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2003-09-10 16:28 mmeineke |
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2004-02-10 16:33 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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* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
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libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
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single version of energy minimization is working. |
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2003-09-09 16:50 mmeineke |
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2004-02-09 15:38 mmeineke |
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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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* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
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the massive memory overusage by OOPSE |
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2004-02-09 09:48 chrisfen |
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|
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* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
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hardwired LJ_rcut |
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|
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2004-02-06 19:14 tim |
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|
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* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
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message] |
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2004-02-06 16:37 tim |
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|
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* ChangeLog, libBASS/Globals.cpp, |
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libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
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libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
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libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
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energy minimization for argon is working, need to add constraint |
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2004-02-06 14:05 tim |
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* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
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one more file into Makefile.in |
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2004-02-06 13:58 tim |
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|
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* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
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libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
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libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
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libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
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libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
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libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
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libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
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libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
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libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
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libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
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some lines into global.cpp to make it work with energy minimization |
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|
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2004-02-04 17:26 tim |
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|
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* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
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Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
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Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
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NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
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Single version of conjugate gradient with golden search linesearch |
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pass a couple of functions test. Brent's algorithm is still broken |
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|
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2004-02-03 17:54 tim |
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|
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* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
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Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
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NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
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SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
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2004-02-03 15:47 tim |
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|
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* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
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ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
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NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
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SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
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SteepestDescent.hpp: [no log message] |
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|
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2004-02-03 15:43 tim |
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|
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* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
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Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
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MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
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NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
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constraint class |
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|
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2004-02-03 12:10 tim |
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|
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* libmdtools/Functor.hpp: Functor.hpp pass unit test |
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|
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2004-02-03 10:21 tim |
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|
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* ChangeLog, libmdtools/Minimizer1D.cpp, |
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libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
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2004-02-02 15:29 tim |
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|
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* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
