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tim |
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2003-07-31 10:38 tim |
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* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
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to the globals |
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2003-07-31 10:35 tim |
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* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
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Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
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NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
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SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
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Added Z constraint. |
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2003-07-30 16:17 chuckv |
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* libmdtools/: EAM_FF.cpp, ForceFields.hpp, ReadWrite.hpp, |
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calc_eam.F90, do_Forces.F90, wrappers.F90: More bug fixes for eam. |
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2003-07-29 11:32 mmeineke |
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* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
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libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
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working on the props code |
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2003-07-29 11:32 mmeineke |
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* libBASS/Globals.cpp: [no log message] |
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2003-07-25 15:00 chuckv |
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* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
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notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
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2003-07-24 16:22 chuckv |
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* ac-tools/configure.in: Changed configure to look for both upper |
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and lower cass .mod files |
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2003-07-24 14:57 chuckv |
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* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
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eam and do_forces. |
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2003-07-23 17:13 chuckv |
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* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
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force_globals.F90, simulation_module.F90, status_module.F90: |
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Finished most code for eam.... |
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2003-07-22 16:49 mmeineke |
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* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
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function to the DumpReader. It should now save the start of each |
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frame in a vector. |
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2003-07-22 15:05 mmeineke |
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* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
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to read dump files |
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2003-07-22 14:54 tim |
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* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
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Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
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NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
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message] |
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2003-07-22 11:41 mmeineke |
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* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
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SimSetup.cpp: Fixed a current time initialization bug in |
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InitFromFile. |
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2003-07-21 16:27 mmeineke |
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* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
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Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
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friends to accomadate random file access |
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2003-07-21 11:23 mmeineke |
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* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
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one sets it. |
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2003-07-21 11:23 mmeineke |
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* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
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ReadWrite.hpp: fixed Initializefrom file to start the simulation |
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from the time specified in the init file. |
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2003-07-17 16:49 gezelter |
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* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
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DumpReader.cpp: Started work on a DumpReader |
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2003-07-17 15:38 gezelter |
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* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
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2003-07-17 15:32 gezelter |
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* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
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libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
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Changes for SSD/E |
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2003-07-17 14:38 mmeineke |
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* libmdtools/do_Forces.F90: commented out an eam line |
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2003-07-17 14:32 chuckv |
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* libmdtools/atype_module.F90: fixed spelling issue |
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2003-07-17 14:29 chuckv |
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* libmdtools/: fInfo.c, status_module.F90: added info module |
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2003-07-17 14:25 chuckv |
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* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
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atype_module.F90, calc_eam.F90, do_Forces.F90, |
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fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
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mpiSimulation_module.F90: Added massive changes for eam.... |
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2003-07-16 16:49 chuckv |
