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2003-10-24 18:17 mmeineke |
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2004-04-28 21:11 tim |
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* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
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unmatched c/fortran interface |
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2004-04-28 18:09 tim |
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* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
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keep the previous position of cantilever in SMD |
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2004-04-28 17:34 tim |
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* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
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libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
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in Molecule.cpp which initialize massRatio before creat the array. |
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fix two bugs in ZconsVisitor |
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2004-04-28 17:06 gezelter |
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* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
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Adding molecular cutoffs |
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2004-04-28 16:39 gezelter |
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* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
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fSimulation.h, force_globals.F90, simulation_module.F90: work on |
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molecular cutoffs |
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2004-04-28 16:39 gezelter |
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* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
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Globals |
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2004-04-27 11:26 tim |
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* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
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ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
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fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
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molecule and massRation into atom class |
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2004-04-26 16:16 mmeineke |
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* libBASS/Globals.cpp: modified the defaults for the system init |
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time and system init state. |
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2004-04-26 09:29 gezelter |
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* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
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calc_charge_charge.F90 |
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2004-04-23 23:31 tim |
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* ChangeLog, libmdtools/AtomVisitor.cpp, |
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libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
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reaction field correction to charge-charge interaction |
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2004-04-22 16:33 tim |
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* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
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Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
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calculation of pressure tensor |
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2004-04-22 09:55 tim |
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* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
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another bug in InitFromFile. MPI verion of OOPSE is working again |
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2004-04-21 22:29 tim |
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* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
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InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
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SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
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bugs in MPI version of InitfromFile and one unmatch MPI command in |
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DumpWriter |
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2004-04-21 00:32 tim |
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* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
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libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
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utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
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useless files |
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2004-04-20 11:56 tim |
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* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
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SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
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velocitize at thermo |
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2004-04-20 00:39 tim |
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* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
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libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
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libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
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libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
| 95 |
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libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
| 96 |
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libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
| 97 |
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utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
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utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
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2004-04-19 17:13 gezelter |
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* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
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Thermo.cpp: Fixed a charge bug |
| 104 |
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| 105 |
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2004-04-19 15:54 tim |
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* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
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libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
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libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
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a bug in CompositeVisitor which cause the double counting problem |
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| 112 |
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2004-04-19 12:44 tim |
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* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
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libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
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libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
| 117 |
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libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
| 118 |
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libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
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Dump2XYZ is almost working except atoms in rigidbody are double |
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counted |
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2004-04-18 22:52 tim |
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* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
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libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
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libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
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libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
| 128 |
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libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
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libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
| 130 |
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libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
| 131 |
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libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
| 132 |
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libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
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libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
| 134 |
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libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 135 |
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libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
| 136 |
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libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
| 137 |
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libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
| 138 |
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libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
| 139 |
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utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
| 140 |
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implement of quickLate using visitor and composite pattern |
| 141 |
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| 142 |
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2004-04-15 17:15 tim |
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* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
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exclude list |
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| 147 |
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2004-04-15 11:18 tim |
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* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
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libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
| 151 |
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libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
| 152 |
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libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
| 153 |
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libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 154 |
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libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
| 155 |
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libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
| 156 |
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whole bunch of bugs :-) |
| 157 |
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2004-04-14 12:20 chrisfen |
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* forceFields/WATER.frc: Added the WATER.frc force field |
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2004-04-14 11:32 gezelter |
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* libmdtools/Molecule.cpp: fixed for get_potential |
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2004-04-14 10:37 tim |
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* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
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libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
| 170 |
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libmdtools/Integrator.hpp, libmdtools/Make.dep, |
| 171 |
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libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
| 172 |
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libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
| 173 |
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libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 174 |
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libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 175 |
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libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
| 176 |
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libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
| 177 |
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libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
| 178 |
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Change DumpWriter and InitFromFile |
| 179 |
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2004-04-13 11:26 gezelter |
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* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
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molecules can keep track of their own IntegrableObjects (and |
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RigidBodies). Also a bug-fix so that SimInfo can keep track of |
| 185 |
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RigidBodies (which was done incorrectly before). |
| 186 |
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2004-04-13 11:25 gezelter |
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* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
| 190 |
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(will back out momentarily) |
| 191 |
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| 192 |
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2004-04-13 10:10 gezelter |
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* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
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Those were old. |
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2004-04-13 10:09 gezelter |
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* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
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to add IntegrableObjects |
| 201 |
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| 202 |
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2004-04-12 16:02 gezelter |
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* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
| 205 |
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2004-04-12 15:32 gezelter |
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* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
| 209 |
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test run |
| 210 |
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| 211 |
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2004-04-12 15:32 gezelter |
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* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
| 214 |
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DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
| 215 |
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DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
| 216 |
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ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
| 217 |
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Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
