--- trunk/OOPSE/ChangeLog 2003/03/21 17:42:12 378 +++ trunk/OOPSE/ChangeLog 2003/08/27 16:16:01 727 @@ -1,3 +1,1658 @@ -2/19/2003 - finished porting the packge into autoconf and automake. Incremented version to 0.6 +2003-08-26 15:37 tim -2/13/2003 - Starting to port the package into the OOPSE distribution + * 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 +