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2003-09-10 16:28 mmeineke |
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2004-05-26 11:41 gezelter |
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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/do_Forces.F90: Compacted all of the 8 copies of the |
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force loop into one. |
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2003-09-09 16:50 mmeineke |
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2004-05-24 17:24 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/: calc_eam.F90, calc_gb.F90: pressure tensor fixes |
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|
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2004-05-24 16:23 chrisfen |
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|
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* libmdtools/Restraints.cpp: Removed unnecessary variables and |
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changed error messages in Restraints.cpp |
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|
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2004-05-24 16:03 gezelter |
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|
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* libmdtools/: Thermo.cpp, calc_LJ_FF.F90, calc_charge_charge.F90, |
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calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
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calc_reaction_field.F90, calc_sticky_pair.F90, do_Forces.F90: Fixes |
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for stress / pressure tensor by cutoff group |
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|
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2004-05-22 15:55 chrisfen |
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|
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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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|
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2004-05-22 13:17 chrisfen |
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|
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* libBASS/: Globals.cpp, Globals.hpp: Added Bass keyword |
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useThermInt. |
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|
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2004-05-22 13:16 chrisfen |
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|
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* libmdtools/: Atom.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
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ForceFields.cpp, ForceFields.hpp, Integrator.cpp, Integrator.hpp, |
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Restraints.cpp, Restraints.hpp, RigidBody.cpp, RigidBody.hpp, |
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SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp, |
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StuntDouble.cpp, StuntDouble.hpp: Fixed Thermodynamic integration |
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code. |
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|
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2004-05-21 10:58 gezelter |
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|
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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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|
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2004-05-21 09:22 gezelter |
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|
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* configure, ac-tools/configure.in, forceFields/LJ.vdw, |
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forceFields/amber99.vdw, forceFields/charmm27.vdw, |
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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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|
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2004-05-20 15:27 chrisfen |
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|
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* libBASS/: Globals.cpp, Globals.hpp: Hopefully this commit |
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included the bass keywords |
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|
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2004-05-20 15:24 chrisfen |
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|
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* libmdtools/: ForceFields.cpp, ForceFields.hpp, Integrator.cpp, |
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Integrator.hpp, Makefile.in, ReadWrite.hpp, Restraints.cpp, |
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Restraints.hpp, SimInfo.hpp, SimSetup.cpp, StatWriter.cpp: Several |
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additions... Restraints.cpp and .hpp were included for restraining |
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particles in thermodynamic integration. By including these, |
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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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|
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2004-05-13 16:08 gezelter |
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|
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* libmdtools/: Integrator.cpp, do_Forces.F90: fixes for skip list |
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|
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2004-05-12 17:01 tim |
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|
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* samples/: argon/Makefile, argon/argonEM.bass, |
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argon/init_argon.eor, minimizer/argon/Makefile, |
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minimizer/argon/argonEM.bass, minimizer/argon/init_argon.eor, |
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minimizer/water/Makefile, minimizer/water/Makefile.in, |
81 |
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minimizer/water/WATER.frc, minimizer/water/init_ssd.eor, |
82 |
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minimizer/water/ssdEM.bass, minimizer/water/tip4p_two.bass, |
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minimizer/water/tip4p_two.init, minimizer/water/water.mdl: add |
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minimizer sample |
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|
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2004-05-12 16:54 gezelter |
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|
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* libmdtools/: Utility.cpp, Utility.hpp: fixes for MacOS X |
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compilation |
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|
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2004-05-12 15:54 gezelter |
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|
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* libmdtools/: RigidBody.cpp, RigidBody.hpp, SimSetup.cpp: Fixes |
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for compilation under Mac OS X with IBM's xl compilers |
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|
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2004-05-12 15:14 gezelter |
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|
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* src/: oopse.cpp, oose.cpp: Added a nifty neato banner |
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|
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2004-05-12 15:14 gezelter |
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|
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* libmdtools/LJFF.cpp: Removed an extraneous write |
103 |
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|
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2004-05-12 15:13 gezelter |
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|
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* libBASS/simError.h: Starting to change the error model |
107 |
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|
108 |
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2004-05-12 14:45 gezelter |
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|
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* utils/Dump2XYZ.cpp: const char* fix |
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|
112 |
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2004-05-12 14:44 gezelter |
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|
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* libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
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src/oopse.cpp, src/oose.cpp: MPI fixes and removal of extraneous |
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write statements |
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|
118 |
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2004-05-12 11:38 tim |
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|
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* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
