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2003-09-10 16:28 mmeineke |
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2004-06-09 11:16 tim |
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* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |
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work on getting gofR working. |
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* libmdtools/: ConstraintAlgorithm.hpp, ConstraintElement.hpp, |
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Euler3.cpp, Euler3.hpp, Integrator.hpp, Make.dep, Makefile.in, |
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Mat3x3d.cpp, Mat3x3d.hpp, Quaternion.cpp, Quaternion.hpp, |
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Rattle.cpp, Rattle.hpp, RigidBody.cpp, RigidBody.hpp, Roll.cpp, |
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Roll.hpp, Shake.cpp, Shake.hpp, Vector3d.cpp, Vector3d.hpp: 1. |
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adding some useful math classes(Mat3x3d, Vector3d, Quaternion, |
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Euler3) these classes use anonymous union and struct to support |
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double[3], double[3][3] and double[4] 2. adding roll constraint |
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algorithm |
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2003-09-09 16:50 mmeineke |
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2004-06-08 11:49 gezelter |
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* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the |
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beginings of the GofR pair correlation. |
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* libmdtools/: NPT.cpp, NPTf.cpp, StuntDouble.cpp, Thermo.cpp: |
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Fixed a bug in NPTf (vScale was declared in the cpp file in |
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addition to the declaration in Integrator.hpp file) |
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2004-06-07 09:26 gezelter |
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* libBASS/Globals.cpp, libmdtools/AtomVisitor.cpp, |
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libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.hpp, |
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libmdtools/ConstraintIterator.hpp, |
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libmdtools/ConstraintManager.hpp, libmdtools/ConstraintPair.hpp, |
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libmdtools/DirectionalAtom.cpp, libmdtools/DumpReader.cpp, |
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libmdtools/DumpWriter.cpp, libmdtools/MatVec3.c, |
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libmdtools/MatVec3.h, libmdtools/StreamTokenizer.hpp, |
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libmdtools/ZConsReader.cpp: Fixes from gcc -Wall |
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2004-06-07 09:09 chrisfen |
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* libmdtools/Thermo.cpp: Dan cleaned up the pressure calculation a |
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bit... Got rid of some unnecessary lines of code in Thermo.cpp |
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2004-06-04 16:00 gezelter |
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* libmdtools/: ConstraintIterator.hpp, OOPSEMinimizer.cpp, |
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StuntDouble.cpp: small bugfixes |
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2004-06-04 15:29 tim |
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* libmdtools/Integrator.hpp: [no log message] |
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2004-06-04 14:30 tim |
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* ChangeLog, libmdtools/CallbackFunctor.cpp, |
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libmdtools/CallbackFunctor.hpp, libmdtools/ConstraintAlgorithm.cpp, |
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libmdtools/ConstraintAlgorithm.hpp, libmdtools/Integrator.hpp, |
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libmdtools/OOPSEMinimizer.cpp, libmdtools/Rattle.hpp, |
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libmdtools/Shake.hpp, libmdtools/ShakeMin.cpp, |
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libmdtools/ShakeMin.hpp: constraint algorithm for minimization is |
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working |
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2004-06-04 11:23 gezelter |
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* forceFields/charmm27.vdw: Moved to SHAPES |
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2004-06-04 11:23 gezelter |
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* forceFields/: LJ.vdw, amber99.vdw, gaff.vdw, oplsaal.vdw: [no log |
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message] |
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2004-06-04 09:59 gezelter |
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* libmdtools/: notifyCutoffs.F90, status_module.F90, wrappers.F90: |
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More work on Fortran side of error handler |
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2004-06-04 09:59 gezelter |
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* configure, ac-tools/aclocal.m4: fixed a typo in autoconf script |
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2004-06-04 09:35 gezelter |
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* libmdtools/: Makefile.in, fInfo.c, status_module.F90: Unifying |
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the error handlers |
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2004-06-04 09:17 gezelter |
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* libBASS/: MemberStamp.cpp, MemberStamp.hpp: Not used anymore |
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2004-06-04 09:11 gezelter |
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* libBASS/: config.h.in, fError.c: forgot to add these |
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2004-06-03 22:15 tim |
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* ChangeLog, libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
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libmdtools/CallbackFunctor.cpp, libmdtools/ConstraintAlgorithm.cpp, |
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libmdtools/ConstraintManager.cpp, libmdtools/GenericData.cpp, |
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libmdtools/GenericData.hpp, libmdtools/Integrator.cpp, |
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libmdtools/Integrator.hpp, libmdtools/Make.dep, |
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libmdtools/Makefile.in, libmdtools/Molecule.cpp, |
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libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NVT.cpp, |
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libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, |
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libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
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libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
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libmdtools/SimSetup.cpp, libmdtools/StuntDouble.cpp, |
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libmdtools/StuntDouble.hpp, utils/Vector3.hpp: new rattle algorithm |
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is working |
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2004-06-03 21:38 gezelter |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
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libBASS/Makefile.in, libBASS/mpiBASS.h, libBASS/simError.c, |
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libBASS/simError.h, libmdtools/Makefile.in, libmdtools/config.h.in, |
| 106 |
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libmdtools/notifyCutoffs.F90, src/Makefile.in: Config changes for |
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fortran access to SimError |
| 108 |
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2004-06-03 16:51 tim |
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* libmdtools/: CallbackFunctor.cpp, CallbackFunctor.hpp, |
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ConstraintAlgorithm.cpp, ConstraintAlgorithm.hpp, |
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ConstraintElement.cpp, ConstraintElement.hpp, |
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ConstraintIterator.hpp, ConstraintManager.cpp, |
| 115 |
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ConstraintManager.hpp, ConstraintPair.hpp, Rattle.cpp, Rattle.hpp, |
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Shake.cpp, Shake.hpp, ShakeMin.cpp, ShakeMin.hpp, TypeInfo.hpp: new |
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implementation of constraint |
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2004-06-03 16:06 tim |
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* libmdtools/DumpWriter.cpp: fixed a bug which only writes out the |
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first atom of a molecule |
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2004-06-03 15:02 gezelter |
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* libmdtools/SimSetup.cpp: Fixed groupOffset bug |
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2004-06-03 15:02 gezelter |
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* ac-tools/: aclocal.m4, configure.in: Working on MPI scripting for |
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autoconf |
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2004-06-02 13:28 gezelter |
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* samples/: argon/Makefile, minimizer/argon/Makefile: Shouldn't |
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have been in CVS |
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2004-06-02 13:28 gezelter |
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* samples/: argon/Makefile, minimizer/argon/Makefile: Why is this |
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in CVS? |
| 142 |
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2004-06-02 13:27 gezelter |
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* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Make.dep, |
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Makefile.in, WATER.cpp: formatting error messages, dependency fixes |
| 147 |
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2004-06-02 13:27 gezelter |
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* libBASS/simError.h: starting fortran-usable version of simError |
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2004-06-02 09:56 chrisfen |
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* samples/: argon/Makefile, minimizer/argon/Makefile: Probably |
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shouldn't be in CVS |
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2004-06-02 09:56 chrisfen |
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* libmdtools/: Integrator.cpp, NVT.cpp, ReadWrite.hpp, |
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Restraints.cpp, SimInfo.cpp, StatWriter.cpp: Formatting Changes, |
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removed writeRaw |
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2004-06-02 09:56 chrisfen |
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* libBASS/simError.c: Formatting Changes |
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2004-06-02 09:21 gezelter |
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* libBASS/simError.c, libBASS/simError.h, libmdtools/SimInfo.cpp: |
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severity levels in simError |
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2004-06-01 16:45 gezelter |
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* libmdtools/: Exclude.cpp, SimInfo.cpp, calc_LJ_FF.F90, |
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do_Forces.F90, mpiSimulation.cpp, neighborLists.F90, |
| 176 |