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Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
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Adding GoldenSection and Brent LineSearch Method |
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|
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2004-01-30 16:47 tim |
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|
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* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
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MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
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NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
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MinimizerBase instead of a functor to do line seach |
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|
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2004-01-30 10:00 chrisfen |
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|
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* forceFields/Makefile.in, libmdtools/Atom.cpp, |
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libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
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libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
108 |
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libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
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libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
110 |
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libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
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libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
112 |
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has a working WATER.cpp forcefield and parser. This involved |
113 |
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changes to WATER.cpp and ForceFields amoung other files. One |
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important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
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This will be removed on the next commit... |
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|
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2004-01-29 18:00 gezelter |
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|
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* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
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libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
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libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
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libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
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libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
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libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
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libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
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libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
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member list fixes for rigid bodies |
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|
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2004-01-29 16:44 tim |
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|
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* libmdtools/MinimizerParameterSet.hpp: Adding |
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MinimizerParameterSet class. |
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|
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2004-01-28 17:44 tim |
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|
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* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
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NLModel0 and NLModel1 |
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|
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2004-01-28 15:40 tim |
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|
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* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
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of NLModel |
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|
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2004-01-27 15:34 gezelter |
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|
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* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
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water.mdl file, updated ssd.bass to use new SSD name |
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|
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2004-01-27 15:34 gezelter |
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|
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* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
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MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
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stuff |
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|
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2004-01-27 14:39 gezelter |
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|
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* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
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2004-01-27 14:39 gezelter |
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* samples/metals/Au.bass: Longer run time to test gold in MPI |
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2004-01-27 14:38 gezelter |
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|
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* samples/argon/argon.bass: Longer run time to test argon |
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|
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2004-01-27 14:38 gezelter |
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|
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* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
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changes to do new rigidBody scheme a copy of WATER.cpp from this |
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morning |
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|
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2004-01-27 14:37 gezelter |
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|
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* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
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BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
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MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
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MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
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interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
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node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
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do new rigidBody scheme |
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|