| 218 |
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MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
| 219 |
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NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
| 220 |
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SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
| 221 |
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SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
| 222 |
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WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
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(Somewhat extensive) |
| 224 |
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2004-04-12 15:31 gezelter |
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* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
| 228 |
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libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
| 229 |
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utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
| 230 |
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Changes for RigidBody dynamics |
| 231 |
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2004-03-17 09:22 tim |
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* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
| 235 |
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libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
| 236 |
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libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
| 237 |
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libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
| 238 |
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does not sound a good choice, next commit will seperate SMD and |
| 239 |
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ZConstraint |
| 240 |
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2004-03-16 14:22 tim |
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* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 244 |
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libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
| 245 |
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libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
| 246 |
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libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
| 247 |
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now can support sequential moving. Refactorying is needed to |
| 248 |
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support SMD in ZConstraint |
| 249 |
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2004-03-02 15:32 tim |
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* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
| 253 |
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StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
| 254 |
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support large file |
| 255 |
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| 256 |
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2004-03-01 16:17 tim |
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* utils/zsub.cpp: Fix a couple of bugs in zsub |
| 259 |
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| 260 |
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2004-03-01 15:01 tim |
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* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
| 263 |
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libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
| 264 |
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libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
| 265 |
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utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
| 266 |
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utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
| 267 |
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program which can be used to replace atom type for zconstraint into |
| 268 |
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OOPSE |
| 269 |
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| 270 |
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2004-02-24 11:36 tim |
| 271 |
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| 272 |
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* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 273 |
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libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
| 274 |
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message] |
| 275 |
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| 276 |
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2004-02-24 10:49 tim |
| 277 |
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| 278 |
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* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
| 279 |
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Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
| 280 |
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ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
| 281 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
| 282 |
> |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
| 283 |
> |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
| 284 |
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SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
| 285 |
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| 286 |
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2004-02-24 10:44 tim |
| 287 |
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* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
| 289 |
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Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
| 290 |
> |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
| 291 |
> |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
| 292 |
> |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
| 293 |
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compose to implement Minimizer both versions are working |
| 294 |
> |
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| 295 |
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2004-02-17 14:23 tim |
| 296 |
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| 297 |
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* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
| 298 |
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libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 299 |
> |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
| 300 |
> |
libmdtools/MinimizerParameterSet.hpp, |
| 301 |
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libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
| 302 |
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to remove the constraint force along bond direction |
| 303 |
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| 304 |
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2004-02-10 16:33 tim |
| 305 |
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| 306 |
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* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
| 307 |
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libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
| 308 |
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single version of energy minimization is working. |
| 309 |
> |
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| 310 |
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2004-02-09 15:38 mmeineke |
| 311 |
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| 312 |
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* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
| 313 |
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the massive memory overusage by OOPSE |
| 314 |
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| 315 |
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2004-02-09 09:48 chrisfen |
| 316 |
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| 317 |
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* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
| 318 |
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hardwired LJ_rcut |
| 319 |
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| 320 |
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2004-02-06 19:14 tim |
| 321 |
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* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
| 323 |
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message] |
| 324 |
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| 325 |
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2004-02-06 16:37 tim |
| 326 |
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| 327 |
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* ChangeLog, libBASS/Globals.cpp, |
| 328 |
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libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
| 329 |
> |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
| 330 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
| 331 |
> |
energy minimization for argon is working, need to add constraint |
| 332 |
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| 333 |
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2004-02-06 14:05 tim |
| 334 |
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* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
| 336 |
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one more file into Makefile.in |
| 337 |
> |
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| 338 |
> |
2004-02-06 13:58 tim |
| 339 |
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| 340 |
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* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 341 |
> |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
| 342 |
> |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
| 343 |
> |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
| 344 |
> |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
| 345 |
> |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
| 346 |
> |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
| 347 |
> |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
| 348 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 349 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
| 350 |
> |
some lines into global.cpp to make it work with energy minimization |
| 351 |
> |
|
| 352 |
> |
2004-02-04 17:26 tim |
| 353 |
> |
|
| 354 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
| 355 |
> |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
| 356 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
| 357 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
| 358 |
> |
Single version of conjugate gradient with golden search linesearch |
| 359 |
> |
pass a couple of functions test. Brent's algorithm is still broken |
| 360 |
> |
|
| 361 |
> |
2004-02-03 17:54 tim |
| 362 |
> |
|
| 363 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
| 364 |
> |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
| 365 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
| 366 |
> |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
| 367 |
> |
|
| 368 |
> |
2004-02-03 15:47 tim |
| 369 |
> |
|
| 370 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
| 371 |
> |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
| 372 |
> |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
| 373 |
> |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
| 374 |
> |
SteepestDescent.hpp: [no log message] |
| 375 |
> |
|
| 376 |
> |
2004-02-03 15:43 tim |
| 377 |
> |
|
| 378 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
| 379 |
> |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
| 380 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
| 381 |
> |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
| 382 |
> |
constraint class |
| 383 |
> |
|
| 384 |
> |
2004-02-03 12:10 tim |
| 385 |
> |
|
| 386 |
> |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
| 387 |
> |
|
| 388 |
> |
2004-02-03 10:21 tim |
| 389 |
> |
|
| 390 |
> |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
| 391 |
> |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
| 392 |
> |
|
| 393 |
> |
2004-02-02 15:29 tim |
| 394 |
> |
|
| 395 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
| 396 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
| 397 |
> |
Adding GoldenSection and Brent LineSearch Method |
| 398 |
> |
|
| 399 |
> |
2004-01-30 16:47 tim |
| 400 |
> |
|
| 401 |
> |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
| 402 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
| 403 |
> |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
| 404 |
> |
MinimizerBase instead of a functor to do line seach |
| 405 |
> |
|
| 406 |
> |
2004-01-30 10:00 chrisfen |
| 407 |
> |
|
| 408 |
> |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
| 409 |
> |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
| 410 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
| 411 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 412 |
> |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
| 413 |
> |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
| 414 |
> |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
| 415 |
> |
has a working WATER.cpp forcefield and parser. This involved |
| 416 |
> |
changes to WATER.cpp and ForceFields amoung other files. One |
| 417 |
> |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
| 418 |
> |
This will be removed on the next commit... |
| 419 |
> |
|
| 420 |
> |
2004-01-29 18:00 gezelter |
| 421 |
> |
|
| 422 |
> |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
| 423 |
> |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
| 424 |
> |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
| 425 |
> |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
| 426 |
> |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
| 427 |
> |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
| 428 |
> |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
| 429 |
> |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
| 430 |
> |
member list fixes for rigid bodies |
| 431 |
> |
|
| 432 |
> |
2004-01-29 16:44 tim |
| 433 |
> |
|
| 434 |
> |
* libmdtools/MinimizerParameterSet.hpp: Adding |
| 435 |
> |
MinimizerParameterSet class. |
| 436 |
> |
|
| 437 |
> |
2004-01-28 17:44 tim |
| 438 |
> |
|
| 439 |
> |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
| 440 |
> |
NLModel0 and NLModel1 |
| 441 |
> |
|
| 442 |
> |
2004-01-28 15:40 tim |
| 443 |
> |
|
| 444 |
> |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
| 445 |
> |
of NLModel |
| 446 |
> |
|
| 447 |
> |
2004-01-27 15:34 gezelter |
| 448 |
> |
|
| 449 |
> |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
| 450 |
> |
water.mdl file, updated ssd.bass to use new SSD name |
| 451 |
> |
|
| 452 |
> |
2004-01-27 15:34 gezelter |
| 453 |
> |
|
| 454 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
| 455 |
> |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
| 456 |
> |
stuff |
| 457 |
> |
|
| 458 |
> |
2004-01-27 14:39 gezelter |
| 459 |
> |
|
| 460 |
> |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
| 461 |
> |
|
| 462 |
> |
2004-01-27 14:39 gezelter |
| 463 |
> |
|
| 464 |
> |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
| 465 |
> |
|
| 466 |
> |
2004-01-27 14:38 gezelter |
| 467 |
> |
|
| 468 |
> |
* samples/argon/argon.bass: Longer run time to test argon |
| 469 |
> |
|
| 470 |
> |
2004-01-27 14:38 gezelter |
| 471 |
> |
|
| 472 |
> |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
| 473 |
> |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