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simulation_module.F90: Bug fix (fixes of skipList and neighbor list |
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under MPI) |
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2004-06-01 16:44 gezelter |
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* libBASS/MoleculeStamp.cpp: Bug fix (memory leak) |
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2004-06-01 13:43 gezelter |
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* samples/: argon/argon.bass, minimizer/argon/argon.bass: Testing |
| 186 |
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2004-06-01 13:42 gezelter |
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* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
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SimSetup.hpp, do_Forces.F90, fortranWrapDefines.hpp, |
| 191 |
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mpiSimulation.cpp, mpiSimulation_module.F90, simulation_module.F90: |
| 192 |
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Cutoff Groups for MPI |
| 193 |
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2004-06-01 13:07 chrisfen |
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* libmdtools/: ForceFields.cpp, StatWriter.cpp: Fixed bug in |
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useLiquidThermInt routine in ForceFields.cpp |
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2004-06-01 12:15 chrisfen |
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* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
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SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Implemented a separate |
| 203 |
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solid and liquid thermodynamic integration routines |
| 204 |
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2004-06-01 10:57 tim |
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* libmdtools/: CutoffGroup.hpp, SimSetup.cpp: cutoff group in |
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progress |
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2004-06-01 09:27 chrisfen |
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* libBASS/: Globals.cpp, Globals.hpp: Added useLiquidThermInt |
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keyword and changed useThermInt to useSolidThermInt |
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2004-06-01 09:21 chrisfen |
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* libBASS/: Globals.cpp, Globals.hpp: Paving the way for separate |
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solid and liquid thermodynamic integration routines |
| 219 |
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2004-05-28 10:21 gezelter |
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* libmdtools/do_Forces.F90: bugfix starting |
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| 224 |
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2004-05-27 15:06 chrisfen |
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* libmdtools/: Integrator.cpp, StatWriter.cpp: Fixed a bug in |
| 227 |
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Integrator.cpp where it called writeRaw() when useThermInt = |
| 228 |
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false... |
| 229 |
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2004-05-27 14:51 tim |
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* ChangeLog, libmdtools/do_Forces.F90, |
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libmdtools/simulation_module.F90: Bug fix for SkipList |
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2004-05-27 14:26 gezelter |
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* libmdtools/SimSetup.cpp: bugfix in simsetup? |
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2004-05-27 13:59 gezelter |
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* libmdtools/: DumpReader.cpp, DumpWriter.cpp, |
| 242 |
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InitializeFromFile.cpp, SimInfo.cpp, SimSetup.cpp, SimSetup.hpp, |
| 243 |
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ZConsWriter.cpp, ZConstraint.cpp, fortranWrapDefines.hpp, |
| 244 |
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mdProfile.cpp, mpiSimulation.cpp, mpiSimulation.hpp, |
| 245 |
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mpiSimulation_module.F90, randomSPRNG.cpp, simulation_module.F90: |
| 246 |
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Cutoff group changes under MPI |
| 247 |
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2004-05-27 11:20 gezelter |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in: Fixes for |
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xlc++ |
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2004-05-27 10:31 tim |
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* libmdtools/SimInfo.cpp: groupList new bases on global index of |
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atoms |
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2004-05-27 10:21 gezelter |
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* src/: oopse.cpp, oose.cpp: Modified the nifty banner |
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2004-05-27 10:21 gezelter |
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* libmdtools/: Make.dep, do_Forces.F90, simulation_module.F90: |
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Fixed off-by-one error in groupStartRow and groupStartCol |
| 266 |
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2004-05-26 19:48 tim |
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* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/DumpWriter.cpp, |
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libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
| 271 |
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libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 272 |
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libmdtools/ZConsWriter.cpp, libmdtools/calc_LJ_FF.F90, |
| 273 |
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libmdtools/calc_charge_charge.F90, |
| 274 |
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libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
| 275 |
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libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
| 276 |
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libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
| 277 |
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libmdtools/force_globals.F90, libmdtools/mdProfile.cpp, |
| 278 |
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libmdtools/mpiComponentPlan.h, libmdtools/mpiSimulation.cpp, |
| 279 |
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libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
| 280 |
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libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
| 281 |
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libmdtools/simulation_module.F90: in the progress of fixing MPI |
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version of cutoff group |
| 283 |
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2004-05-26 11:41 gezelter |
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* libmdtools/do_Forces.F90: Compacted all of the 8 copies of the |
| 287 |
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force loop into one. |
| 288 |
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2004-05-24 17:24 gezelter |
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* libmdtools/: calc_eam.F90, calc_gb.F90: pressure tensor fixes |
| 292 |
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2004-05-24 16:23 chrisfen |
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* libmdtools/Restraints.cpp: Removed unnecessary variables and |
| 296 |
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changed error messages in Restraints.cpp |
| 297 |
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2004-05-24 16:03 gezelter |
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* libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, |
| 301 |
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calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
| 302 |
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calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes |
| 303 |
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for stress / pressure tensor by cutoff group |
| 304 |
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2004-05-22 15:55 chrisfen |
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* libmdtools/Restraints.cpp: Fixed an error in Restraints.cpp... |
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Too many arguements in a function call. |
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2004-05-22 13:17 chrisfen |
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* libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword |
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useThermInt. |
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2004-05-22 13:16 chrisfen |
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* libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
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ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, |
| 319 |
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Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, |
| 320 |
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SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, |
| 321 |
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StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration |
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code. |
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2004-05-21 10:58 gezelter |
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* libmdtools/: do_Forces.F90, simulation_module.F90: Major changes |
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to skipThisPair for efficiency |
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2004-05-21 09:22 gezelter |
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* configure, ac-tools/configure.in, forceFields/LJ.vdw, |
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forceFields/amber99.vdw, forceFields/charmm27.vdw, |
| 333 |
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forceFields/gaff.vdw, forceFields/oplsaal.vdw, |
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samples/argon/Makefile, samples/minimizer/argon/Makefile: Changes |
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for SHAPES potential |
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2004-05-20 15:27 chrisfen |
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* libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit |
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included the bass keywords |
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2004-05-20 15:24 chrisfen |
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* libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, |
| 345 |
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Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, |
| 346 |
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Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several |
| 347 |
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additions... Restraints.cpp and .hpp were included for restraining |
| 348 |
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particles in thermodynamic integration. By including these, |
| 349 |
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changes were made in Integrator, SimInfo, ForceFeilds, SimSetup, |
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StatWriter, and possibly some other files. Two bass keywords were |
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also added for performing thermodynamic integration: a lambda value |
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one and a k power one. |
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2004-05-13 16:08 gezelter |
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* libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list |
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2004-05-12 17:01 tim |