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2004-01-27 14:15 tim |
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|
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* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
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Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
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MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
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constraint for Nonlinear Optimization Model |
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|
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2004-01-26 17:01 gezelter |
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|
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* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
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Euler angles for orientation instead of unit vectors required |
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changes in MoLocator |
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|
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2004-01-26 16:53 gezelter |
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|
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* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
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beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
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water/water.mdl: Changed orientation lines from unit vectors to |
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euler angles |
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|
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2004-01-26 16:52 gezelter |
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|
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* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
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|
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2004-01-26 16:45 gezelter |
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|
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* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
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use Euler angles in the following order: phi, theta, psi Removed |
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the ability to set orientation using a unit vector |
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|
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2004-01-26 16:26 gezelter |
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|
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* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
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RigidBodyStamp.hpp: Changed default orientation in BASS to use |
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Euler angles in the following order: phi, theta, psi Removed the |
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ability to set orientation using a unit vector |
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|
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2004-01-26 13:52 gezelter |
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|
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* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
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MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
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|
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2004-01-22 12:34 chrisfen |
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|
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* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
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TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
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Corrected spelling in several directories, and stated WATER.cpp |
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|
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2004-01-21 17:16 tim |
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|
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* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
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NLOPModel.hpp: constraint class in energy minimization |
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|
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2004-01-20 15:34 tim |
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|
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* libmdtools/MinimizerBase.hpp: Adding energy minimization |
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|
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2004-01-20 15:32 tim |
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|
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* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
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NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
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|
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2004-01-19 16:17 gezelter |
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|
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* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
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more user-friendly |
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|
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2004-01-19 13:51 chrisfen |
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|
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* forceFields/DUFF.frc: Updated the default water to SSD/E |
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|
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2004-01-19 13:36 tim |
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|
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* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
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time, status time, thermal time and reset time are not divisible by |
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dt |
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2004-01-19 11:10 gezelter |
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|
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* third-party/Makefile.in: Added a bunch of dummy targets so make |
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won't complain |
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2004-01-19 11:10 gezelter |
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|
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* samples/lipid/5x5.bass: Fixed old bass file |
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|
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2004-01-19 11:09 gezelter |
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|
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* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
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required a change in how the MoleculeStamps are used by divideLabor |
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in mpiSimulation.cpp |
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2004-01-19 11:08 gezelter |
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|
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* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
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BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