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ForceFields.cpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
122 |
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SimSetup.cpp, SimState.cpp, SimState.hpp: get rid of rc and |
123 |
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massratio from simState, creat cutoff group forevery atom which |
124 |
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does not belong to cutoff group defined at mdl file |
125 |
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|
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2004-05-12 10:58 gezelter |
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|
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* libmdtools/: CutoffGroup.hpp, do_Forces.F90: efficiency fixes in |
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CutoffGroup |
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|
131 |
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2004-05-12 10:35 gezelter |
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|
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* samples/water/water.mdl: Added the cutoff Groups to the default |
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water.mdl file |
135 |
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|
136 |
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2004-05-12 10:02 tim |
137 |
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|
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* ChangeLog, libmdtools/CutoffGroup.hpp, libmdtools/SimInfo.cpp: |
139 |
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fixed a bug in CutoffGroup::getCOM() |
140 |
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|
141 |
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2004-05-12 09:29 gezelter |
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|
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* libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
144 |
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libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
145 |
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samples/water/ssd.bass: bug fixes for cutoffGroups |
146 |
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|
147 |
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2004-05-11 17:28 tim |
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|
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* utils/Vector3.hpp: adding generic Vector3 class |
150 |
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|
151 |
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2004-05-11 16:44 tim |
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|
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* libmdtools/Integrator.hpp: adding instantiation of |
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Integrator<BaseIntegrator> in order to make OOPSE compiled by icc8 |
155 |
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|
156 |
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2004-05-11 16:31 gezelter |
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|
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* libmdtools/: calc_LJ_FF.F90, calc_charge_charge.F90, |
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calc_dipole_dipole.F90, calc_gb.F90, calc_reaction_field.F90, |
160 |
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calc_sticky_pair.F90, do_Forces.F90, notifyCutoffs.F90: |
161 |
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Fortran-side changes for group-based cutoffs |
162 |
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|
163 |
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2004-05-11 16:20 tim |
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|
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* libmdtools/CutoffGroup.hpp: adding CutoffGroup.hpp |
166 |
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|
167 |
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2004-05-11 16:14 tim |
168 |
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|
169 |
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* libmdtools/: ForceFields.cpp, Make.dep, Molecule.cpp, |
170 |
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SimInfo.cpp: fix two bugs in siminfo which cause infinite loop; fix |
171 |
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anoter one in CutoffGroup which causes seg fault |
172 |
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|
173 |
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2004-05-11 15:33 tim |
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|
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* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
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libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
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libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp: adding cutoffGroup |
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into OOPSE |
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|
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2004-05-11 15:07 gezelter |
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|
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* libBASS/: BASS_parse.c, parse_tree.c: bugfix for cutoffGroup |
183 |
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|
184 |
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2004-05-11 11:00 gezelter |
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|
186 |
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* libmdtools/: Make.dep, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
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fortranWrapDefines.hpp, notifyCutoffs.F90: Fixes to libmdtools to |
188 |
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use the simplified cutoff stuff in the BASS library |
189 |
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|
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2004-05-10 23:21 gezelter |
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|
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* libBASS/: BASS_interface.cpp, BASS_interface.h, BASSyacc.y, |
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CutoffGroupStamp.cpp, CutoffGroupStamp.hpp, Globals.cpp, |
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Globals.hpp, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
195 |
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MoleculeStamp.cpp, MoleculeStamp.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 for adding CutoffGroups to molecules. |
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Also restructured the plethora of cutoff radii into one |
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cutoffRadius and one switchingRadius. Also removed the |
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useMolecularCutoffs keyword |
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|
202 |
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2004-05-10 15:28 tim |
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|
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* ChangeLog, libmdtools/DumpWriter.cpp, src/Makefile.in: optimize |
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DumpWriter |
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|
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2004-05-07 16:36 gezelter |
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|
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* libmdtools/: fSwitchingFunction.h, switch_module.F90: New module |
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for fortran group-based switching function |
211 |
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|
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2004-05-07 16:35 gezelter |
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|
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* libmdtools/: Atom.hpp, ForceFields.cpp, Integrator.cpp, |
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Makefile.in, SimInfo.cpp, SimState.cpp, SimState.hpp, |
216 |
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calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
217 |
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calc_eam.F90, calc_gb.F90, calc_sticky_pair.F90, do_Forces.F90, |
218 |
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force_globals.F90, fortranWrapDefines.hpp, mpiComponentPlan.h, |
219 |
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mpiSimulation_module.F90, neighborLists.F90, notifyCutoffs.F90, |
220 |
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simulation_module.F90: Many changes to get group-based cutoffs to |
221 |
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work |
222 |
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|
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2004-05-01 13:52 tim |
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|
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* ChangeLog, libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
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libmdtools/OOPSEMinimizer.cpp, libmdtools/SimInfo.cpp, |
227 |
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libmdtools/SimInfo.hpp, libmdtools/calc_charge_charge.F90, |
228 |