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> |
|
| 360 |
> |
* samples/: argon/Makefile, argon/argonEM.bass, |
| 361 |
> |
argon/init_argon.eor, minimizer/argon/Makefile, |
| 362 |
> |
minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, |
| 363 |
> |
minimizer/water/Makefile, minimizer/water/Makefile.in, |
| 364 |
> |
minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, |
| 365 |
> |
minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, |
| 366 |
> |
minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add |
| 367 |
> |
minimizer sample |
| 368 |
> |
|
| 369 |
> |
2004-05-12 16:54 gezelter |
| 370 |
> |
|
| 371 |
> |
* libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X |
| 372 |
> |
compilation |
| 373 |
> |
|
| 374 |
> |
2004-05-12 15:54 gezelter |
| 375 |
> |
|
| 376 |
> |
* libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes |
| 377 |
> |
for compilation under Mac OS X with IBM's xl compilers |
| 378 |
> |
|
| 379 |
> |
2004-05-12 15:14 gezelter |
| 380 |
> |
|
| 381 |
> |
* src/: oopse.cpp, oose.cpp: Added a nifty neato banner |
| 382 |
> |
|
| 383 |
> |
2004-05-12 15:14 gezelter |
| 384 |
> |
|
| 385 |
> |
* libmdtools/LJFF.cpp: Removed an extraneous write |
| 386 |
> |
|
| 387 |
> |
2004-05-12 15:13 gezelter |
| 388 |
> |
|
| 389 |
> |
* libBASS/simError.h: Starting to change the error model |
| 390 |
> |
|
| 391 |
> |
2004-05-12 14:45 gezelter |
| 392 |
> |
|
| 393 |
> |
* utils/Dump2XYZ.cpp: const char* fix |
| 394 |
> |
|
| 395 |
> |
2004-05-12 14:44 gezelter |
| 396 |
> |
|
| 397 |
> |
* libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
| 398 |
> |
src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous |
| 399 |
> |
write statements |
| 400 |
> |
|
| 401 |
> |
2004-05-12 11:38 tim |
| 402 |
> |
|
| 403 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
| 404 |
> |
ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
| 405 |
> |
SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and |
| 406 |
> |
massratio from simState, creat cutoff group forevery atom which |
| 407 |
> |
does not belong to cutoff group defined at mdl file |
| 408 |
> |
|
| 409 |
> |
2004-05-12 10:58 gezelter |
| 410 |
> |
|
| 411 |
> |
* libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in |
| 412 |
> |
CutoffGroup |
| 413 |
> |
|
| 414 |
> |
2004-05-12 10:35 gezelter |
| 415 |
> |
|
| 416 |
> |
* samples/water/water.mdl: Added the cutoff Groups to the default |
| 417 |
> |
water.mdl file |
| 418 |
> |
|
| 419 |
> |
2004-05-12 10:02 tim |
| 420 |
> |
|
| 421 |
> |
* ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: |
| 422 |
> |
fixed a bug in CutoffGroup::getCOM() |
| 423 |
> |
|
| 424 |
> |
2004-05-12 09:29 gezelter |
| 425 |
> |
|
| 426 |
> |
* libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 427 |
> |
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
| 428 |
> |
samples/water/ssd.bass: bug fixes for cutoffGroups |
| 429 |
> |
|
| 430 |
> |
2004-05-11 17:28 tim |
| 431 |
> |
|
| 432 |
> |
* utils/Vector3.hpp: adding generic Vector3 class |
| 433 |
> |
|
| 434 |
> |
2004-05-11 16:44 tim |
| 435 |
> |
|
| 436 |
> |
* libmdtools/Integrator.hpp: adding instantiation of |
| 437 |
> |
Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8 |
| 438 |
> |
|
| 439 |
> |
2004-05-11 16:31 gezelter |
| 440 |
> |
|
| 441 |
> |
* libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, |
| 442 |
> |
calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, |
| 443 |
> |
calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: |
| 444 |
> |
Fortran-side changes for group-based cutoffs |
| 445 |
> |
|
| 446 |
> |
2004-05-11 16:20 tim |
| 447 |
> |
|
| 448 |
> |
* libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp |
| 449 |
> |
|
| 450 |
> |
2004-05-11 16:14 tim |
| 451 |
> |
|
| 452 |
> |
* libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, |
| 453 |
> |
SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix |
| 454 |
> |
anoter one in CutoffGroup which causes seg fault |
| 455 |
> |
|
| 456 |
> |
2004-05-11 15:33 tim |
| 457 |
> |
|
| 458 |
> |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
| 459 |
> |
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
| 460 |
> |
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup |
| 461 |
> |
into OOPSE |
| 462 |
> |
|
| 463 |
> |
2004-05-11 15:07 gezelter |
| 464 |
> |
|
| 465 |
> |
* libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup |
| 466 |
> |
|
| 467 |
> |
2004-05-11 11:00 gezelter |
| 468 |
> |
|
| 469 |
> |
* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
| 470 |
> |
fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
| 471 |
> |
use the simplified cutoff stuff in the BASS library |
| 472 |
> |
|
| 473 |
> |
2004-05-10 23:21 gezelter |
| 474 |
> |
|
| 475 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
| 476 |
> |
CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
| 477 |
> |
Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
| 478 |
> |
MoleculeStamp.cpp, MoleculeStamp.hpp, interface.c, make_nodes.c, |
| 479 |
> |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
| 480 |
> |
parse_tree.c: BASS changes for adding CutoffGroups to molecules. |
| 481 |
> |
Also restructured the plethora of cutoff radii into one |
| 482 |
> |
cutoffRadius and one switchingRadius. Also removed the |
| 483 |
> |
useMolecularCutoffs keyword |
| 484 |
> |
|
| 485 |
> |
2004-05-10 15:28 tim |
| 486 |
> |
|
| 487 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
| 488 |
> |
DumpWriter |
| 489 |
> |
|
| 490 |
> |
2004-05-07 16:36 gezelter |
| 491 |
> |
|
| 492 |
> |
* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
| 493 |
> |
for fortran group-based switching function |
| 494 |
> |
|
| 495 |
> |
2004-05-07 16:35 gezelter |
| 496 |
> |
|
| 497 |
> |
* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
| 498 |
> |
Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
| 499 |
> |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
| 500 |
> |
calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
| 501 |
> |
force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
| 502 |
> |
mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
| 503 |
> |
simulation_module.F90: Many changes to get group-based cutoffs to |
| 504 |
> |
work |
| 505 |
> |
|
| 506 |
> |
2004-05-01 13:52 tim |
| 507 |
> |
|
| 508 |
> |
* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 509 |
> |
libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
| 510 |
> |
libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
| 511 |
> |
libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
| 512 |
> |
libmdtools/fortranWrapDefines.hpp, |
| 513 |
> |
libmdtools/simulation_module.F90: C++ pass groupList to fortran |
| 514 |
> |
|
| 515 |
> |
2004-04-29 11:03 tim |
| 516 |
> |
|
| 517 |
> |
* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
| 518 |
> |
calc_charge_charge when using molecular cutoff |
| 519 |
> |
|
| 520 |
> |
2004-04-28 21:11 tim |
| 521 |
> |
|
| 522 |
> |
* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
| 523 |
> |
unmatched c/fortran interface |
| 524 |
> |
|
| 525 |
> |
2004-04-28 18:09 tim |
| 526 |
> |
|
| 527 |
> |
* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
| 528 |
> |
keep the previous position of cantilever in SMD |
| 529 |
> |
|
| 530 |
> |
2004-04-28 17:34 tim |
| 531 |
> |
|
| 532 |
> |
* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
| 533 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
| 534 |
> |
in Molecule.cpp which initialize massRatio before creat the array. |
| 535 |
> |
fix two bugs in ZconsVisitor |
| 536 |
> |
|
| 537 |
> |
2004-04-28 17:06 gezelter |
| 538 |
> |
|
| 539 |
> |
* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
| 540 |
> |
Adding molecular cutoffs |
| 541 |
> |
|
| 542 |
> |
2004-04-28 16:39 gezelter |
| 543 |
> |
|
| 544 |
> |
* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
| 545 |
> |
fSimulation.h, force_globals.F90, simulation_module.F90: work on |
| 546 |
> |
molecular cutoffs |
| 547 |
> |
|
| 548 |
> |
2004-04-28 16:39 gezelter |
| 549 |
> |
|
| 550 |
> |
* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
| 551 |
> |
Globals |
| 552 |
> |
|
| 553 |
> |
2004-04-27 11:26 tim |
| 554 |
> |
|
| 555 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
| 556 |
> |
ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
| 557 |
> |
fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
| 558 |
> |
molecule and massRation into atom class |
| 559 |
> |
|
| 560 |
> |
2004-04-26 16:16 mmeineke |
| 561 |
> |
|
| 562 |
> |
* libBASS/Globals.cpp: modified the defaults for the system init |
| 563 |
> |
time and system init state. |
| 564 |
> |
|
| 565 |
> |
2004-04-26 09:29 gezelter |
| 566 |
> |
|
| 567 |
> |
* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
| 568 |
> |
calc_charge_charge.F90 |
| 569 |
> |
|
| 570 |
> |
2004-04-23 23:31 tim |
| 571 |
> |
|
| 572 |
> |
* ChangeLog, libmdtools/AtomVisitor.cpp, |
| 573 |
> |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
| 574 |
> |
reaction field correction to charge-charge interaction |
| 575 |
> |
|
| 576 |
> |
2004-04-22 16:33 tim |
| 577 |
> |
|
| 578 |
> |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
| 579 |
> |
Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
| 580 |
> |
calculation of pressure tensor |
| 581 |
> |
|
| 582 |
> |
2004-04-22 09:55 tim |
| 583 |
> |
|
| 584 |
> |
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
| 585 |
> |
another bug in InitFromFile. MPI verion of OOPSE is working again |
| 586 |
> |
|
| 587 |
> |
2004-04-21 22:29 tim |
| 588 |
> |
|
| 589 |
> |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
| 590 |
> |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
| 591 |
> |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
| 592 |
> |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
| 593 |
> |
DumpWriter |
| 594 |
> |
|
| 595 |
> |
2004-04-21 00:32 tim |
| 596 |
> |
|
| 597 |
> |
* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
| 598 |
> |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
| 599 |
> |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
| 600 |
> |
useless files |
| 601 |
> |
|
| 602 |
> |
2004-04-20 11:56 tim |
| 603 |
> |
|
| 604 |
> |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
| 605 |
> |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
| 606 |
> |
velocitize at thermo |
| 607 |
> |
|
| 608 |
> |
2004-04-20 00:39 tim |
| 609 |
> |
|
| 610 |
> |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
| 611 |
> |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
| 612 |
> |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
| 613 |
> |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
| 614 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
| 615 |
> |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
| 616 |
> |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
| 617 |
> |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
| 618 |
> |
|
| 619 |
> |
2004-04-19 17:13 gezelter |
| 620 |
> |
|
| 621 |
> |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
| 622 |
> |
Thermo.cpp: Fixed a charge bug |
| 623 |
> |
|
| 624 |
> |
2004-04-19 15:54 tim |
| 625 |
> |
|
| 626 |
> |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
| 627 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
| 628 |
> |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
| 629 |
> |
a bug in CompositeVisitor which cause the double counting problem |
| 630 |
> |
|
| 631 |
> |
2004-04-19 12:44 tim |
| 632 |
> |
|
| 633 |
> |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
| 634 |
> |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
| 635 |
> |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
| 636 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
| 637 |
> |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
| 638 |
> |
Dump2XYZ is almost working except atoms in rigidbody are double |
| 639 |
> |
counted |
| 640 |
> |
|
| 641 |
> |
2004-04-18 22:52 tim |
| 642 |
> |
|
| 643 |
> |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
| 644 |
> |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
| 645 |
> |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
| 646 |
> |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
| 647 |
> |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
| 648 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
