--- trunk/OOPSE/ChangeLog 2003/08/20 19:41:04 705 +++ trunk/OOPSE/ChangeLog 2003/09/12 16:20:05 760 @@ -1,3 +1,227 @@ +2003-09-10 16:28 mmeineke + + * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more + work on getting gofR working. + +2003-09-09 16:50 mmeineke + + * props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the + beginings of the GofR pair correlation. + + added identification of identI in matchI. + +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 + +2003-08-28 11:59 mmeineke + + * props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: + added the first functional parts of the PairCorrType Abstract + classes. + +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, @@ -1339,17 +1563,27 @@ 2003-03-24 20:07 gezelter - * samples/Makefile: moving tests to samples + * samples/Makefile, tests/Makefile: moving tests to samples 2003-03-24 20:06 gezelter - * samples/: alkane/Makefile, alkane/alkanes.mdl, - alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, - argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, - lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, - lipid/lipid.mdl, lipid/water.mdl, water/Makefile, - water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to - samples + * samples/alkane/Makefile, samples/alkane/alkanes.mdl, + samples/alkane/butane.bass, samples/alkane/init_butane.eor, + samples/argon/Makefile, samples/argon/argon.bass, + samples/argon/init_argon.eor, samples/argon/lj.mdl, + samples/lipid/5x5.bass, samples/lipid/Makefile, + samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, + samples/lipid/water.mdl, samples/water/Makefile, + samples/water/init_ssd.eor, samples/water/ssd.bass, + samples/water/water.mdl, tests/alkane/Makefile, + tests/alkane/alkanes.mdl, tests/alkane/butane.bass, + tests/alkane/init_butane.eor, tests/argon/Makefile, + tests/argon/argon.bass, tests/argon/init_argon.eor, + tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, + tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, + tests/lipid/water.mdl, tests/water/Makefile, + tests/water/init_ssd.eor, tests/water/ssd.bass, + tests/water/water.mdl: moved tests to samples 2003-03-24 19:51 gezelter @@ -1357,7 +1591,9 @@ 2003-03-24 19:46 gezelter - * ac-tools/Make.conf.in: Added makefiles in tests directories + * ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, + tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: + Added makefiles in tests directories 2003-03-24 16:55 gezelter @@ -1374,6 +1610,22 @@ * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, do_Forces.F90: little bug fixes here and there +2003-03-24 11:04 mmeineke + + * tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon + test simulation + +2003-03-24 11:02 mmeineke + + * tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, + lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, + water/water.mdl: [no log message] + +2003-03-24 11:02 mmeineke + + * tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added + some test bass files for experimenting with + 2003-03-24 10:26 mmeineke * libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug @@ -1483,8 +1735,8 @@ libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, - libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE - Tree + libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial + revision 2003-03-21 12:42 mmeineke @@ -1541,6 +1793,6 @@ libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, - libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial - revision + libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE + Tree