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libmdtools/do_Forces.F90, libmdtools/fSimulation.h, |
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libmdtools/fortranWrapDefines.hpp, |
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libmdtools/simulation_module.F90: C++ pass groupList to fortran |
231 |
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|
232 |
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2004-04-29 11:03 tim |
233 |
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|
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* ChangeLog, libmdtools/calc_charge_charge.F90: fixed two bugs in |
235 |
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calc_charge_charge when using molecular cutoff |
236 |
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|
237 |
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2004-04-28 21:11 tim |
238 |
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|
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* libmdtools/: ForceFields.cpp, fortranWrapDefines.hpp: fix an |
240 |
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unmatched c/fortran interface |
241 |
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|
242 |
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2004-04-28 18:09 tim |
243 |
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|
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* ChangeLog, libmdtools/Integrator.hpp, libmdtools/ZConstraint.cpp: |
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keep the previous position of cantilever in SMD |
246 |
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|
247 |
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2004-04-28 17:34 tim |
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|
249 |
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* ChangeLog, libmdtools/Molecule.cpp, libmdtools/Molecule.hpp, |
250 |
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libmdtools/OtherVisitor.cpp, libmdtools/ZconsVisitor.cpp: fix a bug |
251 |
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in Molecule.cpp which initialize massRatio before creat the array. |
252 |
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fix two bugs in ZconsVisitor |
253 |
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|
254 |
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2004-04-28 17:06 gezelter |
255 |
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|
256 |
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* libmdtools/: MatVec3.h, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
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Adding molecular cutoffs |
258 |
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|
259 |
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2004-04-28 16:39 gezelter |
260 |
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|
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* libmdtools/: calc_charge_charge.F90, do_Forces.F90, |
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fSimulation.h, force_globals.F90, simulation_module.F90: work on |
263 |
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molecular cutoffs |
264 |
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|
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2004-04-28 16:39 gezelter |
266 |
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|
267 |
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* libBASS/: Globals.cpp, Globals.hpp: useMolecularCutoffs added to |
268 |
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Globals |
269 |
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|
270 |
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2004-04-27 11:26 tim |
271 |
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|
272 |
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* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp, |
273 |
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ForceFields.cpp, Molecule.cpp, SimState.cpp, SimState.hpp, |
274 |
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fSimulation.h, fortranWrapDefines.hpp: add center of mass of the |
275 |
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molecule and massRation into atom class |
276 |
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|
277 |
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2004-04-26 16:16 mmeineke |
278 |
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|
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* libBASS/Globals.cpp: modified the defaults for the system init |
280 |
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time and system init state. |
281 |
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|
282 |
> |
2004-04-26 09:29 gezelter |
283 |
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|
284 |
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* libmdtools/: Thermo.cpp, calc_charge_charge.F90: Fixed a bug in |
285 |
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calc_charge_charge.F90 |
286 |
> |
|
287 |
> |
2004-04-23 23:31 tim |
288 |
> |
|
289 |
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* ChangeLog, libmdtools/AtomVisitor.cpp, |
290 |
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libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: add |
291 |
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reaction field correction to charge-charge interaction |
292 |
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|
293 |
> |
2004-04-22 16:33 tim |
294 |
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|
295 |
> |
* libmdtools/: InitializeFromFile.cpp, SimInfo.cpp, SimInfo.hpp, |
296 |
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Thermo.cpp, calc_charge_charge.F90, do_Forces.F90: change the |
297 |
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calculation of pressure tensor |
298 |
> |
|
299 |
> |
2004-04-22 09:55 tim |
300 |
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|
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* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp: fixed |
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another bug in InitFromFile. MPI verion of OOPSE is working again |
303 |
> |
|
304 |
> |
2004-04-21 22:29 tim |
305 |
> |
|
306 |
> |
* libmdtools/: AtomVisitor.cpp, DumpReader.cpp, DumpWriter.cpp, |
307 |
> |
InitializeFromFile.cpp, NPT.cpp, NVT.cpp, OtherVisitor.cpp, |
308 |
> |
SimSetup.cpp, calc_charge_charge.F90, mpiSimulation.cpp: fixed two |
309 |
> |
bugs in MPI version of InitfromFile and one unmatch MPI command in |
310 |
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DumpWriter |
311 |
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|
312 |
> |
2004-04-21 00:32 tim |
313 |
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|
314 |
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* libmdtools/Functor.hpp, libmdtools/LinearCons.cpp, |
315 |
> |
libmdtools/LinearCons.hpp, utils/CmdlineZsub.c, |
316 |
> |
utils/CmdlineZsub.h, utils/zsub.cpp, utils/zsub.ggo: remove some |
317 |
> |
useless files |
318 |
> |
|
319 |
> |
2004-04-20 11:56 tim |
320 |
> |
|
321 |
> |
* libmdtools/: Integrator.cpp, NVT.cpp, OtherVisitor.cpp, |
322 |
> |
SimInfo.cpp, Thermo.cpp, Thermo.hpp: fixed getCOMVel and |
323 |
> |
velocitize at thermo |
324 |
> |
|
325 |
> |
2004-04-20 00:39 tim |
326 |
> |
|
327 |
> |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
328 |
> |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
329 |
> |
libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
330 |
> |
libmdtools/DirectionalAtom.hpp, libmdtools/GenericData.hpp, |
331 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
332 |
> |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
333 |
> |
utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, |
334 |
> |
utils/Dump2XYZCmd.h: DUMP2XYZ 0.99 version |
335 |
> |
|
336 |
> |
2004-04-19 17:13 gezelter |
337 |
> |
|
338 |
> |
* libmdtools/: Atom.cpp, Integrator.cpp, NVT.cpp, SimInfo.cpp, |
339 |
> |
Thermo.cpp: Fixed a charge bug |
340 |
> |
|
341 |
> |
2004-04-19 15:54 tim |
342 |
> |
|
343 |
> |
* libmdtools/CompositeVisitor.cpp, libmdtools/CompositeVisitor.hpp, |
344 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
345 |
> |
libmdtools/RigidBody.cpp, utils/Make.dep, utils/Makefile.in: fixed |
346 |
> |
a bug in CompositeVisitor which cause the double counting problem |
347 |
> |
|
348 |
> |
2004-04-19 12:44 tim |
349 |
> |
|
350 |
> |
* libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
351 |
> |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
352 |
> |
libmdtools/DumpReader.cpp, libmdtools/Make.dep, |
353 |
> |
libmdtools/OtherVisitor.cpp, libmdtools/RigidBodyVisitor.cpp, |
354 |
> |
libmdtools/ZconsVisitor.cpp, utils/Dump2XYZ.cpp, utils/Makefile.in: |
355 |
> |
Dump2XYZ is almost working except atoms in rigidbody are double |
356 |
> |
counted |
357 |
> |
|
358 |
> |
2004-04-18 22:52 tim |
359 |
> |
|
360 |
> |
* ChangeLog, libmdtools/Atom.cpp, libmdtools/Atom.hpp, |
361 |
> |
libmdtools/AtomVisitor.cpp, libmdtools/AtomVisitor.hpp, |
362 |
> |
libmdtools/BaseVisitor.hpp, libmdtools/CompositeVisitor.cpp, |
363 |
> |
libmdtools/CompositeVisitor.hpp, libmdtools/DumpReader.cpp, |
364 |
> |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
365 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
366 |
> |
libmdtools/MatVec3.h, libmdtools/OtherVisitor.cpp, |