| 649 |
> |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
| 650 |
> |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
| 651 |
> |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
| 652 |
> |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
| 653 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 654 |
> |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
| 655 |
> |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
| 656 |
> |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
| 657 |
> |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
| 658 |
> |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
| 659 |
> |
implement of quickLate using visitor and composite pattern |
| 660 |
> |
|
| 661 |
> |
2004-04-15 17:15 tim |
| 662 |
> |
|
| 663 |
> |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
| 664 |
> |
exclude list |
| 665 |
> |
|
| 666 |
> |
2004-04-15 11:18 tim |
| 667 |
> |
|
| 668 |
> |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
| 669 |
> |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
| 670 |
> |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
| 671 |
> |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
| 672 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 673 |
> |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
| 674 |
> |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
| 675 |
> |
whole bunch of bugs :-) |
| 676 |
> |
|
| 677 |
> |
2004-04-14 12:20 chrisfen |
| 678 |
> |
|
| 679 |
> |
* forceFields/WATER.frc: Added the WATER.frc force field |
| 680 |
> |
|
| 681 |
> |
2004-04-14 11:32 gezelter |
| 682 |
> |
|
| 683 |
> |
* libmdtools/Molecule.cpp: fixed for get_potential |
| 684 |
> |
|
| 685 |
> |
2004-04-14 10:37 tim |
| 686 |
> |
|
| 687 |
> |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
| 688 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
| 689 |
> |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
| 690 |
> |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
| 691 |
> |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
| 692 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 693 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 694 |
> |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
| 695 |
> |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
| 696 |
> |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
| 697 |
> |
Change DumpWriter and InitFromFile |
| 698 |
> |
|
| 699 |
> |
2004-04-13 11:26 gezelter |
| 700 |
> |
|
| 701 |
> |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
| 702 |
> |
molecules can keep track of their own IntegrableObjects (and |
| 703 |
> |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
| 704 |
> |
RigidBodies (which was done incorrectly before). |
| 705 |
> |
|
| 706 |
> |
2004-04-13 11:25 gezelter |
| 707 |
> |
|
| 708 |
> |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
| 709 |
> |
(will back out momentarily) |
| 710 |
> |
|
| 711 |
> |
2004-04-13 10:10 gezelter |
| 712 |
> |
|
| 713 |
> |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
| 714 |
> |
Those were old. |
| 715 |
> |
|
| 716 |
> |
2004-04-13 10:09 gezelter |
| 717 |
> |
|
| 718 |
> |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
| 719 |
> |
to add IntegrableObjects |
| 720 |
> |
|
| 721 |
> |
2004-04-12 16:02 gezelter |
| 722 |
> |
|
| 723 |
> |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
| 724 |
> |
|
| 725 |
> |
2004-04-12 15:32 gezelter |
| 726 |
> |
|
| 727 |
> |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
| 728 |
> |
test run |
| 729 |
> |
|
| 730 |
> |
2004-04-12 15:32 gezelter |
| 731 |
> |
|
| 732 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
| 733 |
> |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
| 734 |
> |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
| 735 |
> |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
| 736 |
> |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
| 737 |
> |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
| 738 |
> |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
| 739 |
> |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
| 740 |
> |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
| 741 |
> |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
| 742 |
> |
(Somewhat extensive) |
| 743 |
> |
|
| 744 |
> |
2004-04-12 15:31 gezelter |
| 745 |
> |
|
| 746 |
> |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
| 747 |
> |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
| 748 |
> |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
| 749 |
> |
Changes for RigidBody dynamics |
| 750 |
> |
|
| 751 |
> |
2004-03-17 09:22 tim |
| 752 |
> |
|
| 753 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
| 754 |
> |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
| 755 |
> |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
| 756 |
> |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
| 757 |
> |
does not sound a good choice, next commit will seperate SMD and |
| 758 |
> |
ZConstraint |
| 759 |
> |
|
| 760 |
> |
2004-03-16 14:22 tim |
| 761 |
> |
|
| 762 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 763 |
> |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
| 764 |
> |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
| 765 |
> |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
| 766 |
> |
now can support sequential moving. Refactorying is needed to |
| 767 |
> |
support SMD in ZConstraint |
| 768 |
> |
|
| 769 |
> |
2004-03-02 15:32 tim |
| 770 |
> |
|
| 771 |
> |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
| 772 |
> |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
| 773 |
> |
support large file |
| 774 |
> |
|
| 775 |
> |
2004-03-01 16:17 tim |
| 776 |
> |
|
| 777 |
> |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
| 778 |
> |
|
| 779 |
> |
2004-03-01 15:01 tim |
| 780 |
> |
|
| 781 |
> |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
| 782 |
> |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
| 783 |
> |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
| 784 |
> |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
| 785 |
> |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
| 786 |
> |
program which can be used to replace atom type for zconstraint into |
| 787 |
> |
OOPSE |
| 788 |
> |
|
| 789 |
> |
2004-02-24 11:36 tim |
| 790 |
> |
|
| 791 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 792 |
> |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
| 793 |
> |
message] |
| 794 |
> |
|
| 795 |
> |
2004-02-24 10:49 tim |
| 796 |
> |
|
| 797 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
| 798 |
> |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
| 799 |
> |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
| 800 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
| 801 |
> |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
| 802 |
> |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
| 803 |
> |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
| 804 |
> |
|
| 805 |
> |
2004-02-24 10:44 tim |
| 806 |
> |
|
| 807 |
> |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
| 808 |
> |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
| 809 |
> |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
| 810 |
> |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
| 811 |
> |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
| 812 |
> |
compose to implement Minimizer both versions are working |
| 813 |
> |
|
| 814 |
> |
2004-02-17 14:23 tim |
| 815 |
> |
|
| 816 |
> |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
| 817 |
> |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
| 818 |
> |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
| 819 |
> |
libmdtools/MinimizerParameterSet.hpp, |
| 820 |
> |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
| 821 |
> |
to remove the constraint force along bond direction |
| 822 |
> |
|
| 823 |
> |
2004-02-10 16:33 tim |
| 824 |
> |
|
| 825 |
> |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
| 826 |
> |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
| 827 |
> |
single version of energy minimization is working. |
| 828 |
> |
|
| 829 |
> |
2004-02-09 15:38 mmeineke |
| 830 |
> |
|
| 831 |
> |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
| 832 |
> |
the massive memory overusage by OOPSE |
| 833 |
> |
|
| 834 |
> |
2004-02-09 09:48 chrisfen |
| 835 |
> |
|
| 836 |
> |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
| 837 |
> |
hardwired LJ_rcut |
| 838 |
> |
|
| 839 |
> |
2004-02-06 19:14 tim |
| 840 |
> |
|
| 841 |
> |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
| 842 |
> |
message] |
| 843 |
> |
|
| 844 |
> |
2004-02-06 16:37 tim |
| 845 |
> |
|
| 846 |
> |
* ChangeLog, libBASS/Globals.cpp, |
| 847 |
> |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
| 848 |
> |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
| 849 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
| 850 |
> |
energy minimization for argon is working, need to add constraint |
| 851 |
> |
|
| 852 |
> |
2004-02-06 14:05 tim |
| 853 |
> |
|
| 854 |
> |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
| 855 |
> |
one more file into Makefile.in |
| 856 |
> |
|
| 857 |
> |
2004-02-06 13:58 tim |
| 858 |
> |
|
| 859 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 860 |
> |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
| 861 |
> |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
| 862 |
> |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
| 863 |
> |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
| 864 |
> |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
| 865 |
> |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
| 866 |
> |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
| 867 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 868 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
| 869 |
> |
some lines into global.cpp to make it work with energy minimization |
| 870 |
> |
|
| 871 |
> |
2004-02-04 17:26 tim |
| 872 |
> |
|
| 873 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
| 874 |
> |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
| 875 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
| 876 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
| 877 |
> |
Single version of conjugate gradient with golden search linesearch |
| 878 |
> |
pass a couple of functions test. Brent's algorithm is still broken |
| 879 |
> |
|
| 880 |
> |
2004-02-03 17:54 tim |
| 881 |
> |
|
| 882 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
| 883 |
> |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
| 884 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
| 885 |
> |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
| 886 |
> |
|
| 887 |
> |
2004-02-03 15:47 tim |
| 888 |
> |
|
| 889 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
| 890 |
> |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
| 891 |
> |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
| 892 |
> |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
| 893 |
> |
SteepestDescent.hpp: [no log message] |
| 894 |
> |
|
| 895 |
> |
2004-02-03 15:43 tim |
| 896 |
> |
|
| 897 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
| 898 |
> |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
| 899 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
| 900 |
> |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
| 901 |
> |
constraint class |
| 902 |
> |
|
| 903 |
> |
2004-02-03 12:10 tim |
| 904 |
> |
|
| 905 |
> |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
| 906 |
> |
|
| 907 |
> |
2004-02-03 10:21 tim |
| 908 |
> |
|
| 909 |
> |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
| 910 |
> |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
| 911 |
> |
|
| 912 |
> |
2004-02-02 15:29 tim |
| 913 |
> |
|
| 914 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
| 915 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
| 916 |
> |
Adding GoldenSection and Brent LineSearch Method |
| 917 |
> |
|
| 918 |
> |
2004-01-30 16:47 tim |
| 919 |
> |
|
| 920 |
> |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
| 921 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
| 922 |
> |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
| 923 |
> |
MinimizerBase instead of a functor to do line seach |
| 924 |
> |
|
