--- trunk/OOPSE/ChangeLog 2004/05/10 20:28:14 1152 +++ trunk/OOPSE/ChangeLog 2004/05/27 19:51:18 1206 @@ -1,3 +1,240 @@ +2004-05-27 10:31 tim + + * libmdtools/SimInfo.cpp: groupList new bases on global index of + atoms + +2004-05-27 10:21 gezelter + + * src/: oopse.cpp, oose.cpp: Modified the nifty banner + +2004-05-27 10:21 gezelter + + * libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90: + Fixed off-by-one error in groupStartRow and groupStartCol + +2004-05-26 19:48 tim + + * ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp, + libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, + libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90, + libmdtools/calc_charge_charge.F90, + libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, + libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, + libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, + libmdtools/force_globals.F90, libmdtools/mdProfile.cpp, + libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp, + libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, + libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, + libmdtools/simulation_module.F90: in the progress of fixing MPI + version of cutoff group + +2004-05-26 11:41 gezelter + + * libmdtools/do_Forces.F90: Compacted all of the 8 copies of the + force loop into one. + +2004-05-24 17:24 gezelter + + * libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes + +2004-05-24 16:23 chrisfen + + * libmdtools/Restraints.cpp: Removed unnecessary variables and + changed error messages in Restraints.cpp + +2004-05-24 16:03 gezelter + + * libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, + calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, + calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes + for stress / pressure tensor by cutoff group + +2004-05-22 15:55 chrisfen + + * libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... + Too many arguements in a function call. + +2004-05-22 13:17 chrisfen + + * libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword + useThermInt. + +2004-05-22 13:16 chrisfen + + * libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, + ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, + Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, + SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, + StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration + code. + +2004-05-21 10:58 gezelter + + * libmdtools/: do_Forces.F90, simulation_module.F90: Major changes + to skipThisPair for efficiency + +2004-05-21 09:22 gezelter + + * configure, ac-tools/configure.in, forceFields/LJ.vdw, + forceFields/amber99.vdw, forceFields/charmm27.vdw, + forceFields/gaff.vdw, forceFields/oplsaal.vdw, + samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes + for SHAPES potential + +2004-05-20 15:27 chrisfen + + * libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit + included the bass keywords + +2004-05-20 15:24 chrisfen + + * libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, + Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, + Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several + additions... Restraints.cpp and .hpp were included for restraining + particles in thermodynamic integration. By including these, + changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, + StatWriter, and possibly some other files. Two bass keywords were + also added for performing thermodynamic integration: a lambda value + one and a k power one. + +2004-05-13 16:08 gezelter + + * libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list + +2004-05-12 17:01 tim + + * samples/: argon/Makefile, argon/argonEM.bass, + argon/init_argon.eor, minimizer/argon/Makefile, + minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, + minimizer/water/Makefile, minimizer/water/Makefile.in, + minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, + minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, + minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add + minimizer sample + +2004-05-12 16:54 gezelter + + * libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X + compilation + +2004-05-12 15:54 gezelter + + * libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes + for compilation under Mac OS X with IBM's xl compilers + +2004-05-12 15:14 gezelter + + * src/: oopse.cpp, oose.cpp: Added a nifty neato banner + +2004-05-12 15:14 gezelter + + * libmdtools/LJFF.cpp: Removed an extraneous write + +2004-05-12 15:13 gezelter + + * libBASS/simError.h: Starting to change the error model + +2004-05-12 14:45 gezelter + + * utils/Dump2XYZ.cpp: const char* fix + +2004-05-12 14:44 gezelter + + * libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, + src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous + write statements + +2004-05-12 11:38 tim + + * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, + ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, + SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and + massratio from simState, creat cutoff group forevery atom which + does not belong to cutoff group defined at mdl file + +2004-05-12 10:58 gezelter + + * libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in + CutoffGroup + +2004-05-12 10:35 gezelter + + * samples/water/water.mdl: Added the cutoff Groups to the default + water.mdl file + +2004-05-12 10:02 tim + + * ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: + fixed a bug in CutoffGroup::getCOM() + +2004-05-12 09:29 gezelter + + * libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, + libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, + samples/water/ssd.bass: bug fixes for cutoffGroups + +2004-05-11 17:28 tim + + * utils/Vector3.hpp: adding generic Vector3 class + +2004-05-11 16:44 tim + + * libmdtools/Integrator.hpp: adding instantiation of + Integrator in order to make OOPSE compiled by icc8 + +2004-05-11 16:31 gezelter + + * libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, + calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, + calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: + Fortran-side changes for group-based cutoffs + +2004-05-11 16:20 tim + + * libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp + +2004-05-11 16:14 tim + + * libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, + SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix + anoter one in CutoffGroup which causes seg fault + +2004-05-11 15:33 tim + + * ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, + libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, + libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup + into OOPSE + +2004-05-11 15:07 gezelter + + * libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup + +2004-05-11 11:00 gezelter + + * libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, + fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to + use the simplified cutoff stuff in the BASS library + +2004-05-10 23:21 gezelter + + * libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, + CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, + Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, + MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, + make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, + parse_tree.c: BASS changes for adding CutoffGroups to molecules. + Also restructured the plethora of cutoff radii into one + cutoffRadius and one switchingRadius. Also removed the + useMolecularCutoffs keyword + +2004-05-10 15:28 tim + + * ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize + DumpWriter + 2004-05-07 16:36 gezelter * libmdtools/: fSwitchingFunction.h, switch_module.F90: New module @@ -495,7 +732,8 @@ 2004-01-27 14:38 gezelter - * samples/argon/argon.bass: Longer run time to test argon + * samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer + run time to test argon 2004-01-27 14:38 gezelter @@ -712,8 +950,8 @@ 2004-01-12 15:37 tim * ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, - samples/water/ssd.bass: Dumpwriter only write out the atoms on - master nodes + samples/minimizer/argon/argon.bass, samples/water/ssd.bass: + Dumpwriter only write out the atoms on master nodes 2004-01-10 04:46 tim @@ -764,9 +1002,9 @@ 2004-01-07 14:26 tim * libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, - samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of - sending message from master node to itself in DumpWriter.cpp and - InitializeFromFile.cpp + samples/argon/argon.bass, samples/minimizer/argon/argon.bass, + samples/water/ssd.bass: Fixed a bug of sending message from master + node to itself in DumpWriter.cpp and InitializeFromFile.cpp 2004-01-06 14:49 chuckv @@ -1072,8 +1310,8 @@ 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. + samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi + and eta to the comment line of dump file. 2003-10-28 17:25 mmeineke @@ -1494,12 +1732,15 @@ 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 + samples/minimizer/argon/Makefile, + samples/minimizer/argon/Makefile.in, + samples/minimizer/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 @@ -2088,8 +2329,9 @@ 2003-07-14 18:06 gezelter * samples/: alkane/init_butane.eor, argon/argon.bass, - argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes - for samples + argon/init_argon.eor, minimizer/argon/argon.bass, + minimizer/argon/init_argon.eor, lipid/init_5x5.eor, + water/init_ssd.eor: Fixes for samples 2003-07-14 18:06 gezelter @@ -2762,7 +3004,8 @@ * libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, - samples/argon/argon.bass: more bug fixes.... + samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more + bug fixes.... 2003-04-01 11:49 mmeineke @@ -2969,7 +3212,8 @@ 2003-03-26 10:37 chuckv * libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, - samples/argon/argon.bass: Fixes for Parallel thermalization + samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes + for Parallel thermalization 2003-03-26 09:55 mmeineke @@ -3001,9 +3245,10 @@ 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 + lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, + minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, + minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, + water/ssd.bass, water/water.mdl: moved tests to samples 2003-03-24 19:51 gezelter