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MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
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RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
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make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
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parse_tree.c: BASS changes to add RigidBodies and LJrcut |
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|
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2004-01-16 16:55 tim |
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|
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* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
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eor file |
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2004-01-16 16:51 mmeineke |
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|
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* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
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write eor files |
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2004-01-16 10:01 mmeineke |
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|
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* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
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initialization of the AtomStruct |
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2004-01-15 16:57 chuckv |
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* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
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2004-01-15 10:51 gezelter |
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|
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* ac-tools/aclocal.m4: Changes for altivec |
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2004-01-15 09:22 gezelter |
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* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
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2004-01-14 23:33 gezelter |
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* libmdtools/do_Forces.F90: changes for charge charge interactions |
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2004-01-14 20:14 gezelter |
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|
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* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
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notifyCutoffs.F90: More work for adding charges |
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2004-01-14 17:41 gezelter |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
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src/Makefile.in: autoconf fixes |
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2004-01-14 11:28 mmeineke |
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|
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* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
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2004-01-14 10:48 gezelter |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
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src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
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changes for icc8 |
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2004-01-13 18:01 gezelter |
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|
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* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
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SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
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fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
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Changes for adding direct charge-charge interactions (with |
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switching function) |
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2004-01-13 17:34 gezelter |
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|
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* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
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oopseMPI_module.F90: Some changes for new MPI organization and |
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direct charge-charge interactions |
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|
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2004-01-13 17:11 tim |
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* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
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2004-01-13 16:22 tim |
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* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
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2004-01-13 15:35 tim |
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* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
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eor file whenever it is used instead of rewinding it |
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2004-01-13 15:04 tim |
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* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
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of writeFrame |
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2004-01-13 10:46 tim |
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|
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* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
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Merge the code of writeFinal and writeDump; |
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Adding sortingIndex into DumpWriter; |
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Fix a bug of writing last frame twice in integrator |
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|
374 |
> |
2004-01-12 17:54 tim |
375 |
> |
|
376 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
377 |
> |
a bug in copying string |
378 |
> |
|
379 |
> |
2004-01-12 15:37 tim |
380 |
> |
|
381 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
382 |
> |
samples/water/ssd.bass: Dumpwriter only write out the atoms on |
383 |
> |
master nodes |
384 |
> |
|
385 |
> |
2004-01-10 04:46 tim |
386 |
> |
|
387 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
388 |
> |
roll it back fix a bug of copying string to a pointer Still have |
389 |
> |
Seg fault, it looks like a random MPI seg fault in totalview |
390 |
> |
|
391 |
> |
2004-01-09 21:15 tim |
392 |
> |
|
393 |
> |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
394 |
> |
|
395 |
> |
2004-01-09 15:29 gezelter |
396 |
> |
|
397 |
> |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
398 |
> |
|
399 |
> |
2004-01-08 17:25 chuckv |
400 |
> |
|
401 |
> |
* libmdtools/DumpWriter.cpp: A work in progress... |
402 |
> |
|
403 |
> |
2004-01-08 13:59 gezelter |
404 |
> |
|
405 |
> |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
406 |
> |
case |
407 |
> |
|
408 |
> |
2004-01-08 13:13 mmeineke |
409 |
> |
|
410 |
> |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
411 |
> |
state bug. |
412 |
> |
|
413 |
> |
2004-01-08 13:05 gezelter |
414 |
> |
|
415 |
> |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
416 |
> |
|
417 |
> |
2004-01-08 12:57 mmeineke |
418 |
> |
|
419 |
> |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
420 |
> |
exstended state bug |
421 |
> |
|
422 |