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* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
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2003-07-16 16:30 mmeineke |
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* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
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SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
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calc_reaction_field.F90, do_Forces.F90, fSimulation.h, |
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fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
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neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, |
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wrappers.F90: Changed how cutoffs were handled from C. Now |
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notifyCutoffs in Fortran notifies those who need the information of |
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any changes to cutoffs. |
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2003-07-16 12:35 gezelter |
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* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
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quickLate is now somewhat more intelligent about periodic |
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boundaries and wrapping. |
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2003-07-16 11:40 chuckv |
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* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
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2003-07-16 10:34 mmeineke |
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* scripts/cleanSrc: added a quick wipe-and-update script for quick |
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rebuilds on BoB |
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2003-07-15 21:11 gezelter |
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* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
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SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
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fixes for box changes |
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2003-07-15 17:29 mmeineke |
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* libmdtools/simulation_module.F90: removed some debugging print |
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statements. |
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2003-07-15 17:22 mmeineke |
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* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
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do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
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do_forces. Rrf was not being used in the neighborlist correctly. |
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rcut was conssistently being set lowere than Rrf causing the dipole |
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cutoff region to be to small. Also led to the removal of the taper |
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region to buffer the dipole cutoff. |
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2003-07-15 16:34 mmeineke |
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* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
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fixing ssd bug |
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2003-07-15 14:56 gezelter |
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* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
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for the NPT ensembles |
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2003-07-15 13:52 mmeineke |
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* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
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simSetup |
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2003-07-15 12:57 mmeineke |
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* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
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SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
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fixed some bugs, Changed entry_plug to info where appropriate |
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2003-07-15 12:25 chuckv |
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* utils/sysBuild.ggo: added more command line arguments |
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2003-07-15 12:11 gezelter |
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* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
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Fixing force field line |
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2003-07-15 12:10 gezelter |
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* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
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calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
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calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
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tensor |
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2003-07-15 10:50 gezelter |
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* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
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2003-07-15 10:42 gezelter |
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* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
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removed old outdated code |
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2003-07-15 09:45 gezelter |
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* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
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2003-07-15 09:28 gezelter |
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* libmdtools/Molecule.cpp: removing get_vx |
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2003-07-14 22:28 gezelter |
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* libmdtools/NPTfm.cpp: Added NPTfm |
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2003-07-14 22:27 gezelter |
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* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
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Bugfix in NPTim, fixes for NPTfm |
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2003-07-14 22:08 gezelter |
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* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
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Checking in changes for NPTim |
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2003-07-14 18:06 gezelter |
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* utils/Makefile: Broken SysBuilder |
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2003-07-14 18:06 gezelter |
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* samples/: alkane/init_butane.eor, argon/argon.bass, |
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argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
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for samples |
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2003-07-14 18:06 gezelter |