| 925 |
> |
2004-01-30 10:00 chrisfen |
| 926 |
> |
|
| 927 |
> |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
| 928 |
> |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
| 929 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
| 930 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
| 931 |
> |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
| 932 |
> |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
| 933 |
> |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
| 934 |
> |
has a working WATER.cpp forcefield and parser. This involved |
| 935 |
> |
changes to WATER.cpp and ForceFields amoung other files. One |
| 936 |
> |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
| 937 |
> |
This will be removed on the next commit... |
| 938 |
> |
|
| 939 |
> |
2004-01-29 18:00 gezelter |
| 940 |
> |
|
| 941 |
> |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
| 942 |
> |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
| 943 |
> |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
| 944 |
> |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
| 945 |
> |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
| 946 |
> |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
| 947 |
> |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
| 948 |
> |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
| 949 |
> |
member list fixes for rigid bodies |
| 950 |
> |
|
| 951 |
> |
2004-01-29 16:44 tim |
| 952 |
> |
|
| 953 |
> |
* libmdtools/MinimizerParameterSet.hpp: Adding |
| 954 |
> |
MinimizerParameterSet class. |
| 955 |
> |
|
| 956 |
> |
2004-01-28 17:44 tim |
| 957 |
> |
|
| 958 |
> |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
| 959 |
> |
NLModel0 and NLModel1 |
| 960 |
> |
|
| 961 |
> |
2004-01-28 15:40 tim |
| 962 |
> |
|
| 963 |
> |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
| 964 |
> |
of NLModel |
| 965 |
> |
|
| 966 |
> |
2004-01-27 15:34 gezelter |
| 967 |
> |
|
| 968 |
> |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
| 969 |
> |
water.mdl file, updated ssd.bass to use new SSD name |
| 970 |
> |
|
| 971 |
> |
2004-01-27 15:34 gezelter |
| 972 |
> |
|
| 973 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
| 974 |
> |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
| 975 |
> |
stuff |
| 976 |
> |
|
| 977 |
> |
2004-01-27 14:39 gezelter |
| 978 |
> |
|
| 979 |
> |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
| 980 |
> |
|
| 981 |
> |
2004-01-27 14:39 gezelter |
| 982 |
> |
|
| 983 |
> |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
| 984 |
> |
|
| 985 |
> |
2004-01-27 14:38 gezelter |
| 986 |
> |
|
| 987 |
> |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer |
| 988 |
> |
run time to test argon |
| 989 |
> |
|
| 990 |
> |
2004-01-27 14:38 gezelter |
| 991 |
> |
|
| 992 |
> |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
| 993 |
> |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
| 994 |
> |
morning |
| 995 |
> |
|
| 996 |
> |
2004-01-27 14:37 gezelter |
| 997 |
> |
|
| 998 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
| 999 |
> |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
| 1000 |
> |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
| 1001 |
> |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
| 1002 |
> |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
| 1003 |
> |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
| 1004 |
> |
do new rigidBody scheme |
| 1005 |
> |
|
| 1006 |
> |
2004-01-27 14:15 tim |
| 1007 |
> |
|
| 1008 |
> |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
| 1009 |
> |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
| 1010 |
> |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
| 1011 |
> |
constraint for Nonlinear Optimization Model |
| 1012 |
> |
|
| 1013 |
> |
2004-01-26 17:01 gezelter |
| 1014 |
> |
|
| 1015 |
> |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
| 1016 |
> |
Euler angles for orientation instead of unit vectors required |
| 1017 |
> |
changes in MoLocator |
| 1018 |
> |
|
| 1019 |
> |
2004-01-26 16:53 gezelter |
| 1020 |
> |
|
| 1021 |
> |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
| 1022 |
> |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
| 1023 |
> |
water/water.mdl: Changed orientation lines from unit vectors to |
| 1024 |
> |
euler angles |
| 1025 |
> |
|
| 1026 |
> |
2004-01-26 16:52 gezelter |
| 1027 |
> |
|
| 1028 |
> |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
| 1029 |
> |
|
| 1030 |
> |
2004-01-26 16:45 gezelter |
| 1031 |
> |
|
| 1032 |
> |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
| 1033 |
> |
use Euler angles in the following order: phi, theta, psi Removed |
| 1034 |
> |
the ability to set orientation using a unit vector |
| 1035 |
> |
|
| 1036 |
> |
2004-01-26 16:26 gezelter |
| 1037 |
> |
|
| 1038 |
> |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
| 1039 |
> |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
| 1040 |
> |
Euler angles in the following order: phi, theta, psi Removed the |
| 1041 |
> |
ability to set orientation using a unit vector |
| 1042 |
> |
|
| 1043 |
> |
2004-01-26 13:52 gezelter |
| 1044 |
> |
|
| 1045 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
| 1046 |
> |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
| 1047 |
> |
|
| 1048 |
> |
2004-01-22 12:34 chrisfen |
| 1049 |
> |
|
| 1050 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
| 1051 |
> |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
| 1052 |
> |
Corrected spelling in several directories, and stated WATER.cpp |
| 1053 |
> |
|
| 1054 |
> |
2004-01-21 17:16 tim |
| 1055 |
> |
|
| 1056 |
> |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
| 1057 |
> |
NLOPModel.hpp: constraint class in energy minimization |
| 1058 |
> |
|
| 1059 |
> |
2004-01-20 15:34 tim |
| 1060 |
> |
|
| 1061 |
> |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
| 1062 |
> |
|
| 1063 |
> |
2004-01-20 15:32 tim |
| 1064 |
> |
|
| 1065 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
| 1066 |
> |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
| 1067 |
> |
|
| 1068 |
> |
2004-01-19 16:17 gezelter |
| 1069 |
> |
|
| 1070 |
> |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
| 1071 |
> |
more user-friendly |
| 1072 |
> |
|
| 1073 |
> |
2004-01-19 13:51 chrisfen |
| 1074 |
> |
|
| 1075 |
> |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
| 1076 |
> |
|
| 1077 |
> |
2004-01-19 13:36 tim |
| 1078 |
> |
|
| 1079 |
> |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
| 1080 |
> |
time, status time, thermal time and reset time are not divisible by |
| 1081 |
> |
dt |
| 1082 |
> |
|
| 1083 |
> |
2004-01-19 11:10 gezelter |
| 1084 |
> |
|
| 1085 |
> |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
| 1086 |
> |
won't complain |
| 1087 |
> |
|
| 1088 |
> |
2004-01-19 11:10 gezelter |
| 1089 |
> |
|
| 1090 |
> |
* samples/lipid/5x5.bass: Fixed old bass file |
| 1091 |
> |
|
| 1092 |
> |
2004-01-19 11:09 gezelter |
| 1093 |
> |
|
| 1094 |
> |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
| 1095 |
> |
required a change in how the MoleculeStamps are used by divideLabor |
| 1096 |
> |
in mpiSimulation.cpp |
| 1097 |
> |
|
| 1098 |
> |
2004-01-19 11:08 gezelter |
| 1099 |
> |
|
| 1100 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
| 1101 |
> |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
| 1102 |
> |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
| 1103 |
> |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
| 1104 |
> |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
| 1105 |
> |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
| 1106 |
> |
|
| 1107 |
> |
2004-01-16 16:55 tim |
| 1108 |
> |
|
| 1109 |
> |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
| 1110 |
> |
eor file |
| 1111 |
> |
|
| 1112 |
> |
2004-01-16 16:51 mmeineke |
| 1113 |
> |
|
| 1114 |
> |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
| 1115 |
> |
write eor files |
| 1116 |
> |
|
| 1117 |
> |
2004-01-16 10:01 mmeineke |
| 1118 |
> |
|
| 1119 |
> |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
| 1120 |
> |
initialization of the AtomStruct |
| 1121 |
> |
|
| 1122 |
> |
2004-01-15 16:57 chuckv |
| 1123 |
> |
|
| 1124 |
> |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
| 1125 |
> |
|
| 1126 |
> |
2004-01-15 10:51 gezelter |
| 1127 |
> |
|
| 1128 |
> |
* ac-tools/aclocal.m4: Changes for altivec |
| 1129 |
> |
|
| 1130 |
> |
2004-01-15 09:22 gezelter |
| 1131 |
> |
|
| 1132 |
> |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
| 1133 |
> |
|
| 1134 |
> |
2004-01-14 23:33 gezelter |
| 1135 |
> |
|
| 1136 |
> |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
| 1137 |
> |
|
| 1138 |
> |
2004-01-14 20:14 gezelter |
| 1139 |
> |
|
| 1140 |
> |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
| 1141 |
> |
notifyCutoffs.F90: More work for adding charges |
| 1142 |
> |
|
| 1143 |
> |
2004-01-14 17:41 gezelter |
| 1144 |
> |
|
| 1145 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1146 |
> |
src/Makefile.in: autoconf fixes |
| 1147 |
> |
|
| 1148 |
> |
2004-01-14 11:28 mmeineke |
| 1149 |
> |
|
| 1150 |
> |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
| 1151 |
> |
|
| 1152 |
> |
2004-01-14 10:48 gezelter |
| 1153 |
> |
|
| 1154 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1155 |
> |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
| 1156 |
> |
changes for icc8 |
| 1157 |
> |
|
| 1158 |
> |
2004-01-13 18:01 gezelter |
| 1159 |
> |
|
| 1160 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
| 1161 |
> |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
| 1162 |
> |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
| 1163 |
> |
Changes for adding direct charge-charge interactions (with |
| 1164 |
> |
switching function) |
| 1165 |
> |
|
| 1166 |
> |
2004-01-13 17:34 gezelter |
| 1167 |
> |
|
| 1168 |
> |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
| 1169 |
> |
oopseMPI_module.F90: Some changes for new MPI organization and |
| 1170 |
> |
direct charge-charge interactions |
| 1171 |
> |
|
| 1172 |
> |
2004-01-13 17:11 tim |
| 1173 |
> |
|
| 1174 |
> |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
| 1175 |
> |
|
| 1176 |
> |
2004-01-13 16:22 tim |
| 1177 |
> |
|
| 1178 |
> |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
| 1179 |
> |
|
| 1180 |
> |
2004-01-13 15:35 tim |
| 1181 |
> |
|
| 1182 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
| 1183 |
> |
eor file whenever it is used instead of rewinding it |
| 1184 |
> |
|
| 1185 |
> |
2004-01-13 15:04 tim |
| 1186 |
> |
|
| 1187 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
| 1188 |
> |
of writeFrame |
| 1189 |
> |
|
| 1190 |
> |
2004-01-13 10:46 tim |
| 1191 |
> |
|
| 1192 |
> |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
| 1193 |
> |
Merge the code of writeFinal and writeDump; |
| 1194 |
> |
Adding sortingIndex into DumpWriter; |
| 1195 |
> |
Fix a bug of writing last frame twice in integrator |
| 1196 |
> |
|
| 1197 |
> |
2004-01-12 17:54 tim |
| 1198 |
> |
|
| 1199 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
| 1200 |
> |
a bug in copying string |
| 1201 |
> |
|
| 1202 |
> |
2004-01-12 15:37 tim |
| 1203 |
> |
|
| 1204 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
| 1205 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: |
| 1206 |
> |
Dumpwriter only write out the atoms on master nodes |
| 1207 |
> |
|
| 1208 |
> |
2004-01-10 04:46 tim |
| 1209 |
> |
|
| 1210 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
| 1211 |
> |
roll it back fix a bug of copying string to a pointer Still have |
| 1212 |
> |
Seg fault, it looks like a random MPI seg fault in totalview |
| 1213 |
> |
|
| 1214 |
> |
2004-01-09 21:15 tim |
| 1215 |
> |
|
| 1216 |
> |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
| 1217 |
> |
|
| 1218 |
> |
2004-01-09 15:29 gezelter |
| 1219 |
> |
|
| 1220 |
> |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
| 1221 |
> |
|
| 1222 |
> |
2004-01-08 17:25 chuckv |
| 1223 |
> |
|
| 1224 |
> |
* libmdtools/DumpWriter.cpp: A work in progress... |
| 1225 |
> |
|
| 1226 |
> |
2004-01-08 13:59 gezelter |
| 1227 |
> |
|
| 1228 |
> |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
| 1229 |
> |
case |
| 1230 |
> |
|
| 1231 |
> |
2004-01-08 13:13 mmeineke |
| 1232 |
> |
|
| 1233 |
> |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
| 1234 |
> |
state bug. |