> |
2004-01-08 12:40 gezelter |
423 |
> |
|
424 |
> |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
425 |
> |
|
426 |
> |
2004-01-08 10:44 mmeineke |
427 |
> |
|
428 |
> |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
429 |
> |
XS state info flag |
430 |
> |
|
431 |
> |
2004-01-07 14:26 tim |
432 |
> |
|
433 |
> |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
434 |
> |
samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of |
435 |
> |
sending message from master node to itself in DumpWriter.cpp and |
436 |
> |
InitializeFromFile.cpp |
437 |
> |
|
438 |
> |
2004-01-06 14:49 chuckv |
439 |
> |
|
440 |
> |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
441 |
> |
performance fixes in the dipole dipole and reaction field code |
442 |
> |
|
443 |
> |
2004-01-06 13:54 chuckv |
444 |
> |
|
445 |
> |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
446 |
> |
little more sane |
447 |
> |
|
448 |
> |
2004-01-05 17:49 chuckv |
449 |
> |
|
450 |
> |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
451 |
> |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
452 |
> |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
453 |
> |
performance by reducing spurious function calls |
454 |
> |
|
455 |
> |
2004-01-05 17:18 chuckv |
456 |
> |
|
457 |
> |
* libmdtools/do_Forces.F90: mangling forces even further |
458 |
> |
|
459 |
> |
2004-01-05 17:18 chuckv |
460 |
> |
|
461 |
> |
* configure, ac-tools/configure.in: mpich mucking |
462 |
> |
|
463 |
> |
2004-01-05 17:12 chuckv |
464 |
> |
|
465 |
> |
* libmdtools/do_Forces.F90: mangled do_forces... |
466 |
> |
|
467 |
> |
2004-01-05 16:00 chuckv |
468 |
> |
|
469 |
> |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
470 |
> |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
471 |
> |
lookup |
472 |
> |
|
473 |
> |
2003-12-29 14:56 chuckv |
474 |
> |
|
475 |
> |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
476 |
> |
third-party directory for code not written by us. Also added |
477 |
> |
Mersenne Twister random number generator code. This will eventually |
478 |
> |
replace sprng as the random number generator used by OOPSE. |
479 |
> |
|
480 |
> |
2003-12-22 16:26 chuckv |
481 |
> |
|
482 |
> |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
483 |
> |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
484 |
> |
Fixes to profile code. |
485 |
> |
|
486 |
> |
2003-12-19 15:36 mmeineke |
487 |
> |
|
488 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
489 |
> |
timing.F90, timing.f90: More profiling fixes. |
490 |
> |
|
491 |
> |
2003-12-19 15:19 chuckv |
492 |
> |
|
493 |
> |
* libmdtools/timing.f90: Another change for MPI in timing. |
494 |
> |
|
495 |
> |
2003-12-19 15:17 chuckv |
496 |
> |
|
497 |
> |
* libmdtools/timing.f90: Small update to timing in MPI |
498 |
> |
|
499 |
> |
2003-12-19 13:53 mmeineke |
500 |
> |
|
501 |
> |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
502 |
> |
profiling commands work now. Will start adding PROFILE ifdefs into |
503 |
> |
the code |
504 |
> |
|
505 |
> |
2003-12-19 12:25 mmeineke |
506 |
> |
|
507 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
508 |
> |
some profiling routines |
509 |
> |
|
510 |
> |
2003-12-19 10:12 mmeineke |
511 |
> |
|
512 |
> |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
513 |
> |
and GofRomega |
514 |
|
|
515 |
< |
added identification of identI in matchI. |
515 |
> |
additional work on randomBilayer |
516 |
|
|
517 |
+ |
2003-12-19 10:12 mmeineke |
518 |
+ |
|
519 |
+ |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
520 |
+ |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
521 |
+ |
GofRomega |
522 |
+ |
|
523 |
+ |
2003-12-18 16:47 mmeineke |
524 |
+ |
|
525 |
+ |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
526 |
+ |
some profile functionality |
527 |
+ |
|
528 |
+ |
2003-12-18 15:46 chuckv |
529 |
+ |
|
530 |
+ |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
531 |
+ |
Added functions for simple profiling in fortran. |
532 |
+ |
|
533 |
+ |
2003-12-17 15:13 chuckv |
534 |
+ |
|
535 |
+ |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
536 |
+ |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
537 |
+ |
rho_col were scattered into the same array. Unfortunately, MPI |
538 |
+ |
zeros the array between scatters so half of the sum was being lost. |
539 |
+ |
Fixed by added a temp array for column scatter, then sum loop over |
540 |
+ |
nlocal. |
541 |
+ |
|
542 |
+ |
2003-12-16 15:49 mmeineke |
543 |
+ |
|
544 |
+ |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
545 |
+ |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
546 |
+ |
gofRomega. both need to be debugged and tested. |
547 |
+ |
|
548 |
+ |
2003-12-12 10:42 gezelter |
549 |
+ |
|
550 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
551 |
+ |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
552 |
+ |
gradients (to do minimizations) |
553 |
+ |
|
554 |
+ |
2003-12-12 10:33 mmeineke |
555 |
+ |
|
556 |
+ |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
557 |
+ |
header |
558 |
+ |
|
559 |
+ |
2003-12-10 11:52 mmeineke |
560 |
+ |
|
561 |
+ |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
562 |
+ |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
563 |
+ |
randomBilayer to the build. Also move the random bilayer builder |
564 |
+ |
from bilayerSys to randomBilayer |
565 |
+ |
|
566 |
+ |
2003-11-25 10:44 mmeineke |
567 |
+ |
|
568 |
+ |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
569 |
+ |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
570 |
+ |
TB3 in DUFF.frc |
571 |
+ |
|
572 |
+ |
2003-11-21 15:09 mmeineke |
573 |
+ |
|
574 |
+ |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
575 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
576 |
+ |
message in SimInfo. Added a more informative error message in |
577 |
+ |
InitializeFromFile |
578 |
+ |
|
579 |
+ |
2003-11-21 15:07 mmeineke |
580 |
+ |
|
581 |
+ |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
582 |
+ |
ing in the GofR,CosTheta |
583 |
+ |
|
584 |
+ |
2003-11-21 14:31 chrisfen |
585 |
+ |
|
586 |
+ |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
587 |
+ |
a bug in SimInfo ordering of radii |
588 |
+ |
|
589 |
+ |
2003-11-11 12:20 mmeineke |
590 |
+ |
|
591 |
+ |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
592 |
+ |
a min function. |
593 |
+ |
|
594 |
+ |
2003-11-10 16:50 mmeineke |
595 |
+ |
|
596 |
+ |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
597 |
+ |
reordered the rcut/ecr/boxSize initialization |
598 |
+ |
|
599 |
+ |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
600 |
+ |
now exit when it runs into rcut or ecr. |
601 |
+ |
|
602 |
+ |
2003-11-07 16:46 chuckv |
603 |
+ |
|
604 |
+ |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
605 |
+ |
oopseMPI_module.F90: Added support for compiling fortran without |
606 |
+ |
use of mpich modules. We use mpif.h instead.: |
607 |
+ |
|
608 |
+ |
2003-11-07 12:09 mmeineke |
609 |
+ |
|
610 |
+ |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
611 |
+ |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
612 |
+ |
the atom loop in the NPT family of integrators. |
613 |
+ |
|
614 |
+ |
2003-11-06 17:01 mmeineke |
615 |
+ |
|
616 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
617 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
618 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
619 |
+ |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
620 |
+ |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
621 |
+ |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
622 |
+ |
* useIntiTime => useInitialTime |
623 |
+ |