| 474 |
> |
morning |
| 475 |
> |
|
| 476 |
> |
2004-01-27 14:37 gezelter |
| 477 |
> |
|
| 478 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
| 479 |
> |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
| 480 |
> |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
| 481 |
> |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
| 482 |
> |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
| 483 |
> |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
| 484 |
> |
do new rigidBody scheme |
| 485 |
> |
|
| 486 |
> |
2004-01-27 14:15 tim |
| 487 |
> |
|
| 488 |
> |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
| 489 |
> |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
| 490 |
> |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
| 491 |
> |
constraint for Nonlinear Optimization Model |
| 492 |
> |
|
| 493 |
> |
2004-01-26 17:01 gezelter |
| 494 |
> |
|
| 495 |
> |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
| 496 |
> |
Euler angles for orientation instead of unit vectors required |
| 497 |
> |
changes in MoLocator |
| 498 |
> |
|
| 499 |
> |
2004-01-26 16:53 gezelter |
| 500 |
> |
|
| 501 |
> |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
| 502 |
> |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
| 503 |
> |
water/water.mdl: Changed orientation lines from unit vectors to |
| 504 |
> |
euler angles |
| 505 |
> |
|
| 506 |
> |
2004-01-26 16:52 gezelter |
| 507 |
> |
|
| 508 |
> |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
| 509 |
> |
|
| 510 |
> |
2004-01-26 16:45 gezelter |
| 511 |
> |
|
| 512 |
> |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
| 513 |
> |
use Euler angles in the following order: phi, theta, psi Removed |
| 514 |
> |
the ability to set orientation using a unit vector |
| 515 |
> |
|
| 516 |
> |
2004-01-26 16:26 gezelter |
| 517 |
> |
|
| 518 |
> |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
| 519 |
> |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
| 520 |
> |
Euler angles in the following order: phi, theta, psi Removed the |
| 521 |
> |
ability to set orientation using a unit vector |
| 522 |
> |
|
| 523 |
> |
2004-01-26 13:52 gezelter |
| 524 |
> |
|
| 525 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
| 526 |
> |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
| 527 |
> |
|
| 528 |
> |
2004-01-22 12:34 chrisfen |
| 529 |
> |
|
| 530 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
| 531 |
> |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
| 532 |
> |
Corrected spelling in several directories, and stated WATER.cpp |
| 533 |
> |
|
| 534 |
> |
2004-01-21 17:16 tim |
| 535 |
> |
|
| 536 |
> |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
| 537 |
> |
NLOPModel.hpp: constraint class in energy minimization |
| 538 |
> |
|
| 539 |
> |
2004-01-20 15:34 tim |
| 540 |
> |
|
| 541 |
> |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
| 542 |
> |
|
| 543 |
> |
2004-01-20 15:32 tim |
| 544 |
> |
|
| 545 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
| 546 |
> |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
| 547 |
> |
|
| 548 |
> |
2004-01-19 16:17 gezelter |
| 549 |
> |
|
| 550 |
> |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
| 551 |
> |
more user-friendly |
| 552 |
> |
|
| 553 |
> |
2004-01-19 13:51 chrisfen |
| 554 |
> |
|
| 555 |
> |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
| 556 |
> |
|
| 557 |
> |
2004-01-19 13:36 tim |
| 558 |
> |
|
| 559 |
> |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
| 560 |
> |
time, status time, thermal time and reset time are not divisible by |
| 561 |
> |
dt |
| 562 |
> |
|
| 563 |
> |
2004-01-19 11:10 gezelter |
| 564 |
> |
|
| 565 |
> |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
| 566 |
> |
won't complain |
| 567 |
> |
|
| 568 |
> |
2004-01-19 11:10 gezelter |
| 569 |
> |
|
| 570 |
> |
* samples/lipid/5x5.bass: Fixed old bass file |
| 571 |
> |
|
| 572 |
> |
2004-01-19 11:09 gezelter |
| 573 |
> |
|
| 574 |
> |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
| 575 |
> |
required a change in how the MoleculeStamps are used by divideLabor |
| 576 |
> |
in mpiSimulation.cpp |
| 577 |
> |
|
| 578 |
> |
2004-01-19 11:08 gezelter |
| 579 |
> |
|
| 580 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
| 581 |
> |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
| 582 |
> |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
| 583 |
> |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
| 584 |
> |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
| 585 |
> |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
| 586 |
> |
|
| 587 |
> |
2004-01-16 16:55 tim |
| 588 |
> |
|
| 589 |
> |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
| 590 |
> |
eor file |
| 591 |
> |
|
| 592 |
> |
2004-01-16 16:51 mmeineke |
| 593 |
> |
|
| 594 |
> |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
| 595 |
> |
write eor files |
| 596 |
> |
|
| 597 |
> |
2004-01-16 10:01 mmeineke |
| 598 |
> |
|
| 599 |
> |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
| 600 |
> |
initialization of the AtomStruct |
| 601 |
> |
|
| 602 |
> |
2004-01-15 16:57 chuckv |
| 603 |
> |
|
| 604 |
> |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
| 605 |
> |
|
| 606 |
> |
2004-01-15 10:51 gezelter |
| 607 |
> |
|
| 608 |
> |
* ac-tools/aclocal.m4: Changes for altivec |
| 609 |
> |
|
| 610 |
> |
2004-01-15 09:22 gezelter |
| 611 |
> |
|
| 612 |
> |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
| 613 |
> |
|
| 614 |
> |
2004-01-14 23:33 gezelter |
| 615 |
> |
|
| 616 |
> |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
| 617 |
> |
|
| 618 |
> |
2004-01-14 20:14 gezelter |
| 619 |
> |
|
| 620 |
> |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
| 621 |
> |
notifyCutoffs.F90: More work for adding charges |
| 622 |
> |
|
| 623 |
> |
2004-01-14 17:41 gezelter |
| 624 |
> |
|
| 625 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 626 |
> |
src/Makefile.in: autoconf fixes |
| 627 |
> |
|
| 628 |
> |
2004-01-14 11:28 mmeineke |
| 629 |
> |
|
| 630 |
> |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
| 631 |
> |
|
| 632 |
> |
2004-01-14 10:48 gezelter |
| 633 |
> |
|
| 634 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 635 |
> |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
| 636 |
> |
changes for icc8 |
| 637 |
> |
|
| 638 |
> |
2004-01-13 18:01 gezelter |
| 639 |
> |
|
| 640 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
| 641 |
> |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
| 642 |
> |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
| 643 |
> |
Changes for adding direct charge-charge interactions (with |
| 644 |
> |
switching function) |
| 645 |
> |
|
| 646 |
> |
2004-01-13 17:34 gezelter |
| 647 |
> |
|
| 648 |
> |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
| 649 |
> |
oopseMPI_module.F90: Some changes for new MPI organization and |
| 650 |
> |
direct charge-charge interactions |
| 651 |
> |
|
| 652 |
> |
2004-01-13 17:11 tim |
| 653 |
> |
|
| 654 |
> |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
| 655 |
> |
|
| 656 |
> |
2004-01-13 16:22 tim |
| 657 |
> |
|
| 658 |
> |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
| 659 |
> |
|
| 660 |
> |
2004-01-13 15:35 tim |
| 661 |
> |
|
| 662 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
| 663 |
> |
eor file whenever it is used instead of rewinding it |
| 664 |
> |
|
| 665 |
> |
2004-01-13 15:04 tim |
| 666 |
> |
|
| 667 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
| 668 |
> |
of writeFrame |
| 669 |
> |
|
| 670 |
> |
2004-01-13 10:46 tim |
| 671 |
> |
|
| 672 |
> |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
| 673 |
> |
Merge the code of writeFinal and writeDump; |
| 674 |
> |
Adding sortingIndex into DumpWriter; |
| 675 |
> |
Fix a bug of writing last frame twice in integrator |
| 676 |
> |
|
| 677 |
> |
2004-01-12 17:54 tim |
| 678 |
> |
|
| 679 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
| 680 |
> |
a bug in copying string |
| 681 |
> |
|
| 682 |
> |
2004-01-12 15:37 tim |
| 683 |
> |
|
| 684 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
| 685 |
> |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
| 686 |
> |
master nodes |
| 687 |
> |
|
| 688 |
> |
2004-01-10 04:46 tim |
| 689 |
> |
|
| 690 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
| 691 |
> |
roll it back fix a bug of copying string to a pointer Still have |
| 692 |
> |
Seg fault, it looks like a random MPI seg fault in totalview |
| 693 |
> |
|
| 694 |
> |
2004-01-09 21:15 tim |
| 695 |
> |
|
| 696 |
> |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
| 697 |
> |
|
| 698 |
> |
2004-01-09 15:29 gezelter |
| 699 |
> |
|
| 700 |
> |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
| 701 |
> |
|
| 702 |
> |
2004-01-08 17:25 chuckv |
| 703 |
> |
|
| 704 |
> |
* libmdtools/DumpWriter.cpp: A work in progress... |
| 705 |
> |
|
| 706 |
> |
2004-01-08 13:59 gezelter |
| 707 |
> |
|
| 708 |
> |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
| 709 |
> |
case |
| 710 |
> |
|
| 711 |
> |
2004-01-08 13:13 mmeineke |
| 712 |
> |
|
| 713 |
> |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
| 714 |
> |
state bug. |
| 715 |
> |
|
| 716 |
> |
2004-01-08 13:05 gezelter |
| 717 |
> |
|
| 718 |
> |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
| 719 |
> |
|
| 720 |
> |
2004-01-08 12:57 mmeineke |
| 721 |
> |
|
| 722 |
> |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
| 723 |
> |
exstended state bug |
| 724 |
> |
|
| 725 |
> |
2004-01-08 12:40 gezelter |
| 726 |
> |
|
| 727 |
> |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
| 728 |
> |
|
| 729 |
> |
2004-01-08 10:44 mmeineke |
| 730 |
> |
|
| 731 |
> |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
| 732 |
> |
XS state info flag |
| 733 |
> |
|
| 734 |
> |
2004-01-07 14:26 tim |
| 735 |
> |
|
| 736 |
> |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
| 737 |
> |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
| 738 |
> |
sending message from master node to itself in DumpWriter.cpp and |
| 739 |
> |
InitializeFromFile.cpp |
| 740 |
> |
|
| 741 |
> |
2004-01-06 14:49 chuckv |
| 742 |
> |
|
| 743 |
> |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
| 744 |
> |
performance fixes in the dipole dipole and reaction field code |
| 745 |
> |
|
| 746 |
> |
2004-01-06 13:54 chuckv |
| 747 |
> |
|
| 748 |
> |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
| 749 |
> |
little more sane |
| 750 |
> |
|
| 751 |
> |
2004-01-05 17:49 chuckv |
| 752 |
> |
|
| 753 |
> |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 754 |
> |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
| 755 |
> |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
| 756 |
> |
performance by reducing spurious function calls |
| 757 |
> |
|
| 758 |
> |
2004-01-05 17:18 chuckv |
| 759 |
> |
|
| 760 |
> |
* libmdtools/do_Forces.F90: mangling forces even further |
| 761 |
> |
|
| 762 |
> |
2004-01-05 17:18 chuckv |
| 763 |
> |
|
| 764 |
> |
* configure, ac-tools/configure.in: mpich mucking |
| 765 |
> |
|
| 766 |
> |
2004-01-05 17:12 chuckv |
| 767 |
> |
|
| 768 |
> |
* libmdtools/do_Forces.F90: mangled do_forces... |
| 769 |
> |
|
| 770 |
> |
2004-01-05 16:00 chuckv |
| 771 |
> |
|
| 772 |
> |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
| 773 |
> |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
| 774 |
> |
lookup |
| 775 |
> |
|
| 776 |
> |
2003-12-29 14:56 chuckv |
| 777 |
> |
|
| 778 |
> |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
| 779 |
> |
third-party directory for code not written by us. Also added |
| 780 |
> |
Mersenne Twister random number generator code. This will eventually |
| 781 |
> |
replace sprng as the random number generator used by OOPSE. |
| 782 |
> |
|
| 783 |
> |
2003-12-22 16:26 chuckv |
| 784 |
> |
|
| 785 |
> |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 786 |
> |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
| 787 |
> |
Fixes to profile code. |
| 788 |
> |
|
| 789 |
> |
2003-12-19 15:36 mmeineke |
| 790 |
> |
|
| 791 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
| 792 |
> |
timing.F90, timing.f90: More profiling fixes. |
| 793 |
> |
|
| 794 |
> |
2003-12-19 15:19 chuckv |
| 795 |
> |
|
| 796 |
> |
* libmdtools/timing.f90: Another change for MPI in timing. |
| 797 |
> |
|
| 798 |
> |
2003-12-19 15:17 chuckv |
| 799 |
> |
|
| 800 |
> |
* libmdtools/timing.f90: Small update to timing in MPI |
| 801 |
> |
|
| 802 |
> |
2003-12-19 13:53 mmeineke |
| 803 |
> |
|
| 804 |
> |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
| 805 |
> |
profiling commands work now. Will start adding PROFILE ifdefs into |
| 806 |
> |
the code |
| 807 |
> |
|
| 808 |
> |
2003-12-19 12:25 mmeineke |
| 809 |
> |
|
| 810 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
| 811 |
> |
some profiling routines |
| 812 |
> |
|
| 813 |
> |
2003-12-19 10:12 mmeineke |
| 814 |
> |
|
| 815 |
> |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
| 816 |
> |
and GofRomega |
| 817 |
> |
|
| 818 |
> |
additional work on randomBilayer |
| 819 |
> |
|
| 820 |
> |
2003-12-19 10:12 mmeineke |
| 821 |
> |
|
| 822 |
> |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
| 823 |
> |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
| 824 |
> |
GofRomega |
| 825 |
> |
|
| 826 |
> |
2003-12-18 16:47 mmeineke |
| 827 |
> |
|
| 828 |
> |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
| 829 |
> |
some profile functionality |
| 830 |
> |
|
| 831 |
> |
2003-12-18 15:46 chuckv |
| 832 |
> |
|
| 833 |
> |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
| 834 |
> |
Added functions for simple profiling in fortran. |
| 835 |
> |
|
| 836 |
> |
2003-12-17 15:13 chuckv |
| 837 |
> |
|
| 838 |
> |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
| 839 |
> |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
| 840 |
> |
rho_col were scattered into the same array. Unfortunately, MPI |
| 841 |
> |
zeros the array between scatters so half of the sum was being lost. |
| 842 |
> |
Fixed by added a temp array for column scatter, then sum loop over |
| 843 |
> |
nlocal. |
| 844 |
> |
|
| 845 |
> |
2003-12-16 15:49 mmeineke |
| 846 |
> |
|
| 847 |
> |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
| 848 |
> |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
| 849 |
> |
gofRomega. both need to be debugged and tested. |
| 850 |
> |
|
| 851 |
> |
2003-12-12 10:42 gezelter |
| 852 |
> |
|
| 853 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 854 |
> |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
| 855 |
> |
gradients (to do minimizations) |
| 856 |
> |
|
| 857 |
> |
2003-12-12 10:33 mmeineke |
| 858 |
> |
|
| 859 |
> |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
| 860 |
> |
header |
| 861 |
> |
|
| 862 |
> |
2003-12-10 11:52 mmeineke |
| 863 |
> |
|
| 864 |
> |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
| 865 |
> |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
| 866 |
> |
randomBilayer to the build. Also move the random bilayer builder |
| 867 |
> |
from bilayerSys to randomBilayer |
| 868 |
> |
|
| 869 |
> |
2003-11-25 10:44 mmeineke |
| 870 |
> |
|
| 871 |
> |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
| 872 |
> |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
| 873 |
> |
TB3 in DUFF.frc |
| 874 |
> |
|
| 875 |
> |
2003-11-21 15:09 mmeineke |
| 876 |
> |
|
| 877 |
> |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
| 878 |
> |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
| 879 |
> |
message in SimInfo. Added a more informative error message in |
| 880 |
> |
InitializeFromFile |
| 881 |
> |
|
| 882 |
> |
2003-11-21 15:07 mmeineke |
| 883 |
> |
|
| 884 |
> |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
| 885 |
> |
ing in the GofR,CosTheta |
| 886 |
> |
|
| 887 |
> |
2003-11-21 14:31 chrisfen |
| 888 |
> |
|
| 889 |
> |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
| 890 |
> |
a bug in SimInfo ordering of radii |
