--- trunk/OOPSE/ChangeLog 2003/08/28 21:09:47 736 +++ trunk/OOPSE/ChangeLog 2004/06/11 17:16:21 1268 @@ -1,1678 +1,3701 @@ -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, - latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, - sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. - Nanobuilder still broke. - -2003-08-15 14:24 tim - - * libBASS/Globals.cpp, libBASS/Globals.hpp, - libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, - libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, - libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp, - libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint - Method - -2003-08-14 11:16 tim - - * libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint - with average force substraction strategy - -2003-08-13 16:20 chuckv - - * libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some - profiling code -DPROFILE. - -2003-08-13 14:21 tim - - * libBASS/Globals.cpp, libBASS/Globals.hpp, - libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, - libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic - potential & z-contraint method - -2003-08-12 16:44 mmeineke - - * libBASS/BASS_interface.cpp, libBASS/Globals.hpp, - libmdtools/Atom.cpp, libmdtools/DUFF.cpp, - libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, - libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really - annoying bug in Directional Atom, where mu was getting written to - pseudorandom memory location. - -2003-08-12 14:56 tim - - * libBASS/BASS_interface.cpp, libBASS/Globals.cpp, - libBASS/Globals.hpp, libmdtools/Atom.hpp, - libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, - libmdtools/SimSetup.cpp: debugging globals - -2003-08-12 13:40 gezelter - - * forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes - and new atypes in LJFF - -2003-08-12 13:15 gezelter - - * forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older - stuff... - -2003-08-12 13:14 chuckv - - * utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. - -2003-08-12 13:04 chuckv - - * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: - Missed del of files before. - -2003-08-12 13:03 chuckv - - * utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log - message] - -2003-08-12 13:01 chuckv - - * utils/sysbuilder/Makefile: commit makefile - -2003-08-12 12:51 tim - - * libBASS/Globals.cpp, libBASS/Globals.hpp, - libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, - libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, - libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added - harmonical potential to z-constraint method - -2003-08-11 17:31 chuckv - - * utils/Makefile: Changed makefile to only build quicklate. - -2003-08-11 17:25 chuckv - - * ac-tools/configure.in: added utils/sysbuilder to be built. - -2003-08-11 17:12 chuckv - - * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, - bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, - sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp, - sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp, - sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c, - sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp, - sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp, - sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp, - sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged - sysbuilder into a subdirectory. Fixed some of sysbuilder to work - with new atom allocation in libmdtools. - -2003-08-11 14:41 tim - - * libmdtools/: Integrator.cpp, Integrator.hpp: added method of - moving zconstraint molecules to specified positions - -2003-08-11 14:39 tim - - * libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] - -2003-08-11 14:38 mmeineke - - * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, - libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, - libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp, - libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c, - libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h, - libBASS/node_list.h, libBASS/parse_interface.h, - libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint - into the BASS language syntax. - -2003-08-11 13:29 mmeineke - - * libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of - degrees of freedom to account for zConstreints - -2003-08-08 16:22 chuckv - - * libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, - 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 - - * libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated - instance of Atom::setZ and Atom::getZ in ZConstaint. - -2003-08-07 16:47 mmeineke - - * libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, - DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, - GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp, - SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp, - SimState.hpp, Torsion.cpp: switched SimInfo to use a system - configuration from SimState rather than arrays from Atom - -2003-08-06 19:47 chuckv - - * libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, - libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, - libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, - samples/metals/Au.bass: Bug fixes for eam... - -2003-08-01 11:18 tim - - * libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of - Z-Constraint - -2003-07-31 14:59 tim - - * ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, - libmdtools/ZConstraint.cpp: add index range checking into - ZConstraint - -2003-07-31 10:38 tim - - * libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters - to the globals - -2003-07-31 10:35 tim - - * libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, - Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, - NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, - SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: - Added Z constraint. - -2003-07-30 16:17 chuckv - - * libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, - libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, - libmdtools/do_Forces.F90, libmdtools/wrappers.F90, - samples/metals/Au.bass: More bug fixes for eam. - -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 - -2003-07-29 11:32 mmeineke - - * libBASS/Globals.cpp: [no log message] - -2003-07-25 15:05 chuckv - - * samples/metals/: Au.bass, metals.mdl: Added bass models for - metals - -2003-07-25 15:00 chuckv - - * libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, - notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. - -2003-07-24 16:22 chuckv - - * ac-tools/configure.in: Changed configure to look for both upper - and lower cass .mod files - -2003-07-24 14:57 chuckv - - * libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for - eam and do_forces. - -2003-07-23 17:13 chuckv - - * libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, - force_globals.F90, simulation_module.F90, status_module.F90: - Finished most code for eam.... - -2003-07-22 16:49 mmeineke - - * libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan - function to the DumpReader. It should now save the start of each - frame in a vector. - -2003-07-22 15:05 mmeineke - - * libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes - to read dump files - -2003-07-22 14:54 tim - - * libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, - Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, - NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log - message] - -2003-07-22 11:41 mmeineke - - * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, - SimSetup.cpp: Fixed a current time initialization bug in - InitFromFile. - -2003-07-21 16:27 mmeineke - - * libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, - Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and - friends to accomadate random file access - -2003-07-21 11:23 mmeineke - - * libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no - one sets it. - -2003-07-21 11:23 mmeineke - - * libmdtools/: InitializeFromFile.cpp, Integrator.cpp, - ReadWrite.hpp: fixed Initializefrom file to start the simulation - from the time specified in the init file. - -2003-07-17 16:49 gezelter - - * libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, - DumpReader.cpp: Started work on a DumpReader - -2003-07-17 15:38 gezelter - - * libmdtools/calc_sticky_pair.F90: Fixes for SSD/E - -2003-07-17 15:32 gezelter - - * forceFields/DUFF.frc, libmdtools/DUFF.cpp, - libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: - Changes for SSD/E - -2003-07-17 14:38 mmeineke - - * libmdtools/do_Forces.F90: commented out an eam line - -2003-07-17 14:32 chuckv - - * libmdtools/atype_module.F90: fixed spelling issue - -2003-07-17 14:29 chuckv - - * libmdtools/: fInfo.c, status_module.F90: added info module - -2003-07-17 14:25 chuckv - - * libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, - atype_module.F90, calc_eam.F90, do_Forces.F90, - fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, - mpiSimulation_module.F90: Added massive changes for eam.... - -2003-07-16 16:49 chuckv - - * libmdtools/EAM_FF.cpp: More up to date version of EAM_FF - -2003-07-16 16:30 mmeineke - - * libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, - SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, - calc_reaction_field.F90, do_Forces.F90, fSimulation.h, - fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, - neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, - wrappers.F90: Changed how cutoffs were handled from C. Now - notifyCutoffs in Fortran notifies those who need the information of - any changes to cutoffs. - -2003-07-16 12:35 gezelter - - * utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. - quickLate is now somewhat more intelligent about periodic - boundaries and wrapping. - -2003-07-16 11:40 chuckv - - * libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists - -2003-07-16 10:34 mmeineke - - * scripts/cleanSrc: added a quick wipe-and-update script for quick - rebuilds on BoB - -2003-07-15 21:11 gezelter - - * libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, - SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more - fixes for box changes - -2003-07-15 17:29 mmeineke - - * libmdtools/simulation_module.F90: removed some debugging print - statements. - -2003-07-15 17:22 mmeineke - - * libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, - do_Forces.F90, simulation_module.F90: fixed a long lived bug in - do_forces. Rrf was not being used in the neighborlist correctly. - rcut was conssistently being set lowere than Rrf causing the dipole - cutoff region to be to small. Also led to the removal of the taper - region to buffer the dipole cutoff. - -2003-07-15 16:34 mmeineke - - * libmdtools/: SimInfo.cpp, simulation_module.F90: working on - fixing ssd bug - -2003-07-15 14:56 gezelter - - * libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes - for the NPT ensembles - -2003-07-15 13:52 mmeineke - - * libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up - simSetup - -2003-07-15 12:57 mmeineke - - * libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, - SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: - fixed some bugs, Changed entry_plug to info where appropriate - -2003-07-15 12:25 chuckv - - * utils/sysBuild.ggo: added more command line arguments - -2003-07-15 12:11 gezelter - - * samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: - Fixing force field line - -2003-07-15 12:10 gezelter - - * libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, - calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, - calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure - tensor - -2003-07-15 10:50 gezelter - - * libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes - -2003-07-15 10:42 gezelter - - * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: - removed old outdated code - -2003-07-15 09:45 gezelter - - * libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx - -2003-07-15 09:28 gezelter - - * libmdtools/Molecule.cpp: removing get_vx - -2003-07-14 22:28 gezelter - - * libmdtools/NPTfm.cpp: Added NPTfm - -2003-07-14 22:27 gezelter - - * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: - Bugfix in NPTim, fixes for NPTfm - -2003-07-14 22:08 gezelter - - * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: - Checking in changes for NPTim - -2003-07-14 18:06 gezelter - - * utils/Makefile: Broken SysBuilder - -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 - -2003-07-14 18:06 gezelter - - * libmdtools/: Integrator.cpp, do_Forces.F90: Removed some - debugging write statements - -2003-07-14 17:38 gezelter - - * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, - NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom - -2003-07-14 16:48 mmeineke - - * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get - and set routines to Atom and DirectionalAtom - -2003-07-14 16:35 chuckv - - * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, - sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder - that takes different cmd line arguments. - -2003-07-14 16:28 mmeineke - - * libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, - ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, - SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors - were not being updated - -2003-07-14 10:04 gezelter - - * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on - NPTim - -2003-07-14 09:55 mmeineke - - * forceFields/DUFF.frc: Switched the bond in the force field back - to constrained, to preserve energy - -2003-07-11 17:34 mmeineke - - * libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, - Integrator.hpp: working on som integrator bugs - -2003-07-11 10:26 gezelter - - * libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting - to worry about all the strtok() calls in our code - -2003-07-11 09:49 gezelter - - * utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness - -2003-07-10 20:15 gezelter - - * libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and - eor. - -2003-07-10 17:15 mmeineke - - * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, - SimInfo.cpp, Thermo.cpp: fixed some bugs - -2003-07-10 14:53 chuckv - - * utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, - nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added - nanoBuilder and a general Lattice builder. - -2003-07-10 12:10 gezelter - - * libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, - Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff - -2003-07-09 17:14 mmeineke - - * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, - Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, - SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the - caclulation of HmatInverse. - -2003-07-09 10:34 mmeineke - - * libBASS/MoleculeStamp.hpp: starting some work for xlate - -2003-07-09 10:33 mmeineke - - * libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff - -2003-07-09 08:56 gezelter - - * libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf - -2003-07-09 08:56 gezelter - - * libBASS/Globals.cpp: Removed Qmass - -2003-07-08 21:15 gezelter - - * libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf - and NPTi - -2003-07-08 20:41 gezelter - - * libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf - -2003-07-08 16:10 gezelter - - * libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] - -2003-07-08 16:06 gezelter - - * libmdtools/NPTi.cpp: fixed box scaling - -2003-07-08 15:56 gezelter - - * libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, - SimInfo.hpp, Thermo.cpp: NPTi - -2003-07-03 14:41 mmeineke - - * libBASS/Makefile, libmdtools/Makefile, src/Makefile, - utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy - scripts in the makefiles - -2003-07-02 16:26 mmeineke - - * libBASS/Makefile, libmdtools/DumpWriter.cpp, - libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, - libmdtools/Makefile, libmdtools/ReadWrite.hpp, - libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, - libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, - utils/Makefile: fixed the bugs introduced by switching the periodic - box to a matrix - -2003-07-01 17:39 gezelter - - * libmdtools/do_Forces.F90: Fortran flexi-BOX - -2003-07-01 17:29 gezelter - - * libmdtools/simulation_module.F90: Fixes for flexi-BOX - -2003-07-01 16:33 mmeineke - - * libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, - fortranWrapDefines.hpp, simulation_module.F90: working on adding - the box matrix to everything. - -2003-06-30 17:03 mmeineke - - * ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - src/oopse.cpp: - Updated the ChangeLog, and Converted most of the SImInfo to use - non-Isotropic boxes. wrapVector needs to be finished. - -2003-06-25 16:12 mmeineke - - * libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds - to Harmonic bonds in the DUFF frc file - - fixed constraints. - -2003-06-25 16:11 mmeineke - - * forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in - the DUFF frc file - -2003-06-24 17:51 gezelter - - * libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! - -2003-06-24 14:57 mmeineke - - * forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, - libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into - the DUFF forcefield and BondExtensions.cpp - -2003-06-23 16:24 mmeineke - - * libmdtools/Integrator.cpp: Doing some work to debug the - constraint code. - -2003-06-20 15:50 gezelter - - * libmdtools/Integrator.hpp: NPT fix - -2003-06-20 15:29 mmeineke - - * libmdtools/Atom.cpp, libmdtools/DUFF.cpp, - libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, - libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, - libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, - libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the - integrator and NVT seem to be working now. - -2003-06-20 11:49 gezelter - - * libmdtools/: Integrator.hpp, NVT.cpp: NVT additions - -2003-06-19 17:02 mmeineke - - * forceFields/DUFF.frc, forceFields/LJFF.frc, - forceFields/LJ_FF.frc, forceFields/Makefile, - forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, - libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, - libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, - libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, - libmdtools/TraPPEFF.cpp: slowly converting to new integrator and - forcefield names. - -2003-06-19 14:21 mmeineke - - * libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: - finished the basics of the integrator and SimSetup.cpp - -2003-06-19 14:11 mmeineke - - * libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it - up / get it to work with the new Integrator. - -2003-06-18 17:20 mmeineke - - * libmdtools/Symplectic.cpp: minor changes in an attempt to fix - output times. - -2003-06-17 16:56 mmeineke - - * libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters - fro the ghost Bend in TraPPE_Ex - - some work on the integrator. ( incomplete) - -2003-06-17 16:55 mmeineke - - * forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost - Bend in TraPPE_Ex - -2003-06-04 16:06 mmeineke - - * libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and - constrainB to the Symplectic integrator - -2003-05-30 16:32 mmeineke - - * utils/bilayerSys.cpp: currently modifiying Symplectic to become - the basic integrator. - - bilayerSys.cpp altered for building tb3. - -2003-05-30 16:31 mmeineke - - * libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, - TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently - modifiying Symplectic to become the basic integrator. - -2003-05-30 15:19 mmeineke - - * libmdtools/Integrator.hpp: added some member variables for - position, velocity, etc. - -2003-05-30 14:07 mmeineke - - * libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT - is now derived from Integrator - -2003-05-20 11:44 mmeineke - - * libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. - -2003-05-17 11:57 mmeineke - - * utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be - working - -2003-05-16 16:37 mmeineke - - * utils/bilayerSys.cpp: still working on the bilayer code - -2003-05-16 09:28 mmeineke - - * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some - work to overhaul sysbuild. - -2003-05-13 16:23 mmeineke - - * libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop - -2003-05-13 15:47 mmeineke - - * samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, - beadLipid/water.mdl: Added bead lipid model to the sample directory - -2003-05-13 15:34 mmeineke - - * forceFields/TraPPE_Ex.frc: finished adding the Tail beads into - the Trappe extended force field - -2003-05-13 12:01 mmeineke - - * forceFields/TraPPE_Ex.frc: added the TailBead atom types to the - TraPPe_Ex forceField - -2003-05-09 14:51 mmeineke - - * samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. - there were some duplicate entries - - added a two chain lipid to the lipid.mdl in sample - -2003-05-09 14:51 mmeineke - - * forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. - there were some duplicate entries - -2003-05-09 11:56 mmeineke - - * forceFields/TraPPE_Ex.frc: added the utils subdirectory to the - configure script - - added the CH branching group to the TraPPE_Ex fource field - -2003-05-09 11:55 mmeineke - - * ac-tools/configure.in: added the utils subdirectory to the - configure script - -2003-04-25 11:02 mmeineke - - * utils/bilayerSys.cpp: i quick fix to th distance in the random - bilayer builder - -2003-04-24 21:00 mmeineke - - * libmdtools/f_verlet_constrained.F90: added a new test for - constraint failure - -2003-04-17 16:54 mmeineke - - * libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, - utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, - utils/bilayerSys.cpp: fixed up sysBuild to where it should now - build our systems - -2003-04-16 16:11 mmeineke - - * utils/: MoLocator.cpp, MoLocator.hpp: almost finished. - -2003-04-15 16:47 mmeineke - - * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys - and sysBuild both will build now. woot! - -2003-04-15 16:20 mmeineke - - * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, - bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp - - sysBuild still need to write the bass file. - - MoLocator.cpp is currently empty - -2003-04-15 15:40 chuckv - - * forceFields/EAM_FF.frc, forceFields/agu3.eam, - forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, - forceFields/pdu3.eam, forceFields/ptu3.eam, - libmdtools/ForceFields.hpp: Added eam force files... - -2003-04-15 11:37 chuckv - - * libmdtools/EAM_FF.cpp: More eam work. - -2003-04-14 16:22 mmeineke - - * libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, - utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: - working on the system builder - -2003-04-14 16:16 chuckv - - * libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed - ordering on NVT calculation in integrators. - -2003-04-14 14:51 mmeineke - - * utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, - obj/placeHolder: working on a system builder - -2003-04-14 14:04 mmeineke - - * utils/Makefile: added Ghost bends to the TraPPE_Ex forceField - - added sysBuild to the utils Makefile - -2003-04-14 14:03 mmeineke - - * forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added - Ghost bends to the TraPPE_Ex forceField - -2003-04-14 13:19 chuckv - - * libmdtools/calc_eam.F90: Added first mangling of EAM. - -2003-04-11 13:46 mmeineke - - * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, - simulation_module.F90: fixed a memory bug in Fortran, where - molMembershipArray was declared nLocal instead of nGlobal. - -2003-04-11 10:16 gezelter - - * libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, - SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, - fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress - for NPT - -2003-04-10 15:08 mmeineke - - * libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a - globalIndex counter to Molecule - -2003-04-10 11:35 gezelter - - * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on - ConstantStress - -2003-04-10 11:27 mmeineke - - * libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. - caused a miscalculation of nLocal. - -2003-04-10 11:21 mmeineke - - * libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, - do_Forces.F90: fixed a bug in symplectic, where presure was only - being calculated the first time through. - -2003-04-09 11:20 chuckv - - * samples/alkane/alkanes.mdl: added pentane to the alkane model - file - -2003-04-09 08:59 gezelter - - * libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, - Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file - -2003-04-08 23:06 gezelter - - * libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, - ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, - SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, - Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, - calc_reaction_field.F90, calc_sticky_pair.F90, - fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and - NVT - -2003-04-08 17:38 chuckv - - * libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, - libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, - libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, - libmdtools/simulation_module.F90, samples/water/ssd.bass: It works - (kinda)... - -2003-04-08 16:35 gezelter - - * libBASS/Globals.cpp, libBASS/Globals.hpp, - libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, - libmdtools/SimSetup.cpp: Fixes for NPT / NVT - -2003-04-08 12:16 chuckv - - * libmdtools/: do_Forces.F90, neighborLists.F90, - simulation_module.F90: Moved expand neighborlist to init_FF. - -2003-04-08 10:20 chuckv - - * libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for - NVT - -2003-04-08 09:39 gezelter - - * libmdtools/Verlet.cpp: fixes for nvt / npt - -2003-04-08 09:34 gezelter - - * libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, - Thermo.cpp, Verlet.cpp: dt/2 fix in nvt - -2003-04-08 07:50 gezelter - - * libmdtools/ExtendedSystem.cpp: Fixes for affine transform - -2003-04-08 07:44 gezelter - - * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, - Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the - NVT and NPT ensembles - -2003-04-07 16:42 gezelter - - * libBASS/Globals.cpp, libBASS/Globals.hpp, - libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, - libmdtools/SimSetup.cpp: Fixes for NPT and NVT - -2003-04-07 16:20 mmeineke - - * libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial - portion of SSD. - -2003-04-07 16:16 mmeineke - - * libmdtools/: ForceFields.cpp, Symplectic.cpp: - doing some testing in sticky through Symplectic. - -2003-04-07 15:51 gezelter - - * libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT - -2003-04-07 15:50 chuckv - - * libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for - tau and virial. - -2003-04-07 15:06 mmeineke - - * libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, - libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, - libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, - src/Makefile: bug fixes - -2003-04-07 11:56 gezelter - - * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, - StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: - Many fixes to add extended system - -2003-04-07 09:30 gezelter - - * src/Makefile: Fixed a bug caused by my experimentation - -2003-04-07 09:30 gezelter - - * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, - Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: - Added ExtendedSystem infrastructure for NPT and NVT calculations - -2003-04-07 09:30 gezelter - - * libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS - -2003-04-04 23:07 gezelter - - * src/Makefile: final mods to try a fortran compiler - -2003-04-04 22:39 gezelter - - * libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, - fortranWrapDefines.hpp: Bug fixes for simulation module rewrites - -2003-04-04 21:56 gezelter - - * libmdtools/: Makefile, atype_module.F90, do_Forces.F90, - fortranWrappers.cpp, wrappers.F90: bug fixes for compilation - -2003-04-04 21:45 gezelter - - * libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug - fixes to fortran wrappers - -2003-04-04 17:22 chuckv - - * libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, - calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, - do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, - simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets - smarter, fortran gets dumber... - -2003-04-04 14:57 mmeineke - - * libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, - neighborLists.F90: fixed a memory read bug in neighborlist - -2003-04-04 14:47 gezelter - - * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, - SimInfo.hpp, Thermo.cpp: Changes for Extended System - -2003-04-04 14:16 gezelter - - * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, - SimInfo.hpp: Fixes for ExtendedSystem - -2003-04-03 20:57 gezelter - - * libmdtools/ExtendedSystem.hpp: Added extended system header - -2003-04-03 20:57 gezelter - - * libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes - for extended system code - -2003-04-03 18:49 gezelter - - * libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to - extendedsystem - -2003-04-03 17:19 mmeineke - - * libmdtools/Molecule.hpp: added some little fixes here and there. - -2003-04-03 17:01 mmeineke - - * libmdtools/TraPPE_ExFF.cpp: fixed a possible call before - initialize bug. - -2003-04-03 16:12 mmeineke - - * libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just - little things like deleteing unused variables and such. - -2003-04-03 15:57 mmeineke - - * libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to - simError.h also some fixes to Molecule.hpp - -2003-04-03 15:57 mmeineke - - * libBASS/simError.h: a few fixes to simError.h - -2003-04-03 15:21 mmeineke - - * libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, - libBASS/simError.h, libmdtools/DumpWriter.cpp, - libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, - libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, - libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, - src/Makefile, src/oopse.cpp: fixed some small things with - simError.h - -2003-04-03 15:19 gezelter - - * libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT - -2003-04-03 14:58 gezelter - - * libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for - now) - -2003-04-03 08:42 gezelter - - * README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: - Changed Readme, added some files - -2003-04-02 17:19 mmeineke - - * libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, - Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: - dipoles mostly work, but there is a memory leak somewhere. - -2003-04-02 10:01 mmeineke - - * libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting - the proper atomIdents. - -2003-04-01 11:50 chuckv - - * libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, - libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, - samples/argon/argon.bass: more bug fixes.... - -2003-04-01 11:49 mmeineke - - * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed - DumpWriter to be more robust to errors. also added a little - namespace to InitFromFile to wrap it's helper functions in MPI - -2003-03-31 17:09 chuckv - - * libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local - not zeroed. - -2003-03-31 16:50 chuckv - - * libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, - libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, - libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, - libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, - libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, - samples/alkane/butane.bass: Fixes in MPI force calc and in - Trappe_Ex parsing. - -2003-03-28 17:34 chuckv - - * libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp - -2003-03-28 16:45 chuckv - - * libBASS/Makefile, libmdtools/DumpWriter.cpp, - libmdtools/InitializeFromFile.cpp: Bug fixes in read-write - routines. - -2003-03-28 14:33 mmeineke - - * libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, - Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a - bug where the Excludes were not being created properly - -2003-03-28 14:30 chuckv - - * libBASS/Makefile, libmdtools/DumpWriter.cpp, - libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, - libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes - and debugging mpi read write from file. - -2003-03-28 10:28 mmeineke - - * libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range - interactions in Trappe - -2003-03-27 18:33 chuckv - - * libmdtools/: SimSetup.cpp, mpiSimulation.cpp, - mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. - -2003-03-27 17:16 mmeineke - - * libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where - excludes were not being initialized - -2003-03-27 16:52 mmeineke - - * src/Makefile: [no log message] - -2003-03-27 16:52 mmeineke - - * libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. - -2003-03-27 16:07 mmeineke - - * libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, - Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, - Verlet.cpp: fixed the compile time bugs, Source builds and links - -2003-03-27 15:48 mmeineke - - * libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few - more bugs. - -2003-03-27 15:40 mmeineke - - * libmdtools/Molecule.cpp: added the Molecule.cpp file - -2003-03-27 15:39 mmeineke - - * libmdtools/: Makefile, Molecule.hpp: fixed the makefile - -2003-03-27 15:36 mmeineke - - * libmdtools/: AbstractClasses.hpp, ForceFields.cpp, - ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, - SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs - -2003-03-27 15:12 mmeineke - - * libmdtools/: AbstractClasses.hpp, ForceFields.cpp, - Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, - Verlet.cpp: I have implemeted Molecules everywhere I could remember - to. will now attempt to compile. - -2003-03-27 14:21 mmeineke - - * libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, - SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished - updating SimSetup to initialize and use the new MPI division of - labour, and Molecule class - -2003-03-27 12:55 mmeineke - - * libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to - use Molecule - -2003-03-27 12:32 mmeineke - - * libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, - SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been - converted to the new Molecule model. TraPPE_Ex is currently being - updated. SimSetups routines are writtten, but not yet called. - -2003-03-27 10:07 gezelter - - * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, - mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom - numbering in MPI - -2003-03-27 09:30 mmeineke - - * libmdtools/mpiSimulation.cpp: little bug fixes here and there. - -2003-03-26 20:49 gezelter - - * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to - fileio for MPI - -2003-03-26 18:14 gezelter - - * libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, - mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug - fixes many bug fixes - -2003-03-26 17:24 gezelter - - * libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on - sequence of atoms on the other processors. Node 0 now fires - potatoes at other processors to get them to send french fries back. - -2003-03-26 17:02 mmeineke - - * libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for - making the molecules is in place. ForceField needs to be updated - next. - -2003-03-26 16:54 mmeineke - - * libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of - the "static" bugs in Atom and Exclude - -2003-03-26 16:50 mmeineke - - * libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, - SimSetup.cpp: still working on the SimSetup routine. also fixed - some things in Exclude.hpp - -2003-03-26 16:24 gezelter - - * libmdtools/Makefile: Added Atom.cpp and Exclude.cpp - -2003-03-26 16:23 gezelter - - * libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom - and Exclude list - -2003-03-26 16:04 gezelter - - * libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and - delete ranges of atoms - -2003-03-26 15:45 mmeineke - - * libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class - with static arrays similar to the Atom class - -2003-03-26 15:22 mmeineke - - * libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm - overhauling the molecule class to contain it's own bonds, bends, - and torsions. - - may god have mercy on my soul. - -2003-03-26 14:34 chuckv - - * libmdtools/mpiSimulation.cpp: Finished globalIndex. - -2003-03-26 13:02 gezelter - - * libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, - mpiSimulation.hpp: MPI stuff for passing out molecules - -2003-03-26 11:12 chuckv - - * libmdtools/mpiSimulation.cpp: working on load balancing - -2003-03-26 10:37 chuckv - - * libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, - samples/argon/argon.bass: Fixes for Parallel thermalization - -2003-03-26 09:55 mmeineke - - * libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in - THermo.cpp - -2003-03-25 17:54 chuckv - - * libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation - of potential energy and temperature. - -2003-03-25 09:29 mmeineke - - * libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, - src/MPIobj/dummy, src/obj/dummy: [no log message] - -2003-03-25 09:29 mmeineke - - * libBASS/MPIobj/dummy: added dummy files to keep the build - deirectories from being pruned. - -2003-03-24 20:07 gezelter - - * samples/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 - -2003-03-24 19:51 gezelter - - * ac-tools/configure.in: Tests are becoming samples - -2003-03-24 19:46 gezelter - - * ac-tools/Make.conf.in: Added makefiles in tests directories - -2003-03-24 16:55 gezelter - - * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, - libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, - libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, - libmdtools/calc_reaction_field.F90, - libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, - libmdtools/simulation_module.F90: electrostatic changes for dipole - / RF separation - -2003-03-24 13:33 mmeineke - - * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, - do_Forces.F90: little bug fixes here and there - -2003-03-24 10:26 mmeineke - - * libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug - where short range interactions were not being calculated. - - removed some debug print statements - -2003-03-21 17:11 chuckv - - * libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, - do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: - various write statements for debugging - -2003-03-21 16:26 chuckv - - * forceFields/Makefile: added links to the makefile in forceFields - -2003-03-21 15:52 gezelter - - * ac-tools/Make.conf.in, ac-tools/configure.in, - libmdtools/Makefile: Fixed F_MACH_DEP bug - -2003-03-21 15:37 gezelter - - * ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, - ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, - libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, - src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, - autoconf fixes - -2003-03-21 14:58 gezelter - - * LICENSE: Added license file - -2003-03-21 14:55 gezelter - - * forceFields/Makefile: Fixed makefile - -2003-03-21 14:49 gezelter - - * forceFields/Makefile: Makefile for forceFields - -2003-03-21 14:42 gezelter - - * README: Readme changes - -2003-03-21 12:52 mmeineke - - * src/Makefile: [no log message] - -2003-03-21 12:52 mmeineke - - * libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends - -2003-03-21 12:42 mmeineke - - * AUTHORS, ChangeLog, NEWS, Makefile, README, - ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, - ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, - ac-tools/install-sh, forceFields/DipoleTest.frc, - forceFields/LJ_FF.frc, forceFields/TraPPE.frc, - forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, - libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, - libBASS/BASS_interface.h, libBASS/BASS_parse.c, - libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, - libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, - libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, - libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, - libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, - libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, - libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, - libBASS/MakeStamps.hpp, libBASS/Makefile, - libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, - libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, - libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, - libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, - libBASS/parse_interface.h, libBASS/parse_me.h, - libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, - libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, - utils/sfmakedepend, ac-tools/shtool, - libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, - libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, - libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, - libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, - libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, - libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, - libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, - libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, - libmdtools/Makefile, libmdtools/Molecule.hpp, - libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, - libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, - libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, - libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, - libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, - libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, - libmdtools/Verlet.cpp, libmdtools/atype_module.F90, - libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, - libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, - libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, - libmdtools/fForceField.h, libmdtools/fSimulation.h, - libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, - libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, - libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, - libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, - libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, - 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 - -2003-03-21 12:42 mmeineke - - * AUTHORS, ChangeLog, NEWS, Makefile, README, - ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, - ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, - ac-tools/install-sh, forceFields/DipoleTest.frc, - forceFields/LJ_FF.frc, forceFields/TraPPE.frc, - forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, - libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, - libBASS/BASS_interface.h, libBASS/BASS_parse.c, - libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, - libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, - libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, - libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, - libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, - libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, - libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, - libBASS/MakeStamps.hpp, libBASS/Makefile, - libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, - libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, - libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, - libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, - libBASS/parse_interface.h, libBASS/parse_me.h, - libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, - libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, - utils/sfmakedepend, ac-tools/shtool, - libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, - libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, - libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, - libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, - libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, - libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, - libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, - libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, - libmdtools/Makefile, libmdtools/Molecule.hpp, - libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, - libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, - libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, - libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, - libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, - libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, - libmdtools/Verlet.cpp, libmdtools/atype_module.F90, - libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, - libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, - libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, - libmdtools/fForceField.h, libmdtools/fSimulation.h, - libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, - libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, - libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, - libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, - libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, - 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 +2004-06-09 11:59 tim + + * ChangeLog, libmdtools/Roll.cpp: Roll in progress + +2004-06-09 11:16 tim + + * libmdtools/: ConstraintAlgorithm.hpp, ConstraintElement.hpp, + Euler3.cpp, Euler3.hpp, Integrator.hpp, Make.dep, Makefile.in, + Mat3x3d.cpp, Mat3x3d.hpp, Quaternion.cpp, Quaternion.hpp, + Rattle.cpp, Rattle.hpp, RigidBody.cpp, RigidBody.hpp, Roll.cpp, + Roll.hpp, Shake.cpp, Shake.hpp, Vector3d.cpp, Vector3d.hpp: 1. + adding some useful math classes(Mat3x3d, Vector3d, Quaternion, + Euler3) these classes use anonymous union and struct to support + double[3], double[3][3] and double[4] 2. adding roll constraint + algorithm + +2004-06-08 11:49 gezelter + + * libmdtools/: NPT.cpp, NPTf.cpp, StuntDouble.cpp, Thermo.cpp: + Fixed a bug in NPTf (vScale was declared in the cpp file in + addition to the declaration in Integrator.hpp file) + +2004-06-07 09:26 gezelter + + * libBASS/Globals.cpp, libmdtools/AtomVisitor.cpp, + libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.hpp, + libmdtools/ConstraintIterator.hpp, + libmdtools/ConstraintManager.hpp, libmdtools/ConstraintPair.hpp, + libmdtools/DirectionalAtom.cpp, libmdtools/DumpReader.cpp, + libmdtools/DumpWriter.cpp, libmdtools/MatVec3.c, + libmdtools/MatVec3.h, libmdtools/StreamTokenizer.hpp, + libmdtools/ZConsReader.cpp: Fixes from gcc -Wall + +2004-06-07 09:09 chrisfen + + * libmdtools/Thermo.cpp: Dan cleaned up the pressure calculation a + bit... Got rid of some unnecessary lines of code in Thermo.cpp + +2004-06-04 16:00 gezelter + + * libmdtools/: ConstraintIterator.hpp, OOPSEMinimizer.cpp, + StuntDouble.cpp: small bugfixes + +2004-06-04 15:29 tim + + * libmdtools/Integrator.hpp: [no log message] + +2004-06-04 14:30 tim + + * ChangeLog, libmdtools/CallbackFunctor.cpp, + libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.cpp, + libmdtools/ConstraintAlgorithm.hpp, libmdtools/Integrator.hpp, + libmdtools/OOPSEMinimizer.cpp, libmdtools/Rattle.hpp, + libmdtools/Shake.hpp, libmdtools/ShakeMin.cpp, + libmdtools/ShakeMin.hpp: constraint algorithm for minimization is + working + +2004-06-04 11:23 gezelter + + * forceFields/charmm27.vdw: Moved to SHAPES + +2004-06-04 11:23 gezelter + + * forceFields/: LJ.vdw, amber99.vdw, gaff.vdw, oplsaal.vdw: [no log + message] + +2004-06-04 09:59 gezelter + + * libmdtools/: notifyCutoffs.F90, status_module.F90, wrappers.F90: + More work on Fortran side of error handler + +2004-06-04 09:59 gezelter + + * configure, ac-tools/aclocal.m4: fixed a typo in autoconf script + +2004-06-04 09:35 gezelter + + * libmdtools/: Makefile.in, fInfo.c, status_module.F90: Unifying + the error handlers + +2004-06-04 09:17 gezelter + + * libBASS/: MemberStamp.cpp, MemberStamp.hpp: Not used anymore + +2004-06-04 09:11 gezelter + + * libBASS/: config.h.in, fError.c: forgot to add these + +2004-06-03 22:15 tim + + * ChangeLog, libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, + libmdtools/CallbackFunctor.cpp, libmdtools/ConstraintAlgorithm.cpp, + libmdtools/ConstraintManager.cpp, libmdtools/GenericData.cpp, + libmdtools/GenericData.hpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/Make.dep, + libmdtools/Makefile.in, libmdtools/Molecule.cpp, + libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NVT.cpp, + libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, + libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/StuntDouble.cpp, + libmdtools/StuntDouble.hpp, utils/Vector3.hpp: new rattle algorithm + is working + +2004-06-03 21:38 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + libBASS/Makefile.in, libBASS/mpiBASS.h, libBASS/simError.c, + libBASS/simError.h, libmdtools/Makefile.in, libmdtools/config.h.in, + libmdtools/notifyCutoffs.F90, src/Makefile.in: Config changes for + fortran access to SimError + +2004-06-03 16:51 tim + + * libmdtools/: CallbackFunctor.cpp, CallbackFunctor.hpp, + ConstraintAlgorithm.cpp, ConstraintAlgorithm.hpp, + ConstraintElement.cpp, ConstraintElement.hpp, + ConstraintIterator.hpp, ConstraintManager.cpp, + ConstraintManager.hpp, ConstraintPair.hpp, Rattle.cpp, Rattle.hpp, + Shake.cpp, Shake.hpp, ShakeMin.cpp, ShakeMin.hpp, TypeInfo.hpp: new + implementation of constraint + +2004-06-03 16:06 tim + + * libmdtools/DumpWriter.cpp: fixed a bug which only writes out the + first atom of a molecule + +2004-06-03 15:02 gezelter + + * libmdtools/SimSetup.cpp: Fixed groupOffset bug + +2004-06-03 15:02 gezelter + + * ac-tools/: aclocal.m4, configure.in: Working on MPI scripting for + autoconf + +2004-06-02 13:28 gezelter + + * samples/: argon/Makefile, minimizer/argon/Makefile: Shouldn't + have been in CVS + +2004-06-02 13:28 gezelter + + * samples/: argon/Makefile, minimizer/argon/Makefile: Why is this + in CVS? + +2004-06-02 13:27 gezelter + + * libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Make.dep, + Makefile.in, WATER.cpp: formatting error messages, dependency fixes + +2004-06-02 13:27 gezelter + + * libBASS/simError.h: starting fortran-usable version of simError + +2004-06-02 09:56 chrisfen + + * samples/: argon/Makefile, minimizer/argon/Makefile: Probably + shouldn't be in CVS + +2004-06-02 09:56 chrisfen + + * libmdtools/: Integrator.cpp, NVT.cpp, ReadWrite.hpp, + Restraints.cpp, SimInfo.cpp, StatWriter.cpp: Formatting Changes, + removed writeRaw + +2004-06-02 09:56 chrisfen + + * libBASS/simError.c: Formatting Changes + +2004-06-02 09:21 gezelter + + * libBASS/simError.c, libBASS/simError.h, libmdtools/SimInfo.cpp: + severity levels in simError + +2004-06-01 16:45 gezelter + + * libmdtools/: Exclude.cpp, SimInfo.cpp, calc_LJ_FF.F90, + do_Forces.F90, mpiSimulation.cpp, neighborLists.F90, + simulation_module.F90: Bug fix (fixes of skipList and neighbor list + under MPI) + +2004-06-01 16:44 gezelter + + * libBASS/MoleculeStamp.cpp: Bug fix (memory leak) + +2004-06-01 13:43 gezelter + + * samples/: argon/argon.bass, minimizer/argon/argon.bass: Testing + +2004-06-01 13:42 gezelter + + * libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, + SimSetup.hpp, do_Forces.F90, fortranWrapDefines.hpp, + mpiSimulation.cpp, mpiSimulation_module.F90, simulation_module.F90: + Cutoff Groups for MPI + +2004-06-01 13:07 chrisfen + + * libmdtools/: ForceFields.cpp, StatWriter.cpp: Fixed bug in + useLiquidThermInt routine in ForceFields.cpp + +2004-06-01 12:15 chrisfen + + * libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, + SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Implemented a separate + solid and liquid thermodynamic integration routines + +2004-06-01 10:57 tim + + * libmdtools/: CutoffGroup.hpp, SimSetup.cpp: cutoff group in + progress + +2004-06-01 09:27 chrisfen + + * libBASS/: Globals.cpp, Globals.hpp: Added useLiquidThermInt + keyword and changed useThermInt to useSolidThermInt + +2004-06-01 09:21 chrisfen + + * libBASS/: Globals.cpp, Globals.hpp: Paving the way for separate + solid and liquid thermodynamic integration routines + +2004-05-28 10:21 gezelter + + * libmdtools/do_Forces.F90: bugfix starting + +2004-05-27 15:06 chrisfen + + * libmdtools/: Integrator.cpp, StatWriter.cpp: Fixed a bug in + Integrator.cpp where it called writeRaw() when useThermInt = + false... + +2004-05-27 14:51 tim + + * ChangeLog, libmdtools/do_Forces.F90, + libmdtools/simulation_module.F90: Bug fix for SkipList + +2004-05-27 14:26 gezelter + + * libmdtools/SimSetup.cpp: bugfix in simsetup? + +2004-05-27 13:59 gezelter + + * libmdtools/: DumpReader.cpp, DumpWriter.cpp, + InitializeFromFile.cpp, SimInfo.cpp, SimSetup.cpp, SimSetup.hpp, + ZConsWriter.cpp, ZConstraint.cpp, fortranWrapDefines.hpp, + mdProfile.cpp, mpiSimulation.cpp, mpiSimulation.hpp, + mpiSimulation_module.F90, randomSPRNG.cpp, simulation_module.F90: + Cutoff group changes under MPI + +2004-05-27 11:20 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in: Fixes for + xlc++ + +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 + for fortran group-based switching function + +2004-05-07 16:35 gezelter + + * libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, + Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, + calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, + calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, + force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, + mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, + simulation_module.F90: Many changes to get group-based cutoffs to + work + +2004-05-01 13:52 tim + + * ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, + libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, + libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, + libmdtools/do_Forces.F90, libmdtools/fSimulation.h, + libmdtools/fortranWrapDefines.hpp, + libmdtools/simulation_module.F90: C++ pass groupList to fortran + +2004-04-29 11:03 tim + + * ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in + calc_charge_charge when using molecular cutoff + +2004-04-28 21:11 tim + + * libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an + unmatched c/fortran interface + +2004-04-28 18:09 tim + + * ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: + keep the previous position of cantilever in SMD + +2004-04-28 17:34 tim + + * ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, + libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug + in Molecule.cpp which initialize massRatio before creat the array. + fix two bugs in ZconsVisitor + +2004-04-28 17:06 gezelter + + * libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: + Adding molecular cutoffs + +2004-04-28 16:39 gezelter + + * libmdtools/: calc_charge_charge.F90, do_Forces.F90, + fSimulation.h, force_globals.F90, simulation_module.F90: work on + molecular cutoffs + +2004-04-28 16:39 gezelter + + * libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to + Globals + +2004-04-27 11:26 tim + + * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, + ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, + fSimulation.h, fortranWrapDefines.hpp: add center of mass of the + molecule and massRation into atom class + +2004-04-26 16:16 mmeineke + + * libBASS/Globals.cpp: modified the defaults for the system init + time and system init state. + +2004-04-26 09:29 gezelter + + * libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in + calc_charge_charge.F90 + +2004-04-23 23:31 tim + + * ChangeLog, libmdtools/AtomVisitor.cpp, + libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add + reaction field correction to charge-charge interaction + +2004-04-22 16:33 tim + + * libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, + Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the + calculation of pressure tensor + +2004-04-22 09:55 tim + + * libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed + another bug in InitFromFile. MPI verion of OOPSE is working again + +2004-04-21 22:29 tim + + * libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, + InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, + SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two + bugs in MPI version of InitfromFile and one unmatch MPI command in + DumpWriter + +2004-04-21 00:32 tim + + * libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, + libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, + utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some + useless files + +2004-04-20 11:56 tim + + * libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, + SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and + velocitize at thermo + +2004-04-20 00:39 tim + + * ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, + libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, + libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, + libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, + libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, + libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, + utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, + utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version + +2004-04-19 17:13 gezelter + + * libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, + Thermo.cpp: Fixed a charge bug + +2004-04-19 15:54 tim + + * libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, + libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, + libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed + a bug in CompositeVisitor which cause the double counting problem + +2004-04-19 12:44 tim + + * libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, + libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, + libmdtools/DumpReader.cpp, libmdtools/Make.dep, + libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, + libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: + Dump2XYZ is almost working except atoms in rigidbody are double + counted + +2004-04-18 22:52 tim + + * ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, + libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, + libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, + libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, + libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, + libmdtools/Integrator.cpp, libmdtools/Makefile.in, + libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, + libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, + libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, + libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, + libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, + libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, + libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, + utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new + implement of quickLate using visitor and composite pattern + +2004-04-15 17:15 tim + + * libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting + exclude list + +2004-04-15 11:18 tim + + * ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, + libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, + libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, + libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, + libmdtools/Thermo.cpp, libmdtools/WATER.cpp, + libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix + whole bunch of bugs :-) + +2004-04-14 12:20 chrisfen + + * forceFields/WATER.frc: Added the WATER.frc force field + +2004-04-14 11:32 gezelter + + * libmdtools/Molecule.cpp: fixed for get_potential + +2004-04-14 10:37 tim + + * AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, + libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/Make.dep, + libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, + libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, + libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, + libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, + libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: + Change DumpWriter and InitFromFile + +2004-04-13 11:26 gezelter + + * libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now + molecules can keep track of their own IntegrableObjects (and + RigidBodies). Also a bug-fix so that SimInfo can keep track of + RigidBodies (which was done incorrectly before). + +2004-04-13 11:25 gezelter + + * libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable + (will back out momentarily) + +2004-04-13 10:10 gezelter + + * libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. + Those were old. + +2004-04-13 10:09 gezelter + + * libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot + to add IntegrableObjects + +2004-04-12 16:02 gezelter + + * libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code + +2004-04-12 15:32 gezelter + + * samples/: alkane/butane.bass, water/ssd.bass: Slightly longer + test run + +2004-04-12 15:32 gezelter + + * libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, + DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, + DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, + ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, + Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, + MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, + NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, + SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, + SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, + WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics + (Somewhat extensive) + +2004-04-12 15:31 gezelter + + * libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, + libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, + utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: + Changes