|
624 |
+ |
2003-11-06 14:24 mmeineke |
625 |
+ |
|
626 |
+ |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
627 |
+ |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
628 |
+ |
parse_tree.h: fixed the includes in the Make.dep |
629 |
+ |
|
630 |
+ |
2003-11-06 14:11 mmeineke |
631 |
+ |
|
632 |
+ |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
633 |
+ |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
634 |
+ |
new-templateless branch to the main trunk. |
635 |
+ |
|
636 |
+ |
bug Fixes include: * fixed the switching function from ortho to |
637 |
+ |
non-ortho box. !!!!! THis was responsible for all of the |
638 |
+ |
sudden deaths we saw. * some formating in the string when we |
639 |
+ |
write out the extended system state. * added NPT.cpp to the |
640 |
+ |
makefile.in |
641 |
+ |
|
642 |
+ |
2003-11-06 13:20 mmeineke |
643 |
+ |
|
644 |
+ |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
645 |
+ |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
646 |
+ |
bug. The box was not switching between orthorhombic and |
647 |
+ |
non-orthorhombic wrapping correctly. we added a fabs() to |
648 |
+ |
the check.which should fix it. |
649 |
+ |
|
650 |
+ |
2003-11-05 14:16 mmeineke |
651 |
+ |
|
652 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
653 |
+ |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
654 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
655 |
+ |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
656 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
657 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
658 |
+ |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
659 |
+ |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
660 |
+ |
some work on trying to find the compression bug |
661 |
+ |
|
662 |
+ |
2003-11-03 17:07 mmeineke |
663 |
+ |
|
664 |
+ |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
665 |
+ |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
666 |
+ |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
667 |
+ |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
668 |
+ |
most of standard template library from OOPSE. |
669 |
+ |
|
670 |
+ |
2003-10-31 16:06 mmeineke |
671 |
+ |
|
672 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
673 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
674 |
+ |
SimSetup.cpp: started work on template removal. |
675 |
+ |
|
676 |
+ |
2003-10-31 13:28 mmeineke |
677 |
+ |
|
678 |
+ |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
679 |
+ |
added template stuff to the Maikefile template |
680 |
+ |
|
681 |
+ |
little changes to some printf format statements |
682 |
+ |
|
683 |
+ |
2003-10-31 13:28 mmeineke |
684 |
+ |
|
685 |
+ |
* libBASS/Makefile.in: added template stuff to the Maikefile |
686 |
+ |
template |
687 |
+ |
|
688 |
+ |
2003-10-30 13:59 gezelter |
689 |
+ |
|
690 |
+ |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
691 |
+ |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
692 |
+ |
rList problems |
693 |
+ |
|
694 |
+ |
2003-10-30 09:11 gezelter |
695 |
+ |
|
696 |
+ |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
697 |
+ |
queried before q0 was allocated. |
698 |
+ |
|
699 |
+ |
2003-10-29 15:41 mmeineke |
700 |
+ |
|
701 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
702 |
+ |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
703 |
+ |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
704 |
+ |
in bass.l |
705 |
+ |
|
706 |
+ |
fixed a little bug in the first time step, regarding the setting of |
707 |
+ |
ecr and est in fortran |
708 |
+ |
|
709 |
+ |
2003-10-29 15:40 mmeineke |
710 |
+ |
|
711 |
+ |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
712 |
+ |
|
713 |
+ |
2003-10-29 12:55 mmeineke |
714 |
+ |
|
715 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
716 |
+ |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
717 |
+ |
rcut is setup, as well as additional debugging comments. |
718 |
+ |
|
719 |
+ |
2003-10-29 09:28 gezelter |
720 |
+ |
|
721 |
+ |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
722 |
+ |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
723 |
+ |
templates |
724 |
+ |
|
725 |
+ |
2003-10-28 22:16 gezelter |
726 |
+ |
|
727 |
+ |
* src/Makefile.in: Refixed broken makefile |
728 |
+ |
|
729 |
+ |
2003-10-28 22:06 gezelter |
730 |
+ |
|
731 |
+ |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
732 |
+ |
fixes |
733 |
+ |
|
734 |
+ |
2003-10-28 19:19 tim |
735 |
+ |
|
736 |
+ |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
737 |
+ |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
738 |
+ |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
739 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
740 |
+ |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
741 |
+ |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
742 |
+ |
samples/water/ssd.bass: add chi and eta to the comment line of dump |
743 |
+ |
file. |
744 |
+ |
|
745 |
+ |
2003-10-28 17:25 mmeineke |
746 |
+ |
|
747 |
+ |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
748 |
+ |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
749 |
+ |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
750 |
+ |
how c calls fortran. All function pointers and fortran calls are |
751 |
+ |
rigidly typecast now. |
752 |
+ |
|
753 |
+ |
2003-10-28 15:42 gezelter |
754 |
+ |
|
755 |
+ |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
756 |
+ |
Portability fixes |
757 |
+ |
|
758 |
+ |
2003-10-28 15:09 gezelter |
759 |
+ |
|
760 |
+ |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
761 |
+ |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
762 |
+ |
src/Makefile.in: Compatibility fixes |
763 |
+ |
|
764 |
+ |
2003-10-28 12:08 mmeineke |
765 |
+ |
|
766 |
+ |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
767 |
+ |
started work on template removal |
768 |
+ |
|
769 |
+ |
2003-10-28 12:04 gezelter |
770 |
+ |
|
771 |
+ |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
772 |
+ |
trying to understand extern "C" stuff for pointers |
773 |
+ |
|
774 |
+ |
2003-10-28 11:20 gezelter |
775 |
+ |
|
776 |
+ |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
777 |
+ |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
778 |
+ |
|
779 |
+ |
2003-10-28 11:03 gezelter |
780 |
+ |
|
781 |
+ |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
782 |
+ |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
783 |
+ |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
784 |
+ |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
785 |
+ |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
786 |
+ |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
787 |
+ |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
788 |
+ |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
789 |
+ |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
790 |
+ |
more portable c header stuff Also, mod file fixes and portability |
791 |
+ |
changes Some fortran changes will need to be reversed. |
792 |
+ |
|
793 |
+ |
2003-10-28 11:03 gezelter |
794 |
+ |
|
795 |
+ |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
796 |
+ |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
797 |
+ |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
798 |
+ |
portable c header stuff Also, mod file fixes and portability |
799 |
+ |
changes |
800 |
+ |
|
801 |
+ |
2003-10-28 11:02 gezelter |
802 |
+ |
|
803 |
+ |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
804 |
+ |
stuff |
805 |
+ |
|
806 |
+ |
2003-10-27 18:00 gezelter |
807 |
+ |
|
808 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
809 |
+ |