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* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
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debugging write statements |
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2003-07-14 17:38 gezelter |
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* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
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NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
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2003-07-14 16:48 mmeineke |
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* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
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and set routines to Atom and DirectionalAtom |
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2003-07-14 16:35 chuckv |
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* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
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sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
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that takes different cmd line arguments. |
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2003-07-14 16:28 mmeineke |
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* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
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ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
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SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
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were not being updated |
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2003-07-14 10:04 gezelter |
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* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
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NPTim |
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2003-07-14 09:55 mmeineke |
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* forceFields/DUFF.frc: Switched the bond in the force field back |
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to constrained, to preserve energy |
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2003-07-11 17:34 mmeineke |
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* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
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Integrator.hpp: working on som integrator bugs |
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2003-07-11 10:26 gezelter |
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* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
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to worry about all the strtok() calls in our code |
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2003-07-11 09:49 gezelter |
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* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
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2003-07-10 20:15 gezelter |
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* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
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eor. |
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2003-07-10 17:15 mmeineke |
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* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
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SimInfo.cpp, Thermo.cpp: fixed some bugs |
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2003-07-10 14:53 chuckv |
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* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
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nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
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nanoBuilder and a general Lattice builder. |
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2003-07-10 12:10 gezelter |
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* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
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Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
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2003-07-09 17:14 mmeineke |
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* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
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Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
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SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
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caclulation of HmatInverse. |
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2003-07-09 10:34 mmeineke |
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* libBASS/MoleculeStamp.hpp: starting some work for xlate |
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2003-07-09 10:33 mmeineke |
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* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
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2003-07-09 08:56 gezelter |
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* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
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2003-07-09 08:56 gezelter |
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* libBASS/Globals.cpp: Removed Qmass |
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2003-07-08 21:15 gezelter |
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* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
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and NPTi |
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2003-07-08 20:41 gezelter |
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* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
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2003-07-08 16:10 gezelter |
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* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
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2003-07-08 16:06 gezelter |
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* libmdtools/NPTi.cpp: fixed box scaling |
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366 |
|
|
2003-07-08 15:56 gezelter |
367 |
|
|
|
368 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
369 |
|
|
SimInfo.hpp, Thermo.cpp: NPTi |
370 |
|
|
|
371 |
|
|
2003-07-03 14:41 mmeineke |
372 |
|
|
|
373 |
|
|
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
374 |
|
|
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
375 |
|
|
scripts in the makefiles |
376 |
|
|
|
377 |
|
|
2003-07-02 16:26 mmeineke |
378 |
|
|
|
379 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
380 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
381 |
|
|
libmdtools/Makefile, libmdtools/ReadWrite.hpp, |
382 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
383 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
384 |
|
|
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, |
385 |
|
|
utils/Makefile: fixed the bugs introduced by switching the periodic |
386 |
|
|
box to a matrix |
387 |
|
|
|
388 |
|
|
2003-07-01 17:39 gezelter |
389 |
|
|
|
390 |
|
|
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
391 |
|
|
|
392 |
|
|
2003-07-01 17:29 gezelter |
393 |
|
|
|
394 |
|
|
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
395 |
|
|
|
396 |
|
|
2003-07-01 16:33 mmeineke |
397 |
|
|
|
398 |
|
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
399 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