| 891 |
> |
|
| 892 |
> |
2003-11-11 12:20 mmeineke |
| 893 |
|
|
| 894 |
+ |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
| 895 |
+ |
a min function. |
| 896 |
+ |
|
| 897 |
+ |
2003-11-10 16:50 mmeineke |
| 898 |
+ |
|
| 899 |
+ |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
| 900 |
+ |
reordered the rcut/ecr/boxSize initialization |
| 901 |
+ |
|
| 902 |
+ |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
| 903 |
+ |
now exit when it runs into rcut or ecr. |
| 904 |
+ |
|
| 905 |
+ |
2003-11-07 16:46 chuckv |
| 906 |
+ |
|
| 907 |
+ |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
| 908 |
+ |
oopseMPI_module.F90: Added support for compiling fortran without |
| 909 |
+ |
use of mpich modules. We use mpif.h instead.: |
| 910 |
+ |
|
| 911 |
+ |
2003-11-07 12:09 mmeineke |
| 912 |
+ |
|
| 913 |
+ |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
| 914 |
+ |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
| 915 |
+ |
the atom loop in the NPT family of integrators. |
| 916 |
+ |
|
| 917 |
+ |
2003-11-06 17:01 mmeineke |
| 918 |
+ |
|
| 919 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
| 920 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
| 921 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 922 |
+ |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
| 923 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
| 924 |
+ |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
| 925 |
+ |
* useIntiTime => useInitialTime |
| 926 |
+ |
|
| 927 |
+ |
2003-11-06 14:24 mmeineke |
| 928 |
+ |
|
| 929 |
+ |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
| 930 |
+ |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
| 931 |
+ |
parse_tree.h: fixed the includes in the Make.dep |
| 932 |
+ |
|
| 933 |
+ |
2003-11-06 14:11 mmeineke |
| 934 |
+ |
|
| 935 |
+ |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
| 936 |
+ |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
| 937 |
+ |
new-templateless branch to the main trunk. |
| 938 |
+ |
|
| 939 |
+ |
bug Fixes include: * fixed the switching function from ortho to |
| 940 |
+ |
non-ortho box. !!!!! THis was responsible for all of the |
| 941 |
+ |
sudden deaths we saw. * some formating in the string when we |
| 942 |
+ |
write out the extended system state. * added NPT.cpp to the |
| 943 |
+ |
makefile.in |
| 944 |
+ |
|
| 945 |
+ |
2003-11-06 13:20 mmeineke |
| 946 |
+ |
|
| 947 |
+ |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
| 948 |
+ |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
| 949 |
+ |
bug. The box was not switching between orthorhombic and |
| 950 |
+ |
non-orthorhombic wrapping correctly. we added a fabs() to |
| 951 |
+ |
the check.which should fix it. |
| 952 |
+ |
|
| 953 |
+ |
2003-11-05 14:16 mmeineke |
| 954 |
+ |
|
| 955 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
| 956 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
| 957 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
| 958 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
| 959 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
| 960 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
| 961 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
| 962 |
+ |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
| 963 |
+ |
some work on trying to find the compression bug |
| 964 |
+ |
|
| 965 |
+ |
2003-11-03 17:07 mmeineke |
| 966 |
+ |
|
| 967 |
+ |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
| 968 |
+ |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
| 969 |
+ |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
| 970 |
+ |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
| 971 |
+ |
most of standard template library from OOPSE. |
| 972 |
+ |
|
| 973 |
+ |
2003-10-31 16:06 mmeineke |
| 974 |
+ |
|
| 975 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
| 976 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
| 977 |
+ |
SimSetup.cpp: started work on template removal. |
| 978 |
+ |
|
| 979 |
+ |
2003-10-31 13:28 mmeineke |
| 980 |
+ |
|
| 981 |
+ |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
| 982 |
+ |
added template stuff to the Maikefile template |
| 983 |
+ |
|
| 984 |
+ |
little changes to some printf format statements |
| 985 |
+ |
|
| 986 |
+ |
2003-10-31 13:28 mmeineke |
| 987 |
+ |
|
| 988 |
+ |
* libBASS/Makefile.in: added template stuff to the Maikefile |
| 989 |
+ |
template |
| 990 |
+ |
|
| 991 |
+ |
2003-10-30 13:59 gezelter |
| 992 |
+ |
|
| 993 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
| 994 |
+ |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
| 995 |
+ |
rList problems |
| 996 |
+ |
|
| 997 |
+ |
2003-10-30 09:11 gezelter |
| 998 |
+ |
|
| 999 |
+ |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
| 1000 |
+ |
queried before q0 was allocated. |
| 1001 |
+ |
|
| 1002 |
+ |
2003-10-29 15:41 mmeineke |
| 1003 |
+ |
|
| 1004 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
| 1005 |
+ |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
| 1006 |
+ |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
| 1007 |
+ |
in bass.l |
| 1008 |
+ |
|
| 1009 |
+ |
fixed a little bug in the first time step, regarding the setting of |
| 1010 |
+ |
ecr and est in fortran |
| 1011 |
+ |
|
| 1012 |
+ |
2003-10-29 15:40 mmeineke |
| 1013 |
+ |
|
| 1014 |
+ |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
| 1015 |
+ |
|
| 1016 |
+ |
2003-10-29 12:55 mmeineke |
| 1017 |
+ |
|
| 1018 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
| 1019 |
+ |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
| 1020 |
+ |
rcut is setup, as well as additional debugging comments. |
| 1021 |
+ |
|
| 1022 |
+ |
2003-10-29 09:28 gezelter |
| 1023 |
+ |
|
| 1024 |
+ |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
| 1025 |
+ |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
| 1026 |
+ |
templates |
| 1027 |
+ |
|
| 1028 |
+ |
2003-10-28 22:16 gezelter |
| 1029 |
+ |
|
| 1030 |
+ |
* src/Makefile.in: Refixed broken makefile |
| 1031 |
+ |
|
| 1032 |
+ |
2003-10-28 22:06 gezelter |
| 1033 |
+ |
|
| 1034 |
+ |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
| 1035 |
+ |
fixes |
| 1036 |
+ |
|
| 1037 |
+ |
2003-10-28 19:19 tim |
| 1038 |
+ |
|
| 1039 |
+ |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
| 1040 |
+ |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
| 1041 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
| 1042 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
| 1043 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
| 1044 |
+ |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
| 1045 |
+ |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
| 1046 |
+ |
file. |
| 1047 |
+ |
|
| 1048 |
+ |
2003-10-28 17:25 mmeineke |
| 1049 |
+ |
|
| 1050 |
+ |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
| 1051 |
+ |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
| 1052 |
+ |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
| 1053 |
+ |
how c calls fortran. All function pointers and fortran calls are |
| 1054 |
+ |
rigidly typecast now. |
| 1055 |
+ |
|
| 1056 |
+ |
2003-10-28 15:42 gezelter |
| 1057 |
+ |
|
| 1058 |
+ |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
| 1059 |
+ |
Portability fixes |
| 1060 |
+ |
|
| 1061 |
+ |
2003-10-28 15:09 gezelter |
| 1062 |
+ |
|
| 1063 |
+ |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
| 1064 |
+ |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
| 1065 |
+ |
src/Makefile.in: Compatibility fixes |
| 1066 |
+ |
|
| 1067 |
+ |
2003-10-28 12:08 mmeineke |
| 1068 |
+ |
|
| 1069 |
+ |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
| 1070 |
+ |
started work on template removal |
| 1071 |
+ |
|
| 1072 |
+ |
2003-10-28 12:04 gezelter |
| 1073 |
+ |
|
| 1074 |
+ |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
| 1075 |
+ |
trying to understand extern "C" stuff for pointers |
| 1076 |
+ |
|
| 1077 |
+ |
2003-10-28 11:20 gezelter |
| 1078 |
+ |
|
| 1079 |
+ |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
| 1080 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
| 1081 |
+ |
|
| 1082 |
+ |
2003-10-28 11:03 gezelter |
| 1083 |
+ |
|
| 1084 |
+ |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
| 1085 |
+ |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
| 1086 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
| 1087 |
+ |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
| 1088 |
+ |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
| 1089 |
+ |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
| 1090 |
+ |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
| 1091 |
+ |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
| 1092 |
+ |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
| 1093 |
+ |
more portable c header stuff Also, mod file fixes and portability |
| 1094 |
+ |
changes Some fortran changes will need to be reversed. |
| 1095 |
+ |
|
| 1096 |
+ |
2003-10-28 11:03 gezelter |
| 1097 |
+ |
|
| 1098 |
+ |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
| 1099 |
+ |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
| 1100 |
+ |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
| 1101 |
+ |
portable c header stuff Also, mod file fixes and portability |
| 1102 |
+ |
changes |
| 1103 |
+ |
|
| 1104 |
+ |
2003-10-28 11:02 gezelter |
| 1105 |
+ |
|
| 1106 |
+ |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
| 1107 |
+ |
stuff |
| 1108 |
+ |
|
| 1109 |
+ |
2003-10-27 18:00 gezelter |
| 1110 |
+ |
|
| 1111 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
| 1112 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, |
| 1113 |
+ |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
| 1114 |
+ |
|
| 1115 |
+ |
2003-10-27 17:08 mmeineke |
| 1116 |
+ |
|
| 1117 |
|
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
| 1118 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
| 1119 |
+ |
added routines for the sysbuilder to work with simSetup |
| 1120 |
+ |
|
| 1121 |
+ |
remved the QuickBass routines, and had all parsing go through |
| 1122 |
+ |
SimSetup. LatticeBilayer is in complete working order now. |
| 1123 |
+ |
|
| 1124 |
+ |
2003-10-27 17:07 mmeineke |
| 1125 |
+ |
|
| 1126 |
+ |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
| 1127 |
+ |
routines for the sysbuilder to work with simSetup |
| 1128 |
+ |
|
| 1129 |
+ |
2003-10-27 11:20 gezelter |
| 1130 |
+ |
|
| 1131 |
+ |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
| 1132 |
+ |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
| 1133 |
+ |
|
| 1134 |
+ |
2003-10-24 17:17 mmeineke |
| 1135 |
+ |
|
| 1136 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
| 1137 |
|
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
| 1138 |
|
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
| 1139 |
|
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
| 1140 |
|
overhauled latticeBilayer into its own program. Removed sysBuild |
| 1141 |
|
from the Makefile |
| 1142 |
|
|
| 1143 |
< |
2003-10-24 13:36 gezelter |
| 1143 |
> |
2003-10-24 12:36 gezelter |
| 1144 |
|
|
| 1145 |
|
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
| 1146 |
|
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
| 1147 |
|
builder |
| 1148 |
|
|
| 1149 |
< |
2003-10-24 13:35 gezelter |
| 1149 |
> |
2003-10-24 12:35 gezelter |
| 1150 |
|
|
| 1151 |
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
| 1152 |
|
merge problem |
| 1153 |
|
|
| 1154 |
< |
2003-10-23 15:57 mmeineke |
| 1154 |
> |
2003-10-23 14:57 mmeineke |
| 1155 |
|
|
| 1156 |
|
* samples/metals/Makefile.in: added eam ForceField files to the |
| 1157 |
|
init |
| 1160 |
|
|
| 1161 |
|
added the init file to the makefile |
| 1162 |
|
|
| 1163 |
< |
2003-10-23 15:57 mmeineke |
| 1163 |
> |
2003-10-23 14:57 mmeineke |
| 1164 |
|
|
| 1165 |
|
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
| 1166 |
|
to the init |
| 1167 |
|
|
| 1168 |
|
fixed an eam mpi parmeter setup bug |
| 1169 |
|
|
| 1170 |
< |
2003-10-23 15:57 mmeineke |
| 1170 |
> |
2003-10-23 14:57 mmeineke |
| 1171 |
|
|
| 1172 |
|
* forceFields/Makefile.in: added eam ForceField files to the init |
| 1173 |
|
|
| 1174 |
< |
2003-10-22 17:17 mmeineke |
| 1174 |
> |
2003-10-22 16:17 mmeineke |
| 1175 |
|
|
| 1176 |
|
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
| 1177 |
|
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
| 1178 |
|
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
| 1179 |
|
no box skew allowed. |
| 1180 |
|
|
| 1181 |
< |
2003-10-21 15:33 mmeineke |
| 1181 |
> |
2003-10-21 14:33 mmeineke |
| 1182 |
|
|
| 1183 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 1184 |
|
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
| 1187 |
|
of the time stamp in the .init file * default=> useInitTime = |
| 1188 |
|
true; |
| 1189 |
|
|
| 1190 |
< |
2003-10-17 17:19 mmeineke |
| 1190 |
> |
2003-10-17 16:19 mmeineke |
| 1191 |
|
|
| 1192 |
|
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
| 1193 |
|
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
| 1197 |
|
fixed a number of bugs in the staticProps code. gofr is now |
| 1198 |
|
working. |
| 1199 |
|
|
| 1200 |
< |
2003-10-17 17:18 mmeineke |
| 1200 |
> |
2003-10-17 16:18 mmeineke |
| 1201 |
|
|
| 1202 |
|
* ac-tools/configure.in: added the staticProps directory to the |
| 1203 |
|
build list for both configure and configure.in |
| 1204 |
|
|
| 1205 |
< |
2003-10-17 17:17 mmeineke |
| 1205 |
> |
2003-10-17 16:17 mmeineke |
| 1206 |
|
|
| 1207 |
|
* configure: added the staticProps directory to the build list |
| 1208 |
|
|
| 1209 |
< |
2003-10-16 15:16 mmeineke |
| 1209 |
> |
2003-10-16 14:16 mmeineke |
| 1210 |
|
|
| 1211 |
|
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
| 1212 |
|
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
| 1220 |
|
a frame is written. This lets the .eor file represent the last |
| 1221 |
|
written frame of a simulation. |
| 1222 |
|
|
| 1223 |
< |
2003-10-10 13:10 mmeineke |
| 1223 |
> |
2003-10-10 12:10 mmeineke |
| 1224 |
|
|
| 1225 |
< |
* props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp, |
| 1226 |
< |
props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp, |
| 1227 |
< |
props/PairCorrList.hpp, props/PairCorrType.cpp, |
| 1228 |
< |
props/PairCorrType.hpp, props/staticProps.cpp, |
| 1229 |
< |
staticProps/AllCorr.cpp, staticProps/AllCorr.hpp, |
| 97 |
< |
staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp, |
| 98 |
< |
staticProps/GofR.cpp, staticProps/Makefile.in, |
| 99 |
< |
staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp, |
| 100 |
< |
staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp, |
| 101 |
< |
staticProps/staticProps.cpp: removed the props directory, and moved |
| 102 |
< |
everything over to staticProps |
| 1225 |
> |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
| 1226 |
> |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
| 1227 |
> |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
| 1228 |
> |
staticProps.cpp: removed the props directory, and moved everything |
| 1229 |
> |
over to staticProps |
| 1230 |
|
|
| 1231 |
< |
2003-10-09 18:09 mmeineke |
| 1231 |
> |
2003-10-09 17:09 mmeineke |
| 1232 |
|
|
| 1233 |
< |
* libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp, |
| 107 |
< |
props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp, |
| 108 |
< |
props/PairCorrType.cpp, props/PairCorrType.hpp, |
| 109 |
< |
props/staticProps.cpp: Contiuned work on staticProps. should be in |
| 1233 |
> |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
| 1234 |
|
a position where it will compile and run first runs. |
| 1235 |
|
|
| 1236 |
< |
2003-10-04 14:46 chuckv |
| 1236 |
> |
2003-10-04 13:46 chuckv |
| 1237 |
|
|
| 1238 |
|
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
| 1239 |
|
samples/metals/Au.bass: Fixed bug in calc_eam. |
| 1240 |
|
|
| 1241 |
< |
2003-10-04 14:08 chuckv |
| 1241 |
> |
2003-10-04 13:08 chuckv |
| 1242 |
|
|
| 1243 |
|
* samples/metals/init_au.in: added Au init file for eam. |
| 1244 |