367 |
> |
libmdtools/OtherVisitor.hpp, libmdtools/ReadWrite.hpp, |
368 |
> |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
369 |
> |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
370 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
371 |
> |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
372 |
> |
libmdtools/Thermo.cpp, libmdtools/ZConsReader.cpp, |
373 |
> |
libmdtools/ZConsReader.hpp, libmdtools/ZconsVisitor.cpp, |
374 |
> |
libmdtools/ZconsVisitor.hpp, utils/Dump2XYZ.cpp, |
375 |
> |
utils/Dump2XYZ.ggo, utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h: new |
376 |
> |
implement of quickLate using visitor and composite pattern |
377 |
> |
|
378 |
> |
2004-04-15 17:15 tim |
379 |
> |
|
380 |
> |
* libmdtools/SimSetup.cpp, utils/zsub.cpp: fix a bug in setting |
381 |
> |
exclude list |
382 |
> |
|
383 |
> |
2004-04-15 11:18 tim |
384 |
> |
|
385 |
> |
* ChangeLog, forceFields/DUFF.frc, libBASS/MoleculeStamp.cpp, |
386 |
> |
libmdtools/Atom.hpp, libmdtools/InitializeFromFile.cpp, |
387 |
> |
libmdtools/Integrator.cpp, libmdtools/Molecule.cpp, |
388 |
> |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
389 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
390 |
> |
libmdtools/Thermo.cpp, libmdtools/WATER.cpp, |
391 |
> |
libmdtools/calc_charge_charge.F90, libmdtools/do_Forces.F90: fix |
392 |
> |
whole bunch of bugs :-) |
393 |
> |
|
394 |
> |
2004-04-14 12:20 chrisfen |
395 |
> |
|
396 |
> |
* forceFields/WATER.frc: Added the WATER.frc force field |
397 |
> |
|
398 |
> |
2004-04-14 11:32 gezelter |
399 |
> |
|
400 |
> |
* libmdtools/Molecule.cpp: fixed for get_potential |
401 |
> |
|
402 |
> |
2004-04-14 10:37 tim |
403 |
> |
|
404 |
> |
* AUTHORS, ChangeLog, libmdtools/DumpWriter.cpp, |
405 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
406 |
> |
libmdtools/Integrator.hpp, libmdtools/Make.dep, |
407 |
> |
libmdtools/Molecule.hpp, libmdtools/OOPSEMinimizer.cpp, |
408 |
> |
libmdtools/ReadWrite.hpp, libmdtools/RigidBody.hpp, |
409 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
410 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
411 |
> |
libmdtools/StuntDouble.cpp, libmdtools/StuntDouble.hpp, |
412 |
> |
libmdtools/ZConsReader.cpp, libmdtools/mpiSimulation.cpp, |
413 |
> |
libmdtools/mpiSimulation.hpp, utils/quickLate.c, utils/zsub.cpp: |
414 |
> |
Change DumpWriter and InitFromFile |
415 |
> |
|
416 |
> |
2004-04-13 11:26 gezelter |
417 |
> |
|
418 |
> |
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: Now |
419 |
> |
molecules can keep track of their own IntegrableObjects (and |
420 |
> |
RigidBodies). Also a bug-fix so that SimInfo can keep track of |
421 |
> |
RigidBodies (which was done incorrectly before). |
422 |
> |
|
423 |
> |
2004-04-13 11:25 gezelter |
424 |
> |
|
425 |
> |
* libBASS/: MoleculeStamp.cpp, MoleculeStamp.hpp: Added Integrable |
426 |
> |
(will back out momentarily) |
427 |
> |
|
428 |
> |
2004-04-13 10:10 gezelter |
429 |
> |
|
430 |
> |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Oops. |
431 |
> |
Those were old. |
432 |
> |
|
433 |
> |
2004-04-13 10:09 gezelter |
434 |
> |
|
435 |
> |
* libmdtools/: IntegrableObjects.cpp, IntegrableObjects.hpp: Forgot |
436 |
> |
to add IntegrableObjects |
437 |
> |
|
438 |
> |
2004-04-12 16:02 gezelter |
439 |
> |
|
440 |
> |
* libmdtools/: RigidBody.cpp, RigidBody.hpp: Adding RigidBody code |
441 |
> |
|
442 |
> |
2004-04-12 15:32 gezelter |
443 |
> |
|
444 |
> |
* samples/: alkane/butane.bass, water/ssd.bass: Slightly longer |
445 |
> |
test run |
446 |
> |
|
447 |
> |
2004-04-12 15:32 gezelter |
448 |
> |
|
449 |
> |
* libmdtools/: Atom.cpp, Atom.hpp, DUFF.cpp, DipoleTestFF.cpp, |
450 |
> |
DirectionalAtom.cpp, DirectionalAtom.hpp, DumpReader.cpp, |
451 |
> |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, Exclude.hpp, |
452 |
> |
ForceFields.cpp, ForceFields.hpp, InitializeFromFile.cpp, |
453 |
> |
Integrator.cpp, Integrator.hpp, LJFF.cpp, Make.dep, Makefile.in, |
454 |
> |
MatVec3.c, MatVec3.h, Molecule.cpp, Molecule.hpp, NPT.cpp, |
455 |
> |
NPTf.cpp, NPTxyz.cpp, NVT.cpp, OOPSEMinimizer.cpp, SRI.hpp, |
456 |
> |
SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SkipList.cpp, |
457 |
> |
SkipList.hpp, StuntDouble.cpp, StuntDouble.hpp, TraPPE_ExFF.cpp, |
458 |
> |
WATER.cpp, ZConsReader.cpp: Changes for RigidBody dynamics |
459 |
> |
(Somewhat extensive) |
460 |
> |
|
461 |
> |
2004-04-12 15:31 gezelter |
462 |
> |
|
463 |
> |
* libBASS/BASSyacc.y, libBASS/Globals.cpp, libBASS/MakeStamps.cpp, |
464 |
> |
libBASS/RigidBodyStamp.cpp, libBASS/RigidBodyStamp.hpp, |
465 |
> |
utils/sysbuilder/MoLocator.cpp, utils/sysbuilder/MoLocator.hpp: |
466 |
> |
Changes for RigidBody dynamics |
467 |
> |
|
468 |
> |
2004-03-17 09:22 tim |
469 |
> |
|
470 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/ZconStamp.cpp, |
471 |
> |
libBASS/ZconStamp.hpp, libmdtools/GenericData.hpp, |
472 |
> |
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
473 |
> |
libmdtools/ZConstraint.cpp: incorporate SMD into ZConstraint,it |
474 |
> |
does not sound a good choice, next commit will seperate SMD and |
475 |
> |
ZConstraint |
476 |
> |
|
477 |
> |
2004-03-16 14:22 tim |
478 |
> |
|
479 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
480 |
> |
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
481 |
> |
libmdtools/SimSetup.cpp, libmdtools/ZConsWriter.cpp, |
482 |
> |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp: ZConstraint |
483 |
> |
now can support sequential moving. Refactorying is needed to |
484 |
> |
support SMD in ZConstraint |
485 |
> |
|
486 |
> |
2004-03-02 15:32 tim |
487 |
> |
|
488 |
> |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, ReadWrite.hpp, |
489 |
> |
StatWriter.cpp, ZConsWriter.hpp: add LARGEFILE_SOURCE64 macro to |
490 |
> |
support large file |
491 |
> |
|
492 |
> |
2004-03-01 16:17 tim |
493 |
> |
|
494 |
> |
* utils/zsub.cpp: Fix a couple of bugs in zsub |
495 |
> |
|
496 |
> |
2004-03-01 15:01 tim |
497 |
> |
|
498 |
> |
* ChangeLog, libmdtools/DumpReader.cpp, libmdtools/Makefile.in, |
499 |
> |
libmdtools/OOPSEMinimizer.cpp, libmdtools/ReadWrite.hpp, |
500 |
> |
libmdtools/ZConsReader.cpp, libmdtools/ZConsReader.hpp, |
501 |
> |
utils/CmdlineZsub.c, utils/CmdlineZsub.h, utils/Makefile.in, |
502 |
> |
utils/quickLate.c, utils/zsub.cpp, utils/zsub.ggo: Adding zsub, a |
503 |
> |
program which can be used to replace atom type for zconstraint into |
504 |
> |
OOPSE |
505 |
> |
|
506 |
> |
2004-02-24 11:36 tim |
507 |
> |
|
508 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
509 |
> |
libmdtools/PRCG.cpp, libmdtools/SimSetup.cpp, src/oose.cpp: [no log |
510 |
> |
message] |
511 |
> |
|
512 |
> |
2004-02-24 10:49 tim |
513 |
> |
|
514 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
515 |
> |
Constraint.cpp, Constraint.hpp, ConstraintList.cpp, |
516 |
> |
ConstraintList.hpp, Minimizer.hpp, Minimizer1D.cpp, |
517 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, NLModel.hpp, NLModel0.cpp, |
518 |
> |
NLModel1.cpp, NonlinearCons.cpp, NonlinearCons.hpp, |
519 |
> |
OOPSEMinimizerBase.cpp, SteepestDescent.cpp, SteepestDescent.hpp, |
520 |
> |
SymMatrix.hpp: remove the old implement of minimizer from cvs tree |
521 |
> |
|
522 |
> |
2004-02-24 10:44 tim |
523 |
> |
|
524 |
> |
* libmdtools/: CGFamilyMinimizer.cpp, ConjugateMinimizer.cpp, |
525 |
> |
Integrator.hpp, Makefile.in, Minimizer1D.cpp, |
526 |
> |
MinimizerParameterSet.hpp, OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, |
527 |
> |
OOPSEMinimizerBase.cpp, PRCG.cpp, SDMinimizer.cpp, SimInfo.hpp, |
528 |
> |
SimSetup.cpp, Utility.cpp, Utility.hpp: Using inherit instead of |
529 |
> |
compose to implement Minimizer both versions are working |
530 |
> |
|
531 |
> |
2004-02-17 14:23 tim |
532 |
> |
|
533 |
> |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
534 |
> |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
535 |
> |
libmdtools/Minimizer1D.cpp, libmdtools/Minimizer1D.hpp, |
536 |
> |
libmdtools/MinimizerParameterSet.hpp, |
537 |
> |
libmdtools/OOPSEMinimizerBase.cpp: adding function shakeF in order |
538 |
> |
to remove the constraint force along bond direction |
539 |
> |
|
540 |
> |
2004-02-10 16:33 tim |
541 |
> |
|
542 |
> |
* ChangeLog, libmdtools/ConjugateMinimizer.cpp, |
543 |
> |
libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: |
544 |
> |
single version of energy minimization is working. |
545 |
> |
|
546 |
> |
2004-02-09 15:38 mmeineke |
547 |
> |
|
548 |
> |
* staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on |
549 |
> |
the massive memory overusage by OOPSE |
550 |
> |
|
551 |
> |
2004-02-09 09:48 chrisfen |
552 |
> |
|
553 |
> |
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the |
554 |
> |
hardwired LJ_rcut |
555 |
> |
|
556 |
> |
2004-02-06 19:14 tim |
557 |
> |
|
558 |
> |
* libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log |
559 |
> |
message] |
560 |
> |
|
561 |
> |
2004-02-06 16:37 tim |
562 |
> |
|
563 |
> |
* ChangeLog, libBASS/Globals.cpp, |
564 |
> |
libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, |
565 |
> |
libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, |
566 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of |
567 |
> |
energy minimization for argon is working, need to add constraint |
568 |
> |
|
569 |
> |
2004-02-06 14:05 tim |
570 |
> |
|
571 |
> |
* libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add |
572 |