400 |
|
|
the box matrix to everything. |
401 |
|
|
|
402 |
|
|
2003-06-30 17:03 mmeineke |
403 |
|
|
|
404 |
|
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
405 |
|
|
src/oopse.cpp: |
406 |
|
|
Updated the ChangeLog, and Converted most of the SImInfo to use |
407 |
|
|
non-Isotropic boxes. wrapVector needs to be finished. |
408 |
|
|
|
409 |
mmeineke |
568 |
2003-06-25 16:12 mmeineke |
410 |
|
|
|
411 |
|
|
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
412 |
|
|
to Harmonic bonds in the DUFF frc file |
413 |
|
|
|
414 |
|
|
fixed constraints. |
415 |
|
|
|
416 |
|
|
2003-06-25 16:11 mmeineke |
417 |
|
|
|
418 |
|
|
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
419 |
|
|
the DUFF frc file |
420 |
|
|
|
421 |
|
|
2003-06-24 17:51 gezelter |
422 |
|
|
|
423 |
|
|
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
424 |
|
|
|
425 |
|
|
2003-06-24 14:57 mmeineke |
426 |
|
|
|
427 |
|
|
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
428 |
|
|
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
429 |
|
|
the DUFF forcefield and BondExtensions.cpp |
430 |
|
|
|
431 |
|
|
2003-06-23 16:24 mmeineke |
432 |
|
|
|
433 |
|
|
* libmdtools/Integrator.cpp: Doing some work to debug the |
434 |
|
|
constraint code. |
435 |
|
|
|
436 |
|
|
2003-06-20 15:50 gezelter |
437 |
|
|
|
438 |
|
|
* libmdtools/Integrator.hpp: NPT fix |
439 |
|
|
|
440 |
|
|
2003-06-20 15:29 mmeineke |
441 |
|
|
|
442 |
|
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
443 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
444 |
|
|
libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
445 |
|
|
libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
446 |
|
|
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
447 |
|
|
integrator and NVT seem to be working now. |
448 |
|
|
|
449 |
|
|
2003-06-20 11:49 gezelter |
450 |
|
|
|
451 |
|
|
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
452 |
|
|
|
453 |
|
|
2003-06-19 17:02 mmeineke |
454 |
|
|
|
455 |
|
|
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
456 |
|
|
forceFields/LJ_FF.frc, forceFields/Makefile, |
457 |
|
|
forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
458 |
|
|
libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
459 |
|
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
460 |
|
|
libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, |
461 |
|
|
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
462 |
|
|
forcefield names. |
463 |
|
|
|
464 |
|
|
2003-06-19 14:21 mmeineke |
465 |
|
|
|
466 |
|
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
467 |
|
|
finished the basics of the integrator and SimSetup.cpp |
468 |
|
|
|
469 |
|
|
2003-06-19 14:11 mmeineke |
470 |
|
|
|
471 |
|
|
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
472 |
|
|
up / get it to work with the new Integrator. |
473 |
|
|
|
474 |
|
|
2003-06-18 17:20 mmeineke |
475 |
|
|
|
476 |
|
|
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
477 |
|
|
output times. |
478 |
|
|
|
479 |
|
|
2003-06-17 16:56 mmeineke |
480 |
|
|
|
481 |
|
|
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
482 |
|
|
fro the ghost Bend in TraPPE_Ex |
483 |
|
|
|
484 |
|
|
some work on the integrator. ( incomplete) |
485 |
|
|
|
486 |
|
|
2003-06-17 16:55 mmeineke |
487 |
|
|
|
488 |
|
|
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
489 |
|
|
Bend in TraPPE_Ex |
490 |
|
|
|
491 |
|
|
2003-06-04 16:06 mmeineke |
492 |
|
|
|
493 |
|
|
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
494 |
|
|
constrainB to the Symplectic integrator |
495 |
|
|
|
496 |
|
|
2003-05-30 16:32 mmeineke |
497 |
|
|
|
498 |
|
|
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
499 |
|
|
the basic integrator. |
500 |
|
|
|
501 |
|
|
bilayerSys.cpp altered for building tb3. |
502 |
|
|
|
503 |
|
|
2003-05-30 16:31 mmeineke |
504 |
|
|
|
505 |
|
|
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
506 |
|
|
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
507 |
|
|
modifiying Symplectic to become the basic integrator. |
508 |
|
|
|
509 |
|
|
2003-05-30 15:19 mmeineke |
510 |
|
|
|
511 |
|
|
* libmdtools/Integrator.hpp: added some member variables for |
512 |
|
|
position, velocity, etc. |
513 |
|
|
|
514 |
|
|
2003-05-30 14:07 mmeineke |
515 |
|
|
|
516 |
|
|
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
517 |
|
|
is now derived from Integrator |
518 |
|
|
|
519 |
|
|
2003-05-20 11:44 mmeineke |
520 |
|
|
|
521 |
|
|
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
522 |
|
|
|
523 |
|
|
2003-05-17 11:57 mmeineke |
524 |
|
|
|
525 |
|
|
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
526 |
|
|
working |
527 |
|
|
|
528 |
|
|
2003-05-16 16:37 mmeineke |
529 |
|
|
|
530 |
|
|
* utils/bilayerSys.cpp: still working on the bilayer code |
531 |
|
|
|
532 |
|
|
2003-05-16 09:28 mmeineke |
533 |
|
|
|
534 |
|
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
535 |
|
|
work to overhaul sysbuild. |
536 |
|
|
|
537 |
|
|
2003-05-13 16:23 mmeineke |
538 |
|
|
|
539 |
|
|
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
540 |
|
|
|
541 |
|
|
2003-05-13 15:47 mmeineke |
542 |
|
|
|
543 |
|
|
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
544 |
|
|
beadLipid/water.mdl: Added bead lipid model to the sample directory |
545 |
|
|
|
546 |
|
|
2003-05-13 15:34 mmeineke |
547 |
|
|
|
548 |
|
|
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
549 |
|
|
the Trappe extended force field |
550 |
|
|
|
551 |
|
|
2003-05-13 12:01 mmeineke |
552 |
|
|
|
553 |
|
|
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
554 |
|
|
TraPPe_Ex forceField |
555 |
|
|
|
556 |
|
|
2003-05-09 14:51 mmeineke |
557 |
|
|
|
558 |
|
|
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
559 |
|
|
there were some duplicate entries |
560 |
|
|
|
561 |
|
|
added a two chain lipid to the lipid.mdl in sample |
562 |
|
|
|
563 |
|
|
2003-05-09 14:51 mmeineke |
564 |
|
|
|
565 |
|
|
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
566 |
|
|
there were some duplicate entries |
567 |
|
|
|
568 |
|
|
2003-05-09 11:56 mmeineke |
569 |
|
|
|
570 |
|
|
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
571 |
|
|
configure script |
572 |
|
|
|
573 |
|
|
added the CH branching group to the TraPPE_Ex fource field |
574 |
|
|
|
575 |
|
|
2003-05-09 11:55 mmeineke |
576 |
|
|
|
577 |
|
|
* ac-tools/configure.in: added the utils subdirectory to the |
578 |
|
|
configure script |
579 |
|
|
|
580 |
|
|
2003-04-25 11:02 mmeineke |
581 |
|
|
|
582 |
|
|
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
583 |
|
|
bilayer builder |
584 |
|
|
|
585 |
|
|
2003-04-24 21:00 mmeineke |
586 |
|
|
|
587 |
|
|
* libmdtools/f_verlet_constrained.F90: added a new test for |
588 |
|
|
constraint failure |
589 |
|
|
|
590 |
|
|
2003-04-17 16:54 mmeineke |
591 |
|
|
|
592 |
|
|
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
593 |
|
|
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
594 |
|
|
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
595 |
|
|
build our systems |
596 |
|
|
|
597 |
|
|
2003-04-16 16:11 mmeineke |
598 |
|
|
|
599 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
600 |
|
|
|
601 |
|
|
2003-04-15 16:47 mmeineke |
602 |
|
|
|
603 |
|
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
604 |
|
|
and sysBuild both will build now. woot! |
605 |
|
|
|
606 |
|
|
2003-04-15 16:20 mmeineke |
607 |
|
|
|
608 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
609 |
|
|
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
610 |
|
|
|
611 |
|
|
sysBuild still need to write the bass file. |