ac-tools/configure.in, ac-tools/fortran90.m4, |
810 |
+ |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
811 |
+ |
|
812 |
+ |
2003-10-27 17:08 mmeineke |
813 |
+ |
|
814 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
815 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
816 |
+ |
added routines for the sysbuilder to work with simSetup |
817 |
+ |
|
818 |
+ |
remved the QuickBass routines, and had all parsing go through |
819 |
+ |
SimSetup. LatticeBilayer is in complete working order now. |
820 |
+ |
|
821 |
+ |
2003-10-27 17:07 mmeineke |
822 |
+ |
|
823 |
+ |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
824 |
+ |
routines for the sysbuilder to work with simSetup |
825 |
+ |
|
826 |
+ |
2003-10-27 11:20 gezelter |
827 |
+ |
|
828 |
+ |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
829 |
+ |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
830 |
+ |
|
831 |
+ |
2003-10-24 17:17 mmeineke |
832 |
+ |
|
833 |
+ |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
834 |
+ |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
835 |
+ |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
836 |
+ |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
837 |
+ |
overhauled latticeBilayer into its own program. Removed sysBuild |
838 |
+ |
from the Makefile |
839 |
+ |
|
840 |
+ |
2003-10-24 12:36 gezelter |
841 |
+ |
|
842 |
+ |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
843 |
+ |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
844 |
+ |
builder |
845 |
+ |
|
846 |
+ |
2003-10-24 12:35 gezelter |
847 |
+ |
|
848 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
849 |
+ |
merge problem |
850 |
+ |
|
851 |
+ |
2003-10-23 14:57 mmeineke |
852 |
+ |
|
853 |
+ |
* samples/metals/Makefile.in: added eam ForceField files to the |
854 |
+ |
init |
855 |
+ |
|
856 |
+ |
fixed an eam mpi parmeter setup bug |
857 |
+ |
|
858 |
+ |
added the init file to the makefile |
859 |
+ |
|
860 |
+ |
2003-10-23 14:57 mmeineke |
861 |
+ |
|
862 |
+ |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
863 |
+ |
to the init |
864 |
+ |
|
865 |
+ |
fixed an eam mpi parmeter setup bug |
866 |
+ |
|
867 |
+ |
2003-10-23 14:57 mmeineke |
868 |
+ |
|
869 |
+ |
* forceFields/Makefile.in: added eam ForceField files to the init |
870 |
+ |
|
871 |
+ |
2003-10-22 16:17 mmeineke |
872 |
+ |
|
873 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
874 |
+ |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
875 |
+ |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
876 |
+ |
no box skew allowed. |
877 |
+ |
|
878 |
+ |
2003-10-21 14:33 mmeineke |
879 |
+ |
|
880 |
+ |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
881 |
+ |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
882 |
+ |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
883 |
+ |
* useInitTime = false: sets the origin time to 0.0 regardless |
884 |
+ |
of the time stamp in the .init file * default=> useInitTime = |
885 |
+ |
true; |
886 |
+ |
|
887 |
+ |
2003-10-17 16:19 mmeineke |
888 |
+ |
|
889 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
890 |
+ |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
891 |
+ |
staticProps.cpp, obj/placeholder: added the staticProps directory |
892 |
+ |
to the build list for both configure and configure.in |
893 |
+ |
|
894 |
+ |
fixed a number of bugs in the staticProps code. gofr is now |
895 |
+ |
working. |
896 |
+ |
|
897 |
+ |
2003-10-17 16:18 mmeineke |
898 |
+ |
|
899 |
+ |
* ac-tools/configure.in: added the staticProps directory to the |
900 |
+ |
build list for both configure and configure.in |
901 |
+ |
|
902 |
+ |
2003-10-17 16:17 mmeineke |
903 |
+ |
|
904 |
+ |
* configure: added the staticProps directory to the build list |
905 |
+ |
|
906 |
+ |
2003-10-16 14:16 mmeineke |
907 |
+ |
|
908 |
+ |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
909 |
+ |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
910 |
+ |
use linked lists instead of a vector. |
911 |
+ |
|
912 |
+ |
Fixed the makefile to build DumpReader.cpp |
913 |
+ |
|
914 |
+ |
Removed a comment output in Exclude.cpp |
915 |
+ |
|
916 |
+ |
Modified DumpWriter and Integrator to write an eor file every time |
917 |
+ |
a frame is written. This lets the .eor file represent the last |
918 |
+ |
written frame of a simulation. |
919 |
+ |
|
920 |
+ |
2003-10-10 12:10 mmeineke |
921 |
+ |
|
922 |
+ |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
923 |
+ |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
924 |
+ |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
925 |
+ |
staticProps.cpp: removed the props directory, and moved everything |
926 |
+ |
over to staticProps |
927 |
+ |
|
928 |
+ |
2003-10-09 17:09 mmeineke |
929 |
+ |
|
930 |
+ |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
931 |
+ |
a position where it will compile and run first runs. |
932 |
+ |
|
933 |
+ |
2003-10-04 13:46 chuckv |
934 |
+ |
|
935 |
+ |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
936 |
+ |
samples/metals/Au.bass: Fixed bug in calc_eam. |
937 |
+ |
|
938 |
+ |
2003-10-04 13:08 chuckv |
939 |
+ |
|
940 |
+ |
* samples/metals/init_au.in: added Au init file for eam. |
941 |
+ |
|
942 |
+ |
2003-10-03 17:11 mmeineke |
943 |
+ |
|
944 |
+ |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
945 |
+ |
entahlpy from the statwriter and thermo. |
946 |
+ |
|
947 |
+ |
2003-10-03 17:02 mmeineke |
948 |
+ |
|
949 |
+ |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
950 |
+ |
statements in simError |
951 |
+ |
|
952 |
+ |
added a function to get the maxCutoff |
953 |
+ |
|
954 |
+ |
2003-10-03 17:01 mmeineke |
955 |
+ |
|
956 |
+ |
* libBASS/simError.c: changed the formating ogf the error |
957 |
+ |
statements in simError |
958 |
+ |
|
959 |
+ |
2003-09-30 11:00 mmeineke |
960 |
+ |
|
961 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
962 |
+ |
f90Flags so they are no longer overwritten by the compiler. |
963 |
+ |
|
964 |
+ |
2003-09-29 17:06 mmeineke |
965 |
+ |
|
966 |
+ |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
967 |
+ |
for conifig.in |
968 |
+ |
|
969 |
+ |
fixed wrappers to extern "C" |
970 |
+ |
|
971 |
+ |
2003-09-29 17:06 mmeineke |
972 |
+ |
|
973 |
+ |
* ac-tools/configure.in: added mpif90 mod check back same for |
974 |
+ |
conifig.in |
975 |
+ |
|
976 |
+ |
2003-09-29 17:05 mmeineke |
977 |
+ |
|
978 |
+ |
* configure: added mpif90 mod check back |
979 |
+ |
|
980 |
+ |
2003-09-29 16:16 mmeineke |
981 |
+ |
|
982 |
+ |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
983 |
+ |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
984 |
+ |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
985 |
+ |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
986 |
+ |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
987 |
+ |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
988 |
+ |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
989 |
+ |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
990 |
+ |
found with SUN's SUNWspro.s1s7 |
991 |
+ |
|
992 |
+ |
2003-09-29 12:38 mmeineke |
993 |
+ |
|
994 |
+ |
* libmdtools/GenericData.hpp: light change in syntax. no |
995 |
+ |
signifigant change. |
996 |
+ |
|
997 |
+ |
2003-09-25 16:17 mmeineke |
998 |
+ |
|
999 |
+ |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
1000 |
+ |
additional remarks from icc -w3 (extra verbose output) |
1001 |
+ |
|
1002 |
+ |
2003-09-25 14:27 mmeineke |
1003 |
+ |
|
1004 |
+ |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1005 |
+ |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
1006 |
+ |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
1007 |