> |
one more file into Makefile.in |
573 |
> |
|
574 |
> |
2004-02-06 13:58 tim |
575 |
> |
|
576 |
> |
* ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, |
577 |
> |
libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, |
578 |
> |
libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, |
579 |
> |
libmdtools/Integrator.hpp, libmdtools/Makefile.in, |
580 |
> |
libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, |
581 |
> |
libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, |
582 |
> |
libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, |
583 |
> |
libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, |
584 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
585 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add |
586 |
> |
some lines into global.cpp to make it work with energy minimization |
587 |
> |
|
588 |
> |
2004-02-04 17:26 tim |
589 |
> |
|
590 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
591 |
> |
Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, |
592 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, |
593 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) |
594 |
> |
Single version of conjugate gradient with golden search linesearch |
595 |
> |
pass a couple of functions test. Brent's algorithm is still broken |
596 |
> |
|
597 |
> |
2004-02-03 17:54 tim |
598 |
> |
|
599 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, |
600 |
> |
Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, |
601 |
> |
NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, |
602 |
> |
SteepestDescent.hpp: NLModel0, NLModel1 pass uit test |
603 |
> |
|
604 |
> |
2004-02-03 15:47 tim |
605 |
> |
|
606 |
> |
* libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, |
607 |
> |
ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, |
608 |
> |
NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, |
609 |
> |
SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, |
610 |
> |
SteepestDescent.hpp: [no log message] |
611 |
> |
|
612 |
> |
2004-02-03 15:43 tim |
613 |
> |
|
614 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, |
615 |
> |
Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, |
616 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
617 |
> |
NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory |
618 |
> |
constraint class |
619 |
> |
|
620 |
> |
2004-02-03 12:10 tim |
621 |
> |
|
622 |
> |
* libmdtools/Functor.hpp: Functor.hpp pass unit test |
623 |
> |
|
624 |
> |
2004-02-03 10:21 tim |
625 |
> |
|
626 |
> |
* ChangeLog, libmdtools/Minimizer1D.cpp, |
627 |
> |
libmdtools/Minimizer1D.hpp: begin unit test of minimizer |
628 |
> |
|
629 |
> |
2004-02-02 15:29 tim |
630 |
> |
|
631 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, |
632 |
> |
Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: |
633 |
> |
Adding GoldenSection and Brent LineSearch Method |
634 |
> |
|
635 |
> |
2004-01-30 16:47 tim |
636 |
> |
|
637 |
> |
* libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, |
638 |
> |
MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, |
639 |
> |
NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from |
640 |
> |
MinimizerBase instead of a functor to do line seach |
641 |
> |
|
642 |
> |
2004-01-30 10:00 chrisfen |
643 |
> |
|
644 |
> |
* forceFields/Makefile.in, libmdtools/Atom.cpp, |
645 |
> |
libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, |
646 |
> |
libmdtools/Integrator.cpp, libmdtools/Makefile.in, |
647 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
648 |
> |
libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, |
649 |
> |
libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, |
650 |
> |
libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now |
651 |
> |
has a working WATER.cpp forcefield and parser. This involved |
652 |
> |
changes to WATER.cpp and ForceFields amoung other files. One |
653 |
> |
important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. |
654 |
> |
This will be removed on the next commit... |
655 |
> |
|
656 |
> |
2004-01-29 18:00 gezelter |
657 |
> |
|
658 |
> |
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
659 |
> |
libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
660 |
> |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, |
661 |
> |
libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, |
662 |
> |
libBASS/RigidBodyStamp.hpp, libBASS/interface.c, |
663 |
> |
libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, |
664 |
> |
libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, |
665 |
> |
libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: |
666 |
> |
member list fixes for rigid bodies |
667 |
> |
|
668 |
> |
2004-01-29 16:44 tim |
669 |
> |
|
670 |
> |
* libmdtools/MinimizerParameterSet.hpp: Adding |
671 |
> |
MinimizerParameterSet class. |
672 |
> |
|
673 |
> |
2004-01-28 17:44 tim |
674 |
> |
|
675 |
> |
* libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of |
676 |
> |
NLModel0 and NLModel1 |
677 |
> |
|
678 |
> |
2004-01-28 15:40 tim |
679 |
> |
|
680 |
> |
* libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision |
681 |
> |
of NLModel |
682 |
> |
|
683 |
> |
2004-01-27 15:34 gezelter |
684 |
> |
|
685 |
> |
* samples/water/: ssd.bass, water.mdl: Added point-charge models to |
686 |
> |
water.mdl file, updated ssd.bass to use new SSD name |
687 |
> |
|
688 |
> |
2004-01-27 15:34 gezelter |
689 |
> |
|
690 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
691 |
> |
MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody |
692 |
> |
stuff |
693 |
> |
|
694 |
> |
2004-01-27 14:39 gezelter |
695 |
> |
|
696 |
> |
* samples/water/ssd.bass: Longer run time to test SSD water in MPI |
697 |
> |
|
698 |
> |
2004-01-27 14:39 gezelter |
699 |
> |
|
700 |
> |
* samples/metals/Au.bass: Longer run time to test gold in MPI |
701 |
> |
|
702 |
> |
2004-01-27 14:38 gezelter |
703 |
> |
|
704 |
> |
* samples/: argon/argon.bass, minimizer/argon/argon.bass: Longer |
705 |
> |
run time to test argon |
706 |
> |
|
707 |
> |
2004-01-27 14:38 gezelter |
708 |
> |
|
709 |
> |
* libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS |
710 |
> |
changes to do new rigidBody scheme a copy of WATER.cpp from this |
711 |
> |
morning |
712 |
> |
|
713 |
> |
2004-01-27 14:37 gezelter |
714 |
> |
|
715 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
716 |
> |
BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, |
717 |
> |
MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, |
718 |
> |
MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, |
719 |
> |
interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, |
720 |
> |
node_list.h, parse_interface.h, parse_tree.c: More BASS changes to |
721 |
> |
do new rigidBody scheme |
722 |
> |
|
723 |
> |
2004-01-27 14:15 tim |
724 |
> |
|
725 |
> |
* libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, |
726 |
> |
Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, |
727 |
> |
MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of |
728 |
> |
constraint for Nonlinear Optimization Model |
729 |
> |
|
730 |
> |
2004-01-26 17:01 gezelter |
731 |
> |
|
732 |
> |
* utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use |
733 |
> |
Euler angles for orientation instead of unit vectors required |
734 |
> |
changes in MoLocator |
735 |
> |
|
736 |
> |
2004-01-26 16:53 gezelter |
737 |
> |
|
738 |
> |
* samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, |
739 |
> |
beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, |
740 |
> |
water/water.mdl: Changed orientation lines from unit vectors to |
741 |
> |
euler angles |
742 |
> |
|
743 |
> |
2004-01-26 16:52 gezelter |
744 |
> |
|
745 |
> |
* libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians |
746 |
> |
|
747 |
> |
2004-01-26 16:45 gezelter |
748 |
> |
|
749 |
> |
* libmdtools/SimSetup.cpp: Changed default orientation in BASS to |
750 |
> |
use Euler angles in the following order: phi, theta, psi Removed |
751 |
> |
the ability to set orientation using a unit vector |
752 |
> |
|
753 |
> |
2004-01-26 16:26 gezelter |
754 |
> |
|
755 |
> |
* libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, |
756 |
> |
RigidBodyStamp.hpp: Changed default orientation in BASS to use |
757 |
> |
Euler angles in the following order: phi, theta, psi Removed the |
758 |
> |
ability to set orientation using a unit vector |
759 |
> |
|
760 |
> |
2004-01-26 13:52 gezelter |
761 |
> |
|
762 |
> |
* libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, |
763 |
> |
MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies |
764 |
> |
|
765 |
> |
2004-01-22 12:34 chrisfen |
766 |
> |
|
767 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, |
768 |
> |
TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: |
769 |
> |
Corrected spelling in several directories, and stated WATER.cpp |
770 |
> |
|
771 |
> |
2004-01-21 17:16 tim |
772 |
> |
|
773 |
> |
* libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, |
774 |
> |
NLOPModel.hpp: constraint class in energy minimization |
775 |
> |
|
776 |
> |
2004-01-20 15:34 tim |
777 |
> |
|
778 |
> |
* libmdtools/MinimizerBase.hpp: Adding energy minimization |
779 |
> |
|
780 |
> |
2004-01-20 15:32 tim |
781 |
> |
|
782 |
> |
* libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, |
783 |
> |
NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer |
784 |
> |
|
785 |
> |
2004-01-19 16:17 gezelter |
786 |
> |
|
787 |
> |
* libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages |
788 |
> |
more user-friendly |
789 |
> |
|
790 |
> |
2004-01-19 13:51 chrisfen |
791 |
> |
|
792 |
> |
* forceFields/DUFF.frc: Updated the default water to SSD/E |
793 |
> |
|
794 |
> |
2004-01-19 13:36 tim |
795 |
> |
|
796 |
> |
* libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample |
797 |
> |
time, status time, thermal time and reset time are not divisible by |
798 |
> |
dt |
799 |
> |
|
800 |
> |
2004-01-19 11:10 gezelter |
801 |
> |
|
802 |
> |
* third-party/Makefile.in: Added a bunch of dummy targets so make |
803 |
> |
won't complain |
804 |
> |
|
805 |
> |
2004-01-19 11:10 gezelter |
806 |
> |
|
807 |
> |
* samples/lipid/5x5.bass: Fixed old bass file |
808 |
> |
|
809 |
> |
2004-01-19 11:09 gezelter |
810 |
> |
|
811 |
> |
* libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies |
812 |
> |
required a change in how the MoleculeStamps are used by divideLabor |
813 |
> |
in mpiSimulation.cpp |
814 |
> |
|
815 |
> |
2004-01-19 11:08 gezelter |
816 |
> |
|
817 |
> |
* libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, |
818 |
> |
BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, |
819 |
> |
MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, |
820 |
> |
RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, |
821 |
> |
make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, |
822 |
> |
parse_tree.c: BASS changes to add RigidBodies and LJrcut |
823 |
> |
|
824 |
> |
2004-01-16 16:55 tim |
825 |
> |
|
826 |
> |
* libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating |
827 |
> |
eor file |
828 |
> |
|
829 |
> |
2004-01-16 16:51 mmeineke |
830 |
> |
|
831 |
> |
* libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could |
832 |
> |
write eor files |
833 |
> |
|
834 |
> |
2004-01-16 10:01 mmeineke |
835 |
> |
|
836 |
> |
* libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi |
837 |
> |
initialization of the AtomStruct |
838 |
> |
|
839 |
> |
2004-01-15 16:57 chuckv |
840 |
> |
|
841 |
> |
* configure, libmdtools/DumpWriter.cpp: Fixes for Dumps |
842 |
> |
|
843 |
> |
2004-01-15 10:51 gezelter |
844 |
> |
|
845 |
> |
* ac-tools/aclocal.m4: Changes for altivec |
846 |
> |
|
847 |
> |
2004-01-15 09:22 gezelter |
848 |
> |
|
849 |
> |
* libmdtools/DumpWriter.cpp: Documented the Spud Toss |
850 |
> |
|
851 |
> |
2004-01-14 23:33 gezelter |
852 |
> |
|
853 |
> |
* libmdtools/do_Forces.F90: changes for charge charge interactions |
854 |
> |
|
855 |
> |
2004-01-14 20:14 gezelter |
856 |
> |
|
857 |
> |
* libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, |
858 |
> |
notifyCutoffs.F90: More work for adding charges |
859 |
> |
|
860 |
> |
2004-01-14 17:41 gezelter |
861 |
> |
|
862 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
863 |
> |
src/Makefile.in: autoconf fixes |
864 |
> |
|
865 |
> |
2004-01-14 11:28 mmeineke |
866 |
> |
|
867 |
> |
* utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug |
868 |
> |
|
869 |
> |
2004-01-14 10:48 gezelter |
870 |
> |
|
871 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
872 |
> |
src/Makefile.in, third-party/Makefile.in: autoconf compatibility |
873 |
> |
changes for icc8 |
874 |
> |
|
875 |
> |
2004-01-13 18:01 gezelter |
876 |
> |
|
877 |
> |
* libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, |
878 |
> |
SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, |
879 |
> |
fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: |
880 |
> |
Changes for adding direct charge-charge interactions (with |
881 |
> |
switching function) |
882 |
> |
|
883 |
> |
2004-01-13 17:34 gezelter |
884 |
> |
|
885 |
> |
* libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, |
886 |
> |
oopseMPI_module.F90: Some changes for new MPI organization and |
887 |
> |
direct charge-charge interactions |
888 |
> |
|
889 |
> |
2004-01-13 17:11 tim |
890 |
> |
|
891 |
> |
* Functor.hpp, libmdtools/Functor.hpp: [no log message] |
892 |
> |
|
893 |
> |
2004-01-13 16:22 tim |
894 |
> |
|
895 |
> |
* Functor.hpp, samples/water/ssd.bass: Energy Minimization method |
896 |
> |
|
897 |
> |
2004-01-13 15:35 tim |
898 |
> |
|
899 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the |
900 |
> |
eor file whenever it is used instead of rewinding it |
901 |
> |
|
902 |
> |
2004-01-13 15:04 tim |
903 |
> |
|
904 |
> |
* libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface |
905 |
> |
of writeFrame |
906 |
> |
|
907 |
> |
2004-01-13 10:46 tim |
908 |
> |
|
909 |
> |
* libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: |
910 |
> |
Merge the code of writeFinal and writeDump; |
911 |
> |
Adding sortingIndex into DumpWriter; |
912 |
> |
Fix a bug of writing last frame twice in integrator |
913 |
> |
|
914 |
> |
2004-01-12 17:54 tim |
915 |
> |
|
916 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix |
917 |
> |
a bug in copying string |
918 |
> |
|
919 |
> |
2004-01-12 15:37 tim |
920 |
> |
|
921 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, |
922 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: |
923 |
> |
Dumpwriter only write out the atoms on master nodes |
924 |
> |
|
925 |
> |
2004-01-10 04:46 tim |
926 |
> |
|
927 |
> |
* ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just |
928 |
> |
roll it back fix a bug of copying string to a pointer Still have |
929 |
> |
Seg fault, it looks like a random MPI seg fault in totalview |
930 |
> |
|
931 |
> |
2004-01-09 21:15 tim |
932 |
> |
|
933 |
> |
* libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub |
934 |
> |
|
935 |
> |
2004-01-09 15:29 gezelter |
936 |
> |
|
937 |
> |
* libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) |
938 |
> |
|
939 |
> |
2004-01-08 17:25 chuckv |
940 |
> |
|
941 |
> |
* libmdtools/DumpWriter.cpp: A work in progress... |
942 |
> |
|
943 |
> |
2004-01-08 13:59 gezelter |
944 |
> |
|
945 |
> |
* libmdtools/DumpWriter.cpp: null terminate some strings just in |
946 |
> |
case |
947 |
> |
|
948 |
> |
2004-01-08 13:13 mmeineke |
949 |
> |
|
950 |
> |
* libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS |
951 |
> |
state bug. |
952 |
> |
|
953 |
> |
2004-01-08 13:05 gezelter |
954 |
> |
|
955 |
> |
* libmdtools/DumpWriter.cpp: added strncpy to DumpWriter |
956 |
> |
|
957 |
> |
2004-01-08 12:57 mmeineke |
958 |
> |
|
959 |
> |
* libmdtools/InitializeFromFile.cpp: fixed the restart from NVT |
960 |
> |
exstended state bug |
961 |
> |
|
962 |
> |
2004-01-08 12:40 gezelter |
963 |
> |
|
964 |
> |
* libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter |
965 |
> |
|
966 |
> |
2004-01-08 10:44 mmeineke |
967 |
> |
|
968 |
> |
* libmdtools/InitializeFromFile.cpp: added support for the ignore |
969 |
> |
XS state info flag |
970 |
> |
|
971 |
> |
2004-01-07 14:26 tim |
972 |
> |
|
973 |
> |
* libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, |
974 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass, |
975 |
> |
samples/water/ssd.bass: Fixed a bug of sending message from master |
976 |
> |
node to itself in DumpWriter.cpp and InitializeFromFile.cpp |
977 |
> |
|
978 |
> |
2004-01-06 14:49 chuckv |
979 |
> |
|
980 |
> |
* libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: |
981 |
> |
performance fixes in the dipole dipole and reaction field code |
982 |
> |
|
983 |
> |
2004-01-06 13:54 chuckv |
984 |
> |
|
985 |
> |
* libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a |
986 |
> |
little more sane |
987 |
> |
|
988 |
> |
2004-01-05 17:49 chuckv |
989 |
> |
|
990 |
> |
* libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, |
991 |
> |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
992 |
> |
calc_sticky_pair.F90, do_Forces.F90: Attempting to increase |
993 |
> |
performance by reducing spurious function calls |
994 |
> |
|
995 |
> |
2004-01-05 17:18 chuckv |
996 |
> |
|
997 |
> |
* libmdtools/do_Forces.F90: mangling forces even further |
998 |
> |
|
999 |
> |
2004-01-05 17:18 chuckv |
1000 |
> |
|
1001 |
> |
* configure, ac-tools/configure.in: mpich mucking |
1002 |
> |
|
1003 |
> |
2004-01-05 17:12 chuckv |
1004 |
> |
|
1005 |
> |
* libmdtools/do_Forces.F90: mangled do_forces... |
1006 |
> |
|
1007 |
> |
2004-01-05 16:00 chuckv |
1008 |
> |
|
1009 |
> |
* ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, |
1010 |
> |
libmdtools/do_Forces.F90: Added bitmask to do_forces property |
1011 |
> |
lookup |
1012 |
> |
|
1013 |
> |
2003-12-29 14:56 chuckv |
1014 |
> |
|
1015 |
> |
* samples/metals/Au.bass, third-party/mt19937ar.c: Added |
1016 |
> |
third-party directory for code not written by us. Also added |
1017 |
> |
Mersenne Twister random number generator code. This will eventually |
1018 |
> |
replace sprng as the random number generator used by OOPSE. |
1019 |
> |
|
1020 |
> |
2003-12-22 16:26 chuckv |
1021 |
> |
|
1022 |
> |
* libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
1023 |
> |
libmdtools/mdProfile.cpp, libmdtools/timing.F90, src/oopse.cpp: |
1024 |
> |
Fixes to profile code. |
1025 |
> |
|
1026 |
> |
2003-12-19 15:36 mmeineke |
1027 |
> |
|
1028 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp, |
1029 |
> |
timing.F90, timing.f90: More profiling fixes. |
1030 |
> |
|
1031 |
> |
2003-12-19 15:19 chuckv |
1032 |
> |
|
1033 |
> |
* libmdtools/timing.f90: Another change for MPI in timing. |
1034 |
> |
|
1035 |
> |
2003-12-19 15:17 chuckv |
1036 |
> |
|
1037 |
> |
* libmdtools/timing.f90: Small update to timing in MPI |
1038 |
> |
|
1039 |
> |