for RigidBody dynamics + +2004-03-17 09:22 tim + + * libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, + libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, + libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, + libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it + does not sound a good choice, next commit will seperate SMD and + ZConstraint + +2004-03-16 14:22 tim + + * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, + libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, + libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint + now can support sequential moving. Refactorying is needed to + support SMD in ZConstraint + +2004-03-02 15:32 tim + + * libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, + StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to + support large file + +2004-03-01 16:17 tim + + * utils/zsub.cpp: Fix a couple of bugs in zsub + +2004-03-01 15:01 tim + + * ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, + libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, + libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, + utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, + utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a + program which can be used to replace atom type for zconstraint into + OOPSE + +2004-02-24 11:36 tim + + * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log + message] + +2004-02-24 10:49 tim + + * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, + Constraint.cpp, Constraint.hpp, ConstraintList.cpp, + ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, + Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, + NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, + OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, + SymMatrix.hpp: remove the old implement of minimizer from cvs tree + +2004-02-24 10:44 tim + + * libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, + Integrator.hpp, Makefile.in, Minimizer1D.cpp, + MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, + OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, + SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of + compose to implement Minimizer both versions are working + +2004-02-17 14:23 tim + + * ChangeLog, libmdtools/ConjugateMinimizer.cpp, + libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, + libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, + libmdtools/MinimizerParameterSet.hpp, + libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order + to remove the constraint force along bond direction + +2004-02-10 16:33 tim + + * ChangeLog, libmdtools/ConjugateMinimizer.cpp, + libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: + single version of energy minimization is working. + +2004-02-09 15:38 mmeineke + + * staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on + the massive memory overusage by OOPSE + +2004-02-09 09:48 chrisfen + + * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the + hardwired LJ_rcut + +2004-02-06 19:14 tim + + * libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log + message] + +2004-02-06 16:37 tim + + * ChangeLog, libBASS/Globals.cpp, + libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, + libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of + energy minimization for argon is working, need to add constraint + +2004-02-06 14:05 tim + + * libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add + one more file into Makefile.in + +2004-02-06 13:58 tim + + * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, + libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, + libmdtools/Integrator.hpp, libmdtools/Makefile.in, + libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, + libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, + libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, + libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add + some lines into global.cpp to make it work with energy minimization + +2004-02-04 17:26 tim + + * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, + Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, + Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, + NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) + Single version of conjugate gradient with golden search linesearch + pass a couple of functions test. Brent's algorithm is still broken + +2004-02-03 17:54 tim + + * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, + Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, + NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, + SteepestDescent.hpp: NLModel0, NLModel1 pass uit test + +2004-02-03 15:47 tim + + * libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, + ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, + NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, + SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, + SteepestDescent.hpp: [no log message] + +2004-02-03 15:43 tim + + * libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, + Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, + MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, + NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory + constraint class + +2004-02-03 12:10 tim + + * libmdtools/Functor.hpp: Functor.hpp pass unit test + +2004-02-03 10:21 tim + + * ChangeLog, libmdtools/Minimizer1D.cpp, + libmdtools/Minimizer1D.hpp: begin unit test of minimizer + +2004-02-02 15:29 tim + + * libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, + Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: + Adding GoldenSection and Brent LineSearch Method + +2004-01-30 16:47 tim + + * libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, + MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, + NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from + MinimizerBase instead of a functor to do line seach + +2004-01-30 10:00 chrisfen + + * forceFields/Makefile.in, libmdtools/Atom.cpp, + libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, + libmdtools/Integrator.cpp, libmdtools/Makefile.in, + libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, + libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, + libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, + libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now + has a working WATER.cpp forcefield and parser. This involved + changes to WATER.cpp and ForceFields amoung other files. One + important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. + This will be removed on the next commit... + +2004-01-29 18:00 gezelter + + * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, + libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, + libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, + libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, + libBASS/RigidBodyStamp.hpp, libBASS/interface.c, + libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, + libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, + libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: + member list fixes for rigid bodies + +2004-01-29 16:44 tim + + * libmdtools/MinimizerParameterSet.hpp: Adding + MinimizerParameterSet class. + +2004-01-28 17:44 tim + + * libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of + NLModel0 and NLModel1 + +2004-01-28 15:40 tim + + * libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision + of NLModel + +2004-01-27 15:34 gezelter + + * samples/water/: ssd.bass, water.mdl: Added point-charge models to + water.mdl file, updated ssd.bass to use new SSD name + +2004-01-27 15:34 gezelter + + * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, + MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody + stuff + +2004-01-27 14:39 gezelter + + * samples/water/ssd.bass: Longer run time to test SSD water in MPI + +2004-01-27 14:39 gezelter + + * samples/metals/Au.bass: Longer run time to test gold in MPI + +2004-01-27 14:38 gezelter + + * samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer + run time to test argon + +2004-01-27 14:38 gezelter + + * libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS + changes to do new rigidBody scheme a copy of WATER.cpp from this + morning + +2004-01-27 14:37 gezelter + + * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, + BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, + MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, + MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, + interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, + node_list.h, parse_interface.h, parse_tree.c: More BASS changes to + do new rigidBody scheme + +2004-01-27 14:15 tim + + * libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, + Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, + MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of + constraint for Nonlinear Optimization Model + +2004-01-26 17:01 gezelter + + * utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use + Euler angles for orientation instead of unit vectors required + changes in MoLocator + +2004-01-26 16:53 gezelter + + * samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, + beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, + water/water.mdl: Changed orientation lines from unit vectors to + euler angles + +2004-01-26 16:52 gezelter + + * libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians + +2004-01-26 16:45 gezelter + + * libmdtools/SimSetup.cpp: Changed default orientation in BASS to + use Euler angles in the following order: phi, theta, psi Removed + the ability to set orientation using a unit vector + +2004-01-26 16:26 gezelter + + * libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, + RigidBodyStamp.hpp: Changed default orientation in BASS to use + Euler angles in the following order: phi, theta, psi Removed the + ability to set orientation using a unit vector + +2004-01-26 13:52 gezelter + + * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, + MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies + +2004-01-22 12:34 chrisfen + + * libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, + TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: + Corrected spelling in several directories, and stated WATER.cpp + +2004-01-21 17:16 tim + + * libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, + NLOPModel.hpp: constraint class in energy minimization + +2004-01-20 15:34 tim + + * libmdtools/MinimizerBase.hpp: Adding energy minimization + +2004-01-20 15:32 tim + + * libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, + NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer + +2004-01-19 16:17 gezelter + + * libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages + more user-friendly + +2004-01-19 13:51 chrisfen + + * forceFields/DUFF.frc: Updated the default water to SSD/E + +2004-01-19 13:36 tim + + * libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample + time, status time, thermal time and reset time are not divisible by + dt + +2004-01-19 11:10 gezelter + + * third-party/Makefile.in: Added a bunch of dummy targets so make + won't complain + +2004-01-19 11:10 gezelter + + * samples/lipid/5x5.bass: Fixed old bass file + +2004-01-19 11:09 gezelter + + * libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies + required a change in how the MoleculeStamps are used by divideLabor + in mpiSimulation.cpp + +2004-01-19 11:08 gezelter + + * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, + BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, + MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, + RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, + make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, + parse_tree.c: BASS changes to add RigidBodies and LJrcut + +2004-01-16 16:55 tim + + * libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating + eor file + +2004-01-16 16:51 mmeineke + + * libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could + write eor files + +2004-01-16 10:01 mmeineke + + * libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi + initialization of the AtomStruct + +2004-01-15 16:57 chuckv + + * configure, libmdtools/DumpWriter.cpp: Fixes for Dumps + +2004-01-15 10:51 gezelter + + * ac-tools/aclocal.m4: Changes for altivec + +2004-01-15 09:22 gezelter + + * libmdtools/DumpWriter.cpp: Documented the Spud Toss + +2004-01-14 23:33 gezelter + + * libmdtools/do_Forces.F90: changes for charge charge interactions + +2004-01-14 20:14 gezelter + + * libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, + notifyCutoffs.F90: More work for adding charges + +2004-01-14 17:41 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + src/Makefile.in: autoconf fixes + +2004-01-14 11:28 mmeineke + + * utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug + +2004-01-14 10:48 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + src/Makefile.in, third-party/Makefile.in: autoconf compatibility + changes for icc8 + +2004-01-13 18:01 gezelter + + * libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, + SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, + fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: + Changes for adding direct charge-charge interactions (with + switching function) + +2004-01-13 17:34 gezelter + + * libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, + oopseMPI_module.F90: Some changes for new MPI organization and + direct charge-charge interactions + +2004-01-13 17:11 tim + + * Functor.hpp, libmdtools/Functor.hpp: [no log message] + +2004-01-13 16:22 tim + + * Functor.hpp, samples/water/ssd.bass: Energy Minimization method + +2004-01-13 15:35 tim + + * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the + eor file whenever it is used instead of rewinding it + +2004-01-13 15:04 tim + + * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface + of writeFrame + +2004-01-13 10:46 tim + + * libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: + Merge the code of writeFinal and writeDump; + Adding sortingIndex into DumpWriter; + Fix a bug of writing last frame twice in integrator + +2004-01-12 17:54 tim + + * ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix + a bug in copying string + +2004-01-12 15:37 tim + + * ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, + samples/minimizer/argon/argon.bass, samples/water/ssd.bass: + Dumpwriter only write out the atoms on master nodes + +2004-01-10 04:46 tim + + * ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just + roll it back fix a bug of copying string to a pointer Still have + Seg fault, it looks like a random MPI seg fault in totalview + +2004-01-09 21:15 tim + + * libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub + +2004-01-09 15:29 gezelter + + * libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) + +2004-01-08 17:25 chuckv + + * libmdtools/DumpWriter.cpp: A work in progress... + +2004-01-08 13:59 gezelter + + * libmdtools/DumpWriter.cpp: null terminate some strings just in + case + +2004-01-08 13:13 mmeineke + + * libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS + state bug. + +2004-01-08 13:05 gezelter + + * libmdtools/DumpWriter.cpp: added strncpy to DumpWriter + +2004-01-08 12:57 mmeineke + + * libmdtools/InitializeFromFile.cpp: fixed the restart from NVT + exstended state bug + +2004-01-08 12:40 gezelter + + * libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter + +2004-01-08 10:44 mmeineke + + * libmdtools/InitializeFromFile.cpp: added support for the ignore + XS state info flag + +2004-01-07 