| 1235 |
> |
|
| 1236 |
> |
2004-01-08 13:05 gezelter |
| 1237 |
> |
|
| 1238 |
> |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
| 1239 |
> |
|
| 1240 |
> |
2004-01-08 12:57 mmeineke |
| 1241 |
> |
|
| 1242 |
> |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
| 1243 |
> |
exstended state bug |
| 1244 |
> |
|
| 1245 |
> |
2004-01-08 12:40 gezelter |
| 1246 |
> |
|
| 1247 |
> |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
| 1248 |
> |
|
| 1249 |
> |
2004-01-08 10:44 mmeineke |
| 1250 |
> |
|
| 1251 |
> |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
| 1252 |
> |
XS state info flag |
| 1253 |
> |
|
| 1254 |
> |
2004-01-07 14:26 tim |
| 1255 |
> |
|
| 1256 |
> |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
| 1257 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass, |
| 1258 |
> |
samples/water/ssd.bass: Fixed a bug of sending message from master |
| 1259 |
> |
node to itself in DumpWriter.cpp and InitializeFromFile.cpp |
| 1260 |
> |
|
| 1261 |
> |
2004-01-06 14:49 chuckv |
| 1262 |
> |
|
| 1263 |
> |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
| 1264 |
> |
performance fixes in the dipole dipole and reaction field code |
| 1265 |
> |
|
| 1266 |
> |
2004-01-06 13:54 chuckv |
| 1267 |
> |
|
| 1268 |
> |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
| 1269 |
> |
little more sane |
| 1270 |
> |
|
| 1271 |
> |
2004-01-05 17:49 chuckv |
| 1272 |
> |
|
| 1273 |
> |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
| 1274 |
> |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
| 1275 |
> |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
| 1276 |
> |
performance by reducing spurious function calls |
| 1277 |
> |
|
| 1278 |
> |
2004-01-05 17:18 chuckv |
| 1279 |
> |
|
| 1280 |
> |
* libmdtools/do_Forces.F90: mangling forces even further |
| 1281 |
> |
|
| 1282 |
> |
2004-01-05 17:18 chuckv |
| 1283 |
> |
|
| 1284 |
> |
* configure, ac-tools/configure.in: mpich mucking |
| 1285 |
> |
|
| 1286 |
> |
2004-01-05 17:12 chuckv |
| 1287 |
> |
|
| 1288 |
> |
* libmdtools/do_Forces.F90: mangled do_forces... |
| 1289 |
> |
|
| 1290 |
> |
2004-01-05 16:00 chuckv |
| 1291 |
> |
|
| 1292 |
> |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
| 1293 |
> |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
| 1294 |
> |
lookup |
| 1295 |
> |
|
| 1296 |
> |
2003-12-29 14:56 chuckv |
| 1297 |
> |
|
| 1298 |
> |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
| 1299 |
> |
third-party directory for code not written by us. Also added |
| 1300 |
> |
Mersenne Twister random number generator code. This will eventually |
| 1301 |
> |
replace sprng as the random number generator used by OOPSE. |
| 1302 |
> |
|
| 1303 |
> |
2003-12-22 16:26 chuckv |
| 1304 |
> |
|
| 1305 |
> |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
| 1306 |
> |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
| 1307 |
> |
Fixes to profile code. |
| 1308 |
> |
|
| 1309 |
> |
2003-12-19 15:36 mmeineke |
| 1310 |
> |
|
| 1311 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
| 1312 |
> |
timing.F90, timing.f90: More profiling fixes. |
| 1313 |
> |
|
| 1314 |
> |
2003-12-19 15:19 chuckv |
| 1315 |
> |
|
| 1316 |
> |
* libmdtools/timing.f90: Another change for MPI in timing. |
| 1317 |
> |
|
| 1318 |
> |
2003-12-19 15:17 chuckv |
| 1319 |
> |
|
| 1320 |
> |
* libmdtools/timing.f90: Small update to timing in MPI |
| 1321 |
> |
|
| 1322 |
> |
2003-12-19 13:53 mmeineke |
| 1323 |
> |
|
| 1324 |
> |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
| 1325 |
> |
profiling commands work now. Will start adding PROFILE ifdefs into |
| 1326 |
> |
the code |
| 1327 |
> |
|
| 1328 |
> |
2003-12-19 12:25 mmeineke |
| 1329 |
> |
|
| 1330 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
| 1331 |
> |
some profiling routines |
| 1332 |
> |
|
| 1333 |
> |
2003-12-19 10:12 mmeineke |
| 1334 |
> |
|
| 1335 |
> |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
| 1336 |
> |
and GofRomega |
| 1337 |
|
|
| 1338 |
< |
added identification of identI in matchI. |
| 1338 |
> |
additional work on randomBilayer |
| 1339 |
> |
|
| 1340 |
> |
2003-12-19 10:12 mmeineke |
| 1341 |
> |
|
| 1342 |
> |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
| 1343 |
> |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
| 1344 |
> |
GofRomega |
| 1345 |
> |
|
| 1346 |
> |
2003-12-18 16:47 mmeineke |
| 1347 |
> |
|
| 1348 |
> |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
| 1349 |
> |
some profile functionality |
| 1350 |
> |
|
| 1351 |
> |
2003-12-18 15:46 chuckv |
| 1352 |
> |
|
| 1353 |
> |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
| 1354 |
> |
Added functions for simple profiling in fortran. |
| 1355 |
> |
|
| 1356 |
> |
2003-12-17 15:13 chuckv |
| 1357 |
> |
|
| 1358 |
> |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
| 1359 |
> |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
| 1360 |
> |
rho_col were scattered into the same array. Unfortunately, MPI |
| 1361 |
> |
zeros the array between scatters so half of the sum was being lost. |
| 1362 |
> |
Fixed by added a temp array for column scatter, then sum loop over |
| 1363 |
> |
nlocal. |
| 1364 |
> |
|
| 1365 |
> |
2003-12-16 15:49 mmeineke |
| 1366 |
> |
|
| 1367 |
> |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
| 1368 |
> |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
| 1369 |
> |
gofRomega. both need to be debugged and tested. |
| 1370 |
> |
|
| 1371 |
> |
2003-12-12 10:42 gezelter |
| 1372 |
> |
|
| 1373 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1374 |
> |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
| 1375 |
> |
gradients (to do minimizations) |
| 1376 |
> |
|
| 1377 |
> |
2003-12-12 10:33 mmeineke |
| 1378 |
> |
|
| 1379 |
> |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
| 1380 |
> |
header |
| 1381 |
> |
|
| 1382 |
> |
2003-12-10 11:52 mmeineke |
| 1383 |
> |
|
| 1384 |
> |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
| 1385 |
> |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
| 1386 |
> |
randomBilayer to the build. Also move the random bilayer builder |
| 1387 |
> |
from bilayerSys to randomBilayer |
| 1388 |
> |
|
| 1389 |
> |
2003-11-25 10:44 mmeineke |
| 1390 |
> |
|
| 1391 |
> |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
| 1392 |
> |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
| 1393 |
> |
TB3 in DUFF.frc |
| 1394 |
> |
|
| 1395 |
> |
2003-11-21 15:09 mmeineke |
| 1396 |
> |
|
| 1397 |
> |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
| 1398 |
> |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
| 1399 |
> |
message in SimInfo. Added a more informative error message in |
| 1400 |
> |
InitializeFromFile |
| 1401 |
> |
|
| 1402 |
> |
2003-11-21 15:07 mmeineke |
| 1403 |
> |
|
| 1404 |
> |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
| 1405 |
> |
ing in the GofR,CosTheta |
| 1406 |
> |
|
| 1407 |
> |
2003-11-21 14:31 chrisfen |
| 1408 |
> |
|
| 1409 |
> |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
| 1410 |
> |
a bug in SimInfo ordering of radii |
| 1411 |
> |
|
| 1412 |
> |
2003-11-11 12:20 mmeineke |
| 1413 |
> |
|
| 1414 |
> |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
| 1415 |
> |
a min function. |
| 1416 |
> |
|
| 1417 |
> |
2003-11-10 16:50 mmeineke |
| 1418 |
> |
|
| 1419 |
> |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
| 1420 |
> |
reordered the rcut/ecr/boxSize initialization |
| 1421 |
> |
|
| 1422 |
> |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
| 1423 |
> |
now exit when it runs into rcut or ecr. |
| 1424 |
> |
|
| 1425 |
> |
2003-11-07 16:46 chuckv |
| 1426 |
> |
|
| 1427 |
> |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
| 1428 |
> |
oopseMPI_module.F90: Added support for compiling fortran without |
| 1429 |
> |
use of mpich modules. We use mpif.h instead.: |
| 1430 |
> |
|
| 1431 |
> |
2003-11-07 12:09 mmeineke |
| 1432 |
> |
|
| 1433 |
> |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
| 1434 |
> |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
| 1435 |
> |
the atom loop in the NPT family of integrators. |
| 1436 |
> |
|
| 1437 |
> |
2003-11-06 17:01 mmeineke |
| 1438 |
> |
|
| 1439 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
| 1440 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
| 1441 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 1442 |
> |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
| 1443 |
> |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
| 1444 |
> |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
| 1445 |
> |
* useIntiTime => useInitialTime |
| 1446 |
> |
|
| 1447 |
> |
2003-11-06 14:24 mmeineke |
| 1448 |
> |
|
| 1449 |
> |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
| 1450 |
> |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
| 1451 |
> |
parse_tree.h: fixed the includes in the Make.dep |
| 1452 |
> |
|
| 1453 |
> |
2003-11-06 14:11 mmeineke |
| 1454 |
> |
|
| 1455 |
> |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
| 1456 |
> |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
| 1457 |
> |
new-templateless branch to the main trunk. |
| 1458 |
> |
|
| 1459 |
> |
bug Fixes include: * fixed the switching function from ortho to |
| 1460 |
> |
non-ortho box. !!!!! THis was responsible for all of the |
| 1461 |
> |
sudden deaths we saw. * some formating in the string when we |
| 1462 |
> |
write out the extended system state. * added NPT.cpp to the |
| 1463 |
> |
makefile.in |
| 1464 |
> |
|
| 1465 |
> |
2003-11-06 13:20 mmeineke |
| 1466 |
> |
|
| 1467 |
> |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
| 1468 |
> |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
| 1469 |
> |
bug. The box was not switching between orthorhombic and |
| 1470 |
> |
non-orthorhombic wrapping correctly. we added a fabs() to |
| 1471 |
> |
the check.which should fix it. |
| 1472 |
> |
|
| 1473 |
> |
2003-11-05 14:16 mmeineke |
| 1474 |
> |
|
| 1475 |
> |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
| 1476 |
> |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
| 1477 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
| 1478 |
> |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
| 1479 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
| 1480 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
| 1481 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
| 1482 |
> |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
| 1483 |
> |
some work on trying to find the compression bug |
| 1484 |
> |
|
| 1485 |
> |
2003-11-03 17:07 mmeineke |
| 1486 |
> |
|
| 1487 |
> |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
| 1488 |
> |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
| 1489 |
> |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
| 1490 |
> |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
| 1491 |
> |
most of standard template library from OOPSE. |
| 1492 |
> |
|
| 1493 |
> |
2003-10-31 16:06 mmeineke |
| 1494 |
> |
|
| 1495 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
| 1496 |
> |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
| 1497 |
> |
SimSetup.cpp: started work on template removal. |
| 1498 |
> |
|
| 1499 |
> |
2003-10-31 13:28 mmeineke |
| 1500 |
> |
|
| 1501 |
> |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
| 1502 |
> |
added template stuff to the Maikefile template |
| 1503 |
> |
|
| 1504 |
> |
little changes to some printf format statements |
| 1505 |
> |
|
| 1506 |
> |
2003-10-31 13:28 mmeineke |
| 1507 |
> |
|
| 1508 |
> |
* libBASS/Makefile.in: added template stuff to the Maikefile |
| 1509 |
> |
template |
| 1510 |
> |
|
| 1511 |
> |
2003-10-30 13:59 gezelter |
| 1512 |
> |
|
| 1513 |
> |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
| 1514 |
> |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
| 1515 |
> |
rList problems |
| 1516 |
> |
|
| 1517 |
> |
2003-10-30 09:11 gezelter |
| 1518 |
> |
|
| 1519 |
> |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
| 1520 |
> |
queried before q0 was allocated. |
| 1521 |
> |
|
| 1522 |
> |
2003-10-29 15:41 mmeineke |
| 1523 |
> |
|
| 1524 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
| 1525 |
> |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
| 1526 |
> |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
| 1527 |
> |
in bass.l |
| 1528 |
> |
|
| 1529 |
> |
fixed a little bug in the first time step, regarding the setting of |
| 1530 |