2003-12-19 13:53 mmeineke |
1040 |
> |
|
1041 |
> |
* libmdtools/mdProfile.cpp, src/oopse.cpp, src/oose.cpp: the |
1042 |
> |
profiling commands work now. Will start adding PROFILE ifdefs into |
1043 |
> |
the code |
1044 |
> |
|
1045 |
> |
2003-12-19 12:25 mmeineke |
1046 |
> |
|
1047 |
> |
* libmdtools/: Makefile.in, do_Forces.F90, mdProfile.cpp: added |
1048 |
> |
some profiling routines |
1049 |
> |
|
1050 |
> |
2003-12-19 10:12 mmeineke |
1051 |
> |
|
1052 |
> |
* utils/sysbuilder/randomBilayer.cpp: working on adding GofRtheta |
1053 |
> |
and GofRomega |
1054 |
|
|
1055 |
< |
added identification of identI in matchI. |
1055 |
> |
additional work on randomBilayer |
1056 |
> |
|
1057 |
> |
2003-12-19 10:12 mmeineke |
1058 |
> |
|
1059 |
> |
* staticProps/: AllCorr.cpp, GofRomega.cpp, GofRtheta.cpp, |
1060 |
> |
PairCorrList.hpp, staticProps.cpp: working on adding GofRtheta and |
1061 |
> |
GofRomega |
1062 |
> |
|
1063 |
> |
2003-12-18 16:47 mmeineke |
1064 |
> |
|
1065 |
> |
* libmdtools/: Makefile.in, mdProfile.cpp, mdProfile.hpp: added |
1066 |
> |
some profile functionality |
1067 |
> |
|
1068 |
> |
2003-12-18 15:46 chuckv |
1069 |
> |
|
1070 |
> |
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90, timing.f90: |
1071 |
> |
Added functions for simple profiling in fortran. |
1072 |
> |
|
1073 |
> |
2003-12-17 15:13 chuckv |
1074 |
> |
|
1075 |
> |
* libmdtools/calc_eam.F90, libmdtools/mpiSimulation_module.F90, |
1076 |
> |
samples/metals/init_au.in: Fixed bug in parallel EAM. rho_row and |
1077 |
> |
rho_col were scattered into the same array. Unfortunately, MPI |
1078 |
> |
zeros the array between scatters so half of the sum was being lost. |
1079 |
> |
Fixed by added a temp array for column scatter, then sum loop over |
1080 |
> |
nlocal. |
1081 |
> |
|
1082 |
> |
2003-12-16 15:49 mmeineke |
1083 |
> |
|
1084 |
> |
* staticProps/: GofRomega.cpp, GofRtheta.cpp, Makefile.in, |
1085 |
> |
PairCorrType.cpp, PairCorrType.hpp: finished gofRtheta and added |
1086 |
> |
gofRomega. both need to be debugged and tested. |
1087 |
> |
|
1088 |
> |
2003-12-12 10:42 gezelter |
1089 |
> |
|
1090 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1091 |
> |
libmdtools/Atom.hpp, libmdtools/DirectionalAtom.cpp: Changes for |
1092 |
> |
gradients (to do minimizations) |
1093 |
> |
|
1094 |
> |
2003-12-12 10:33 mmeineke |
1095 |
> |
|
1096 |
> |
* utils/sysbuilder/randomBilayer.hpp: removed the randombilayer |
1097 |
> |
header |
1098 |
> |
|
1099 |
> |
2003-12-10 11:52 mmeineke |
1100 |
> |
|
1101 |
> |
* utils/sysbuilder/: Makefile.in, bilayerSys.cpp, bilayerSys.hpp, |
1102 |
> |
randomBilayer.cpp, randomBilayer.hpp: edited the makefile to add |
1103 |
> |
randomBilayer to the build. Also move the random bilayer builder |
1104 |
> |
from bilayerSys to randomBilayer |
1105 |
> |
|
1106 |
> |
2003-11-25 10:44 mmeineke |
1107 |
> |
|
1108 |
> |
* forceFields/: DUFF.frc, backup.DUFF.frc: backed up the old |
1109 |
> |
DUFF.frc to backup.DUFF.frc alte4red masses and epsilons of TB2 and |
1110 |
> |
TB3 in DUFF.frc |
1111 |
> |
|
1112 |
> |
2003-11-21 15:09 mmeineke |
1113 |
> |
|
1114 |
> |
* libmdtools/InitializeFromFile.cpp, libmdtools/SimInfo.cpp, |
1115 |
> |
utils/sysbuilder/latticeBilayer.cpp: added a more verbose error |
1116 |
> |
message in SimInfo. Added a more informative error message in |
1117 |
> |
InitializeFromFile |
1118 |
> |
|
1119 |
> |
2003-11-21 15:07 mmeineke |
1120 |
> |
|
1121 |
> |
* staticProps/: GofRtheta.cpp, PairCorrType.hpp: begun work on add |
1122 |
> |
ing in the GofR,CosTheta |
1123 |
> |
|
1124 |
> |
2003-11-21 14:31 chrisfen |
1125 |
> |
|
1126 |
> |
* libmdtools/: SimInfo.cpp, do_Forces.F90, neighborLists.F90: Fixed |
1127 |
> |
a bug in SimInfo ordering of radii |
1128 |
> |
|
1129 |
> |
2003-11-11 12:20 mmeineke |
1130 |
> |
|
1131 |
> |
* libmdtools/SimInfo.cpp: added a routine to SimInfo.cpp to inline |
1132 |
> |
a min function. |
1133 |
> |
|
1134 |
> |
2003-11-10 16:50 mmeineke |
1135 |
> |
|
1136 |
> |
* libmdtools/: EAM_FF.cpp, SimInfo.cpp, SimInfo.hpp, SimSetup.cpp: |
1137 |
> |
reordered the rcut/ecr/boxSize initialization |
1138 |
> |
|
1139 |
> |
removed the rcut/ecr shrink and grow algorithm. the simulation will |
1140 |
> |
now exit when it runs into rcut or ecr. |
1141 |
> |
|
1142 |
> |
2003-11-07 16:46 chuckv |
1143 |
> |
|
1144 |
> |
* libmdtools/: Makefile.in, mpiSimulation_module.F90, |
1145 |
> |
oopseMPI_module.F90: Added support for compiling fortran without |
1146 |
> |
use of mpich modules. We use mpif.h instead.: |
1147 |
> |
|
1148 |
> |
2003-11-07 12:09 mmeineke |
1149 |
> |
|
1150 |
> |
* libmdtools/: Integrator.hpp, NPT.cpp, NPTf.cpp, NPTi.cpp, |
1151 |
> |
NPTxyz.cpp: moved the velocity scale matrix calculation outside of |
1152 |
> |
the atom loop in the NPT family of integrators. |
1153 |
> |
|
1154 |
> |
2003-11-06 17:01 mmeineke |
1155 |
> |
|
1156 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/Make.dep, |
1157 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
1158 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1159 |
> |
libmdtools/SimSetup.cpp, utils/sysbuilder/Make.dep, |
1160 |
> |
utils/sysbuilder/latticeBilayer.cpp: added the following parameters |
1161 |
> |
to BASS: * useInitialExtendedSystemState * orthoBoxTolerance |
1162 |
> |
* useIntiTime => useInitialTime |
1163 |
> |
|
1164 |
> |
2003-11-06 14:24 mmeineke |
1165 |
> |
|
1166 |
> |
* libBASS/: BASS_parse.c, BASSlex.l, BASSyacc.y, interface.c, |
1167 |
> |
make_nodes.c, make_nodes.h, parse_interface.h, parse_tree.c, |
1168 |
> |
parse_tree.h: fixed the includes in the Make.dep |
1169 |
> |
|
1170 |
> |
2003-11-06 14:11 mmeineke |
1171 |
> |
|
1172 |
> |
* libmdtools/: Makefile.in, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1173 |
> |
NVT.cpp, SimInfo.cpp, Thermo.cpp: did a merge by hand from the |
1174 |
> |
new-templateless branch to the main trunk. |
1175 |
> |
|
1176 |
> |
bug Fixes include: * fixed the switching function from ortho to |
1177 |
> |
non-ortho box. !!!!! THis was responsible for all of the |
1178 |
> |
sudden deaths we saw. * some formating in the string when we |
1179 |
> |
write out the extended system state. * added NPT.cpp to the |
1180 |
> |
makefile.in |
1181 |
> |
|
1182 |
> |
2003-11-06 13:20 mmeineke |
1183 |
> |
|
1184 |
> |
* libmdtools/: Integrator.cpp, Makefile.in, NPT.cpp, NPTf.cpp, |
1185 |
> |
SimInfo.cpp, Thermo.cpp, do_Forces.F90: fixed the "Sudden Death" |
1186 |
> |
bug. The box was not switching between orthorhombic and |
1187 |
> |
non-orthorhombic wrapping correctly. we added a fabs() to |
1188 |
> |
the check.which should fix it. |
1189 |
> |
|
1190 |
> |
2003-11-05 14:16 mmeineke |
1191 |
> |
|
1192 |
> |
* libmdtools/AbstractClasses.hpp, libmdtools/DumpReader.cpp, |
1193 |
> |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
1194 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
1195 |
> |
libmdtools/Integrator.hpp, libmdtools/Make.dep, libmdtools/NPT.cpp, |
1196 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, |
1197 |
> |
libmdtools/NVT.cpp, libmdtools/SimInfo.hpp, |
1198 |
> |
libmdtools/SimSetup.cpp, samples/water/ssd.bass, src/Make.dep, |
1199 |
> |
utils/sysbuilder/Make.dep, utils/sysbuilder/latticeBilayer.cpp: |
1200 |
> |
some work on trying to find the compression bug |
1201 |
> |
|
1202 |
> |
2003-11-03 17:07 mmeineke |
1203 |
> |
|
1204 |
> |
* libmdtools/: DumpReader.cpp, GenericData.cpp, GenericData.hpp, |
1205 |
> |
InitializeFromFile.cpp, Integrator.hpp, Make.dep, NPT.cpp, |
1206 |
> |
NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
1207 |
> |
SimSetup.cpp, SimSetup.hpp: begun work on removing templates and |
1208 |
> |
most of standard template library from OOPSE. |
1209 |
> |
|
1210 |
> |
2003-10-31 16:06 mmeineke |
1211 |
> |
|
1212 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1213 |
> |
Makefile.in, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, NVT.cpp, |
1214 |
> |
SimSetup.cpp: started work on template removal. |
1215 |
> |
|
1216 |
> |
2003-10-31 13:28 mmeineke |
1217 |
> |
|
1218 |
> |
* libmdtools/: DumpReader.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp: |
1219 |
> |
added template stuff to the Maikefile template |
1220 |
> |
|
1221 |
> |
little changes to some printf format statements |
1222 |
> |
|
1223 |
> |
2003-10-31 13:28 mmeineke |
1224 |
> |
|
1225 |
> |
* libBASS/Makefile.in: added template stuff to the Maikefile |
1226 |
> |
template |
1227 |
> |
|
1228 |
> |
2003-10-30 13:59 gezelter |
1229 |
> |
|
1230 |
> |
* libmdtools/: SimInfo.cpp, SimInfo.hpp, SimSetup.cpp, |
1231 |
> |
do_Forces.F90, neighborLists.F90, notifyCutoffs.F90: bug fixes for |
1232 |
> |
rList problems |
1233 |
> |
|
1234 |
> |
2003-10-30 09:11 gezelter |
1235 |
> |
|
1236 |
> |
* libmdtools/neighborLists.F90: Fixed bug that size(q0) was being |
1237 |
> |
queried before q0 was allocated. |
1238 |
> |
|
1239 |
> |
2003-10-29 15:41 mmeineke |
1240 |
> |
|
1241 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, Integrator.hpp, |
1242 |
> |
SimInfo.cpp, SimSetup.cpp, calc_dipole_dipole.F90, |
1243 |
> |
calc_sticky_pair.F90, do_Forces.F90: fixed a stdlib.h include error |
1244 |
> |
in bass.l |
1245 |
> |
|
1246 |
> |
fixed a little bug in the first time step, regarding the setting of |
1247 |
> |
ecr and est in fortran |
1248 |
> |
|
1249 |
> |
2003-10-29 15:40 mmeineke |
1250 |
> |
|
1251 |
> |
* libBASS/BASSlex.l: fixed a stdlib.h include error |