+ |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
1008 |
+ |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
1009 |
+ |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
1010 |
+ |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1011 |
+ |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1012 |
+ |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
1013 |
+ |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
1014 |
+ |
gcc -Wall and g++ -Wall |
1015 |
+ |
|
1016 |
+ |
2003-09-25 13:54 gezelter |
1017 |
+ |
|
1018 |
+ |
* configure, ac-tools/configure.in: fixed a bug in configure |
1019 |
+ |
|
1020 |
+ |
2003-09-25 11:42 gezelter |
1021 |
+ |
|
1022 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1023 |
+ |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
1024 |
+ |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
1025 |
+ |
fixes for configure |
1026 |
+ |
|
1027 |
+ |
2003-09-24 14:34 mmeineke |
1028 |
+ |
|
1029 |
+ |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
1030 |
+ |
that it is called before the first Statistics are written. |
1031 |
+ |
|
1032 |
+ |
2003-09-23 15:36 gezelter |
1033 |
+ |
|
1034 |
+ |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
1035 |
+ |
bunch of Make.dep files to CVS |
1036 |
+ |
|
1037 |
+ |
2003-09-23 15:34 mmeineke |
1038 |
+ |
|
1039 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
1040 |
+ |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
1041 |
+ |
|
1042 |
+ |
Some small syntax cleaning in NPTfm and SimSetup |
1043 |
+ |
|
1044 |
+ |
2003-09-22 18:07 tim |
1045 |
+ |
|
1046 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1047 |
+ |
SimInfo.hpp: fix bug in calculating maxCutoff |
1048 |
+ |
|
1049 |
+ |
2003-09-22 16:23 mmeineke |
1050 |
+ |
|
1051 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
1052 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
1053 |
+ |
Converted NPTf to work with the NPT base class. |
1054 |
+ |
|
1055 |
+ |
Removed NPTfm and NPTim from cvs |
1056 |
+ |
|
1057 |
+ |
2003-09-19 15:00 mmeineke |
1058 |
+ |
|
1059 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1060 |
+ |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
1061 |
+ |
class. NPTi is up to date. NPTf is not. |
1062 |
+ |
|
1063 |
+ |
2003-09-19 11:03 mmeineke |
1064 |
+ |
|
1065 |
+ |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
1066 |
+ |
makefile |
1067 |
+ |
|
1068 |
+ |
2003-09-19 11:01 gezelter |
1069 |
+ |
|
1070 |
+ |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
1071 |
+ |
|
1072 |
+ |
2003-09-19 11:01 gezelter |
1073 |
+ |
|
1074 |
+ |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
1075 |
+ |
(nearly) conserved quantities for both NPTi and NPTf |
1076 |
+ |
|
1077 |
+ |
2003-09-19 10:20 mmeineke |
1078 |
+ |
|
1079 |
+ |
* utils/Makefile.in: fixed a typo in the makefile. |
1080 |
+ |
|
1081 |
+ |
2003-09-19 09:55 gezelter |
1082 |
+ |
|
1083 |
+ |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
1084 |
+ |
samples/water/ssd.bass: [no log message] |
1085 |
+ |
|
1086 |
+ |
2003-09-19 09:22 tim |
1087 |
+ |
|
1088 |
+ |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
1089 |
+ |
|
1090 |
+ |
2003-09-17 09:22 mmeineke |
1091 |
+ |
|
1092 |
+ |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
1093 |
+ |
work with constraints. |
1094 |
+ |
|
1095 |
+ |
2003-09-16 15:02 tim |
1096 |
+ |
|
1097 |
+ |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
1098 |
+ |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
1099 |
+ |
|
1100 |
+ |
fixed conserved quantity in NPT (Still some small bug) |
1101 |
+ |
|
1102 |
+ |
NPTi appears very stable. |
1103 |
+ |
|
1104 |
+ |
2003-09-15 11:52 tim |
1105 |
+ |
|
1106 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
1107 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
1108 |
+ |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
1109 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1110 |
+ |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
1111 |
+ |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
1112 |
+ |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
1113 |
+ |
statWriter fix bug of vector wrapping at NPTi |
1114 |
+ |
|
1115 |
+ |
2003-09-12 11:20 gezelter |
1116 |
+ |
|
1117 |
+ |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
1118 |
+ |
Makefile.in |
1119 |
+ |
|
1120 |
+ |
2003-09-12 11:20 gezelter |
1121 |
+ |
|
1122 |
+ |
* ChangeLog: Entered changes for configure into ChangeLog |
1123 |
+ |
|
1124 |
|
2003-09-09 15:35 mmeineke |
1125 |
|
|
1126 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
1194 |
|
* ChangeLog, libmdtools/GenericData.cpp, |
1195 |
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
1196 |
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
86 |
– |
|
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. |
1197 |
|
|
1198 |
|
2003-08-27 14:23 tim |
1199 |
|
|
1465 |
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
1466 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
1467 |
|
works..... |
363 |
– |
|
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) |
1468 |
|
|
1469 |
|
2003-08-08 12:48 mmeineke |
1470 |
|
|
1522 |
|
2003-07-29 11:32 mmeineke |
1523 |
|
|
1524 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
1525 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
1526 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
429 |
< |
src/Makefile: working on the props code |
1525 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
1526 |
> |
working on the props code |
1527 |
|
|
1528 |
|
2003-07-29 11:32 mmeineke |
1529 |
|
|
2650 |
|
|
2651 |
|
2003-03-25 09:29 mmeineke |
2652 |
|
|
2653 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
2653 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
2654 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
2655 |
|
|
2656 |
|
2003-03-25 09:29 mmeineke |
2660 |
|
|
2661 |
|
2003-03-24 20:07 gezelter |
2662 |
|
|
2663 |
< |
* samples/Makefile, tests/Makefile: moving tests to samples |
2663 |
> |
* samples/Makefile: moving tests to samples |
2664 |
|
|
2665 |
|
2003-03-24 20:06 gezelter |
2666 |
|
|
2667 |
< |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
2668 |
< |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
2669 |
< |
samples/argon/Makefile, samples/argon/argon.bass, |
2670 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
2671 |
< |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
2672 |
< |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
2673 |
< |
samples/lipid/water.mdl, samples/water/Makefile, |
1577 |
< |
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 |
2667 |
> |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
2668 |
> |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
2669 |
> |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
2670 |
> |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
2671 |
> |
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
2672 |
> |
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
2673 |
> |
samples |
2674 |
|
|
2675 |
|
2003-03-24 19:51 gezelter |
2676 |
|
|
2678 |
|
|
2679 |
|
2003-03-24 19:46 gezelter |
2680 |
|
|
2681 |
< |
* 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 |
2681 |
> |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
2682 |
|
|
2683 |
|
2003-03-24 16:55 gezelter |
2684 |
|
|
2695 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
2696 |
|
do_Forces.F90: little bug fixes here and there |
2697 |
|
|
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 |
– |
|
2698 |
|
2003-03-24 10:26 mmeineke |
2699 |
|
|
2700 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |