOPSE/ChangeLog 2004/01/05 21:00:05 894 @@ -1,3 +1,860 @@ +2003-12-29 14:56 chuckv + + * samples/metals/Au.bass, third-party/mt19937ar.c: Added + third-party directory for code not written by us. Also added + Mersenne Twister random number generator code. This will eventually + replace sprng as the random number generator used by OOPSE. + +2003-12-22 16:26 chuckv + + * libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, + libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: + Fixes to profile code. + +2003-12-19 15:36 mmeineke + + * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, + timing.F90, timing.f90: More profiling fixes. + +2003-12-19 15:19 chuckv + + * libmdtools/timing.f90: Another change for MPI in timing. + +2003-12-19 15:17 chuckv + + * libmdtools/timing.f90: Small update to timing in MPI + +2003-12-19 13:53 mmeineke + + * libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the + profiling commands work now. Will start adding PROFILE ifdefs into + the code + +2003-12-19 12:25 mmeineke + + * libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added + some profiling routines + +2003-12-19 10:12 mmeineke + + * utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta + and GofRomega + + additional work on randomBilayer + +2003-12-19 10:12 mmeineke + + * staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, + PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and + GofRomega + +2003-12-18 16:47 mmeineke + + * libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added + some profile functionality + +2003-12-18 15:46 chuckv + + * libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: + Added functions for simple profiling in fortran. + +2003-12-17 15:13 chuckv + + * libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, + samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and + rho_col were scattered into the same array. Unfortunately, MPI + zeros the array between scatters so half of the sum was being lost. + Fixed by added a temp array for column scatter, then sum loop over + nlocal. + +2003-12-16 15:49 mmeineke + + * staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, + PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added + gofRomega. both need to be debugged and tested. + +2003-12-12 10:42 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for + gradients (to do minimizations) + +2003-12-12 10:33 mmeineke + + * utils/sysbuilder/randomBilayer.hpp: removed the randombilayer + header + +2003-12-10 11:52 mmeineke + + * utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, + randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add + randomBilayer to the build. Also move the random bilayer builder + from bilayerSys to randomBilayer + +2003-11-25 10:44 mmeineke + + * forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old + DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and + TB3 in DUFF.frc + +2003-11-21 15:09 mmeineke + + * libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, + utils/sysbuilder/latticeBilayer.cpp: added a more verbose error + message in SimInfo. Added a more informative error message in + InitializeFromFile + +2003-11-21 15:07 mmeineke + + * staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add + ing in the GofR,CosTheta + +2003-11-21 14:31 chrisfen + + * libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed + a bug in SimInfo ordering of radii + +2003-11-11 12:20 mmeineke + + * libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline + a min function. + +2003-11-10 16:50 mmeineke + + * libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: + reordered the rcut/ecr/boxSize initialization + + removed the rcut/ecr shrink and grow algorithm. the simulation will + now exit when it runs into rcut or ecr. + +2003-11-07 16:46 chuckv + + * libmdtools/: Makefile.in, mpiSimulation_module.F90, + oopseMPI_module.F90: Added support for compiling fortran without + use of mpich modules. We use mpif.h instead.: + +2003-11-07 12:09 mmeineke + + * libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, + NPTxyz.cpp: moved the velocity scale matrix calculation outside of + the atom loop in the NPT family of integrators. + +2003-11-06 17:01 mmeineke + + * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, + libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, + libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, + utils/sysbuilder/latticeBilayer.cpp: added the following parameters + to BASS: * useInitialExtendedSystemState * orthoBoxTolerance + * useIntiTime => useInitialTime + +2003-11-06 14:24 mmeineke + + * libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, + make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, + parse_tree.h: fixed the includes in the Make.dep + +2003-11-06 14:11 mmeineke + + * libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, + NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the + new-templateless branch to the main trunk. + + bug Fixes include: * fixed the switching function from ortho to + non-ortho box. !!!!! THis was responsible for all of the + sudden deaths we saw. * some formating in the string when we + write out the extended system state. * added NPT.cpp to the + makefile.in + +2003-11-06 13:20 mmeineke + + * libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, + SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" + bug. The