|
|
| 1245 |
< |
2003-10-03 18:11 mmeineke |
| 1245 |
> |
2003-10-03 17:11 mmeineke |
| 1246 |
|
|
| 1247 |
|
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
| 1248 |
|
entahlpy from the statwriter and thermo. |
| 1249 |
|
|
| 1250 |
< |
2003-10-03 18:02 mmeineke |
| 1250 |
> |
2003-10-03 17:02 mmeineke |
| 1251 |
|
|
| 128 |
– |
* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
| 129 |
– |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
| 130 |
– |
staticProps.cpp: changed the formating ogf the error statements in |
| 131 |
– |
simError |
| 132 |
– |
|
| 133 |
– |
added a function to get the maxCutoff |
| 134 |
– |
|
| 135 |
– |
near completion of the staticProps code. still needs the pair loop, |
| 136 |
– |
and the loop to allocate and read each frame. |
| 137 |
– |
|
| 138 |
– |
2003-10-03 18:02 mmeineke |
| 139 |
– |
|
| 1252 |
|
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
| 1253 |
|
statements in simError |
| 1254 |
|
|
| 1255 |
|
added a function to get the maxCutoff |
| 1256 |
|
|
| 1257 |
< |
2003-10-03 18:01 mmeineke |
| 1257 |
> |
2003-10-03 17:01 mmeineke |
| 1258 |
|
|
| 1259 |
|
* libBASS/simError.c: changed the formating ogf the error |
| 1260 |
|
statements in simError |
| 1261 |
|
|
| 1262 |
< |
2003-10-02 18:06 mmeineke |
| 1262 |
> |
2003-09-30 11:00 mmeineke |
| 1263 |
|
|
| 152 |
– |
* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
| 153 |
– |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
| 154 |
– |
staticProps.cpp: finishing up the constructs needed to get this |
| 155 |
– |
program up and running |
| 156 |
– |
|
| 157 |
– |
2003-09-30 12:00 mmeineke |
| 158 |
– |
|
| 1264 |
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
| 1265 |
|
f90Flags so they are no longer overwritten by the compiler. |
| 1266 |
|
|
| 1267 |
< |
2003-09-29 18:06 mmeineke |
| 1267 |
> |
2003-09-29 17:06 mmeineke |
| 1268 |
|
|
| 1269 |
|
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
| 1270 |
|
for conifig.in |
| 1271 |
|
|
| 1272 |
|
fixed wrappers to extern "C" |
| 1273 |
|
|
| 1274 |
< |
2003-09-29 18:06 mmeineke |
| 1274 |
> |
2003-09-29 17:06 mmeineke |
| 1275 |
|
|
| 1276 |
|
* ac-tools/configure.in: added mpif90 mod check back same for |
| 1277 |
|
conifig.in |
| 1278 |
|
|
| 1279 |
< |
2003-09-29 18:05 mmeineke |
| 1279 |
> |
2003-09-29 17:05 mmeineke |
| 1280 |
|
|
| 1281 |
|
* configure: added mpif90 mod check back |
| 1282 |
|
|
| 1283 |
< |
2003-09-29 17:16 mmeineke |
| 1283 |
> |
2003-09-29 16:16 mmeineke |
| 1284 |
|
|
| 1285 |
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1286 |
|
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
| 1292 |
|
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
| 1293 |
|
found with SUN's SUNWspro.s1s7 |
| 1294 |
|
|
| 1295 |
< |
2003-09-29 13:38 mmeineke |
| 1295 |
> |
2003-09-29 12:38 mmeineke |
| 1296 |
|
|
| 1297 |
|
* libmdtools/GenericData.hpp: light change in syntax. no |
| 1298 |
|
signifigant change. |
| 1299 |
|
|
| 1300 |
< |
2003-09-25 17:17 mmeineke |
| 1300 |
> |
2003-09-25 16:17 mmeineke |
| 1301 |
|
|
| 1302 |
|
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
| 1303 |
|
additional remarks from icc -w3 (extra verbose output) |
| 1304 |
|
|
| 1305 |
< |
2003-09-25 15:27 mmeineke |
| 1305 |
> |
2003-09-25 14:27 mmeineke |
| 1306 |
|
|
| 1307 |
|
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 1308 |
|
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
| 1316 |
|
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
| 1317 |
|
gcc -Wall and g++ -Wall |
| 1318 |
|
|
| 1319 |
< |
2003-09-25 14:54 gezelter |
| 1319 |
> |
2003-09-25 13:54 gezelter |
| 1320 |
|
|
| 1321 |
|
* configure, ac-tools/configure.in: fixed a bug in configure |
| 1322 |
|
|
| 1323 |
< |
2003-09-25 12:42 gezelter |
| 1323 |
> |
2003-09-25 11:42 gezelter |
| 1324 |
|
|
| 1325 |
|
* Makefile.in, configure, ac-tools/aclocal.m4, |
| 1326 |
|
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
| 1327 |
|
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
| 1328 |
|
fixes for configure |
| 1329 |
|
|
| 1330 |
< |
2003-09-24 15:34 mmeineke |
| 1330 |
> |
2003-09-24 14:34 mmeineke |
| 1331 |
|
|
| 1332 |
|
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
| 1333 |
|
that it is called before the first Statistics are written. |
| 1334 |
|
|
| 1335 |
< |
2003-09-23 16:36 gezelter |
| 1335 |
> |
2003-09-23 15:36 gezelter |
| 1336 |
|
|
| 1337 |
|
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
| 1338 |
|
bunch of Make.dep files to CVS |
| 1339 |
|
|
| 1340 |
< |
2003-09-23 16:34 mmeineke |
| 1340 |
> |
2003-09-23 15:34 mmeineke |
| 1341 |
|
|
| 1342 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
| 1343 |
|
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
| 1344 |
|
|
| 1345 |
|
Some small syntax cleaning in NPTfm and SimSetup |
| 1346 |
|
|
| 1347 |
< |
2003-09-22 19:07 tim |
| 1347 |
> |
2003-09-22 18:07 tim |
| 1348 |
|
|
| 1349 |
|
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
| 1350 |
|
SimInfo.hpp: fix bug in calculating maxCutoff |
| 1351 |
|
|
| 1352 |
< |
2003-09-22 17:23 mmeineke |
| 1352 |
> |
2003-09-22 16:23 mmeineke |
| 1353 |
|
|
| 1354 |
|
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
| 1355 |
|
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
| 1357 |
|
|
| 1358 |
|
Removed NPTfm and NPTim from cvs |
| 1359 |
|
|
| 1360 |
< |
2003-09-19 16:00 mmeineke |
| 1360 |
> |
2003-09-19 15:00 mmeineke |
| 1361 |
|
|
| 1362 |
|
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
| 1363 |
|
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
| 1364 |
|
class. NPTi is up to date. NPTf is not. |
| 1365 |
|
|
| 1366 |
< |
2003-09-19 12:03 mmeineke |
| 1366 |
> |
2003-09-19 11:03 mmeineke |
| 1367 |
|
|
| 1368 |
|
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
| 1369 |
|
makefile |
| 1370 |
|
|
| 1371 |
< |
2003-09-19 12:01 gezelter |
| 1371 |
> |
2003-09-19 11:01 gezelter |
| 1372 |
|
|
| 1373 |
|
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
| 1374 |
|
|
| 1375 |
< |
2003-09-19 12:01 gezelter |
| 1375 |
> |
2003-09-19 11:01 gezelter |
| 1376 |
|
|
| 1377 |
|
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
| 1378 |
|
(nearly) conserved quantities for both NPTi and NPTf |
| 1379 |
|
|
| 1380 |
< |
2003-09-19 11:20 mmeineke |
| 1380 |
> |
2003-09-19 10:20 mmeineke |
| 1381 |
|
|
| 1382 |
|
* utils/Makefile.in: fixed a typo in the makefile. |
| 1383 |
|
|
| 1384 |
< |
2003-09-19 10:55 gezelter |
| 1384 |
> |
2003-09-19 09:55 gezelter |
| 1385 |
|
|
| 1386 |
|
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
| 1387 |
|
samples/water/ssd.bass: [no log message] |
| 1388 |
|
|
| 1389 |
< |
2003-09-19 10:22 tim |
| 1389 |
> |
2003-09-19 09:22 tim |
| 1390 |
|
|
| 1391 |
|
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
| 1392 |
|
|
| 1393 |
< |
2003-09-17 10:22 mmeineke |
| 1393 |
> |
2003-09-17 09:22 mmeineke |
| 1394 |
|
|
| 1395 |
|
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
| 1396 |
|
work with constraints. |
| 1397 |
|
|
| 1398 |
< |
2003-09-16 16:02 tim |
| 1398 |
> |
2003-09-16 15:02 tim |
| 1399 |
|
|
| 1400 |
|
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
| 1401 |
|
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
| 1404 |
|
|
| 1405 |
|
NPTi appears very stable. |
| 1406 |
|
|
| 1407 |
< |
2003-09-15 12:52 tim |
| 1407 |
> |
2003-09-15 11:52 tim |
| 1408 |
|
|
| 1409 |
|
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
| 1410 |
|
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
| 1415 |
|
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
| 1416 |
|
statWriter fix bug of vector wrapping at NPTi |
| 1417 |
|
|
| 1418 |
< |
2003-09-12 16:51 mmeineke |
| 1418 |
> |
2003-09-12 11:20 gezelter |
| 1419 |
|
|
| 315 |
– |
* props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp, |
| 316 |
– |
PairCorrType.hpp: added AllCorr. It eill still need some work |
| 317 |
– |
|
| 318 |
– |
2003-09-12 12:20 gezelter |
| 319 |
– |
|
| 1420 |
|
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
| 1421 |
|
Makefile.in |
| 1422 |
|
|
| 1423 |
< |
2003-09-12 12:20 gezelter |
| 1423 |
> |
2003-09-12 11:20 gezelter |
| 1424 |
|
|
| 1425 |
|
* ChangeLog: Entered changes for configure into ChangeLog |
| 1426 |
|
|
| 1427 |
< |
2003-09-10 17:28 mmeineke |
| 328 |
< |
|
| 329 |
< |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |
| 330 |
< |
work on getting gofR working. |
| 331 |
< |
|
| 332 |
< |
2003-09-09 17:50 mmeineke |
| 333 |
< |
|
| 334 |
< |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the |
| 335 |
< |
beginings of the GofR pair correlation. |
| 336 |
< |
|
| 337 |
< |
added identification of identI in matchI. |
| 338 |
< |
|
| 339 |
< |
2003-09-09 16:35 mmeineke |
| 1427 |
> |
2003-09-09 15:35 mmeineke |
| 1428 |
|
|
| 1429 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
| 1430 |
|
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
| 1431 |
|
|
| 1432 |
|
added two new NPT integrators, they still need work. |
| 1433 |
|
|
| 1434 |
< |
2003-09-09 16:34 mmeineke |
| 1434 |
> |
2003-09-09 15:34 mmeineke |
| 1435 |
|
|
| 1436 |
|
* ChangeLog: updated the ChangeLog |
| 1437 |
|
|
| 1438 |
< |
2003-09-05 18:45 gezelter |
| 1438 |
> |
2003-09-05 17:45 gezelter |
| 1439 |
|
|
| 1440 |
|
* libmdtools/Make.dep: dependency on config.h |
| 1441 |
|
|
| 1442 |
< |
2003-09-05 18:36 gezelter |
| 1442 |
> |
2003-09-05 17:36 gezelter |
| 1443 |
|
|
| 1444 |
|
* configure, ac-tools/aclocal.m4: fixed sprng problem |
| 1445 |
|
|
| 1446 |
< |
2003-09-05 17:29 gezelter |
| 1446 |
> |
2003-09-05 16:29 gezelter |
| 1447 |
|
|
| 1448 |
|
* samples/metals/Makefile.in: New Makefile for metals sample |
| 1449 |
|
|
| 1450 |
< |
2003-09-05 17:27 gezelter |
| 1450 |
> |
2003-09-05 16:27 gezelter |
| 1451 |
|
|
| 1452 |
|
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
| 1453 |
|
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
| 1471 |
|
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
| 1472 |
|
autoconf / configure method of configuring OOPSE |
| 1473 |
|
|
| 1474 |
< |
2003-09-04 17:48 mmeineke |
| 1474 |
> |
2003-09-04 16:48 mmeineke |
| 1475 |
|
|
| 1476 |
|
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 1477 |
|
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
| 1481 |
|
|
| 1482 |
|
added ability to reset the integrators in the NVT and NPT family. |
| 1483 |
|
|
| 1484 |
< |
2003-09-04 17:48 mmeineke |
| 1484 |
> |
2003-09-04 16:48 mmeineke |
| 1485 |
|
|
| 1486 |
|
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
| 1487 |
|
namespace. |
| 1488 |
|
|
| 1489 |
< |
2003-09-02 10:30 tim |
| 1489 |
> |
2003-09-02 09:30 tim |
| 1490 |
|
|
| 1491 |
|
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
| 1492 |
|
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
| 1493 |
|
PolicyByMass |
| 1494 |
|
|
| 1495 |
< |
2003-08-28 17:09 tim |
| 1495 |
> |
2003-08-28 16:09 tim |
| 1496 |
|
|
| 1497 |
|
* ChangeLog, libmdtools/GenericData.cpp, |
| 1498 |
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
| 1499 |
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
| 1500 |
|
|
| 1501 |
< |
2003-08-28 12:59 mmeineke |
| 1501 |
> |
2003-08-27 14:23 tim |
| 1502 |
|
|
| 415 |
– |
* props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: |
| 416 |
– |
added the first functional parts of the PairCorrType Abstract |
| 417 |
– |
classes. |
| 418 |
– |
|
| 419 |
– |
2003-08-27 15:23 tim |
| 420 |
– |
|
| 1503 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
| 1504 |
|
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
| 1505 |
|
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
| 1506 |
|
turn on the optimization flag, it causes a seg fault |
| 1507 |
|
|
| 1508 |
< |
2003-08-27 12:25 gezelter |
| 1508 |
> |
2003-08-27 11:25 gezelter |
| 1509 |
|
|
| 1510 |
|
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
| 1511 |
|
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
| 1512 |
|
stress tensor parallel bug. |
| 1513 |
|
|
| 1514 |
< |
2003-08-27 12:16 tim |
| 1514 |
> |
2003-08-27 11:16 tim |
| 1515 |
|
|
| 1516 |
|
* ChangeLog, libmdtools/DUFF.cpp, |
| 1517 |
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
| 1518 |
|
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
| 1519 |
|
molMembershipList use global index instead of local index |
| 1520 |
|
|
| 1521 |
< |
2003-08-26 16:37 tim |
| 1521 |
> |
2003-08-26 15:37 tim |
| 1522 |
|
|
| 1523 |
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
| 1524 |
|
mpiSimulation.cpp: set default force substraction policy to |
| 1525 |
|
PolicyByMass |
| 1526 |
|
|
| 1527 |
< |
2003-08-26 16:29 tim |
| 1527 |
> |
2003-08-26 15:29 tim |
| 1528 |
|
|
| 1529 |
|
* libmdtools/Integrator.cpp: [no log message] |
| 1530 |
|
|
| 1531 |
< |
2003-08-26 16:13 mmeineke |
| 1531 |
> |
2003-08-26 15:13 mmeineke |
| 1532 |
|
|
| 1533 |
|
* utils/sysbuilder/bilayerSys.cpp: added define statemewnt to |
| 1534 |
|
Statwriter and Dumpwriter to handle files larger than 2 gb. |
| 1537 |
|
|
| 1538 |
|
hard coding some system init into bilayer.sys |
| 1539 |
|
|
| 1540 |
< |
2003-08-26 16:12 mmeineke |
| 1540 |
> |
2003-08-26 15:12 mmeineke |
| 1541 |
|
|
| 1542 |
|
* libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: |
| 1543 |
|
added define statemewnt to Statwriter and Dumpwriter to handle |
| 1545 |
|
|
| 1546 |
|
commented out some print statements in Zconstraint |
| 1547 |
|
|
| 1548 |
< |
2003-08-26 16:02 tim |
| 1548 |
> |
2003-08-26 15:02 tim |
| 1549 |
|
|
| 1550 |
|
* libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed |
| 1551 |
|
and check the seed which is specified by user at least contains 9 |
| 1552 |
|
digits |
| 1553 |
|
|
| 1554 |
< |
2003-08-26 14:32 mmeineke |
| 1554 |
> |
2003-08-26 13:32 mmeineke |
| 1555 |
|
|
| 1556 |
|
* libmdtools/DUFF.cpp: changed the Makefiel a litle. |
| 1557 |
|
|
| 1559 |
|
constucted in MPI. (The MPI struct had 6 doubles declared versus |
| 1560 |
|
the actual 11) |
| 1561 |
|
|
| 1562 |
< |
2003-08-26 14:30 mmeineke |
| 1562 |
> |
2003-08-26 13:30 mmeineke |
| 1563 |
|
|
| 1564 |
|
* Makefile: changed the Makefiel a litle. |
| 1565 |
|
|
| 1566 |
< |
2003-08-25 18:17 gezelter |
| 1566 |
> |
2003-08-25 17:17 gezelter |
| 1567 |
|
|
| 1568 |
|
* utils/sysbuilder/Makefile: More FreeBSD fixes |
| 1569 |
|
|
| 1570 |
< |
2003-08-25 17:51 gezelter |
| 1570 |
> |
2003-08-25 16:51 gezelter |
| 1571 |
|
|
| 1572 |
|
* libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, |
| 1573 |
|
libmdtools/Makefile, src/Makefile: [no log message] |
| 1574 |
|
|
| 1575 |
< |
2003-08-22 16:04 mmeineke |
| 1575 |
> |
2003-08-22 15:04 mmeineke |
| 1576 |
|
|
| 1577 |
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on |
| 1578 |
|
frequency of output dumps. |
| 1579 |
|
|
| 1580 |
< |
2003-08-20 18:23 tim |
| 1580 |
> |
2003-08-20 17:23 tim |
| 1581 |
|
|
| 1582 |
|
* libBASS/Globals.hpp, libmdtools/SimInfo.hpp, |
| 1583 |
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 1585 |
|
if he does not specify any value for seed, oopse will take the |
| 1586 |
|
value of seconds of system time as seed |
| 1587 |
|
|
| 1588 |
< |
2003-08-20 15:42 mmeineke |
| 1588 |
> |
2003-08-20 14:42 mmeineke |
| 1589 |
|
|
| 1590 |
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 1591 |
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, |
| 1598 |
|
fixed a bug where ghostbend atom b was not being set. ( recent bug |
| 1599 |
|
from SimState conversion) |
| 1600 |
|
|
| 1601 |
< |
2003-08-20 15:41 mmeineke |
| 1601 |
> |
2003-08-20 14:41 mmeineke |
| 1602 |
|
|
| 1603 |
|
* libBASS/Globals.hpp: updated the Changelog. |
| 1604 |
|
|
| 1605 |
|
added some bug fixes for setting the random number generator seed |
| 1606 |
|
value. |
| 1607 |
|
|
| 1608 |
< |
2003-08-20 15:41 mmeineke |
| 1608 |
> |
2003-08-20 14:41 mmeineke |
| 1609 |
|
|
| 1610 |
|
* ChangeLog: updated the Changelog. |
| 1611 |
|
|
| 1612 |
< |
2003-08-20 15:11 tim |
| 1612 |
> |
2003-08-20 14:11 tim |
| 1613 |
|
|
| 1614 |
|
* libBASS/Globals.cpp, libmdtools/DUFF.cpp, |