> |
ecr and est in fortran |
| 1531 |
|
|
| 1532 |
+ |
2003-10-29 15:40 mmeineke |
| 1533 |
+ |
|
| 1534 |
+ |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
| 1535 |
+ |
|
| 1536 |
+ |
2003-10-29 12:55 mmeineke |
| 1537 |
+ |
|
| 1538 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
| 1539 |
+ |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
| 1540 |
+ |
rcut is setup, as well as additional debugging comments. |
| 1541 |
+ |
|
| 1542 |
+ |
2003-10-29 09:28 gezelter |
| 1543 |
+ |
|
| 1544 |
+ |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
| 1545 |
+ |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
| 1546 |
+ |
templates |
| 1547 |
+ |
|
| 1548 |
+ |
2003-10-28 22:16 gezelter |
| 1549 |
+ |
|
| 1550 |
+ |
* src/Makefile.in: Refixed broken makefile |
| 1551 |
+ |
|
| 1552 |
+ |
2003-10-28 22:06 gezelter |
| 1553 |
+ |
|
| 1554 |
+ |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
| 1555 |
+ |
fixes |
| 1556 |
+ |
|
| 1557 |
+ |
2003-10-28 19:19 tim |
| 1558 |
+ |
|
| 1559 |
+ |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
| 1560 |
+ |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
| 1561 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
| 1562 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
| 1563 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
| 1564 |
+ |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
| 1565 |
+ |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi |
| 1566 |
+ |
and eta to the comment line of dump file. |
| 1567 |
+ |
|
| 1568 |
+ |
2003-10-28 17:25 mmeineke |
| 1569 |
+ |
|
| 1570 |
+ |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
| 1571 |
+ |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
| 1572 |
+ |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
| 1573 |
+ |
how c calls fortran. All function pointers and fortran calls are |
| 1574 |
+ |
rigidly typecast now. |
| 1575 |
+ |
|
| 1576 |
+ |
2003-10-28 15:42 gezelter |
| 1577 |
+ |
|
| 1578 |
+ |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
| 1579 |
+ |
Portability fixes |
| 1580 |
+ |
|
| 1581 |
+ |
2003-10-28 15:09 gezelter |
| 1582 |
+ |
|
| 1583 |
+ |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
| 1584 |
+ |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
| 1585 |
+ |
src/Makefile.in: Compatibility fixes |
| 1586 |
+ |
|
| 1587 |
+ |
2003-10-28 12:08 mmeineke |
| 1588 |
+ |
|
| 1589 |
+ |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
| 1590 |
+ |
started work on template removal |
| 1591 |
+ |
|
| 1592 |
+ |
2003-10-28 12:04 gezelter |
| 1593 |
+ |
|
| 1594 |
+ |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
| 1595 |
+ |
trying to understand extern "C" stuff for pointers |
| 1596 |
+ |
|
| 1597 |
+ |
2003-10-28 11:20 gezelter |
| 1598 |
+ |
|
| 1599 |
+ |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
| 1600 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
| 1601 |
+ |
|
| 1602 |
+ |
2003-10-28 11:03 gezelter |
| 1603 |
+ |
|
| 1604 |
+ |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
| 1605 |
+ |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
| 1606 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
| 1607 |
+ |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
| 1608 |
+ |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
| 1609 |
+ |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
| 1610 |
+ |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
| 1611 |
+ |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
| 1612 |
+ |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
| 1613 |
+ |
more portable c header stuff Also, mod file fixes and portability |
| 1614 |
+ |
changes Some fortran changes will need to be reversed. |
| 1615 |
+ |
|
| 1616 |
+ |
2003-10-28 11:03 gezelter |
| 1617 |
+ |
|
| 1618 |
+ |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
| 1619 |
+ |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
| 1620 |
+ |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
| 1621 |
+ |
portable c header stuff Also, mod file fixes and portability |
| 1622 |
+ |
changes |
| 1623 |
+ |
|
| 1624 |
+ |
2003-10-28 11:02 gezelter |
| 1625 |
+ |
|
| 1626 |
+ |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
| 1627 |
+ |
stuff |
| 1628 |
+ |
|
| 1629 |
+ |
2003-10-27 18:00 gezelter |
| 1630 |
+ |
|
| 1631 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
| 1632 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, |
| 1633 |
+ |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
| 1634 |
+ |
|
| 1635 |
+ |
2003-10-27 17:08 mmeineke |
| 1636 |
+ |
|
| 1637 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
| 1638 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
| 1639 |
+ |
added routines for the sysbuilder to work with simSetup |
| 1640 |
+ |
|
| 1641 |
+ |
remved the QuickBass routines, and had all parsing go through |
| 1642 |
+ |
SimSetup. LatticeBilayer is in complete working order now. |
| 1643 |
+ |
|
| 1644 |
+ |
2003-10-27 17:07 mmeineke |
| 1645 |
+ |
|
| 1646 |
+ |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
| 1647 |
+ |
routines for the sysbuilder to work with simSetup |
| 1648 |
+ |
|
| 1649 |
+ |
2003-10-27 11:20 gezelter |
| 1650 |
+ |
|
| 1651 |
+ |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
| 1652 |
+ |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
| 1653 |
+ |
|
| 1654 |
+ |
2003-10-24 17:17 mmeineke |
| 1655 |
+ |
|
| 1656 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
| 1657 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
| 1658 |
+ |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
| 1659 |
+ |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
| 1660 |
+ |
overhauled latticeBilayer into its own program. Removed sysBuild |
| 1661 |
+ |
from the Makefile |
| 1662 |
+ |
|
| 1663 |
+ |
2003-10-24 12:36 gezelter |
| 1664 |
+ |
|
| 1665 |
+ |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
| 1666 |
+ |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
| 1667 |
+ |
builder |
| 1668 |
+ |
|
| 1669 |
+ |
2003-10-24 12:35 gezelter |
| 1670 |
+ |
|
| 1671 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
| 1672 |
+ |
merge problem |
| 1673 |
+ |
|
| 1674 |
+ |
2003-10-23 14:57 mmeineke |
| 1675 |
+ |
|
| 1676 |
+ |
* samples/metals/Makefile.in: added eam ForceField files to the |
| 1677 |
+ |
init |
| 1678 |
+ |
|
| 1679 |
+ |
fixed an eam mpi parmeter setup bug |
| 1680 |
+ |
|
| 1681 |
+ |
added the init file to the makefile |
| 1682 |
+ |
|
| 1683 |
+ |
2003-10-23 14:57 mmeineke |
| 1684 |
+ |
|
| 1685 |
+ |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
| 1686 |
+ |
to the init |
| 1687 |
+ |
|
| 1688 |
+ |
fixed an eam mpi parmeter setup bug |
| 1689 |
+ |
|
| 1690 |
+ |
2003-10-23 14:57 mmeineke |
| 1691 |
+ |
|
| 1692 |
+ |
* forceFields/Makefile.in: added eam ForceField files to the init |
| 1693 |
+ |
|
| 1694 |
+ |
2003-10-22 16:17 mmeineke |
| 1695 |
+ |
|
| 1696 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
| 1697 |
+ |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
| 1698 |
+ |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
| 1699 |
+ |
no box skew allowed. |
| 1700 |
+ |
|
| 1701 |
+ |
2003-10-21 14:33 mmeineke |
| 1702 |
+ |
|
| 1703 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
| 1704 |
+ |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
| 1705 |
+ |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
| 1706 |
+ |
* useInitTime = false: sets the origin time to 0.0 regardless |
| 1707 |
+ |
of the time stamp in the .init file * default=> useInitTime = |
| 1708 |
+ |
true; |
| 1709 |
+ |
|
| 1710 |
+ |
2003-10-17 16:19 mmeineke |
| 1711 |
+ |
|
| 1712 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
| 1713 |
+ |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
| 1714 |
+ |
staticProps.cpp, obj/placeholder: added the staticProps directory |
| 1715 |
+ |
to the build list for both configure and configure.in |
| 1716 |
+ |
|
| 1717 |
+ |
fixed a number of bugs in the staticProps code. gofr is now |
| 1718 |
+ |
working. |
| 1719 |
+ |
|
| 1720 |
+ |
2003-10-17 16:18 mmeineke |
| 1721 |
+ |
|
| 1722 |
+ |
* ac-tools/configure.in: added the staticProps directory to the |
| 1723 |
+ |
build list for both configure and configure.in |
| 1724 |
+ |
|
| 1725 |
+ |
2003-10-17 16:17 mmeineke |
| 1726 |
+ |
|
| 1727 |
+ |
* configure: added the staticProps directory to the build list |
| 1728 |
+ |
|
| 1729 |
+ |
2003-10-16 14:16 mmeineke |
| 1730 |
+ |
|
| 1731 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
| 1732 |
+ |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
| 1733 |
+ |
use linked lists instead of a vector. |
| 1734 |
+ |
|
| 1735 |
+ |
Fixed the makefile to build DumpReader.cpp |
| 1736 |
+ |
|
| 1737 |
+ |
Removed a comment output in Exclude.cpp |
| 1738 |
+ |
|
| 1739 |
+ |
Modified DumpWriter and Integrator to write an eor file every time |
| 1740 |
+ |
a frame is written. This lets the .eor file represent the last |
| 1741 |
+ |
written frame of a simulation. |
| 1742 |
+ |
|
| 1743 |
+ |
2003-10-10 12:10 mmeineke |
| 1744 |
+ |
|
| 1745 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
| 1746 |
+ |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
| 1747 |
+ |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
| 1748 |
+ |
staticProps.cpp: removed the props directory, and moved everything |
| 1749 |
+ |
over to staticProps |
| 1750 |
+ |
|
| 1751 |
+ |
2003-10-09 17:09 mmeineke |
| 1752 |
+ |
|
| 1753 |
+ |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
| 1754 |
+ |
a position where it will compile and run first runs. |
| 1755 |
+ |
|
| 1756 |
+ |
2003-10-04 13:46 chuckv |
| 1757 |
+ |
|
| 1758 |
+ |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
| 1759 |
+ |
samples/metals/Au.bass: Fixed bug in calc_eam. |
| 1760 |
+ |
|
| 1761 |
+ |
2003-10-04 13:08 chuckv |
| 1762 |
+ |
|
| 1763 |
+ |
* samples/metals/init_au.in: added Au init file for eam. |
| 1764 |
+ |
|
| 1765 |
+ |
2003-10-03 17:11 mmeineke |
| 1766 |
+ |
|
| 1767 |
+ |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
| 1768 |
+ |
entahlpy from the statwriter and thermo. |
| 1769 |
+ |
|
| 1770 |
+ |
2003-10-03 17:02 mmeineke |
| 1771 |
+ |
|
| 1772 |
+ |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
| 1773 |
+ |
statements in simError |
| 1774 |
+ |
|
| 1775 |
+ |
added a function to get the maxCutoff |
| 1776 |
+ |
|
| 1777 |
+ |
2003-10-03 17:01 mmeineke |
| 1778 |
+ |
|
| 1779 |
+ |
* libBASS/simError.c: changed the formating ogf the error |
| 1780 |
+ |
statements in simError |
| 1781 |
+ |
|
| 1782 |
+ |
2003-09-30 11:00 mmeineke |
| 1783 |
+ |
|
| 1784 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
| 1785 |
+ |
f90Flags so they are no longer overwritten by the compiler. |
| 1786 |
+ |
|
| 1787 |
+ |
2003-09-29 17:06 mmeineke |
| 1788 |
+ |
|
| 1789 |
+ |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
| 1790 |
+ |
for conifig.in |
| 1791 |
+ |
|
| 1792 |
+ |
fixed wrappers to extern "C" |
| 1793 |
+ |
|
| 1794 |
+ |
2003-09-29 17:06 mmeineke |
| 1795 |
+ |
|
| 1796 |
+ |
* ac-tools/configure.in: added mpif90 mod check back same for |
| 1797 |
+ |
conifig.in |
| 1798 |
+ |
|
| 1799 |
+ |
2003-09-29 17:05 mmeineke |
| 1800 |
+ |
|
| 1801 |
+ |
* configure: added mpif90 mod check back |
| 1802 |
+ |
|
| 1803 |
+ |
2003-09-29 16:16 mmeineke |
| 1804 |
+ |
|
| 1805 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
| 1806 |
+ |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
| 1807 |
+ |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
| 1808 |
+ |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
| 1809 |
+ |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
| 1810 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
| 1811 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
| 1812 |
+ |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
| 1813 |
+ |
found with SUN's SUNWspro.s1s7 |
| 1814 |
+ |
|
| 1815 |
+ |
2003-09-29 12:38 mmeineke |
| 1816 |
+ |
|
| 1817 |
+ |
* libmdtools/GenericData.hpp: light change in syntax. no |
| 1818 |
+ |
signifigant change. |
| 1819 |
+ |
|
| 1820 |
+ |
2003-09-25 16:17 mmeineke |
| 1821 |
+ |
|
| 1822 |
+ |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
| 1823 |
+ |
additional remarks from icc -w3 (extra verbose output) |
| 1824 |
+ |
|
| 1825 |
+ |
2003-09-25 14:27 mmeineke |
| 1826 |
+ |
|
| 1827 |
+ |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