box was not switching between orthorhombic and + non-orthorhombic wrapping correctly. we added a fabs() to + the check.which should fix it. + +2003-11-05 14:16 mmeineke + + * libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, + libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, + libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, + libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, + libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, + utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: + some work on trying to find the compression bug + +2003-11-03 17:07 mmeineke + + * libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, + InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, + NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, + SimSetup.cpp, SimSetup.hpp: begun work on removing templates and + most of standard template library from OOPSE. + +2003-10-31 16:06 mmeineke + + * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, + Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, + SimSetup.cpp: started work on template removal. + +2003-10-31 13:28 mmeineke + + * libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: + added template stuff to the Maikefile template + + little changes to some printf format statements + +2003-10-31 13:28 mmeineke + + * libBASS/Makefile.in: added template stuff to the Maikefile + template + +2003-10-30 13:59 gezelter + + * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, + do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for + rList problems + +2003-10-30 09:11 gezelter + + * libmdtools/neighborLists.F90: Fixed bug that size(q0) was being + queried before q0 was allocated. + +2003-10-29 15:41 mmeineke + + * libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, + SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, + calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error + in bass.l + + fixed a little bug in the first time step, regarding the setting of + ecr and est in fortran + +2003-10-29 15:40 mmeineke + + * libBASS/BASSlex.l: fixed a stdlib.h include error + +2003-10-29 12:55 mmeineke + + * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, + SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way + rcut is setup, as well as additional debugging comments. + +2003-10-29 09:28 gezelter + + * configure, ac-tools/configure.in, libBASS/Makefile.in, + libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for + templates + +2003-10-28 22:16 gezelter + + * src/Makefile.in: Refixed broken makefile + +2003-10-28 22:06 gezelter + + * configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility + fixes + +2003-10-28 19:19 tim + + * ChangeLog, libmdtools/AbstractClasses.hpp, + libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, + libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, + libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, + libmdtools/ReadWrite.hpp, samples/argon/argon.bass, + samples/water/ssd.bass: add chi and eta to the comment line of dump + file. + +2003-10-28 17:25 mmeineke + + * libmdtools/: ForceFields.hpp, SimInfo.hpp, + fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, + mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of + how c calls fortran. All function pointers and fortran calls are + rigidly typecast now. + +2003-10-28 15:42 gezelter + + * staticProps/Makefile.in, utils/sysbuilder/Makefile.in: + Portability fixes + +2003-10-28 15:09 gezelter + + * libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, + libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, + src/Makefile.in: Compatibility fixes + +2003-10-28 12:08 mmeineke + + * libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: + started work on template removal + +2003-10-28 12:04 gezelter + + * libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started + trying to understand extern "C" stuff for pointers + +2003-10-28 11:20 gezelter + + * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, + ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility + +2003-10-28 11:03 gezelter + + * libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, + DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, + DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, + ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, + Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, + ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, + StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, + calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, + mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with + more portable c header stuff Also, mod file fixes and portability + changes Some fortran changes will need to be reversed. + +2003-10-28 11:03 gezelter + + * libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, + Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, + Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more + portable c header stuff Also, mod file fixes and portability + changes + +2003-10-28 11:02 gezelter + + * configure, ac-tools/aclocal.m4: mod file fixes and portability + stuff + +2003-10-27 18:00 gezelter + + * Makefile.in, configure, ac-tools/aclocal.m4, + ac-tools/configure.in, ac-tools/fortran90.m4, + libmdtools/Makefile.in: Stuff for MOD support in