612 |
|
|
|
613 |
|
|
MoLocator.cpp is currently empty |
614 |
|
|
|
615 |
|
|
2003-04-15 15:40 chuckv |
616 |
|
|
|
617 |
|
|
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
618 |
|
|
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
619 |
|
|
forceFields/pdu3.eam, forceFields/ptu3.eam, |
620 |
|
|
libmdtools/ForceFields.hpp: Added eam force files... |
621 |
|
|
|
622 |
|
|
2003-04-15 11:37 chuckv |
623 |
|
|
|
624 |
|
|
* libmdtools/EAM_FF.cpp: More eam work. |
625 |
|
|
|
626 |
|
|
2003-04-14 16:22 mmeineke |
627 |
|
|
|
628 |
|
|
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
629 |
|
|
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
630 |
|
|
working on the system builder |
631 |
|
|
|
632 |
|
|
2003-04-14 16:16 chuckv |
633 |
|
|
|
634 |
|
|
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
635 |
|
|
ordering on NVT calculation in integrators. |
636 |
|
|
|
637 |
|
|
2003-04-14 14:51 mmeineke |
638 |
|
|
|
639 |
|
|
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
640 |
|
|
obj/placeHolder: working on a system builder |
641 |
|
|
|
642 |
|
|
2003-04-14 14:04 mmeineke |
643 |
|
|
|
644 |
|
|
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
645 |
|
|
|
646 |
|
|
added sysBuild to the utils Makefile |
647 |
|
|
|
648 |
|
|
2003-04-14 14:03 mmeineke |
649 |
|
|
|
650 |
|
|
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
651 |
|
|
Ghost bends to the TraPPE_Ex forceField |
652 |
|
|
|
653 |
|
|
2003-04-14 13:19 chuckv |
654 |
|
|
|
655 |
|
|
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
656 |
|
|
|
657 |
|
|
2003-04-11 13:46 mmeineke |
658 |
|
|
|
659 |
|
|
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
660 |
|
|
simulation_module.F90: fixed a memory bug in Fortran, where |
661 |
|
|
molMembershipArray was declared nLocal instead of nGlobal. |
662 |
|
|
|
663 |
|
|
2003-04-11 10:16 gezelter |
664 |
|
|
|
665 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
666 |
|
|
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
667 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
668 |
|
|
for NPT |
669 |
|
|
|
670 |
|
|
2003-04-10 15:08 mmeineke |
671 |
|
|
|
672 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
673 |
|
|
globalIndex counter to Molecule |
674 |
|
|
|
675 |
|
|
2003-04-10 11:35 gezelter |
676 |
|
|
|
677 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
678 |
|
|
ConstantStress |
679 |
|
|
|
680 |
|
|
2003-04-10 11:27 mmeineke |
681 |
|
|
|
682 |
|
|
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
683 |
|
|
caused a miscalculation of nLocal. |
684 |
|
|
|
685 |
|
|
2003-04-10 11:21 mmeineke |
686 |
|
|
|
687 |
|
|
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
688 |
|
|
do_Forces.F90: fixed a bug in symplectic, where presure was only |
689 |
|
|
being calculated the first time through. |
690 |
|
|
|
691 |
|
|
2003-04-09 11:20 chuckv |
692 |
|
|
|
693 |
|
|
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
694 |
|
|
file |
695 |
|
|
|
696 |
|
|
2003-04-09 08:59 gezelter |
697 |
|
|
|
698 |
|
|
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
699 |
|
|
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
700 |
|
|
|
701 |
|
|
2003-04-08 23:06 gezelter |
702 |
|
|
|
703 |
|
|
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
704 |
|
|
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
705 |
|
|
SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, |
706 |
|
|
Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
707 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90, |
708 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
709 |
|
|
NVT |
710 |
|
|
|
711 |
|
|
2003-04-08 17:38 chuckv |
712 |
|
|
|
713 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
714 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
715 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
716 |
|
|
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
717 |
|
|
(kinda)... |
718 |
|
|
|
719 |
|
|
2003-04-08 16:35 gezelter |
720 |
|
|
|
721 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
722 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
723 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
724 |
|
|
|
725 |
|
|
2003-04-08 12:16 chuckv |
726 |
|
|
|
727 |
|
|
* libmdtools/: do_Forces.F90, neighborLists.F90, |
728 |
|
|
simulation_module.F90: Moved expand neighborlist to init_FF. |
729 |
|
|
|
730 |
|
|
2003-04-08 10:20 chuckv |
731 |
|
|
|
732 |
|
|
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
733 |
|
|
NVT |
734 |
|
|
|
735 |
|
|
2003-04-08 09:39 gezelter |
736 |
|
|
|
737 |
|
|
* libmdtools/Verlet.cpp: fixes for nvt / npt |
738 |
|
|
|
739 |
|
|
2003-04-08 09:34 gezelter |
740 |
|
|
|
741 |
|
|
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
742 |
|
|
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
743 |
|
|
|
744 |
|
|
2003-04-08 07:50 gezelter |
745 |
|
|
|
746 |
|
|
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
747 |
|
|
|
748 |
|
|
2003-04-08 07:44 gezelter |
749 |
|
|
|
750 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
751 |
|
|
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
752 |
|
|
NVT and NPT ensembles |
753 |
|
|
|
754 |
|
|
2003-04-07 16:42 gezelter |
755 |
|
|
|
756 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
757 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
758 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
759 |
|
|
|
760 |
|
|
2003-04-07 16:20 mmeineke |
761 |
|
|
|
762 |
|
|
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
763 |
|
|
portion of SSD. |
764 |
|
|
|
765 |
|
|
2003-04-07 16:16 mmeineke |
766 |
|
|
|
767 |
|
|
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
768 |
|
|
doing some testing in sticky through Symplectic. |
769 |
|
|
|
770 |
|
|
2003-04-07 15:51 gezelter |
771 |
|
|
|
772 |
|
|
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
773 |
|
|
|
774 |
|
|
2003-04-07 15:50 chuckv |
775 |
|
|
|
776 |
|
|
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
777 |
|
|
tau and virial. |
778 |
|
|
|
779 |
|
|
2003-04-07 15:06 mmeineke |
780 |
|
|
|
781 |
|
|
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
782 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
783 |
|
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
784 |
|
|
src/Makefile: bug fixes |
785 |
|
|
|
786 |
|
|
2003-04-07 11:56 gezelter |
787 |
|
|
|
788 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
789 |
|
|
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
790 |
|
|
Many fixes to add extended system |
791 |
|
|
|
792 |
|
|
2003-04-07 09:30 gezelter |
793 |
|
|
|
794 |
|
|
* src/Makefile: Fixed a bug caused by my experimentation |
795 |
|
|
|
796 |
|
|
2003-04-07 09:30 gezelter |
797 |
|
|
|
798 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
799 |
|
|
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
800 |
|
|
Added ExtendedSystem infrastructure for NPT and NVT calculations |
801 |
|
|
|
802 |
|
|
2003-04-07 09:30 gezelter |
803 |
|
|
|
804 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
805 |
|
|
|
806 |
|
|
2003-04-04 23:07 gezelter |
807 |
|
|
|
808 |
|
|
* src/Makefile: final mods to try a fortran compiler |
809 |
|
|
|
810 |
|
|
2003-04-04 22:39 gezelter |
811 |
|
|
|
812 |
|
|
* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, |
813 |
|
|
fortranWrapDefines.hpp: Bug fixes for simulation module rewrites |
814 |
|
|
|
815 |
|
|
2003-04-04 21:56 gezelter |
816 |
|
|
|
817 |
|
|
* libmdtools/: Makefile, atype_module.F90, do_Forces.F90, |
818 |
|
|
fortranWrappers.cpp, wrappers.F90: bug fixes for compilation |