14:26 tim + + * libmdtools/DumpWriter.cpp, libmdtools/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 + + * libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: + performance fixes in the dipole dipole and reaction field code + +2004-01-06 13:54 chuckv + + * libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a + little more sane + +2004-01-05 17:49 chuckv + + * libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, + calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, + calc_sticky_pair.F90, do_Forces.F90: Attempting to increase + performance by reducing spurious function calls + +2004-01-05 17:18 chuckv + + * libmdtools/do_Forces.F90: mangling forces even further + +2004-01-05 17:18 chuckv + + * configure, ac-tools/configure.in: mpich mucking + +2004-01-05 17:12 chuckv + + * libmdtools/do_Forces.F90: mangled do_forces... + +2004-01-05 16:00 chuckv + + * ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, + libmdtools/do_Forces.F90: Added bitmask to do_forces property + lookup + +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/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 + + * 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/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 + + * 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, + latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, + sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. + Nanobuilder still broke. + +2003-08-15 14:24 tim + + * libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, + libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp, + libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint + Method + +2003-08-14 11:16 tim + + * libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint + with average force substraction strategy + +2003-08-13 16:20 chuckv + + * libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some + profiling code -DPROFILE. + +2003-08-13 14:21 tim + + * libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, + libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic + potential & z-contraint method + +2003-08-12 16:44 mmeineke + + * libBASS/BASS_interface.cpp, libBASS/Globals.hpp, + libmdtools/Atom.cpp, libmdtools/DUFF.cpp, + libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, + libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really + annoying bug in Directional Atom, where mu was getting written to + pseudorandom memory location. + +2003-08-12 14:56 tim + + * libBASS/BASS_interface.cpp, libBASS/Globals.cpp, + libBASS/Globals.hpp, libmdtools/Atom.hpp, + libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, + libmdtools/SimSetup.cpp: debugging globals + +2003-08-12 13:40 gezelter + + * forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes + and new atypes in LJFF + +2003-08-12 13:15 gezelter + + * forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older + stuff... + +2003-08-12 13:14 chuckv + + * utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. + +2003-08-12 13:04 chuckv + + * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: + Missed del of files before. + +2003-08-12 13:03 chuckv + + * utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log + message] + +2003-08-12 13:01 chuckv + + * utils/sysbuilder/Makefile: commit makefile + +2003-08-12 12:51 tim + + * libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, + libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, + libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added + harmonical potential to z-constraint method + +2003-08-11 17:31 chuckv + + * utils/Makefile: Changed makefile to only build quicklate. + +2003-08-11 17:25 chuckv + + * ac-tools/configure.in: added utils/sysbuilder to be built. + +2003-08-11 17:12 chuckv + + * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, + bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, + sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp, + sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp, + sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c, + sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp, + sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp, + sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp, + sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged + sysbuilder into a subdirectory. Fixed some of sysbuilder to work + with new atom allocation in libmdtools. + +2003-08-11 14:41 tim + + * libmdtools/: Integrator.cpp, Integrator.hpp: added method of + moving zconstraint molecules to specified positions + +2003-08-11 14:39 tim + + * libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] + +2003-08-11 14:38 mmeineke + + * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, + libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, + libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp, + libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c, + libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h, + libBASS/node_list.h, libBASS/parse_interface.h, + libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint + into the BASS language syntax. + +2003-08-11 13:29 mmeineke + + * libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of + degrees of freedom to account for zConstreints + +2003-08-08 16:22 chuckv + + * libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, + libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, + samples/metals/Au.bass: EAM works...... Neighbor list also + works..... + +2003-08-08 12:48 mmeineke + + * libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated + instance of Atom::setZ and Atom::getZ in ZConstaint. + +2003-08-07 16:47 mmeineke + + * libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, + DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, + GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp, + SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp, + SimState.hpp, Torsion.cpp: switched SimInfo to use a system + configuration from SimState rather than arrays from Atom + +2003-08-06 19:47 chuckv + + * libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, + libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, + libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, + samples/metals/Au.bass: Bug fixes for eam... + +2003-08-01 11:18 tim + + * libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of + Z-Constraint + +2003-07-31 14:59 tim + + * ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, + libmdtools/ZConstraint.cpp: add index range checking into + ZConstraint + +2003-07-31 10:38 tim + + * libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters + to the globals + +2003-07-31 10:35 tim + + * libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, + Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, + NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, + SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: + Added Z constraint. + +2003-07-30 16:17 chuckv + + * libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, + libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, + libmdtools/do_Forces.F90, libmdtools/wrappers.F90, + samples/metals/Au.bass: More bug fixes for eam. + +2003-07-29 11:32 mmeineke + + * libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: + working on the props code + +2003-07-29 11:32 mmeineke + + * libBASS/Globals.cpp: [no log message] + +2003-07-25 15:05 chuckv + + * samples/metals/: Au.bass, metals.mdl: Added bass models for + metals + +2003-07-25 15:00 chuckv + + * libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, + notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. + +2003-07-24 16:22 chuckv + + * ac-tools/configure.in: Changed configure to look for both upper + and lower cass .mod files + +2003-07-24 14:57 chuckv + + * libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for + eam and do_forces. + +2003-07-23 17:13 chuckv + + * libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, + force_globals.F90, simulation_module.F90, status_module.F90: + Finished most code for eam.... + +2003-07-22 16:49 mmeineke + + * libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan + function to the DumpReader. It should now save the start of each + frame in a vector. + +2003-07-22 15:05 mmeineke + + * libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes + to read dump files + +2003-07-22 14:54 tim + + * libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, + Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, + NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log + message] + +2003-07-22 11:41 mmeineke + + * libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, + SimSetup.cpp: Fixed a current time initialization bug in + InitFromFile. + +2003-07-21 16:27 mmeineke + + * libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, + Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and + friends to accomadate random file access + +2003-07-21 11:23 mmeineke + + * libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no + one sets it. + +2003-07-21 11:23 mmeineke + + * libmdtools/: InitializeFromFile.cpp, Integrator.cpp, + ReadWrite.hpp: fixed Initializefrom file to start the simulation + from the time specified in the init file. + +2003-07-17 16:49 gezelter + + * libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, + DumpReader.cpp: Started work on a DumpReader + +2003-07-17 15:38 gezelter + + * libmdtools/calc_sticky_pair.F90: Fixes for SSD/E + +2003-07-17 15:32 gezelter + + * forceFields/DUFF.frc, libmdtools/DUFF.cpp, + libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: + Changes for SSD/E + +2003-07-17 14:38 mmeineke + + * libmdtools/do_Forces.F90: commented out an eam line + +2003-07-17 14:32 chuckv + + * libmdtools/atype_module.F90: fixed spelling issue + +2003-07-17 14:29 chuckv + + * libmdtools/: fInfo.c, status_module.F90: added info module + +2003-07-17 14:25 chuckv + + * libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, + atype_module.F90, calc_eam.F90, do_Forces.F90, + fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, + mpiSimulation_module.F90: Added massive changes for eam.... + +2003-07-16 16:49 chuckv + + * libmdtools/EAM_FF.cpp: More up to date version of EAM_FF + +2003-07-16 16:30 mmeineke + + * libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, + SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, + calc_reaction_field.F90, do_Forces.F90, fSimulation.h, + fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, + neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, + wrappers.F90: Changed how cutoffs were handled from C. Now + notifyCutoffs in Fortran notifies those who need the information of + any changes to cutoffs. + +2003-07-16 12:35 gezelter + + * utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. + quickLate is now somewhat more intelligent about periodic + boundaries and wrapping. + +2003-07-16 11:40 chuckv + + * libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists + +2003-07-16 10:34 mmeineke + + * scripts/cleanSrc: added a quick wipe-and-update script for quick + rebuilds on BoB + +2003-07-15 21:11 gezelter + + * libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, + SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more + fixes for box changes + +2003-07-15 17:29 mmeineke + + * libmdtools/simulation_module.F90: removed some debugging print + statements. + +2003-07-15 17:22 mmeineke + + * libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, + do_Forces.F90, simulation_module.F90: fixed a long lived bug in + do_forces. Rrf was not being used in the neighborlist correctly. + rcut was conssistently being set lowere than Rrf causing the dipole + cutoff region to be to small. Also led to the removal of the taper + region to buffer the dipole cutoff. + +2003-07-15 16:34 mmeineke + + * libmdtools/: SimInfo.cpp, simulation_module.F90: working on + fixing ssd bug + +2003-07-15 14:56 gezelter + + * libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes + for the NPT ensembles + +2003-07-15 13:52 mmeineke + + * libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up + simSetup + +2003-07-15 12:57 mmeineke + + * libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, + SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: + fixed some bugs, Changed entry_plug to info where appropriate + +2003-07-15 12:25 chuckv + + * utils/sysBuild.ggo: added more command line arguments + +2003-07-15 12:11 gezelter + + * samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: + Fixing force field line + +2003-07-15 12:10 gezelter + + * libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, + calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, + calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure + tensor + +2003-07-15 10:50 gezelter + + * libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes + +2003-07-15 10:42 gezelter + + * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: + removed old outdated code + +2003-07-15 09:45 gezelter + + * libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx + +2003-07-15 09:28 gezelter + + * libmdtools/Molecule.cpp: removing get_vx + +2003-07-14 22:28 gezelter + + * libmdtools/NPTfm.cpp: Added NPTfm + +2003-07-14 22:27 gezelter + + * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: + Bugfix in NPTim, fixes for NPTfm + +2003-07-14 22:08 gezelter + + * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: + Checking in changes for NPTim + +2003-07-14 18:06 gezelter + + * utils/Makefile: Broken SysBuilder + +2003-07-14 18:06 gezelter + + * samples/: alkane/init_butane.eor, argon/argon.bass, + 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 + + * libmdtools/: Integrator.cpp, do_Forces.F90: Removed some + debugging write statements + +2003-07-14 17:38 gezelter + + * libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, + NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom + +2003-07-14 16:48 mmeineke + + * libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get + and set routines to Atom and DirectionalAtom + +2003-07-14 16:35 chuckv + + * utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, + sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder + that takes different cmd line arguments. + +2003-07-14 16:28 mmeineke + + * libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, + ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, + SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors + were not being updated + +2003-07-14 10:04 gezelter + + * libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on + NPTim + +2003-07-14 09:55 mmeineke + + * forceFields/DUFF.frc: Switched the bond in the force field back + to constrained, to preserve energy + +2003-07-11 17:34 mmeineke + + * libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, + Integrator.hpp: working on som integrator bugs + +2003-07-11 10:26 gezelter + + * libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting + to worry about all the strtok() calls in our code + +2003-07-11 09:49 gezelter + + * utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness + +2003-07-10 20:15 gezelter + + * libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and + eor. + +2003-07-10 17:15 mmeineke + + * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, + SimInfo.cpp, Thermo.cpp: fixed some bugs + +2003-07-10 14:53 chuckv + + * utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, + nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added + nanoBuilder and a general Lattice builder. + +2003-07-10 12:10 gezelter + + * libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, + Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff + +2003-07-09 17:14 mmeineke + + * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, + Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, + SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the + caclulation of HmatInverse. + +2003-07-09 10:34 mmeineke + + * libBASS/MoleculeStamp.hpp: starting some work for xlate + +2003-07-09 10:33 mmeineke + + * libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff + +2003-07-09 08:56 gezelter + + * libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf + +2003-07-09 08:56 gezelter + + * libBASS/Globals.cpp: Removed Qmass + +2003-07-08 21:15 gezelter + + * libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf + and NPTi + +2003-07-08 20:41 gezelter + + * libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf + +2003-07-08 16:10 gezelter + + * libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] + +2003-07-08 16:06 gezelter + + * libmdtools/NPTi.cpp: fixed box scaling + +2003-07-08 15:56 gezelter + + * libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, + SimInfo.hpp, Thermo.cpp: NPTi + +2003-07-03 14:41 mmeineke + + * libBASS/Makefile, libmdtools/Makefile, src/Makefile, + utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy + scripts in the makefiles + +2003-07-02 16:26 mmeineke + + * libBASS/Makefile, libmdtools/DumpWriter.cpp, + libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, + libmdtools/Makefile, libmdtools/ReadWrite.