other compilers + +2003-10-27 17:08 mmeineke + + * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, + MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: + added routines for the sysbuilder to work with simSetup + + remved the QuickBass routines, and had all parsing go through + SimSetup. LatticeBilayer is in complete working order now. + +2003-10-27 17:07 mmeineke + + * libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added + routines for the sysbuilder to work with simSetup + +2003-10-27 11:20 gezelter + + * configure, ac-tools/configure.in, samples/water/ssd.bass, + utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild + +2003-10-24 17:17 mmeineke + + * utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, + MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, + latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put + QuickBass, MoLocator, and latticeBuilder into a Builder Library + overhauled latticeBilayer into its own program. Removed sysBuild + from the Makefile + +2003-10-24 12:36 gezelter + + * utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, + latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer + builder + +2003-10-24 12:35 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a + merge problem + +2003-10-23 14:57 mmeineke + + * samples/metals/Makefile.in: added eam ForceField files to the + init + + fixed an eam mpi parmeter setup bug + + added the init file to the makefile + +2003-10-23 14:57 mmeineke + + * libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files + to the init + + fixed an eam mpi parmeter setup bug + +2003-10-23 14:57 mmeineke + + * forceFields/Makefile.in: added eam ForceField files to the init + +2003-10-22 16:17 mmeineke + + * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, + NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT + integrator, NPTxyz. It scales the x, y, and z direction sepeartely. + no box skew allowed. + +2003-10-21 14:33 mmeineke + + * libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, + staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. + * useInitTime = false: sets the origin time to 0.0 regardless + of the time stamp in the .init file * default=> useInitTime = + true; + +2003-10-17 16:19 mmeineke + + * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, + Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, + staticProps.cpp, obj/placeholder: added the staticProps directory + to the build list for both configure  and configure.in + + fixed a number of bugs in the staticProps code. gofr is now + working. + +2003-10-17 16:18 mmeineke + + * ac-tools/configure.in: added the staticProps directory to the + build list for both configure  and configure.in + +2003-10-17 16:17 mmeineke + + * configure: added the staticProps directory to the build list + +2003-10-16 14:16 mmeineke + + * libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, + Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to + use linked lists instead of a vector. + + Fixed the makefile to build DumpReader.cpp + + Removed a comment output in Exclude.cpp + + Modified DumpWriter and Integrator to write an eor file every time + a frame is written. This lets the .eor file represent the last + written frame of a simulation. + +2003-10-10 12:10 mmeineke + + * staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, + CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, + PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, + staticProps.cpp: removed the props directory, and moved everything + over to staticProps + +2003-10-09 17:09 mmeineke + + * libmdtools/Atom.hpp: Contiuned work on staticProps. should be in + a position where it will compile and run first runs. + +2003-10-04 13:46 chuckv + + * libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, + samples/metals/Au.bass: Fixed bug in calc_eam. + +2003-10-04 13:08 chuckv + + * samples/metals/init_au.in: added Au init file for eam. + +2003-10-03 17:11 mmeineke + + * libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed + entahlpy from the statwriter and thermo. + +2003-10-03 17:02 mmeineke + + * libmdtools/SimInfo.hpp: changed the formating ogf the error + statements in simError + + added a function to get the maxCutoff + +2003-10-03 17:01 mmeineke + + * libBASS/simError.c: changed the formating ogf the error + statements in simError + +2003-09-30 11:00 mmeineke + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed + f90Flags so they are no longer overwritten by the compiler. + +2003-09-29 17:06 mmeineke + + * libmdtools/fortranWrappers.cpp: added mpif90 mod check back same + for conifig.in + + fixed wrappers to extern "C" + +2003-09-29 17:06 mmeineke + + * ac-tools/configure.in: added mpif90 mod check back same for + conifig.in + +2003-09-29 17:05 mmeineke + + * configure: added mpif90 mod check back + +2003-09-29 16:16 mmeineke + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, + libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, + libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, + libBASS/ZconStamp.cpp, libBASS/simError.c, + libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, + libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, + libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors + found with SUN's SUNWspro.s1s7 + +2003-09-29 12:38 mmeineke + + * libmdtools/GenericData.hpp: light change in syntax. no + signifigant change. + +2003-09-25 16:17 mmeineke + + * libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some + additional remarks from icc -w3 (extra verbose output) + +2003-09-25 14:27 mmeineke + + * libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, + libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, + libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, + libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, + libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, + libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, + libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, + libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with + gcc -Wall and g++ -Wall + +2003-09-25 13:54 gezelter + + * configure, ac-tools/configure.in: fixed a bug in configure + +2003-09-25 11:42 gezelter + + * Makefile.in, configure, ac-tools/aclocal.m4, + ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, + src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: + fixes for configure + +2003-09-24 14:34 mmeineke + + * libmdtools/Integrator.cpp: moved readyCheck in the integrator so + that it is called before the first Statistics are written. + +2003-09-23 15:36 gezelter + + * src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a + bunch of Make.dep files to CVS + +2003-09-23 15:34 mmeineke + + * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, + SimSetup.cpp: Removed NPTfm from Integrator.hpp. + + Some small syntax cleaning in NPTfm and SimSetup + +2003-09-22 18:07 tim + + * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, + SimInfo.hpp: fix bug in calculating maxCutoff + +2003-09-22 16:23 mmeineke + + * libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, + Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: + Converted NPTf to work with the NPT base class. + + Removed NPTfm and NPTim from cvs + +2003-09-19 15:00 mmeineke + + * libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, + NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base + class. NPTi is up to date. NPTf is not. + +2003-09-19 11:03 mmeineke + + * utils/Makefile.in, src/Makefile.in: removed mpi++ from the + makefile + +2003-09-19 11:01 gezelter + + * samples/water/ssd.bass: goofing off to test NPTf and NPTi + +2003-09-19 11:01 gezelter + + * libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found + (nearly) conserved quantities for both NPTi and NPTf + +2003-09-19 10:20 mmeineke + + * utils/Makefile.in: fixed a typo in the makefile. + +2003-09-19 09:55 gezelter + + * libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, + samples/water/ssd.bass: [no log message] + +2003-09-19 09:22 tim + + * libmdtools/: NPTi.cpp, NVT.cpp: [no log message] + +2003-09-17 09:22 mmeineke + + * libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now + work with constraints. + +2003-09-16 15:02 tim + + * libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, + SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo + + fixed conserved quantity in NPT (Still some small bug) + + NPTi appears very stable. + +2003-09-15 11:52 tim + + * libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, + libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, + libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, + libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, + utils/sysbuilder/bilayerSys.cpp: add conserved quantity to + statWriter fix bug of vector wrapping at NPTi + +2003-09-12 11:20 gezelter + + * libmdtools/: Make.dep, Makefile.in: Added integrators to + Makefile.in + +2003-09-12 11:20 gezelter + + * ChangeLog: Entered changes for configure into ChangeLog + +2003-09-09 15:35 mmeineke + + * libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, + NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog + + added two new NPT integrators, they still need work. + +2003-09-09 15:34 mmeineke + + * ChangeLog: updated the ChangeLog + +2003-09-05 17:45 gezelter + + * libmdtools/Make.dep: dependency on config.h + +2003-09-05 17:36 gezelter + + * configure, ac-tools/aclocal.m4: fixed sprng problem + +2003-09-05 16:29 gezelter + + * samples/metals/Makefile.in: New Makefile for metals sample + +2003-09-05 16:27 gezelter + + * Makefile, Makefile.in, ac-tools/aclocal.m4, + ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, + forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, + libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, + libBASS/Makefile.in, libmdtools/Integrator.hpp, + libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, + libmdtools/Makefile, libmdtools/Makefile.in, + libmdtools/calc_eam.F90, libmdtools/config.h.in, + libmdtools/definitions_module.F90, libmdtools/fInfo.c, + libmdtools/fortranWrappers.cpp, + libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, + libmdtools/simulation_module.F90, samples/Makefile, + samples/Makefile.in, samples/alkane/Makefile, + samples/alkane/Makefile.in, samples/argon/Makefile, + samples/argon/Makefile.in, samples/argon/argon.bass, + samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, + samples/lipid/Makefile, samples/lipid/Makefile.in, + samples/water/Makefile, samples/water/Makefile.in, src/Makefile, + src/Makefile.in, utils/Makefile, utils/Makefile.in, + utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to + autoconf / configure method of configuring OOPSE + +2003-09-04 16:48 mmeineke + + * libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, + libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, + libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, + libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: + added resetTime to the Global namespace. + + added ability to reset the integrators in the NVT and NPT family. + +2003-09-04 16:48 mmeineke + + * libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global + namespace. + +2003-09-02 09:30 tim + + * libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, + ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of + PolicyByMass + +2003-08-28 16:09 tim + + * ChangeLog, libmdtools/GenericData.cpp, + libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, + libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex + +2003-08-27 14:23 tim + + * libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix + bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to + MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we + turn on the optimization flag, it causes a seg fault + +2003-08-27 11:25 gezelter + + * libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, + calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for + stress tensor parallel bug. + +2003-08-27 11:16 tim + + * ChangeLog, libmdtools/DUFF.cpp, + libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: + fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 + molMembershipList use global index instead of local index + +2003-08-26 15:37 tim + + * libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, + mpiSimulation.cpp: set default force substraction policy to + PolicyByMass + +2003-08-26 15:29 tim + + * libmdtools/Integrator.cpp: [no log message] + +2003-08-26 15:13 mmeineke + + * utils/sysbuilder/bilayerSys.cpp: added define statemewnt to + Statwriter and Dumpwriter to handle files larger than 2 gb. + + commented out some print statements in Zconstraint + + hard coding some system init into bilayer.sys + +2003-08-26 15:12 mmeineke + + * libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: + added define statemewnt to Statwriter and Dumpwriter to handle + files larger than 2 gb. + + commented out some print statements in Zconstraint + +2003-08-26 15:02 tim + + * libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed + and check the seed which is specified by user at least contains 9 + digits + +2003-08-26 13:32 mmeineke + + * libmdtools/DUFF.cpp: changed the Makefiel a litle. + + Fixed a bug in MPI_DUFF. The atom block type was not being properly + constucted in MPI. (The MPI struct had 6 doubles declared versus + the actual 11) + +2003-08-26 13:30 mmeineke + + * Makefile: changed the Makefiel a litle. + +2003-08-25 17:17 gezelter + + * utils/sysbuilder/Makefile: More FreeBSD fixes + +2003-08-25 16:51 gezelter + + * libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, + libmdtools/Makefile, src/Makefile: [no log message] + +2003-08-22 15:04 mmeineke + + * libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on + frequency of output dumps. + +2003-08-20 17:23 tim + + * libBASS/Globals.hpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, + libmdtools/mpiSimulation.cpp: user can setup seed in bass file now, + if he does not specify any value for seed, oopse will take the + value of seconds of system time as seed + +2003-08-20 14:42 mmeineke + + * libmdtools/Atom.cpp, libmdtools/DUFF.cpp, + libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimState.cpp, + utils/sysbuilder/bilayerSys.cpp: updated the Changelog. + + added some bug fixes for setting the random number generator seed + value. + + fixed a bug where ghostbend atom b was not being set. ( recent bug + from SimState conversion) + +2003-08-20 14:41 mmeineke + + * libBASS/Globals.hpp: updated the Changelog. + + added some bug fixes for setting the random number generator seed + value. + +2003-08-20 14:41 mmeineke + + * ChangeLog: updated the Changelog. + +2003-08-20 14:11 tim + + * libBASS/Globals.cpp, libmdtools/DUFF.cpp, + libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost + bend class + +2003-08-20 10:13 mmeineke + + * utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in + make links. added -f to ln -s. + +2003-08-20 09:50 tim + + * libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] + +2003-08-20 09:34 tim + + * libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, + ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg + printing + 2003-08-18 15:59 chuckv * utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, @@ -136,13 +993,6 @@ libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, samples/metals/Au.bass: EAM works...... Neighbor list also works..... - -2003-08-08 13:32 mmeineke - - * props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: - moved frameCount's functionality into DumpReader. also split props - into staticProps and dynamicProps. (currently only have - staticProps) 2003-08-08 12:48 mmeineke @@ -200,9 +1050,8 @@ 2003-07-29 11:32 mmeineke * libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, - props/frameCount.c, props/frameCount.h, props/props.cpp, - src/Makefile: working on the props code + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: + working on the props code 2003-07-29 11:32 mmeineke