819 |
|
|
|
820 |
|
|
2003-04-04 21:45 gezelter |
821 |
|
|
|
822 |
|
|
* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug |
823 |
|
|
fixes to fortran wrappers |
824 |
|
|
|
825 |
|
|
2003-04-04 17:22 chuckv |
826 |
|
|
|
827 |
|
|
* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
828 |
|
|
calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, |
829 |
|
|
do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, |
830 |
|
|
simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets |
831 |
|
|
smarter, fortran gets dumber... |
832 |
|
|
|
833 |
|
|
2003-04-04 14:57 mmeineke |
834 |
|
|
|
835 |
|
|
* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, |
836 |
|
|
neighborLists.F90: fixed a memory read bug in neighborlist |
837 |
|
|
|
838 |
|
|
2003-04-04 14:47 gezelter |
839 |
|
|
|
840 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
841 |
|
|
SimInfo.hpp, Thermo.cpp: Changes for Extended System |
842 |
|
|
|
843 |
|
|
2003-04-04 14:16 gezelter |
844 |
|
|
|
845 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
846 |
|
|
SimInfo.hpp: Fixes for ExtendedSystem |
847 |
|
|
|
848 |
|
|
2003-04-03 20:57 gezelter |
849 |
|
|
|
850 |
|
|
* libmdtools/ExtendedSystem.hpp: Added extended system header |
851 |
|
|
|
852 |
|
|
2003-04-03 20:57 gezelter |
853 |
|
|
|
854 |
|
|
* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes |
855 |
|
|
for extended system code |
856 |
|
|
|
857 |
|
|
2003-04-03 18:49 gezelter |
858 |
|
|
|
859 |
|
|
* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to |
860 |
|
|
extendedsystem |
861 |
|
|
|
862 |
|
|
2003-04-03 17:19 mmeineke |
863 |
|
|
|
864 |
|
|
* libmdtools/Molecule.hpp: added some little fixes here and there. |
865 |
|
|
|
866 |
|
|
2003-04-03 17:01 mmeineke |
867 |
|
|
|
868 |
|
|
* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before |
869 |
|
|
initialize bug. |
870 |
|
|
|
871 |
|
|
2003-04-03 16:12 mmeineke |
872 |
|
|
|
873 |
|
|
* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just |
874 |
|
|
little things like deleteing unused variables and such. |
875 |
|
|
|
876 |
|
|
2003-04-03 15:57 mmeineke |
877 |
|
|
|
878 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to |
879 |
|
|
simError.h also some fixes to Molecule.hpp |
880 |
|
|
|
881 |
|
|
2003-04-03 15:57 mmeineke |
882 |
|
|
|
883 |
|
|
* libBASS/simError.h: a few fixes to simError.h |
884 |
|
|
|
885 |
|
|
2003-04-03 15:21 mmeineke |
886 |
|
|
|
887 |
|
|
* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, |
888 |
|
|
libBASS/simError.h, libmdtools/DumpWriter.cpp, |
889 |
|
|
libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, |
890 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, |
891 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, |
892 |
|
|
src/Makefile, src/oopse.cpp: fixed some small things with |
893 |
|
|
simError.h |
894 |
|
|
|
895 |
|
|
2003-04-03 15:19 gezelter |
896 |
|
|
|
897 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT |
898 |
|
|
|
899 |
|
|
2003-04-03 14:58 gezelter |
900 |
|
|
|
901 |
|
|
* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for |
902 |
|
|
now) |
903 |
|
|
|
904 |
|
|
2003-04-03 08:42 gezelter |
905 |
|
|
|
906 |
|
|
* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: |
907 |
|
|
Changed Readme, added some files |
908 |
|
|
|
909 |
|
|
2003-04-02 17:19 mmeineke |
910 |
|
|
|
911 |
|
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, |
912 |
|
|
Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: |
913 |
|
|
dipoles mostly work, but there is a memory leak somewhere. |
914 |
|
|
|
915 |
|
|
2003-04-02 10:01 mmeineke |
916 |
|
|
|
917 |
|
|
* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting |
918 |
|
|
the proper atomIdents. |
919 |
|
|
|
920 |
|
|
2003-04-01 11:50 chuckv |
921 |
|
|
|
922 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
923 |
|
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
924 |
|
|
samples/argon/argon.bass: more bug fixes.... |
925 |
|
|
|
926 |
|
|
2003-04-01 11:49 mmeineke |
927 |
|
|
|
928 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed |
929 |
|
|
DumpWriter to be more robust to errors. also added a little |
930 |
|
|
namespace to InitFromFile to wrap it's helper functions in MPI |
931 |
|
|
|
932 |
|
|
2003-03-31 17:09 chuckv |
933 |
|
|
|
934 |
|
|
* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local |
935 |
|
|
not zeroed. |
936 |
|
|
|
937 |
|
|
2003-03-31 16:50 chuckv |
938 |
|
|
|
939 |
|
|
* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, |
940 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
941 |
|
|
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
942 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
943 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, |
944 |
|
|
samples/alkane/butane.bass: Fixes in MPI force calc and in |
945 |
|
|
Trappe_Ex parsing. |
946 |
|
|
|
947 |
|
|
2003-03-28 17:34 chuckv |
948 |
|
|
|
949 |
|
|
* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp |
950 |
|
|
|
951 |
|
|
2003-03-28 16:45 chuckv |
952 |
|
|
|
953 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
954 |
|
|
libmdtools/InitializeFromFile.cpp: Bug fixes in read-write |
955 |
|
|
routines. |
956 |
|
|
|
957 |
|
|
2003-03-28 14:33 mmeineke |
958 |
|
|
|
959 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, |
960 |
|
|
Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a |
961 |
|
|
bug where the Excludes were not being created properly |
962 |
|
|
|
963 |
|
|
2003-03-28 14:30 chuckv |
964 |
|
|
|
965 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
966 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, |
967 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes |
968 |
|
|
and debugging mpi read write from file. |
969 |
|
|
|
970 |
|
|
2003-03-28 10:28 mmeineke |
971 |
|
|
|
972 |
|
|
* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range |
973 |
|
|
interactions in Trappe |
974 |
|
|
|
975 |
|
|
2003-03-27 18:33 chuckv |
976 |
|
|
|
977 |
|
|
* libmdtools/: SimSetup.cpp, mpiSimulation.cpp, |
978 |
|
|
mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. |
979 |
|
|
|
980 |
|
|
2003-03-27 17:16 mmeineke |
981 |
|
|
|
982 |
|
|
* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where |
983 |
|
|
excludes were not being initialized |
984 |
|
|
|
985 |
|
|
2003-03-27 16:52 mmeineke |
986 |
|
|
|
987 |
|
|
* src/Makefile: [no log message] |
988 |
|
|
|
989 |
|
|
2003-03-27 16:52 mmeineke |
990 |
|
|
|
991 |
|
|
* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. |
992 |
|
|
|
993 |
|
|
2003-03-27 16:07 mmeineke |
994 |
|
|
|
995 |
|
|
* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, |
996 |
|
|
Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, |
997 |
|
|
Verlet.cpp: fixed the compile time bugs, Source builds and links |
998 |
|
|
|
999 |
|
|
2003-03-27 15:48 mmeineke |
1000 |
|
|
|
1001 |
|
|
* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few |
1002 |
|
|
more bugs. |
1003 |
|
|
|
1004 |
|
|
2003-03-27 15:40 mmeineke |
1005 |
|
|
|
1006 |
|
|
* libmdtools/Molecule.cpp: added the Molecule.cpp file |
1007 |
|
|
|
1008 |
|
|
2003-03-27 15:39 mmeineke |
1009 |
|
|
|
1010 |
|
|
* libmdtools/: Makefile, Molecule.hpp: fixed the makefile |
1011 |
|
|
|
1012 |
|
|
2003-03-27 15:36 mmeineke |
1013 |
|
|
|
1014 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
1015 |
|
|
ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, |
1016 |
|
|
SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs |
1017 |
|
|
|
1018 |
|
|
2003-03-27 15:12 mmeineke |
1019 |
|
|
|