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, + libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, + utils/Makefile: fixed the bugs introduced by switching the periodic + box to a matrix + +2003-07-01 17:39 gezelter + + * libmdtools/do_Forces.F90: Fortran flexi-BOX + +2003-07-01 17:29 gezelter + + * libmdtools/simulation_module.F90: Fixes for flexi-BOX + +2003-07-01 16:33 mmeineke + + * libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, + fortranWrapDefines.hpp, simulation_module.F90: working on adding + the box matrix to everything. + +2003-06-30 17:03 mmeineke + + * ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + src/oopse.cpp: + Updated the ChangeLog, and Converted most of the SImInfo to use + non-Isotropic boxes. wrapVector needs to be finished. + +2003-06-25 16:12 mmeineke + + * libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds + to Harmonic bonds in the DUFF frc file + + fixed constraints. + +2003-06-25 16:11 mmeineke + + * forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in + the DUFF frc file + +2003-06-24 17:51 gezelter + + * libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! + +2003-06-24 14:57 mmeineke + + * forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, + libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into + the DUFF forcefield and BondExtensions.cpp + +2003-06-23 16:24 mmeineke + + * libmdtools/Integrator.cpp: Doing some work to debug the + constraint code. + +2003-06-20 15:50 gezelter + + * libmdtools/Integrator.hpp: NPT fix + +2003-06-20 15:29 mmeineke + + * libmdtools/Atom.cpp, libmdtools/DUFF.cpp, + libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, + libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, + libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the + integrator and NVT seem to be working now. + +2003-06-20 11:49 gezelter + + * libmdtools/: Integrator.hpp, NVT.cpp: NVT additions + +2003-06-19 17:02 mmeineke + + * forceFields/DUFF.frc, forceFields/LJFF.frc, + forceFields/LJ_FF.frc, forceFields/Makefile, + forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, + libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, + libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, + libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, + libmdtools/TraPPEFF.cpp: slowly converting to new integrator and + forcefield names. + +2003-06-19 14:21 mmeineke + + * libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: + finished the basics of the integrator and SimSetup.cpp + +2003-06-19 14:11 mmeineke + + * libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it + up / get it to work with the new Integrator. + +2003-06-18 17:20 mmeineke + + * libmdtools/Symplectic.cpp: minor changes in an attempt to fix + output times. + +2003-06-17 16:56 mmeineke + + * libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters + fro the ghost Bend in TraPPE_Ex + + some work on the integrator. ( incomplete) + +2003-06-17 16:55 mmeineke + + * forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost + Bend in TraPPE_Ex + +2003-06-04 16:06 mmeineke + + * libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and + constrainB to the Symplectic integrator + +2003-05-30 16:32 mmeineke + + * utils/bilayerSys.cpp: currently modifiying Symplectic to become + the basic integrator. + + bilayerSys.cpp altered for building tb3. + +2003-05-30 16:31 mmeineke + + * libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, + TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently + modifiying Symplectic to become the basic integrator. + +2003-05-30 15:19 mmeineke + + * libmdtools/Integrator.hpp: added some member variables for + position, velocity, etc. + +2003-05-30 14:07 mmeineke + + * libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT + is now derived from Integrator + +2003-05-20 11:44 mmeineke + + * libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. + +2003-05-17 11:57 mmeineke + + * utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be + working + +2003-05-16 16:37 mmeineke + + * utils/bilayerSys.cpp: still working on the bilayer code + +2003-05-16 09:28 mmeineke + + * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some + work to overhaul sysbuild. + +2003-05-13 16:23 mmeineke + + * libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop + +2003-05-13 15:47 mmeineke + + * samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, + beadLipid/water.mdl: Added bead lipid model to the sample directory + +2003-05-13 15:34 mmeineke + + * forceFields/TraPPE_Ex.frc: finished adding the Tail beads into + the Trappe extended force field + +2003-05-13 12:01 mmeineke + + * forceFields/TraPPE_Ex.frc: added the TailBead atom types to the + TraPPe_Ex forceField + +2003-05-09 14:51 mmeineke + + * samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. + there were some duplicate entries + + added a two chain lipid to the lipid.mdl in sample + +2003-05-09 14:51 mmeineke + + * forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. + there were some duplicate entries + +2003-05-09 11:56 mmeineke + + * forceFields/TraPPE_Ex.frc: added the utils subdirectory to the + configure script + + added the CH branching group to the TraPPE_Ex fource field + +2003-05-09 11:55 mmeineke + + * ac-tools/configure.in: added the utils subdirectory to the + configure script + +2003-04-25 11:02 mmeineke + + * utils/bilayerSys.cpp: i quick fix to th distance in the random + bilayer builder + +2003-04-24 21:00 mmeineke + + * libmdtools/f_verlet_constrained.F90: added a new test for + constraint failure + +2003-04-17 16:54 mmeineke + + * libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, + utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, + utils/bilayerSys.cpp: fixed up sysBuild to where it should now + build our systems + +2003-04-16 16:11 mmeineke + + * utils/: MoLocator.cpp, MoLocator.hpp: almost finished. + +2003-04-15 16:47 mmeineke + + * utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys + and sysBuild both will build now. woot! + +2003-04-15 16:20 mmeineke + + * utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, + bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp + + sysBuild still need to write the bass file. + + MoLocator.cpp is currently empty + +2003-04-15 15:40 chuckv + + * forceFields/EAM_FF.frc, forceFields/agu3.eam, + forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, + forceFields/pdu3.eam, forceFields/ptu3.eam, + libmdtools/ForceFields.hpp: Added eam force files... + +2003-04-15 11:37 chuckv + + * libmdtools/EAM_FF.cpp: More eam work. + +2003-04-14 16:22 mmeineke + + * libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, + utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: + working on the system builder + +2003-04-14 16:16 chuckv + + * libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed + ordering on NVT calculation in integrators. + +2003-04-14 14:51 mmeineke + + * utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, + obj/placeHolder: working on a system builder + +2003-04-14 14:04 mmeineke + + * utils/Makefile: added Ghost bends to the TraPPE_Ex forceField + + added sysBuild to the utils Makefile + +2003-04-14 14:03 mmeineke + + * forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added + Ghost bends to the TraPPE_Ex forceField + +2003-04-14 13:19 chuckv + + * libmdtools/calc_eam.F90: Added first mangling of EAM. + +2003-04-11 13:46 mmeineke + + * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, + simulation_module.F90: fixed a memory bug in Fortran, where + molMembershipArray was declared nLocal instead of nGlobal. + +2003-04-11 10:16 gezelter + + * libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, + SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, + fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress + for NPT + +2003-04-10 15:08 mmeineke + + * libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a + globalIndex counter to Molecule + +2003-04-10 11:35 gezelter + + * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on + ConstantStress + +2003-04-10 11:27 mmeineke + + * libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. + caused a miscalculation of nLocal. + +2003-04-10 11:21 mmeineke + + * libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, + do_Forces.F90: fixed a bug in symplectic, where presure was only + being calculated the first time through. + +2003-04-09 11:20 chuckv + + * samples/alkane/alkanes.mdl: added pentane to the alkane model + file + +2003-04-09 08:59 gezelter + + * libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, + Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file + +2003-04-08 23:06 gezelter + + * libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, + ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, + SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, + Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, + calc_reaction_field.F90, calc_sticky_pair.F90, + fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and + NVT + +2003-04-08 17:38 chuckv + + * libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, + libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, + libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, + libmdtools/simulation_module.F90, samples/water/ssd.bass: It works + (kinda)... + +2003-04-08 16:35 gezelter + + * libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, + libmdtools/SimSetup.cpp: Fixes for NPT / NVT + +2003-04-08 12:16 chuckv + + * libmdtools/: do_Forces.F90, neighborLists.F90, + simulation_module.F90: Moved expand neighborlist to init_FF. + +2003-04-08 10:20 chuckv + + * libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for + NVT + +2003-04-08 09:39 gezelter + + * libmdtools/Verlet.cpp: fixes for nvt / npt + +2003-04-08 09:34 gezelter + + * libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, + Thermo.cpp, Verlet.cpp: dt/2 fix in nvt + +2003-04-08 07:50 gezelter + + * libmdtools/ExtendedSystem.cpp: Fixes for affine transform + +2003-04-08 07:44 gezelter + + * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, + Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the + NVT and NPT ensembles + +2003-04-07 16:42 gezelter + + * libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, + libmdtools/SimSetup.cpp: Fixes for NPT and NVT + +2003-04-07 16:20 mmeineke + + * libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial + portion of SSD. + +2003-04-07 16:16 mmeineke + + * libmdtools/: ForceFields.cpp, Symplectic.cpp: + doing some testing in sticky through Symplectic. + +2003-04-07 15:51 gezelter + + * libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT + +2003-04-07 15:50 chuckv + + * libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for + tau and virial. + +2003-04-07 15:06 mmeineke + + * libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, + libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, + libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, + src/Makefile: bug fixes + +2003-04-07 11:56 gezelter + + * libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, + StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: + Many fixes to add extended system + +2003-04-07 09:30 gezelter + + * src/Makefile: Fixed a bug caused by my experimentation + +2003-04-07 09:30 gezelter + + * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, + Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: + Added ExtendedSystem infrastructure for NPT and NVT calculations + +2003-04-07 09:30 gezelter + + * libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS + +2003-04-04 23:07 gezelter + + * src/Makefile: final mods to try a fortran compiler + +2003-04-04 22:39 gezelter + + * libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, + fortranWrapDefines.hpp: Bug fixes for simulation module rewrites + +2003-04-04 21:56 gezelter + + * libmdtools/: Makefile, atype_module.F90, do_Forces.F90, + fortranWrappers.cpp, wrappers.F90: bug fixes for compilation + +2003-04-04 21:45 gezelter + + * libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug + fixes to fortran wrappers + +2003-04-04 17:22 chuckv + + * libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, + calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, + do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, + simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets + smarter, fortran gets dumber... + +2003-04-04 14:57 mmeineke + + * libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, + neighborLists.F90: fixed a memory read bug in neighborlist + +2003-04-04 14:47 gezelter + + * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, + SimInfo.hpp, Thermo.cpp: Changes for Extended System + +2003-04-04 14:16 gezelter + + * libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, + SimInfo.hpp: Fixes for ExtendedSystem + +2003-04-03 20:57 gezelter + + * libmdtools/ExtendedSystem.hpp: Added extended system header + +2003-04-03 20:57 gezelter + + * libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes + for extended system code + +2003-04-03 18:49 gezelter + + * libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to + extendedsystem + +2003-04-03 17:19 mmeineke + + * libmdtools/Molecule.hpp: added some little fixes here and there. + +2003-04-03 17:01 mmeineke + + * libmdtools/TraPPE_ExFF.cpp: fixed a possible call before + initialize bug. + +2003-04-03 16:12 mmeineke + + * libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just + little things like deleteing unused variables and such. + +2003-04-03 15:57 mmeineke + + * libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to + simError.h also some fixes to Molecule.hpp + +2003-04-03 15:57 mmeineke + + * libBASS/simError.h: a few fixes to simError.h + +2003-04-03 15:21 mmeineke + + * libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, + libBASS/simError.h, libmdtools/DumpWriter.cpp, + libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, + libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, + libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, + src/Makefile, src/oopse.cpp: fixed some small things with + simError.h + +2003-04-03 15:19 gezelter + + * libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT + +2003-04-03 14:58 gezelter + + * libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for + now) + +2003-04-03 08:42 gezelter + + * README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: + Changed Readme, added some files + +2003-04-02 17:19 mmeineke + + * libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, + Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: + dipoles mostly work, but there is a memory leak somewhere. + +2003-04-02 10:01 mmeineke + + * libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting + the proper atomIdents. + +2003-04-01 11:50 chuckv + + * libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, + libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, + samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more + bug fixes.... + +2003-04-01 11:49 mmeineke + + * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed + DumpWriter to be more robust to errors. also added a little + namespace to InitFromFile to wrap it's helper functions in MPI + +2003-03-31 17:09 chuckv + + * libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local + not zeroed. + +2003-03-31 16:50 chuckv + + * libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, + libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, + libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, + libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, + libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, + samples/alkane/butane.bass: Fixes in MPI force calc and in + Trappe_Ex parsing. + +2003-03-28 17:34 chuckv + + * libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp + +2003-03-28 16:45 chuckv + + * libBASS/Makefile, libmdtools/DumpWriter.cpp, + libmdtools/InitializeFromFile.cpp: Bug fixes in read-write + routines. + +2003-03-28 14:33 mmeineke + + * libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, + Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a + bug where the Excludes were not being created properly + +2003-03-28 14:30 chuckv + + * libBASS/Makefile, libmdtools/DumpWriter.cpp, + libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, + libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes + and debugging mpi read write from file. + +2003-03-28 10:28 mmeineke + + * libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range + interactions in Trappe + +2003-03-27 18:33 chuckv + + * libmdtools/: SimSetup.cpp, mpiSimulation.cpp, + mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. + +2003-03-27 17:16 mmeineke + + * libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where + excludes were not being initialized + +2003-03-27 16:52 mmeineke + + * src/Makefile: [no log message] + +2003-03-27 16:52 mmeineke + + * libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. + +2003-03-27 16:07 mmeineke + + * libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, + Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, + Verlet.cpp: fixed the compile time bugs, Source builds and links + +2003-03-27 15:48 mmeineke + + * libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few + more bugs. + +2003-03-27 15:40 mmeineke + + * libmdtools/Molecule.cpp: added the Molecule.cpp file + +2003-03-27 15:39 mmeineke + + * libmdtools/: Makefile, Molecule.hpp: fixed the makefile + +2003-03-27 15:36 mmeineke + + * libmdtools/: AbstractClasses.hpp, ForceFields.cpp, + ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, + SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs + +2003-03-27 15:12 mmeineke + + * libmdtools/: AbstractClasses.hpp, ForceFields.cpp, + Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, + Verlet.cpp: I have implemeted Molecules everywhere I could remember + to. will now attempt to compile. + +2003-03-27 14:21 mmeineke + + * libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, + SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished + updating SimSetup to initialize and use the new MPI division of + labour, and Molecule class + +2003-03-27 12:55 mmeineke + + * libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to + use Molecule + +2003-03-27 12:32 mmeineke + + * libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, + SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been + converted to the new Molecule model. TraPPE_Ex is currently being + updated. SimSetups routines are writtten, but not yet called. + +2003-03-27 10:07 gezelter + + * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, + mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom + numbering in MPI + +2003-03-27 09:30 mmeineke + + * libmdtools/mpiSimulation.cpp: little bug fixes here and there. + +2003-03-26 20:49 gezelter + + * libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to + fileio for MPI + +2003-03-26 18:14 gezelter + + * libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, + mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug + fixes many bug fixes + +2003-03-26 17:24 gezelter + + * libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on + sequence of atoms on the other processors. Node 0 now fires + potatoes at other processors to get them to send french fries back. + +2003-03-26 17:02 mmeineke + + * libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for + making the molecules is in place. ForceField needs to be updated + next. + +2003-03-26 16:54 mmeineke + + * libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of + the "static" bugs in Atom and Exclude + +2003-03-26 16:50 mmeineke + + * libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, + SimSetup.cpp: still working on the SimSetup routine. also fixed + some things in Exclude.hpp + +2003-03-26 16:24 gezelter + + * libmdtools/Makefile: Added Atom.cpp and Exclude.cpp + +2003-03-26 16:23 gezelter + + * libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom + and Exclude list + +2003-03-26 16:04 gezelter + + * libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and + delete ranges of atoms + +2003-03-26 15:45 mmeineke + + * libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class + with static arrays similar to the Atom class + +2003-03-26 15:22 mmeineke + + * libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm + overhauling the molecule class to contain it's own bonds, bends, + and torsions. + + may god have mercy on my soul. + +2003-03-26 14:34 chuckv + + * libmdtools/mpiSimulation.cpp: Finished globalIndex. + +2003-03-26 13:02 gezelter + + * libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, + mpiSimulation.hpp: MPI stuff for passing out molecules + +2003-03-26 11:12 chuckv + + * libmdtools/mpiSimulation.cpp: working on load balancing + +2003-03-26 10:37 chuckv + + * libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, + samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes + for Parallel thermalization + +2003-03-26 09:55 mmeineke + + * libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in + THermo.cpp + +2003-03-25 17:54 chuckv + + * libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation + of potential energy and temperature. + +2003-03-25 09:29 mmeineke + + * libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, + src/MPIobj/dummy, src/obj/dummy: [no log message] + +2003-03-25 09:29 mmeineke + + * libBASS/MPIobj/dummy: added dummy files to keep the build + deirectories from being pruned. + +2003-03-24 20:07 gezelter + + * samples/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, 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 + + * ac-tools/configure.in: Tests are becoming samples + +2003-03-24 19:46 gezelter + + * ac-tools/Make.conf.in: Added makefiles in tests directories + +2003-03-24 16:55 gezelter + + * libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, + libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, + libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, + libmdtools/calc_reaction_field.F90, + libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, + libmdtools/simulation_module.F90: electrostatic changes for dipole + / RF separation + +2003-03-24 13:33 mmeineke + + * libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, + do_Forces.F90: little bug fixes here and there + +2003-03-24 10:26 mmeineke + + * libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug + where short range interactions were not being calculated. + + removed some debug print statements + +2003-03-21 17:11 chuckv + + * libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, + do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: + various write statements for debugging + +2003-03-21 16:26 chuckv + + * forceFields/Makefile: added links to the makefile in forceFields + +2003-03-21 15:52 gezelter + + * ac-tools/Make.conf.in, ac-tools/configure.in, + libmdtools/Makefile: Fixed F_MACH_DEP bug + +2003-03-21 15:37 gezelter + + * ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, + ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, + libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, + src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, + autoconf fixes + +2003-03-21 14:58 gezelter + + * LICENSE: Added license file + +2003-03-21 14:55 gezelter + + * forceFields/Makefile: Fixed makefile + +2003-03-21 14:49 gezelter + + * forceFields/Makefile: Makefile for forceFields + +2003-03-21 14:42 gezelter + + * README: Readme changes + +2003-03-21 12:52 mmeineke + + * src/Makefile: [no log message] + +2003-03-21 12:52 mmeineke + + * libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends + +2003-03-21 12:42 mmeineke + + * AUTHORS, ChangeLog, NEWS, Makefile, README, + ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, + ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, + ac-tools/install-sh, forceFields/DipoleTest.frc, + forceFields/LJ_FF.frc, forceFields/TraPPE.frc, + forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, + libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, + libBASS/BASS_interface.h, libBASS/BASS_parse.c, + libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, + libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, + libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, + libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, + libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, + libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, + libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, + libBASS/MakeStamps.hpp, libBASS/Makefile, + libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, + libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, + libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, + libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, + libBASS/parse_interface.h, libBASS/parse_me.h, + libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, + libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, + utils/sfmakedepend, ac-tools/shtool, + libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, + libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, + libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, + libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, + libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, + libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, + libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, + libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, + libmdtools/Makefile, libmdtools/Molecule.hpp, + libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, + libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, + libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, + libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, + libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, + libmdtools/Verlet.cpp, libmdtools/atype_module.F90, + libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, + libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, + libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, + libmdtools/fForceField.h, libmdtools/fSimulation.h, + libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, + libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, + libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, + libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, + libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, + 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 + +2003-03-21 12:42 mmeineke + + * AUTHORS, ChangeLog, NEWS, Makefile, README, + ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, + ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, + ac-tools/install-sh, forceFields/DipoleTest.frc, + forceFields/LJ_FF.frc, forceFields/TraPPE.frc, + forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, + libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, + libBASS/BASS_interface.h, libBASS/BASS_parse.c, + libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, + libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, + libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, + libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, + libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, + libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, + libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, + libBASS/MakeStamps.hpp, libBASS/Makefile, + libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, + libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, + libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, + libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, + libBASS/parse_interface.h, libBASS/parse_me.h, + libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, + libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, + utils/sfmakedepend, ac-tools/shtool, + libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, + libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, + libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, + libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, + libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, + libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, + libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, + libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, + libmdtools/Makefile, libmdtools/Molecule.hpp, + libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, + libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, + libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, + libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, + libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, + libmdtools/Verlet.cpp, libmdtools/atype_module.F90, + libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, + libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, + libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, + libmdtools/fForceField.h, libmdtools/fSimulation.h, + libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, + libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, + libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, + libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, + libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, + 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