| 1615 |
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost |
| 1616 |
|
bend class |
| 1617 |
|
|
| 1618 |
< |
2003-08-20 11:13 mmeineke |
| 1618 |
> |
2003-08-20 10:13 mmeineke |
| 1619 |
|
|
| 1620 |
|
* utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in |
| 1621 |
|
make links. added -f to ln -s. |
| 1622 |
|
|
| 1623 |
< |
2003-08-20 10:50 tim |
| 1623 |
> |
2003-08-20 09:50 tim |
| 1624 |
|
|
| 1625 |
|
* libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] |
| 1626 |
|
|
| 1627 |
< |
2003-08-20 10:34 tim |
| 1627 |
> |
2003-08-20 09:34 tim |
| 1628 |
|
|
| 1629 |
|
* libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, |
| 1630 |
|
ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg |
| 1631 |
|
printing |
| 1632 |
|
|
| 1633 |
< |
2003-08-18 16:59 chuckv |
| 1633 |
> |
2003-08-18 15:59 chuckv |
| 1634 |
|
|
| 1635 |
|
* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 1636 |
|
latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, |
| 1637 |
|
sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. |
| 1638 |
|
Nanobuilder still broke. |
| 1639 |
|
|
| 1640 |
< |
2003-08-15 15:24 tim |
| 1640 |
> |
2003-08-15 14:24 tim |
| 1641 |
|
|
| 1642 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 1643 |
|
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
| 1646 |
|
libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint |
| 1647 |
|
Method |
| 1648 |
|
|
| 1649 |
< |
2003-08-14 12:16 tim |
| 1649 |
> |
2003-08-14 11:16 tim |
| 1650 |
|
|
| 1651 |
|
* libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint |
| 1652 |
|
with average force substraction strategy |
| 1653 |
|
|
| 1654 |
< |
2003-08-13 17:20 chuckv |
| 1654 |
> |
2003-08-13 16:20 chuckv |
| 1655 |
|
|
| 1656 |
|
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some |
| 1657 |
|
profiling code -DPROFILE. |
| 1658 |
|
|
| 1659 |
< |
2003-08-13 15:21 tim |
| 1659 |
> |
2003-08-13 14:21 tim |
| 1660 |
|
|
| 1661 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 1662 |
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 1663 |
|
libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic |
| 1664 |
|
potential & z-contraint method |
| 1665 |
|
|
| 1666 |
< |
2003-08-12 17:44 mmeineke |
| 1666 |
> |
2003-08-12 16:44 mmeineke |
| 1667 |
|
|
| 1668 |
|
* libBASS/BASS_interface.cpp, libBASS/Globals.hpp, |
| 1669 |
|
libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 1672 |
|
annoying bug in Directional Atom, where mu was getting written to |
| 1673 |
|
pseudorandom memory location. |
| 1674 |
|
|
| 1675 |
< |
2003-08-12 15:56 tim |
| 1675 |
> |
2003-08-12 14:56 tim |
| 1676 |
|
|
| 1677 |
|
* libBASS/BASS_interface.cpp, libBASS/Globals.cpp, |
| 1678 |
|
libBASS/Globals.hpp, libmdtools/Atom.hpp, |
| 1679 |
|
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
| 1680 |
|
libmdtools/SimSetup.cpp: debugging globals |
| 1681 |
|
|
| 1682 |
< |
2003-08-12 14:40 gezelter |
| 1682 |
> |
2003-08-12 13:40 gezelter |
| 1683 |
|
|
| 1684 |
|
* forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes |
| 1685 |
|
and new atypes in LJFF |
| 1686 |
|
|
| 1687 |
< |
2003-08-12 14:15 gezelter |
| 1687 |
> |
2003-08-12 13:15 gezelter |
| 1688 |
|
|
| 1689 |
|
* forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older |
| 1690 |
|
stuff... |
| 1691 |
|
|
| 1692 |
< |
2003-08-12 14:14 chuckv |
| 1692 |
> |
2003-08-12 13:14 chuckv |
| 1693 |
|
|
| 1694 |
|
* utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. |
| 1695 |
|
|
| 1696 |
< |
2003-08-12 14:04 chuckv |
| 1696 |
> |
2003-08-12 13:04 chuckv |
| 1697 |
|
|
| 1698 |
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: |
| 1699 |
|
Missed del of files before. |
| 1700 |
|
|
| 1701 |
< |
2003-08-12 14:03 chuckv |
| 1701 |
> |
2003-08-12 13:03 chuckv |
| 1702 |
|
|
| 1703 |
|
* utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log |
| 1704 |
|
message] |
| 1705 |
|
|
| 1706 |
< |
2003-08-12 14:01 chuckv |
| 1706 |
> |
2003-08-12 13:01 chuckv |
| 1707 |
|
|
| 1708 |
|
* utils/sysbuilder/Makefile: commit makefile |
| 1709 |
|
|
| 1710 |
< |
2003-08-12 13:51 tim |
| 1710 |
> |
2003-08-12 12:51 tim |
| 1711 |
|
|
| 1712 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 1713 |
|
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
| 1715 |
|
libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added |
| 1716 |
|
harmonical potential to z-constraint method |
| 1717 |
|
|
| 1718 |
< |
2003-08-11 18:31 chuckv |
| 1718 |
> |
2003-08-11 17:31 chuckv |
| 1719 |
|
|
| 1720 |
|
* utils/Makefile: Changed makefile to only build quicklate. |
| 1721 |
|
|
| 1722 |
< |
2003-08-11 18:25 chuckv |
| 1722 |
> |
2003-08-11 17:25 chuckv |
| 1723 |
|
|
| 1724 |
|
* ac-tools/configure.in: added utils/sysbuilder to be built. |
| 1725 |
|
|
| 1726 |
< |
2003-08-11 18:12 chuckv |
| 1726 |
> |
2003-08-11 17:12 chuckv |
| 1727 |
|
|
| 1728 |
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 1729 |
|
bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, |
| 1737 |
|
sysbuilder into a subdirectory. Fixed some of sysbuilder to work |
| 1738 |
|
with new atom allocation in libmdtools. |
| 1739 |
|
|
| 1740 |
< |
2003-08-11 15:41 tim |
| 1740 |
> |
2003-08-11 14:41 tim |
| 1741 |
|
|
| 1742 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp: added method of |
| 1743 |
|
moving zconstraint molecules to specified positions |
| 1744 |
|
|
| 1745 |
< |
2003-08-11 15:39 tim |
| 1745 |
> |
2003-08-11 14:39 tim |
| 1746 |
|
|
| 1747 |
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] |
| 1748 |
|
|
| 1749 |
< |
2003-08-11 15:38 mmeineke |
| 1749 |
> |
2003-08-11 14:38 mmeineke |
| 1750 |
|
|
| 1751 |
|
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
| 1752 |
|
libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, |
| 1757 |
|
libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint |
| 1758 |
|
into the BASS language syntax. |
| 1759 |
|
|
| 1760 |
< |
2003-08-11 14:29 mmeineke |
| 1760 |
> |
2003-08-11 13:29 mmeineke |
| 1761 |
|
|
| 1762 |
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of |
| 1763 |
|
degrees of freedom to account for zConstreints |
| 1764 |
|
|
| 1765 |
< |
2003-08-08 17:22 chuckv |
| 1765 |
> |
2003-08-08 16:22 chuckv |
| 1766 |
|
|
| 1767 |
|
* libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, |
| 1768 |
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
| 1769 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
| 1770 |
|
works..... |
| 1771 |
|
|
| 1772 |
< |
2003-08-08 14:32 mmeineke |
| 1772 |
> |
2003-08-08 12:48 mmeineke |
| 1773 |
|
|
| 692 |
– |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
| 693 |
– |
moved frameCount's functionality into DumpReader. also split props |
| 694 |
– |
into staticProps and dynamicProps. (currently only have |
| 695 |
– |
staticProps) |
| 696 |
– |
|
| 697 |
– |
2003-08-08 13:48 mmeineke |
| 698 |
– |
|
| 1774 |
|
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
| 1775 |
|
instance of Atom::setZ and Atom::getZ in ZConstaint. |
| 1776 |
|
|
| 1777 |
< |
2003-08-07 17:47 mmeineke |
| 1777 |
> |
2003-08-07 16:47 mmeineke |
| 1778 |
|
|
| 1779 |
|
* libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
| 1780 |
|
DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, |
| 1783 |
|
SimState.hpp, Torsion.cpp: switched SimInfo to use a system |
| 1784 |
|
configuration from SimState rather than arrays from Atom |
| 1785 |
|
|
| 1786 |
< |
2003-08-06 20:47 chuckv |
| 1786 |
> |
2003-08-06 19:47 chuckv |
| 1787 |
|
|
| 1788 |
|
* libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, |
| 1789 |
|
libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, |
| 1790 |
|
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
| 1791 |
|
samples/metals/Au.bass: Bug fixes for eam... |
| 1792 |
|
|
| 1793 |
< |
2003-08-01 12:18 tim |
| 1793 |
> |
2003-08-01 11:18 tim |
| 1794 |
|
|
| 1795 |
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of |
| 1796 |
|
Z-Constraint |
| 1797 |
|
|
| 1798 |
< |
2003-07-31 15:59 tim |
| 1798 |
> |
2003-07-31 14:59 tim |
| 1799 |
|
|
| 1800 |
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 1801 |
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 1802 |
|
libmdtools/ZConstraint.cpp: add index range checking into |
| 1803 |
|
ZConstraint |
| 1804 |
|
|
| 1805 |
< |
2003-07-31 11:38 tim |
| 1805 |
> |
2003-07-31 10:38 tim |
| 1806 |
|
|
| 1807 |
|
* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
| 1808 |
|
to the globals |
| 1809 |
|
|
| 1810 |
< |
2003-07-31 11:35 tim |
| 1810 |
> |
2003-07-31 10:35 tim |
| 1811 |
|
|
| 1812 |
|
* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
| 1813 |
|
Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
| 1815 |
|
SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
| 1816 |
|
Added Z constraint. |
| 1817 |
|
|
| 1818 |
< |
2003-07-30 17:17 chuckv |
| 1818 |
> |
2003-07-30 16:17 chuckv |
| 1819 |
|
|
| 1820 |
|
* libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, |
| 1821 |
|
libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, |
| 1822 |
|
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, |
| 1823 |
|
samples/metals/Au.bass: More bug fixes for eam. |
| 1824 |
|
|
| 1825 |
< |
2003-07-29 12:32 mmeineke |
| 1825 |
> |
2003-07-29 11:32 mmeineke |
| 1826 |
|
|
| 1827 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
| 1828 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 1829 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
| 755 |
< |
src/Makefile: working on the props code |
| 1828 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
| 1829 |
> |
working on the props code |
| 1830 |
|
|
| 1831 |
< |
2003-07-29 12:32 mmeineke |
| 1831 |
> |
2003-07-29 11:32 mmeineke |
| 1832 |
|
|
| 1833 |
|
* libBASS/Globals.cpp: [no log message] |
| 1834 |
|
|
| 1835 |
< |
2003-07-25 16:05 chuckv |
| 1835 |
> |
2003-07-25 15:05 chuckv |
| 1836 |
|
|
| 1837 |
|
* samples/metals/: Au.bass, metals.mdl: Added bass models for |
| 1838 |
|
metals |
| 1839 |
|
|
| 1840 |
< |
2003-07-25 16:00 chuckv |
| 1840 |
> |
2003-07-25 15:00 chuckv |
| 1841 |
|
|
| 1842 |
|
* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
| 1843 |
|
notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
| 1844 |
|
|
| 1845 |
< |
2003-07-24 17:22 chuckv |
| 1845 |
> |
2003-07-24 16:22 chuckv |
| 1846 |
|
|
| 1847 |
|
* ac-tools/configure.in: Changed configure to look for both upper |
| 1848 |
|
and lower cass .mod files |
| 1849 |
|
|
| 1850 |
< |
2003-07-24 15:57 chuckv |
| 1850 |
> |
2003-07-24 14:57 chuckv |
| 1851 |
|
|
| 1852 |
|
* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
| 1853 |
|
eam and do_forces. |
| 1854 |
|
|
| 1855 |
< |
2003-07-23 18:13 chuckv |
| 1855 |
> |
2003-07-23 17:13 chuckv |
| 1856 |
|
|
| 1857 |
|
* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
| 1858 |
|
force_globals.F90, simulation_module.F90, status_module.F90: |
| 1859 |
|
Finished most code for eam.... |
| 1860 |
|
|
| 1861 |
< |
2003-07-22 17:49 mmeineke |
| 1861 |
> |
2003-07-22 16:49 mmeineke |
| 1862 |
|
|
| 1863 |
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
| 1864 |
|
function to the DumpReader. It should now save the start of each |
| 1865 |
|
frame in a vector. |
| 1866 |
|
|
| 1867 |
< |
2003-07-22 16:05 mmeineke |
| 1867 |
> |
2003-07-22 15:05 mmeineke |
| 1868 |
|
|
| 1869 |
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
| 1870 |
|
to read dump files |
| 1871 |
|
|
| 1872 |
< |
2003-07-22 15:54 tim |
| 1872 |
> |
2003-07-22 14:54 tim |
| 1873 |
|
|
| 1874 |
|
* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
| 1875 |
|
Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
| 1876 |
|
NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
| 1877 |
|
message] |
| 1878 |
|
|
| 1879 |
< |
2003-07-22 12:41 mmeineke |
| 1879 |
> |
2003-07-22 11:41 mmeineke |
| 1880 |
|
|
| 1881 |
|
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
| 1882 |
|
SimSetup.cpp: Fixed a current time initialization bug in |
| 1883 |
|
InitFromFile. |
| 1884 |
|
|
| 1885 |
< |
2003-07-21 17:27 mmeineke |
| 1885 |
> |
2003-07-21 16:27 mmeineke |
| 1886 |
|
|
| 1887 |
|
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
| 1888 |
|
Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
| 1889 |
|
friends to accomadate random file access |
| 1890 |
|
|
| 1891 |
< |
2003-07-21 12:23 mmeineke |
| 1891 |
> |
2003-07-21 11:23 mmeineke |
| 1892 |
|
|
| 1893 |
|
* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
| 1894 |
|
one sets it. |
| 1895 |
|
|
| 1896 |
< |
2003-07-21 12:23 mmeineke |
| 1896 |
> |
2003-07-21 11:23 mmeineke |
| 1897 |
|
|
| 1898 |
|
* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
| 1899 |
|
ReadWrite.hpp: fixed Initializefrom file to start the simulation |
| 1900 |
|
from the time specified in the init file. |
| 1901 |
|
|
| 1902 |
< |
2003-07-17 17:49 gezelter |
| 1902 |
> |
2003-07-17 16:49 gezelter |
| 1903 |
|
|
| 1904 |
|
* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
| 1905 |
|
DumpReader.cpp: Started work on a DumpReader |
| 1906 |
|
|
| 1907 |
< |
2003-07-17 16:38 gezelter |
| 1907 |
> |
2003-07-17 15:38 gezelter |
| 1908 |
|
|
| 1909 |
|
* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
| 1910 |
|
|
| 1911 |
< |
2003-07-17 16:32 gezelter |
| 1911 |
> |
2003-07-17 15:32 gezelter |
| 1912 |
|
|
| 1913 |
|
* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
| 1914 |
|
libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
| 1915 |
|
Changes for SSD/E |
| 1916 |
|
|
| 1917 |
< |
2003-07-17 15:38 mmeineke |
| 1917 |
> |
2003-07-17 14:38 mmeineke |
| 1918 |
|
|
| 1919 |
|
* libmdtools/do_Forces.F90: commented out an eam line |
| 1920 |
|
|
| 1921 |
< |
2003-07-17 15:32 chuckv |
| 1921 |
> |
2003-07-17 14:32 chuckv |
| 1922 |
|
|
| 1923 |
|
* libmdtools/atype_module.F90: fixed spelling issue |
| 1924 |
|
|
| 1925 |
< |
2003-07-17 15:29 chuckv |
| 1925 |
> |
2003-07-17 14:29 chuckv |
| 1926 |
|
|
| 1927 |
|
* libmdtools/: fInfo.c, status_module.F90: added info module |
| 1928 |
|
|
| 1929 |
< |
2003-07-17 15:25 chuckv |
| 1929 |
> |
2003-07-17 14:25 chuckv |
| 1930 |
|
|
| 1931 |
|
* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
| 1932 |
|
atype_module.F90, calc_eam.F90, do_Forces.F90, |
| 1933 |
|
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
| 1934 |
|
mpiSimulation_module.F90: Added massive changes for eam.... |
| 1935 |
|
|
| 1936 |
< |
2003-07-16 17:49 chuckv |
| 1936 |
> |
2003-07-16 16:49 chuckv |
| 1937 |
|
|
| 1938 |
|
* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
| 1939 |
|
|
| 1940 |
< |
2003-07-16 17:30 mmeineke |
| 1940 |
> |
2003-07-16 16:30 mmeineke |
| 1941 |
|
|
| 1942 |
|
* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
| 1943 |
|
SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 1948 |
|
notifyCutoffs in Fortran notifies those who need the information of |
| 1949 |
|
any changes to cutoffs. |
| 1950 |
|
|
| 1951 |
< |
2003-07-16 13:35 gezelter |
| 1951 |
> |
2003-07-16 12:35 gezelter |
| 1952 |
|
|
| 1953 |
|
* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
| 1954 |
|
quickLate is now somewhat more intelligent about periodic |
| 1955 |
|
boundaries and wrapping. |
| 1956 |
|
|
| 1957 |
< |
2003-07-16 12:40 chuckv |
| 1957 |
> |
2003-07-16 11:40 chuckv |
| 1958 |
|
|
| 1959 |
|
* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
| 1960 |
|
|
| 1961 |
< |
2003-07-16 11:34 mmeineke |
| 1961 |
> |
2003-07-16 10:34 mmeineke |
| 1962 |
|
|
| 1963 |
|
* scripts/cleanSrc: added a quick wipe-and-update script for quick |
| 1964 |
|
rebuilds on BoB |
| 1965 |
|
|
| 1966 |
< |
2003-07-15 22:11 gezelter |
| 1966 |
> |
2003-07-15 21:11 gezelter |
| 1967 |
|
|
| 1968 |
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
| 1969 |
|
SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
| 1970 |
|
fixes for box changes |
| 1971 |
|
|
| 1972 |
< |
2003-07-15 18:29 mmeineke |
| 1972 |
> |
2003-07-15 17:29 mmeineke |
| 1973 |
|
|
| 1974 |
|
* libmdtools/simulation_module.F90: removed some debugging print |
| 1975 |
|
statements. |