| 1828 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
| 1829 |
+ |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
| 1830 |
+ |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
| 1831 |
+ |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
| 1832 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
| 1833 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 1834 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
| 1835 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
| 1836 |
+ |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
| 1837 |
+ |
gcc -Wall and g++ -Wall |
| 1838 |
+ |
|
| 1839 |
+ |
2003-09-25 13:54 gezelter |
| 1840 |
+ |
|
| 1841 |
+ |
* configure, ac-tools/configure.in: fixed a bug in configure |
| 1842 |
+ |
|
| 1843 |
+ |
2003-09-25 11:42 gezelter |
| 1844 |
+ |
|
| 1845 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
| 1846 |
+ |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
| 1847 |
+ |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
| 1848 |
+ |
fixes for configure |
| 1849 |
+ |
|
| 1850 |
+ |
2003-09-24 14:34 mmeineke |
| 1851 |
+ |
|
| 1852 |
+ |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
| 1853 |
+ |
that it is called before the first Statistics are written. |
| 1854 |
+ |
|
| 1855 |
+ |
2003-09-23 15:36 gezelter |
| 1856 |
+ |
|
| 1857 |
+ |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
| 1858 |
+ |
bunch of Make.dep files to CVS |
| 1859 |
+ |
|
| 1860 |
+ |
2003-09-23 15:34 mmeineke |
| 1861 |
+ |
|
| 1862 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
| 1863 |
+ |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
| 1864 |
+ |
|
| 1865 |
+ |
Some small syntax cleaning in NPTfm and SimSetup |
| 1866 |
+ |
|
| 1867 |
+ |
2003-09-22 18:07 tim |
| 1868 |
+ |
|
| 1869 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
| 1870 |
+ |
SimInfo.hpp: fix bug in calculating maxCutoff |
| 1871 |
+ |
|
| 1872 |
+ |
2003-09-22 16:23 mmeineke |
| 1873 |
+ |
|
| 1874 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
| 1875 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
| 1876 |
+ |
Converted NPTf to work with the NPT base class. |
| 1877 |
+ |
|
| 1878 |
+ |
Removed NPTfm and NPTim from cvs |
| 1879 |
+ |
|
| 1880 |
+ |
2003-09-19 15:00 mmeineke |
| 1881 |
+ |
|
| 1882 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
| 1883 |
+ |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
| 1884 |
+ |
class. NPTi is up to date. NPTf is not. |
| 1885 |
+ |
|
| 1886 |
+ |
2003-09-19 11:03 mmeineke |
| 1887 |
+ |
|
| 1888 |
+ |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
| 1889 |
+ |
makefile |
| 1890 |
+ |
|
| 1891 |
+ |
2003-09-19 11:01 gezelter |
| 1892 |
+ |
|
| 1893 |
+ |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
| 1894 |
+ |
|
| 1895 |
+ |
2003-09-19 11:01 gezelter |
| 1896 |
+ |
|
| 1897 |
+ |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
| 1898 |
+ |
(nearly) conserved quantities for both NPTi and NPTf |
| 1899 |
+ |
|
| 1900 |
+ |
2003-09-19 10:20 mmeineke |
| 1901 |
+ |
|
| 1902 |
+ |
* utils/Makefile.in: fixed a typo in the makefile. |
| 1903 |
+ |
|
| 1904 |
+ |
2003-09-19 09:55 gezelter |
| 1905 |
+ |
|
| 1906 |
+ |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
| 1907 |
+ |
samples/water/ssd.bass: [no log message] |
| 1908 |
+ |
|
| 1909 |
+ |
2003-09-19 09:22 tim |
| 1910 |
+ |
|
| 1911 |
+ |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
| 1912 |
+ |
|
| 1913 |
+ |
2003-09-17 09:22 mmeineke |
| 1914 |
+ |
|
| 1915 |
+ |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
| 1916 |
+ |
work with constraints. |
| 1917 |
+ |
|
| 1918 |
+ |
2003-09-16 15:02 tim |
| 1919 |
+ |
|
| 1920 |
+ |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
| 1921 |
+ |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
| 1922 |
+ |
|
| 1923 |
+ |
fixed conserved quantity in NPT (Still some small bug) |
| 1924 |
+ |
|
| 1925 |
+ |
NPTi appears very stable. |
| 1926 |
+ |
|
| 1927 |
+ |
2003-09-15 11:52 tim |
| 1928 |
+ |
|
| 1929 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
| 1930 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
| 1931 |
+ |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
| 1932 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
| 1933 |
+ |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
| 1934 |
+ |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
| 1935 |
+ |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
| 1936 |
+ |
statWriter fix bug of vector wrapping at NPTi |
| 1937 |
+ |
|
| 1938 |
+ |
2003-09-12 11:20 gezelter |
| 1939 |
+ |
|
| 1940 |
+ |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
| 1941 |
+ |
Makefile.in |
| 1942 |
+ |
|
| 1943 |
+ |
2003-09-12 11:20 gezelter |
| 1944 |
+ |
|
| 1945 |
+ |
* ChangeLog: Entered changes for configure into ChangeLog |
| 1946 |
+ |
|
| 1947 |
|
2003-09-09 15:35 mmeineke |
| 1948 |
|
|
| 1949 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
| 1984 |
|
samples/Makefile.in, samples/alkane/Makefile, |
| 1985 |
|
samples/alkane/Makefile.in, samples/argon/Makefile, |
| 1986 |
|
samples/argon/Makefile.in, samples/argon/argon.bass, |
| 1987 |
< |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
| 1988 |
< |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
| 1989 |
< |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
| 1990 |
< |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
| 1991 |
< |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
| 1992 |
< |
autoconf / configure method of configuring OOPSE |
| 1987 |
> |
samples/minimizer/argon/Makefile, |
| 1988 |
> |
samples/minimizer/argon/Makefile.in, |
| 1989 |
> |
samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile, |
| 1990 |
> |
samples/beadLipid/Makefile.in, samples/lipid/Makefile, |
| 1991 |
> |
samples/lipid/Makefile.in, samples/water/Makefile, |
| 1992 |
> |
samples/water/Makefile.in, src/Makefile, src/Makefile.in, |
| 1993 |
> |
utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile, |
| 1994 |
> |
utils/sysbuilder/Makefile.in: Changes to autoconf / configure |
| 1995 |
> |
method of configuring OOPSE |
| 1996 |
|
|
| 1997 |
|
2003-09-04 16:48 mmeineke |
| 1998 |
|
|
| 2021 |
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
| 2022 |
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
| 2023 |
|
|
| 87 |
– |
2003-08-28 11:59 mmeineke |
| 88 |
– |
|
| 89 |
– |
* props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: |
| 90 |
– |
added the first functional parts of the PairCorrType Abstract |
| 91 |
– |
classes. |
| 92 |
– |
|
| 2024 |
|
2003-08-27 14:23 tim |
| 2025 |
|
|
| 2026 |
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
| 2292 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
| 2293 |
|
works..... |
| 2294 |
|
|
| 364 |
– |
2003-08-08 13:32 mmeineke |
| 365 |
– |
|
| 366 |
– |
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
| 367 |
– |
moved frameCount's functionality into DumpReader. also split props |
| 368 |
– |
into staticProps and dynamicProps. (currently only have |
| 369 |
– |
staticProps) |
| 370 |
– |
|
| 2295 |
|
2003-08-08 12:48 mmeineke |
| 2296 |
|
|
| 2297 |
|
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
| 2348 |
|
2003-07-29 11:32 mmeineke |
| 2349 |
|
|
| 2350 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
| 2351 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
| 2352 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
| 429 |
< |
src/Makefile: working on the props code |
| 2351 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
| 2352 |
> |
working on the props code |
| 2353 |
|
|
| 2354 |
|
2003-07-29 11:32 mmeineke |
| 2355 |
|
|
| 2581 |
|
2003-07-14 18:06 gezelter |
| 2582 |
|
|
| 2583 |
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
| 2584 |
< |
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
| 2585 |
< |
for samples |
| 2584 |
> |
argon/init_argon.eor, minimizer/argon/argon.bass, |
| 2585 |
> |
minimizer/argon/init_argon.eor, lipid/init_5x5.eor, |
| 2586 |
> |
water/init_ssd.eor: Fixes for samples |
| 2587 |
|
|
| 2588 |
|
2003-07-14 18:06 gezelter |
| 2589 |
|
|
| 3256 |
|
|
| 3257 |
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
| 3258 |
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
| 3259 |
< |
samples/argon/argon.bass: more bug fixes.... |
| 3259 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more |
| 3260 |
> |
bug fixes.... |
| 3261 |
|
|
| 3262 |
|
2003-04-01 11:49 mmeineke |
| 3263 |
|
|
| 3464 |
|
2003-03-26 10:37 chuckv |
| 3465 |
|
|
| 3466 |
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
| 3467 |
< |
samples/argon/argon.bass: Fixes for Parallel thermalization |
| 3467 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes |
| 3468 |
> |
for Parallel thermalization |
| 3469 |
|
|
| 3470 |
|
2003-03-26 09:55 mmeineke |
| 3471 |
|
|
| 3479 |
|
|
| 3480 |
|
2003-03-25 09:29 mmeineke |
| 3481 |
|
|
| 3482 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
| 3482 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
| 3483 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
| 3484 |
|
|
| 3485 |
|
2003-03-25 09:29 mmeineke |
| 3489 |
|
|
| 3490 |
|
2003-03-24 20:07 gezelter |
| 3491 |
|
|
| 3492 |
< |
* samples/Makefile, tests/Makefile: moving tests to samples |
| 3492 |
> |
* samples/Makefile: moving tests to samples |
| 3493 |
|
|
| 3494 |
|
2003-03-24 20:06 gezelter |
| 3495 |
|
|
| 3496 |
< |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
| 3497 |
< |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
| 3498 |
< |
samples/argon/Makefile, samples/argon/argon.bass, |
| 3499 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
| 3500 |
< |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
| 3501 |
< |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
| 3502 |
< |
samples/lipid/water.mdl, samples/water/Makefile, |
| 3503 |
< |
samples/water/init_ssd.eor, samples/water/ssd.bass, |
| 1578 |
< |
samples/water/water.mdl, tests/alkane/Makefile, |
| 1579 |
< |
tests/alkane/alkanes.mdl, tests/alkane/butane.bass, |
| 1580 |
< |
tests/alkane/init_butane.eor, tests/argon/Makefile, |
| 1581 |
< |
tests/argon/argon.bass, tests/argon/init_argon.eor, |
| 1582 |
< |
tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, |
| 1583 |
< |
tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, |
| 1584 |
< |
tests/lipid/water.mdl, tests/water/Makefile, |
| 1585 |
< |
tests/water/init_ssd.eor, tests/water/ssd.bass, |
| 1586 |
< |
tests/water/water.mdl: moved tests to samples |
| 3496 |
> |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
| 3497 |
> |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
| 3498 |
> |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
| 3499 |
> |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
| 3500 |
> |
lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, |
| 3501 |
> |
minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, |
| 3502 |
> |
minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, |
| 3503 |
> |
water/ssd.bass, water/water.mdl: moved tests to samples |
| 3504 |
|
|
| 3505 |
|
2003-03-24 19:51 gezelter |
| 3506 |
|
|
| 3508 |
|
|
| 3509 |
|
2003-03-24 19:46 gezelter |
| 3510 |
|
|
| 3511 |
< |
* ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, |
| 1595 |
< |
tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: |
| 1596 |
< |
Added makefiles in tests directories |
| 3511 |
> |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
| 3512 |
|
|
| 3513 |
|
2003-03-24 16:55 gezelter |
| 3514 |
|
|
| 3525 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
| 3526 |
|
do_Forces.F90: little bug fixes here and there |
| 3527 |
|
|
| 1613 |
– |
2003-03-24 11:04 mmeineke |
| 1614 |
– |
|
| 1615 |
– |
* tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon |
| 1616 |
– |
test simulation |
| 1617 |
– |
|
| 1618 |
– |
2003-03-24 11:02 mmeineke |
| 1619 |
– |
|
| 1620 |
– |
* tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, |
| 1621 |
– |
lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, |
| 1622 |
– |
water/water.mdl: [no log message] |
| 1623 |
– |
|
| 1624 |
– |
2003-03-24 11:02 mmeineke |
| 1625 |
– |
|
| 1626 |
– |
* tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added |
| 1627 |
– |
some test bass files for experimenting with |
| 1628 |
– |
|
| 3528 |
|
2003-03-24 10:26 mmeineke |
| 3529 |
|
|
| 3530 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