1020 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
1021 |
|
|
Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, |
1022 |
|
|
Verlet.cpp: I have implemeted Molecules everywhere I could remember |
1023 |
|
|
to. will now attempt to compile. |
1024 |
|
|
|
1025 |
|
|
2003-03-27 14:21 mmeineke |
1026 |
|
|
|
1027 |
|
|
* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, |
1028 |
|
|
SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished |
1029 |
|
|
updating SimSetup to initialize and use the new MPI division of |
1030 |
|
|
labour, and Molecule class |
1031 |
|
|
|
1032 |
|
|
2003-03-27 12:55 mmeineke |
1033 |
|
|
|
1034 |
|
|
* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to |
1035 |
|
|
use Molecule |
1036 |
|
|
|
1037 |
|
|
2003-03-27 12:32 mmeineke |
1038 |
|
|
|
1039 |
|
|
* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, |
1040 |
|
|
SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been |
1041 |
|
|
converted to the new Molecule model. TraPPE_Ex is currently being |
1042 |
|
|
updated. SimSetups routines are writtten, but not yet called. |
1043 |
|
|
|
1044 |
|
|
2003-03-27 10:07 gezelter |
1045 |
|
|
|
1046 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
1047 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom |
1048 |
|
|
numbering in MPI |
1049 |
|
|
|
1050 |
|
|
2003-03-27 09:30 mmeineke |
1051 |
|
|
|
1052 |
|
|
* libmdtools/mpiSimulation.cpp: little bug fixes here and there. |
1053 |
|
|
|
1054 |
|
|
2003-03-26 20:49 gezelter |
1055 |
|
|
|
1056 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to |
1057 |
|
|
fileio for MPI |
1058 |
|
|
|
1059 |
|
|
2003-03-26 18:14 gezelter |
1060 |
|
|
|
1061 |
|
|
* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, |
1062 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug |
1063 |
|
|
fixes many bug fixes |
1064 |
|
|
|
1065 |
|
|
2003-03-26 17:24 gezelter |
1066 |
|
|
|
1067 |
|
|
* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on |
1068 |
|
|
sequence of atoms on the other processors. Node 0 now fires |
1069 |
|
|
potatoes at other processors to get them to send french fries back. |
1070 |
|
|
|
1071 |
|
|
2003-03-26 17:02 mmeineke |
1072 |
|
|
|
1073 |
|
|
* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for |
1074 |
|
|
making the molecules is in place. ForceField needs to be updated |
1075 |
|
|
next. |
1076 |
|
|
|
1077 |
|
|
2003-03-26 16:54 mmeineke |
1078 |
|
|
|
1079 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of |
1080 |
|
|
the "static" bugs in Atom and Exclude |
1081 |
|
|
|
1082 |
|
|
2003-03-26 16:50 mmeineke |
1083 |
|
|
|
1084 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, |
1085 |
|
|
SimSetup.cpp: still working on the SimSetup routine. also fixed |
1086 |
|
|
some things in Exclude.hpp |
1087 |
|
|
|
1088 |
|
|
2003-03-26 16:24 gezelter |
1089 |
|
|
|
1090 |
|
|
* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp |
1091 |
|
|
|
1092 |
|
|
2003-03-26 16:23 gezelter |
1093 |
|
|
|
1094 |
|
|
* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom |
1095 |
|
|
and Exclude list |
1096 |
|
|
|
1097 |
|
|
2003-03-26 16:04 gezelter |
1098 |
|
|
|
1099 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and |
1100 |
|
|
delete ranges of atoms |
1101 |
|
|
|
1102 |
|
|
2003-03-26 15:45 mmeineke |
1103 |
|
|
|
1104 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class |
1105 |
|
|
with static arrays similar to the Atom class |
1106 |
|
|
|
1107 |
|
|
2003-03-26 15:22 mmeineke |
1108 |
|
|
|
1109 |
|
|
* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm |
1110 |
|
|
overhauling the molecule class to contain it's own bonds, bends, |
1111 |
|
|
and torsions. |
1112 |
|
|
|
1113 |
|
|
may god have mercy on my soul. |
1114 |
|
|
|
1115 |
|
|
2003-03-26 14:34 chuckv |
1116 |
|
|
|
1117 |
|
|
* libmdtools/mpiSimulation.cpp: Finished globalIndex. |
1118 |
|
|
|
1119 |
|
|
2003-03-26 13:02 gezelter |
1120 |
|
|
|
1121 |
|
|
* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, |
1122 |
|
|
mpiSimulation.hpp: MPI stuff for passing out molecules |
1123 |
|
|
|
1124 |
|
|
2003-03-26 11:12 chuckv |
1125 |
|
|
|
1126 |
|
|
* libmdtools/mpiSimulation.cpp: working on load balancing |
1127 |
|
|
|
1128 |
|
|
2003-03-26 10:37 chuckv |
1129 |
|
|
|
1130 |
|
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
1131 |
|
|
samples/argon/argon.bass: Fixes for Parallel thermalization |
1132 |
|
|
|
1133 |
|
|
2003-03-26 09:55 mmeineke |
1134 |
|
|
|
1135 |
|
|
* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in |
1136 |
|
|
THermo.cpp |
1137 |
|
|
|
1138 |
|
|
2003-03-25 17:54 chuckv |
1139 |
|
|
|
1140 |
|
|
* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation |
1141 |
|
|
of potential energy and temperature. |
1142 |
|
|
|
1143 |
|
|
2003-03-25 09:29 mmeineke |
1144 |
|
|
|
1145 |
|
|
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
1146 |
|
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
1147 |
|
|
|
1148 |
|
|
2003-03-25 09:29 mmeineke |
1149 |
|
|
|
1150 |
|
|
* libBASS/MPIobj/dummy: added dummy files to keep the build |
1151 |
|
|
deirectories from being pruned. |
1152 |
|
|
|
1153 |
|
|
2003-03-24 20:07 gezelter |
1154 |
|
|
|
1155 |
|
|
* samples/Makefile: moving tests to samples |
1156 |
|
|
|
1157 |
|
|
2003-03-24 20:06 gezelter |
1158 |
|
|
|
1159 |
|
|
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
1160 |
|
|
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
1161 |
|
|
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
1162 |
|
|
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
1163 |
|
|
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
1164 |
|
|
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
1165 |
|
|
samples |
1166 |
|
|
|
1167 |
|
|
2003-03-24 19:51 gezelter |
1168 |
|
|
|
1169 |
|
|
* ac-tools/configure.in: Tests are becoming samples |
1170 |
|
|
|
1171 |
|
|
2003-03-24 19:46 gezelter |
1172 |
|
|
|
1173 |
|
|
* ac-tools/Make.conf.in: Added makefiles in tests directories |
1174 |
|
|
|
1175 |
|
|
2003-03-24 16:55 gezelter |
1176 |
|
|
|
1177 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, |
1178 |
|
|
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, |
1179 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, |
1180 |
|
|
libmdtools/calc_reaction_field.F90, |
1181 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
1182 |
|
|
libmdtools/simulation_module.F90: electrostatic changes for dipole |
1183 |
|
|
/ RF separation |
1184 |
|
|
|
1185 |
|
|
2003-03-24 13:33 mmeineke |
1186 |
|
|
|
1187 |
|
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
1188 |
|
|
do_Forces.F90: little bug fixes here and there |
1189 |
|
|
|
1190 |
|
|
2003-03-24 10:26 mmeineke |
1191 |
|
|
|
1192 |
|
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
1193 |
|
|
where short range interactions were not being calculated. |
1194 |
|
|
|
1195 |
|
|
removed some debug print statements |
1196 |
|
|
|
1197 |
|
|
2003-03-21 17:11 chuckv |
1198 |
|
|
|
1199 |
|
|
* libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, |
1200 |
|
|
do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: |
1201 |
|
|
various write statements for debugging |
1202 |
|
|
|
1203 |
|
|
2003-03-21 16:26 chuckv |
1204 |
|
|
|
1205 |
|
|
* forceFields/Makefile: added links to the makefile in forceFields |
1206 |
|
|
|
1207 |
|
|
2003-03-21 15:52 gezelter |
1208 |
|
|
|
1209 |
|
|
* ac-tools/Make.conf.in, ac-tools/configure.in, |
1210 |
|
|
libmdtools/Makefile: Fixed F_MACH_DEP bug |
1211 |
|
|
|
1212 |
|
|
2003-03-21 15:37 gezelter |
1213 |
|
|
|
1214 |
|
|
* ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, |
1215 |
|
|
ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, |
1216 |
|
|
libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, |
1217 |
|
|
src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, |
1218 |
|
|
autoconf fixes |
1219 |
|
|
|
1220 |
gezelter |
385 |
2003-03-21 14:58 gezelter |
1221 |
mmeineke |
377 |
|
1222 |
gezelter |
385 |
* LICENSE: Added license file |
1223 |
|
|
|
1224 |
|
|
2003-03-21 14:55 gezelter |
1225 |
|
|
|
1226 |
|
|
* forceFields/Makefile: Fixed makefile |
1227 |
|
|
|
1228 |
|
|
2003-03-21 14:49 gezelter |
1229 |
|
|
|
1230 |
|
|
* forceFields/Makefile: Makefile for forceFields |
1231 |
|
|
|
1232 |
|
|
2003-03-21 14:42 gezelter |
1233 |
|
|
|
1234 |
|
|
* README: Readme changes |
1235 |
|
|
|
1236 |
|
|
2003-03-21 12:52 mmeineke |
1237 |
|
|
|
1238 |
|
|
* src/Makefile: [no log message] |
1239 |
|
|
|
1240 |
|
|
2003-03-21 12:52 mmeineke |
1241 |
|
|
|
1242 |
|
|
* libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends |
1243 |
|
|
|
1244 |
|
|
2003-03-21 12:42 mmeineke |
1245 |
|
|
|
1246 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
1247 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
1248 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
1249 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
1250 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
1251 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
1252 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
1253 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
1254 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
1255 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
1256 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
1257 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
1258 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
1259 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
1260 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
1261 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
1262 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
1263 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
1264 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
1265 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
1266 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
1267 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
1268 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
1269 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
1270 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
1271 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
1272 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
1273 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
1274 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
1275 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
1276 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
1277 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
1278 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
1279 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
1280 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1281 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1282 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
1283 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
1284 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
1285 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
1286 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
1287 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
1288 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
1289 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
1290 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
1291 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
1292 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
1293 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
1294 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
1295 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
1296 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
1297 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
1298 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
1299 |
|
|
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
1300 |
|
|
Tree |
1301 |
|
|
|
1302 |
|
|
2003-03-21 12:42 mmeineke |
1303 |
|
|
|
1304 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
1305 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
1306 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
1307 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
1308 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
1309 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
1310 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
1311 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
1312 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
1313 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
1314 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
1315 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
1316 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
1317 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
1318 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
1319 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
1320 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
1321 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
1322 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
1323 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
1324 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
1325 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
1326 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
1327 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
1328 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
1329 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
1330 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
1331 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
1332 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
1333 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
1334 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
1335 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
1336 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
1337 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
1338 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1339 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1340 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
1341 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
1342 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
1343 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
1344 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
1345 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
1346 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
1347 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
1348 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
1349 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
1350 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
1351 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
1352 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
1353 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
1354 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
1355 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
1356 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
1357 |
|
|
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
1358 |
|
|
revision |
1359 |
|
|
|