| 1976 |
|
|
| 1977 |
< |
2003-07-15 18:22 mmeineke |
| 1977 |
> |
2003-07-15 17:22 mmeineke |
| 1978 |
|
|
| 1979 |
|
* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 1980 |
|
do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
| 1983 |
|
cutoff region to be to small. Also led to the removal of the taper |
| 1984 |
|
region to buffer the dipole cutoff. |
| 1985 |
|
|
| 1986 |
< |
2003-07-15 17:34 mmeineke |
| 1986 |
> |
2003-07-15 16:34 mmeineke |
| 1987 |
|
|
| 1988 |
|
* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
| 1989 |
|
fixing ssd bug |
| 1990 |
|
|
| 1991 |
< |
2003-07-15 15:56 gezelter |
| 1991 |
> |
2003-07-15 14:56 gezelter |
| 1992 |
|
|
| 1993 |
|
* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
| 1994 |
|
for the NPT ensembles |
| 1995 |
|
|
| 1996 |
< |
2003-07-15 14:52 mmeineke |
| 1996 |
> |
2003-07-15 13:52 mmeineke |
| 1997 |
|
|
| 1998 |
|
* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
| 1999 |
|
simSetup |
| 2000 |
|
|
| 2001 |
< |
2003-07-15 13:57 mmeineke |
| 2001 |
> |
2003-07-15 12:57 mmeineke |
| 2002 |
|
|
| 2003 |
|
* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
| 2004 |
|
SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
| 2005 |
|
fixed some bugs, Changed entry_plug to info where appropriate |
| 2006 |
|
|
| 2007 |
< |
2003-07-15 13:25 chuckv |
| 2007 |
> |
2003-07-15 12:25 chuckv |
| 2008 |
|
|
| 2009 |
|
* utils/sysBuild.ggo: added more command line arguments |
| 2010 |
|
|
| 2011 |
< |
2003-07-15 13:11 gezelter |
| 2011 |
> |
2003-07-15 12:11 gezelter |
| 2012 |
|
|
| 2013 |
|
* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
| 2014 |
|
Fixing force field line |
| 2015 |
|
|
| 2016 |
< |
2003-07-15 13:10 gezelter |
| 2016 |
> |
2003-07-15 12:10 gezelter |
| 2017 |
|
|
| 2018 |
|
* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
| 2019 |
|
calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
| 2020 |
|
calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
| 2021 |
|
tensor |
| 2022 |
|
|
| 2023 |
< |
2003-07-15 11:50 gezelter |
| 2023 |
> |
2003-07-15 10:50 gezelter |
| 2024 |
|
|
| 2025 |
|
* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
| 2026 |
|
|
| 2027 |
< |
2003-07-15 11:42 gezelter |
| 2027 |
> |
2003-07-15 10:42 gezelter |
| 2028 |
|
|
| 2029 |
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
| 2030 |
|
removed old outdated code |
| 2031 |
|
|
| 2032 |
< |
2003-07-15 10:45 gezelter |
| 2032 |
> |
2003-07-15 09:45 gezelter |
| 2033 |
|
|
| 2034 |
|
* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
| 2035 |
|
|
| 2036 |
< |
2003-07-15 10:28 gezelter |
| 2036 |
> |
2003-07-15 09:28 gezelter |
| 2037 |
|
|
| 2038 |
|
* libmdtools/Molecule.cpp: removing get_vx |
| 2039 |
|
|
| 2040 |
< |
2003-07-14 23:28 gezelter |
| 2040 |
> |
2003-07-14 22:28 gezelter |
| 2041 |
|
|
| 2042 |
|
* libmdtools/NPTfm.cpp: Added NPTfm |
| 2043 |
|
|
| 2044 |
< |
2003-07-14 23:27 gezelter |
| 2044 |
> |
2003-07-14 22:27 gezelter |
| 2045 |
|
|
| 2046 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
| 2047 |
|
Bugfix in NPTim, fixes for NPTfm |
| 2048 |
|
|
| 2049 |
< |
2003-07-14 23:08 gezelter |
| 2049 |
> |
2003-07-14 22:08 gezelter |
| 2050 |
|
|
| 2051 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
| 2052 |
|
Checking in changes for NPTim |
| 2053 |
|
|
| 2054 |
< |
2003-07-14 19:06 gezelter |
| 2054 |
> |
2003-07-14 18:06 gezelter |
| 2055 |
|
|
| 2056 |
|
* utils/Makefile: Broken SysBuilder |
| 2057 |
|
|
| 2058 |
< |
2003-07-14 19:06 gezelter |
| 2058 |
> |
2003-07-14 18:06 gezelter |
| 2059 |
|
|
| 2060 |
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
| 2061 |
|
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
| 2062 |
|
for samples |
| 2063 |
|
|
| 2064 |
< |
2003-07-14 19:06 gezelter |
| 2064 |
> |
2003-07-14 18:06 gezelter |
| 2065 |
|
|
| 2066 |
|
* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
| 2067 |
|
debugging write statements |
| 2068 |
|
|
| 2069 |
< |
2003-07-14 18:38 gezelter |
| 2069 |
> |
2003-07-14 17:38 gezelter |
| 2070 |
|
|
| 2071 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
| 2072 |
|
NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
| 2073 |
|
|
| 2074 |
< |
2003-07-14 17:48 mmeineke |
| 2074 |
> |
2003-07-14 16:48 mmeineke |
| 2075 |
|
|
| 2076 |
|
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
| 2077 |
|
and set routines to Atom and DirectionalAtom |
| 2078 |
|
|
| 2079 |
< |
2003-07-14 17:35 chuckv |
| 2079 |
> |
2003-07-14 16:35 chuckv |
| 2080 |
|
|
| 2081 |
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
| 2082 |
|
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
| 2083 |
|
that takes different cmd line arguments. |
| 2084 |
|
|
| 2085 |
< |
2003-07-14 17:28 mmeineke |
| 2085 |
> |
2003-07-14 16:28 mmeineke |
| 2086 |
|
|
| 2087 |
|
* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
| 2088 |
|
ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
| 2089 |
|
SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
| 2090 |
|
were not being updated |
| 2091 |
|
|
| 2092 |
< |
2003-07-14 11:04 gezelter |
| 2092 |
> |
2003-07-14 10:04 gezelter |
| 2093 |
|
|
| 2094 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
| 2095 |
|
NPTim |
| 2096 |
|
|
| 2097 |
< |
2003-07-14 10:55 mmeineke |
| 2097 |
> |
2003-07-14 09:55 mmeineke |
| 2098 |
|
|
| 2099 |
|
* forceFields/DUFF.frc: Switched the bond in the force field back |
| 2100 |
|
to constrained, to preserve energy |
| 2101 |
|
|
| 2102 |
< |
2003-07-11 18:34 mmeineke |
| 2102 |
> |
2003-07-11 17:34 mmeineke |
| 2103 |
|
|
| 2104 |
|
* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
| 2105 |
|
Integrator.hpp: working on som integrator bugs |
| 2106 |
|
|
| 2107 |
< |
2003-07-11 11:26 gezelter |
| 2107 |
> |
2003-07-11 10:26 gezelter |
| 2108 |
|
|
| 2109 |
|
* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
| 2110 |
|
to worry about all the strtok() calls in our code |
| 2111 |
|
|
| 2112 |
< |
2003-07-11 10:49 gezelter |
| 2112 |
> |
2003-07-11 09:49 gezelter |
| 2113 |
|
|
| 2114 |
|
* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
| 2115 |
|
|
| 2116 |
< |
2003-07-10 21:15 gezelter |
| 2116 |
> |
2003-07-10 20:15 gezelter |
| 2117 |
|
|
| 2118 |
|
* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
| 2119 |
|
eor. |
| 2120 |
|
|
| 2121 |
< |
2003-07-10 18:15 mmeineke |
| 2121 |
> |
2003-07-10 17:15 mmeineke |
| 2122 |
|
|
| 2123 |
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
| 2124 |
|
SimInfo.cpp, Thermo.cpp: fixed some bugs |
| 2125 |
|
|
| 2126 |
< |
2003-07-10 15:53 chuckv |
| 2126 |
> |
2003-07-10 14:53 chuckv |
| 2127 |
|
|
| 2128 |
|
* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
| 2129 |
|
nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
| 2130 |
|
nanoBuilder and a general Lattice builder. |
| 2131 |
|
|
| 2132 |
< |
2003-07-10 13:10 gezelter |
| 2132 |
> |
2003-07-10 12:10 gezelter |
| 2133 |
|
|
| 2134 |
|
* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
| 2135 |
|
Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
| 2136 |
|
|
| 2137 |
< |
2003-07-09 18:14 mmeineke |
| 2137 |
> |
2003-07-09 17:14 mmeineke |
| 2138 |
|
|
| 2139 |
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
| 2140 |
|
Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
| 2141 |
|
SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
| 2142 |
|
caclulation of HmatInverse. |
| 2143 |
|
|
| 2144 |
< |
2003-07-09 11:34 mmeineke |
| 2144 |
> |
2003-07-09 10:34 mmeineke |
| 2145 |
|
|
| 2146 |
|
* libBASS/MoleculeStamp.hpp: starting some work for xlate |
| 2147 |
|
|
| 2148 |
< |
2003-07-09 11:33 mmeineke |
| 2148 |
> |
2003-07-09 10:33 mmeineke |
| 2149 |
|
|
| 2150 |
|
* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
| 2151 |
|
|
| 2152 |
< |
2003-07-09 09:56 gezelter |
| 2152 |
> |
2003-07-09 08:56 gezelter |
| 2153 |
|
|
| 2154 |
|
* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
| 2155 |
|
|
| 2156 |
< |
2003-07-09 09:56 gezelter |
| 2156 |
> |
2003-07-09 08:56 gezelter |
| 2157 |
|
|
| 2158 |
|
* libBASS/Globals.cpp: Removed Qmass |
| 2159 |
|
|
| 2160 |
< |
2003-07-08 22:15 gezelter |
| 2160 |
> |
2003-07-08 21:15 gezelter |
| 2161 |
|
|
| 2162 |
|
* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
| 2163 |
|
and NPTi |
| 2164 |
|
|
| 2165 |
< |
2003-07-08 21:41 gezelter |
| 2165 |
> |
2003-07-08 20:41 gezelter |
| 2166 |
|
|
| 2167 |
|
* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
| 2168 |
|
|
| 2169 |
< |
2003-07-08 17:10 gezelter |
| 2169 |
> |
2003-07-08 16:10 gezelter |
| 2170 |
|
|
| 2171 |
|
* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
| 2172 |
|
|
| 2173 |
< |
2003-07-08 17:06 gezelter |
| 2173 |
> |
2003-07-08 16:06 gezelter |
| 2174 |
|
|
| 2175 |
|
* libmdtools/NPTi.cpp: fixed box scaling |
| 2176 |
|
|
| 2177 |
< |
2003-07-08 16:56 gezelter |
| 2177 |
> |
2003-07-08 15:56 gezelter |
| 2178 |
|
|
| 2179 |
|
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
| 2180 |
|
SimInfo.hpp, Thermo.cpp: NPTi |
| 2181 |
|
|
| 2182 |
< |
2003-07-03 15:41 mmeineke |
| 2182 |
> |
2003-07-03 14:41 mmeineke |
| 2183 |
|
|
| 2184 |
|
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
| 2185 |
|
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
| 2186 |
|
scripts in the makefiles |
| 2187 |
|
|
| 2188 |
< |
2003-07-02 17:26 mmeineke |
| 2188 |
> |
2003-07-02 16:26 mmeineke |
| 2189 |
|
|
| 2190 |
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
| 2191 |
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 2196 |
|
utils/Makefile: fixed the bugs introduced by switching the periodic |
| 2197 |
|
box to a matrix |
| 2198 |
|
|
| 2199 |
< |
2003-07-01 18:39 gezelter |
| 2199 |
> |
2003-07-01 17:39 gezelter |
| 2200 |
|
|
| 2201 |
|
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
| 2202 |
|
|
| 2203 |
< |
2003-07-01 18:29 gezelter |
| 2203 |
> |
2003-07-01 17:29 gezelter |
| 2204 |
|
|
| 2205 |
|
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
| 2206 |
|
|
| 2207 |
< |
2003-07-01 17:33 mmeineke |
| 2207 |
> |
2003-07-01 16:33 mmeineke |
| 2208 |
|
|
| 2209 |
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
| 2210 |
|
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
| 2211 |
|
the box matrix to everything. |
| 2212 |
|
|
| 2213 |
< |
2003-06-30 18:03 mmeineke |
| 2213 |
> |
2003-06-30 17:03 mmeineke |
| 2214 |
|
|
| 2215 |
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 2216 |
|
src/oopse.cpp: |
| 2217 |
|
Updated the ChangeLog, and Converted most of the SImInfo to use |
| 2218 |
|
non-Isotropic boxes. wrapVector needs to be finished. |
| 2219 |
|
|
| 2220 |
< |
2003-06-25 17:12 mmeineke |
| 2220 |
> |
2003-06-25 16:12 mmeineke |
| 2221 |
|
|
| 2222 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
| 2223 |
|
to Harmonic bonds in the DUFF frc file |
| 2224 |
|
|
| 2225 |
|
fixed constraints. |
| 2226 |
|
|
| 2227 |
< |
2003-06-25 17:11 mmeineke |
| 2227 |
> |
2003-06-25 16:11 mmeineke |
| 2228 |
|
|
| 2229 |
|
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
| 2230 |
|
the DUFF frc file |
| 2231 |
|
|
| 2232 |
< |
2003-06-24 18:51 gezelter |
| 2232 |
> |
2003-06-24 17:51 gezelter |
| 2233 |
|
|
| 2234 |
|
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
| 2235 |
|
|
| 2236 |
< |
2003-06-24 15:57 mmeineke |
| 2236 |
> |
2003-06-24 14:57 mmeineke |
| 2237 |
|
|
| 2238 |
|
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
| 2239 |
|
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
| 2240 |
|
the DUFF forcefield and BondExtensions.cpp |
| 2241 |
|
|
| 2242 |
< |
2003-06-23 17:24 mmeineke |
| 2242 |
> |
2003-06-23 16:24 mmeineke |
| 2243 |
|
|
| 2244 |
|
* libmdtools/Integrator.cpp: Doing some work to debug the |
| 2245 |
|
constraint code. |
| 2246 |
|
|
| 2247 |
< |
2003-06-20 16:50 gezelter |
| 2247 |
> |
2003-06-20 15:50 gezelter |
| 2248 |
|
|
| 2249 |
|
* libmdtools/Integrator.hpp: NPT fix |
| 2250 |
|
|
| 2251 |
< |
2003-06-20 16:29 mmeineke |
| 2251 |
> |
2003-06-20 15:29 mmeineke |
| 2252 |
|
|
| 2253 |
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 2254 |
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 2257 |
|
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
| 2258 |
|
integrator and NVT seem to be working now. |
| 2259 |
|
|
| 2260 |
< |
2003-06-20 12:49 gezelter |
| 2260 |
> |
2003-06-20 11:49 gezelter |
| 2261 |
|
|
| 2262 |
|
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
| 2263 |
|
|
| 2264 |
< |
2003-06-19 18:02 mmeineke |
| 2264 |
> |
2003-06-19 17:02 mmeineke |
| 2265 |
|
|
| 2266 |
|
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
| 2267 |
|
forceFields/LJ_FF.frc, forceFields/Makefile, |
| 2272 |
|
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
| 2273 |
|
forcefield names. |
| 2274 |
|
|
| 2275 |
< |
2003-06-19 15:21 mmeineke |
| 2275 |
> |
2003-06-19 14:21 mmeineke |
| 2276 |
|
|
| 2277 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
| 2278 |
|
finished the basics of the integrator and SimSetup.cpp |
| 2279 |
|
|
| 2280 |
< |
2003-06-19 15:11 mmeineke |
| 2280 |
> |
2003-06-19 14:11 mmeineke |
| 2281 |
|
|
| 2282 |
|
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
| 2283 |
|
up / get it to work with the new Integrator. |
| 2284 |
|
|
| 2285 |
< |
2003-06-18 18:20 mmeineke |
| 2285 |
> |
2003-06-18 17:20 mmeineke |
| 2286 |
|
|
| 2287 |
|
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
| 2288 |
|
output times. |
| 2289 |
|
|
| 2290 |
< |
2003-06-17 17:56 mmeineke |
| 2290 |
> |
2003-06-17 16:56 mmeineke |
| 2291 |
|
|
| 2292 |
|
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
| 2293 |
|
fro the ghost Bend in TraPPE_Ex |
| 2294 |
|
|
| 2295 |
|
some work on the integrator. ( incomplete) |
| 2296 |
|
|
| 2297 |
< |
2003-06-17 17:55 mmeineke |
| 2297 |
> |
2003-06-17 16:55 mmeineke |
| 2298 |
|
|
| 2299 |
|
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
| 2300 |
|
Bend in TraPPE_Ex |
| 2301 |
|
|
| 2302 |
< |
2003-06-04 17:06 mmeineke |
| 2302 |
> |
2003-06-04 16:06 mmeineke |
| 2303 |
|
|
| 2304 |
|
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
| 2305 |
|
constrainB to the Symplectic integrator |
| 2306 |
|
|
| 2307 |
< |
2003-05-30 17:32 mmeineke |
| 2307 |
> |
2003-05-30 16:32 mmeineke |
| 2308 |
|
|
| 2309 |
|
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
| 2310 |
|
the basic integrator. |
| 2311 |
|
|
| 2312 |
|
bilayerSys.cpp altered for building tb3. |
| 2313 |
|
|
| 2314 |
< |
2003-05-30 17:31 mmeineke |
| 2314 |
> |
2003-05-30 16:31 mmeineke |
| 2315 |
|
|
| 2316 |
|
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
| 2317 |
|
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
| 2318 |
|
modifiying Symplectic to become the basic integrator. |
| 2319 |
|
|
| 2320 |
< |
2003-05-30 16:19 mmeineke |
| 2320 |
> |
2003-05-30 15:19 mmeineke |
| 2321 |
|
|
| 2322 |
|
* libmdtools/Integrator.hpp: added some member variables for |
| 2323 |
|
position, velocity, etc. |
| 2324 |
|
|
| 2325 |
< |
2003-05-30 15:07 mmeineke |
| 2325 |
> |
2003-05-30 14:07 mmeineke |
| 2326 |
|
|
| 2327 |
|
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
| 2328 |
|
is now derived from Integrator |
| 2329 |
|
|
| 2330 |
< |
2003-05-20 12:44 mmeineke |
| 2330 |
> |
2003-05-20 11:44 mmeineke |
| 2331 |
|
|
| 2332 |
|
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
| 2333 |
|
|
| 2334 |
< |
2003-05-17 12:57 mmeineke |
| 2334 |
> |
2003-05-17 11:57 mmeineke |
| 2335 |
|
|
| 2336 |
|
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
| 2337 |
|
working |
| 2338 |
|
|
| 2339 |
< |
2003-05-16 17:37 mmeineke |
| 2339 |
> |
2003-05-16 16:37 mmeineke |
| 2340 |
|
|
| 2341 |
|
* utils/bilayerSys.cpp: still working on the bilayer code |
| 2342 |
|
|
| 2343 |
< |
2003-05-16 10:28 mmeineke |
| 2343 |
> |
2003-05-16 09:28 mmeineke |
| 2344 |
|
|
| 2345 |
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
| 2346 |
|
work to overhaul sysbuild. |
| 2347 |
|
|
| 2348 |
< |
2003-05-13 17:23 mmeineke |
| 2348 |
> |
2003-05-13 16:23 mmeineke |
| 2349 |
|
|
| 2350 |
|
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
| 2351 |
|
|
| 2352 |
< |
2003-05-13 16:47 mmeineke |
| 2352 |
> |
2003-05-13 15:47 mmeineke |
| 2353 |
|
|
| 2354 |
|
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
| 2355 |
|
beadLipid/water.mdl: Added bead lipid model to the sample directory |
| 2356 |
|
|
| 2357 |
< |
2003-05-13 16:34 mmeineke |
| 2357 |
> |
2003-05-13 15:34 mmeineke |
| 2358 |
|
|
| 2359 |
|
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
| 2360 |
|
the Trappe extended force field |
| 2361 |
|
|
| 2362 |
< |
2003-05-13 13:01 mmeineke |
| 2362 |
> |
2003-05-13 12:01 mmeineke |
| 2363 |
|
|
| 2364 |
|
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
| 2365 |
|
TraPPe_Ex forceField |
| 2366 |
|
|
| 2367 |
< |
2003-05-09 15:51 mmeineke |
| 2367 |
> |
2003-05-09 14:51 mmeineke |
| 2368 |
|
|
| 2369 |
|
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
| 2370 |
|
there were some duplicate entries |
| 2371 |
|
|
| 2372 |
|
added a two chain lipid to the lipid.mdl in sample |
| 2373 |
|
|
| 2374 |
< |
2003-05-09 15:51 mmeineke |
| 2374 |
> |
2003-05-09 14:51 mmeineke |
| 2375 |
|
|
| 2376 |
|
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
| 2377 |
|
there were some duplicate entries |
| 2378 |
|
|
| 2379 |
< |
2003-05-09 12:56 mmeineke |
| 2379 |
> |
2003-05-09 11:56 mmeineke |
| 2380 |
|
|
| 2381 |
|
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
| 2382 |
|
configure script |
| 2383 |
|
|
| 2384 |
|
added the CH branching group to the TraPPE_Ex fource field |
| 2385 |
|
|
| 2386 |
< |
2003-05-09 12:55 mmeineke |
| 2386 |
> |
2003-05-09 11:55 mmeineke |
| 2387 |
|
|
| 2388 |
|
* ac-tools/configure.in: added the utils subdirectory to the |
| 2389 |
|
configure script |
| 2390 |
|
|
| 2391 |
< |
2003-04-25 12:02 mmeineke |
| 2391 |
> |
2003-04-25 11:02 mmeineke |
| 2392 |
|
|
| 2393 |
|
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
| 2394 |
|
bilayer builder |
| 2395 |
|
|
| 2396 |
< |
2003-04-24 22:00 mmeineke |
| 2396 |
> |
2003-04-24 21:00 mmeineke |
| 2397 |
|
|
| 2398 |
|
* libmdtools/f_verlet_constrained.F90: added a new test for |
| 2399 |
|
constraint failure |
| 2400 |
|
|
| 2401 |
< |
2003-04-17 17:54 mmeineke |
| 2401 |
> |
2003-04-17 16:54 mmeineke |
| 2402 |
|
|
| 2403 |
|
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
| 2404 |
|
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
| 2405 |
|
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
| 2406 |
|
build our systems |
| 2407 |
|
|
| 2408 |
< |
2003-04-16 17:11 mmeineke |
| 2408 |
> |
2003-04-16 16:11 mmeineke |
| 2409 |
|
|
| 2410 |
|
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
| 2411 |
|
|
| 2412 |
< |
2003-04-15 17:47 mmeineke |
| 2412 |
> |
2003-04-15 16:47 mmeineke |
| 2413 |
|
|
| 2414 |
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
| 2415 |
|
and sysBuild both will build now. woot! |
| 2416 |
|
|
| 2417 |
< |
2003-04-15 17:20 mmeineke |
| 2417 |
> |
2003-04-15 16:20 mmeineke |
| 2418 |
|
|
| 2419 |
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
| 2420 |
|
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
| 2423 |
|
|
| 2424 |
|
MoLocator.cpp is currently empty |
| 2425 |
|
|
| 2426 |
< |
2003-04-15 16:40 chuckv |
| 2426 |
> |
2003-04-15 15:40 chuckv |
| 2427 |
|
|
| 2428 |
|
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
| 2429 |
|
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
| 2430 |
|
forceFields/pdu3.eam, forceFields/ptu3.eam, |
| 2431 |
|
libmdtools/ForceFields.hpp: Added eam force files... |
| 2432 |
|
|
| 2433 |
< |
2003-04-15 12:37 chuckv |
| 2433 |
> |
2003-04-15 11:37 chuckv |
| 2434 |
|
|
| 2435 |
|
* libmdtools/EAM_FF.cpp: More eam work. |
| 2436 |
|
|
| 2437 |
< |
2003-04-14 17:22 mmeineke |
| 2437 |
> |
2003-04-14 16:22 mmeineke |
| 2438 |
|
|
| 2439 |
|
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
| 2440 |
|
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
| 2441 |
|
working on the system builder |
| 2442 |
|
|
| 2443 |
< |
2003-04-14 17:16 chuckv |
| 2443 |
> |
2003-04-14 16:16 chuckv |
| 2444 |
|
|
| 2445 |
|
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
| 2446 |
|
ordering on NVT calculation in integrators. |
| 2447 |
|
|
| 2448 |
< |
2003-04-14 15:51 mmeineke |
| 2448 |
> |
2003-04-14 14:51 mmeineke |
| 2449 |
|
|
| 2450 |
|
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
| 2451 |
|
obj/placeHolder: working on a system builder |
| 2452 |
|
|
| 2453 |
< |
2003-04-14 15:04 mmeineke |
| 2453 |
> |
2003-04-14 14:04 mmeineke |
| 2454 |
|
|
| 2455 |
|
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
| 2456 |
|
|
| 2457 |
|
added sysBuild to the utils Makefile |
| 2458 |
|
|
| 2459 |
< |
2003-04-14 15:03 mmeineke |
| 2459 |
> |
2003-04-14 14:03 mmeineke |
| 2460 |
|
|
| 2461 |
|
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
| 2462 |
|
Ghost bends to the TraPPE_Ex forceField |
| 2463 |
|
|
| 2464 |
< |
2003-04-14 14:19 chuckv |
| 2464 |
> |
2003-04-14 13:19 chuckv |
| 2465 |
|
|
| 2466 |
|
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
| 2467 |
|
|
| 2468 |
< |
2003-04-11 14:46 mmeineke |
| 2468 |
> |
2003-04-11 13:46 mmeineke |
| 2469 |
|
|
| 2470 |
|
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
| 2471 |
|
simulation_module.F90: fixed a memory bug in Fortran, where |
| 2472 |
|
molMembershipArray was declared nLocal instead of nGlobal. |
| 2473 |
|
|
| 2474 |
< |
2003-04-11 11:16 gezelter |
| 2474 |
> |
2003-04-11 10:16 gezelter |
| 2475 |
|
|
| 2476 |
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 2477 |
|
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
| 2478 |
|
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
| 2479 |
|
for NPT |
| 2480 |
|
|
| 2481 |
< |
2003-04-10 16:08 mmeineke |
| 2481 |
> |
2003-04-10 15:08 mmeineke |
| 2482 |
|
|
| 2483 |
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
| 2484 |
|
globalIndex counter to Molecule |
| 2485 |
|
|
| 2486 |
< |
2003-04-10 12:35 gezelter |
| 2486 |
> |
2003-04-10 11:35 gezelter |
| 2487 |
|
|
| 2488 |
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
| 2489 |
|
ConstantStress |
| 2490 |
|
|
| 2491 |
< |
2003-04-10 12:27 mmeineke |
| 2491 |
> |
2003-04-10 11:27 mmeineke |
| 2492 |
|
|
| 2493 |
|
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
| 2494 |
|
caused a miscalculation of nLocal. |
| 2495 |
|
|
| 2496 |
< |
2003-04-10 12:21 mmeineke |
| 2496 |
> |
2003-04-10 11:21 mmeineke |
| 2497 |
|
|
| 2498 |
|
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
| 2499 |
|
do_Forces.F90: fixed a bug in symplectic, where presure was only |
| 2500 |
|
being calculated the first time through. |
| 2501 |
|
|
| 2502 |
< |
2003-04-09 12:20 chuckv |
| 2502 |
> |
2003-04-09 11:20 chuckv |
| 2503 |
|
|
| 2504 |
|
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
| 2505 |
|
file |
| 2506 |
|
|
| 2507 |
< |
2003-04-09 09:59 gezelter |
| 2507 |
> |
2003-04-09 08:59 gezelter |
| 2508 |
|
|
| 2509 |
|
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
| 2510 |
|
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
| 2511 |
|
|
| 2512 |
< |
2003-04-09 00:06 gezelter |
| 2512 |
> |
2003-04-08 23:06 gezelter |
| 2513 |
|
|
| 2514 |
|
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
| 2515 |
|
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 2519 |
|
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
| 2520 |
|
NVT |
| 2521 |
|
|
| 2522 |
< |
2003-04-08 18:38 chuckv |
| 2522 |
> |
2003-04-08 17:38 chuckv |
| 2523 |
|
|
| 2524 |
|
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
| 2525 |
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
| 2527 |
|
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
| 2528 |
|
(kinda)... |
| 2529 |
|
|
| 2530 |
< |
2003-04-08 17:35 gezelter |
| 2530 |
> |
2003-04-08 16:35 gezelter |
| 2531 |
|
|
| 2532 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 2533 |
|
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
| 2534 |
|
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
| 2535 |
|
|
| 2536 |
< |
2003-04-08 13:16 chuckv |
| 2536 |
> |
2003-04-08 12:16 chuckv |
| 2537 |
|
|
| 2538 |
|
* libmdtools/: do_Forces.F90, neighborLists.F90, |
| 2539 |
|
simulation_module.F90: Moved expand neighborlist to init_FF. |
| 2540 |
|
|
| 2541 |
< |
2003-04-08 11:20 chuckv |
| 2541 |
> |
2003-04-08 10:20 chuckv |
| 2542 |
|
|
| 2543 |
|
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
| 2544 |
|
NVT |
| 2545 |
|
|
| 2546 |
< |
2003-04-08 10:39 gezelter |
| 2546 |
> |
2003-04-08 09:39 gezelter |
| 2547 |
|
|
| 2548 |
|
* libmdtools/Verlet.cpp: fixes for nvt / npt |
| 2549 |
|
|
| 2550 |
< |
2003-04-08 10:34 gezelter |
| 2550 |
> |
2003-04-08 09:34 gezelter |
| 2551 |
|
|
| 2552 |
|
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
| 2553 |
|
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
| 2554 |
|
|
| 2555 |
< |
2003-04-08 08:50 gezelter |
| 2555 |
> |
2003-04-08 07:50 gezelter |
| 2556 |
|
|
| 2557 |
|
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
| 2558 |
|
|
| 2559 |
< |
2003-04-08 08:44 gezelter |
| 2559 |
> |
2003-04-08 07:44 gezelter |
| 2560 |
|
|
| 2561 |
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
| 2562 |
|
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
| 2563 |
|
NVT and NPT ensembles |
| 2564 |
|
|
| 2565 |
< |
2003-04-07 17:42 gezelter |
| 2565 |
> |
2003-04-07 16:42 gezelter |
| 2566 |
|
|
| 2567 |
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 2568 |
|
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
| 2569 |
|
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
| 2570 |
|
|
| 2571 |
< |
2003-04-07 17:20 mmeineke |
| 2571 |
> |
2003-04-07 16:20 mmeineke |
| 2572 |
|
|
| 2573 |
|
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
| 2574 |
|
portion of SSD. |
| 2575 |
|
|
| 2576 |
< |
2003-04-07 17:16 mmeineke |
| 2576 |
> |
2003-04-07 16:16 mmeineke |
| 2577 |
|
|
| 2578 |
|
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
| 2579 |
|
doing some testing in sticky through Symplectic. |
| 2580 |
|
|
| 2581 |
< |
2003-04-07 16:51 gezelter |
| 2581 |
> |
2003-04-07 15:51 gezelter |
| 2582 |
|
|
| 2583 |
|
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
| 2584 |
|
|
| 2585 |
< |
2003-04-07 16:50 chuckv |
| 2585 |
> |
2003-04-07 15:50 chuckv |
| 2586 |
|
|
| 2587 |
|
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
| 2588 |
|
tau and virial. |
| 2589 |
|
|
| 2590 |
< |
2003-04-07 16:06 mmeineke |
| 2590 |
> |
2003-04-07 15:06 mmeineke |
| 2591 |
|
|
| 2592 |
|
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
| 2593 |
|
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
| 2594 |
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
| 2595 |
|
src/Makefile: bug fixes |
| 2596 |
|
|
| 2597 |
< |
2003-04-07 12:56 gezelter |
| 2597 |
> |
2003-04-07 11:56 gezelter |
| 2598 |
|
|
| 2599 |
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
| 2600 |
|
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
| 2601 |
|
Many fixes to add extended system |
| 2602 |
|
|
| 2603 |
< |
2003-04-07 10:30 gezelter |
| 2603 |
> |
2003-04-07 09:30 gezelter |
| 2604 |
|
|
| 2605 |
|
* src/Makefile: Fixed a bug caused by my experimentation |
| 2606 |
|
|
| 2607 |
< |
2003-04-07 10:30 gezelter |
| 2607 |
> |
2003-04-07 09:30 gezelter |
| 2608 |
|
|
| 2609 |
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
| 2610 |
|
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
| 2611 |
|
Added ExtendedSystem infrastructure for NPT and NVT calculations |
| 2612 |
|
|
| 2613 |
< |
2003-04-07 10:30 gezelter |
| 2613 |
> |
2003-04-07 09:30 gezelter |
| 2614 |
|
|
| 2615 |
|
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
| 2616 |
|
|
| 2953 |
|
|
| 2954 |
|
2003-03-25 09:29 mmeineke |
| 2955 |
|
|
| 2956 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
| 2956 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
| 2957 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
| 2958 |
|
|
| 2959 |
|
2003-03-25 09:29 mmeineke |
| 2963 |
|
|
| 2964 |
|
2003-03-24 20:07 gezelter |
| 2965 |
|
|
| 2966 |
< |
* samples/Makefile, tests/Makefile: moving tests to samples |
| 2966 |
> |
* samples/Makefile: moving tests to samples |
| 2967 |
|
|
| 2968 |
|
2003-03-24 20:06 gezelter |
| 2969 |
|
|
| 2970 |
< |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
| 2971 |
< |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
| 2972 |
< |
samples/argon/Makefile, samples/argon/argon.bass, |
| 2973 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
| 2974 |
< |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
| 2975 |
< |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
| 2976 |
< |
samples/lipid/water.mdl, samples/water/Makefile, |
| 1903 |
< |
samples/water/init_ssd.eor, samples/water/ssd.bass, |
| 1904 |
< |
samples/water/water.mdl, tests/alkane/Makefile, |
| 1905 |
< |
tests/alkane/alkanes.mdl, tests/alkane/butane.bass, |
| 1906 |
< |
tests/alkane/init_butane.eor, tests/argon/Makefile, |
| 1907 |
< |
tests/argon/argon.bass, tests/argon/init_argon.eor, |
| 1908 |
< |
tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, |
| 1909 |
< |
tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, |
| 1910 |
< |
tests/lipid/water.mdl, tests/water/Makefile, |
| 1911 |
< |
tests/water/init_ssd.eor, tests/water/ssd.bass, |
| 1912 |
< |
tests/water/water.mdl: moved tests to samples |
| 2970 |
> |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
| 2971 |
> |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
| 2972 |
> |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
| 2973 |
> |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
| 2974 |
> |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
| 2975 |
> |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
| 2976 |
> |
samples |
| 2977 |
|
|
| 2978 |
|
2003-03-24 19:51 gezelter |
| 2979 |
|
|
| 2981 |
|
|
| 2982 |
|
2003-03-24 19:46 gezelter |
| 2983 |
|
|
| 2984 |
< |
* ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, |
| 1921 |
< |
tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: |
| 1922 |
< |
Added makefiles in tests directories |
| 2984 |
> |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
| 2985 |
|
|
| 2986 |
|
2003-03-24 16:55 gezelter |
| 2987 |
|
|
| 2998 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
| 2999 |
|
do_Forces.F90: little bug fixes here and there |
| 3000 |
|
|
| 1939 |
– |
2003-03-24 11:04 mmeineke |
| 1940 |
– |
|
| 1941 |
– |
* tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon |
| 1942 |
– |
test simulation |
| 1943 |
– |
|
| 1944 |
– |
2003-03-24 11:02 mmeineke |
| 1945 |
– |
|
| 1946 |
– |
* tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, |
| 1947 |
– |
lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, |
| 1948 |
– |
water/water.mdl: [no log message] |
| 1949 |
– |
|
| 1950 |
– |
2003-03-24 11:02 mmeineke |
| 1951 |
– |
|
| 1952 |
– |
* tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added |
| 1953 |
– |
some test bass files for experimenting with |
| 1954 |
– |
|
| 3001 |
|
2003-03-24 10:26 mmeineke |
| 3002 |
|
|
| 3003 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
| 3107 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 3108 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 3109 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 3110 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
| 3111 |
< |
Tree |
| 3110 |
> |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
| 3111 |
> |
revision |
| 3112 |
|
|
| 3113 |
|
2003-03-21 12:42 mmeineke |
| 3114 |
|
|
| 3165 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 3166 |
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 3167 |
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
| 3168 |
< |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
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revision |
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libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
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> |
Tree |
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