1252 |
> |
|
1253 |
> |
2003-10-29 12:55 mmeineke |
1254 |
> |
|
1255 |
> |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1256 |
> |
SimInfo.hpp, SimSetup.cpp, do_Forces.F90: som efixes to the way |
1257 |
> |
rcut is setup, as well as additional debugging comments. |
1258 |
> |
|
1259 |
> |
2003-10-29 09:28 gezelter |
1260 |
> |
|
1261 |
> |
* configure, ac-tools/configure.in, libBASS/Makefile.in, |
1262 |
> |
libmdtools/Makefile.in, src/Makefile.in: C++ compatibility for |
1263 |
> |
templates |
1264 |
> |
|
1265 |
> |
2003-10-28 22:16 gezelter |
1266 |
> |
|
1267 |
> |
* src/Makefile.in: Refixed broken makefile |
1268 |
> |
|
1269 |
> |
2003-10-28 22:06 gezelter |
1270 |
> |
|
1271 |
> |
* configure, ac-tools/aclocal.m4, src/Makefile.in: compatibility |
1272 |
> |
fixes |
1273 |
> |
|
1274 |
> |
2003-10-28 19:19 tim |
1275 |
> |
|
1276 |
> |
* ChangeLog, libmdtools/AbstractClasses.hpp, |
1277 |
> |
libmdtools/DumpWriter.cpp, libmdtools/GenericData.hpp, |
1278 |
> |
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.cpp, |
1279 |
> |
libmdtools/Integrator.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
1280 |
> |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
1281 |
> |
libmdtools/ReadWrite.hpp, samples/argon/argon.bass, |
1282 |
> |
samples/minimizer/argon/argon.bass, samples/water/ssd.bass: add chi |
1283 |
> |
and eta to the comment line of dump file. |
1284 |
> |
|
1285 |
> |
2003-10-28 17:25 mmeineke |
1286 |
> |
|
1287 |
> |
* libmdtools/: ForceFields.hpp, SimInfo.hpp, |
1288 |
> |
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
1289 |
> |
mpiComponentPlan.h, mpiSimulation.hpp: did a complete overhaul of |
1290 |
> |
how c calls fortran. All function pointers and fortran calls are |
1291 |
> |
rigidly typecast now. |
1292 |
> |
|
1293 |
> |
2003-10-28 15:42 gezelter |
1294 |
> |
|
1295 |
> |
* staticProps/Makefile.in, utils/sysbuilder/Makefile.in: |
1296 |
> |
Portability fixes |
1297 |
> |
|
1298 |
> |
2003-10-28 15:09 gezelter |
1299 |
> |
|
1300 |
> |
* libmdtools/calc_LJ_FF.F90, libmdtools/do_Forces.F90, |
1301 |
> |
libmdtools/fForceField.h, libmdtools/mpiSimulation_module.F90, |
1302 |
> |
src/Makefile.in: Compatibility fixes |
1303 |
> |
|
1304 |
> |
2003-10-28 12:08 mmeineke |
1305 |
> |
|
1306 |
> |
* libmdtools/: AbstractClasses.hpp, Integrator.hpp, Makefile.in: |
1307 |
> |
started work on template removal |
1308 |
> |
|
1309 |
> |
2003-10-28 12:04 gezelter |
1310 |
> |
|
1311 |
> |
* libmdtools/: fortranWrappers.cpp, fortranWrappers.hpp: started |
1312 |
> |
trying to understand extern "C" stuff for pointers |
1313 |
> |
|
1314 |
> |
2003-10-28 11:20 gezelter |
1315 |
> |
|
1316 |
> |
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, |
1317 |
> |
ZConsWriter.cpp, ZConstraint.cpp: fixes for compatibility |
1318 |
> |
|
1319 |
> |
2003-10-28 11:03 gezelter |
1320 |
> |
|
1321 |
> |
* libmdtools/: Atom.hpp, BendExtensions.cpp, DUFF.cpp, |
1322 |
> |
DipoleTestFF.cpp, DirectionalAtom.cpp, DumpReader.cpp, |
1323 |
> |
DumpWriter.cpp, EAM_FF.cpp, Exclude.cpp, ForceFields.cpp, |
1324 |
> |
ForceFields.hpp, InitializeFromFile.cpp, Integrator.cpp, LJFF.cpp, |
1325 |
> |
Makefile.in, Molecule.cpp, NPT.cpp, NPTf.cpp, NPTi.cpp, NPTxyz.cpp, |
1326 |
> |
ReadWrite.hpp, SimInfo.cpp, SimSetup.cpp, SimState.cpp, |
1327 |
> |
StatWriter.cpp, Thermo.cpp, TraPPE_ExFF.cpp, ZConstraint.cpp, |
1328 |
> |
calc_LJ_FF.F90, do_Forces.F90, fortranWrappers.cpp, |
1329 |
> |
mpiSimulation.cpp, randomSPRNG.cpp: replace c++ header stuff with |
1330 |
> |
more portable c header stuff Also, mod file fixes and portability |
1331 |
> |
changes Some fortran changes will need to be reversed. |
1332 |
> |
|
1333 |
> |
2003-10-28 11:03 gezelter |
1334 |
> |
|
1335 |
> |
* libBASS/: AtomStamp.cpp, BASS_interface.cpp, Component.cpp, |
1336 |
> |
Globals.cpp, Globals.hpp, LinkedCommand.hpp, MakeStamps.hpp, |
1337 |
> |
Makefile.in, MoleculeStamp.cpp: replace c++ header stuff with more |
1338 |
> |
portable c header stuff Also, mod file fixes and portability |
1339 |
> |
changes |
1340 |
> |
|
1341 |
> |
2003-10-28 11:02 gezelter |
1342 |
> |
|
1343 |
> |
* configure, ac-tools/aclocal.m4: mod file fixes and portability |
1344 |
> |
stuff |
1345 |
> |
|
1346 |
> |
2003-10-27 18:00 gezelter |
1347 |
> |
|
1348 |
> |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1349 |
> |
ac-tools/configure.in, ac-tools/fortran90.m4, |
1350 |
> |
libmdtools/Makefile.in: Stuff for MOD support in other compilers |
1351 |
> |
|
1352 |
> |
2003-10-27 17:08 mmeineke |
1353 |
> |
|
1354 |
> |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1355 |
> |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, latticeBilayer.cpp: |
1356 |
> |
added routines for the sysbuilder to work with simSetup |
1357 |
> |
|
1358 |
> |
remved the QuickBass routines, and had all parsing go through |
1359 |
> |
SimSetup. LatticeBilayer is in complete working order now. |
1360 |
> |
|
1361 |
> |
2003-10-27 17:07 mmeineke |
1362 |
> |
|
1363 |
> |
* libmdtools/: SimInfo.hpp, SimSetup.cpp, SimSetup.hpp: added |
1364 |
> |
routines for the sysbuilder to work with simSetup |
1365 |
> |
|
1366 |
> |
2003-10-27 11:20 gezelter |
1367 |
> |
|
1368 |
> |
* configure, ac-tools/configure.in, samples/water/ssd.bass, |
1369 |
> |
utils/sysbuilder/sysBuild.cpp: fixes for configure, sysBuild |
1370 |
> |
|
1371 |
> |
2003-10-24 17:17 mmeineke |
1372 |
> |
|
1373 |
> |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
1374 |
> |
MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
1375 |
> |
latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
1376 |
> |
QuickBass, MoLocator, and latticeBuilder into a Builder Library |
1377 |
> |
overhauled latticeBilayer into its own program. Removed sysBuild |
1378 |
> |
from the Makefile |
1379 |
> |
|
1380 |
> |
2003-10-24 12:36 gezelter |
1381 |
> |
|
1382 |
> |
* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
1383 |
> |
latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
1384 |
> |
builder |
1385 |
> |
|
1386 |
> |
2003-10-24 12:35 gezelter |
1387 |
> |
|
1388 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
1389 |
> |
merge problem |
1390 |
> |
|
1391 |
> |
2003-10-23 14:57 mmeineke |
1392 |
> |
|
1393 |
> |
* samples/metals/Makefile.in: added eam ForceField files to the |
1394 |
> |
init |
1395 |
> |
|
1396 |
> |
fixed an eam mpi parmeter setup bug |
1397 |
> |
|
1398 |
> |
added the init file to the makefile |
1399 |
> |
|
1400 |
> |
2003-10-23 14:57 mmeineke |
1401 |
> |
|
1402 |
> |
* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
1403 |
> |
to the init |
1404 |
> |
|
1405 |
> |
fixed an eam mpi parmeter setup bug |
1406 |
> |
|
1407 |
> |
2003-10-23 14:57 mmeineke |
1408 |
> |
|
1409 |
> |
* forceFields/Makefile.in: added eam ForceField files to the init |
1410 |
> |
|
1411 |
> |
2003-10-22 16:17 mmeineke |
1412 |
> |
|
1413 |
> |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
1414 |
> |
NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
1415 |
> |
integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
1416 |
> |
no box skew allowed. |
1417 |
> |
|
1418 |
> |
2003-10-21 14:33 mmeineke |
1419 |
> |
|
1420 |
> |
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1421 |
> |
libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
1422 |
> |
staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
1423 |
> |
* useInitTime = false: sets the origin time to 0.0 regardless |
1424 |
> |
of the time stamp in the .init file * default=> useInitTime = |
1425 |
> |
true; |
1426 |
> |
|
1427 |
> |
2003-10-17 16:19 mmeineke |
1428 |
> |
|
1429 |
> |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
1430 |
> |
Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1431 |
> |
staticProps.cpp, obj/placeholder: added the staticProps directory |
1432 |
> |
to the build list for both configure and configure.in |
1433 |
> |
|
1434 |
> |
fixed a number of bugs in the staticProps code. gofr is now |
1435 |
> |
working. |
1436 |
> |
|
1437 |
> |
2003-10-17 16:18 mmeineke |
1438 |
> |
|
1439 |
> |
* ac-tools/configure.in: added the staticProps directory to the |
1440 |
> |
build list for both configure and configure.in |
1441 |
> |
|
1442 |
> |
2003-10-17 16:17 mmeineke |
1443 |
> |
|
1444 |
> |
* configure: added the staticProps directory to the build list |
1445 |
> |
|
1446 |
> |
2003-10-16 14:16 mmeineke |
1447 |
> |
|
1448 |
> |
* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
1449 |
> |
Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
1450 |
> |
use linked lists instead of a vector. |
1451 |
> |
|
1452 |
> |
Fixed the makefile to build DumpReader.cpp |
1453 |
> |
|
1454 |
> |
Removed a comment output in Exclude.cpp |
1455 |
> |
|
1456 |
> |
Modified DumpWriter and Integrator to write an eor file every time |
1457 |
> |
a frame is written. This lets the .eor file represent the last |
1458 |
> |
written frame of a simulation. |
1459 |
> |
|
1460 |
> |
2003-10-10 12:10 mmeineke |
1461 |
> |
|
1462 |
> |
* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, |
1463 |
> |
CorrWrap.hpp, GofR.cpp, Makefile.in, PairCorrList.cpp, |
1464 |
> |
PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
1465 |
> |
staticProps.cpp: removed the props directory, and moved everything |
1466 |
> |
over to staticProps |
1467 |
> |
|
1468 |
> |
2003-10-09 17:09 mmeineke |
1469 |
> |
|
1470 |
> |
* libmdtools/Atom.hpp: Contiuned work on staticProps. should be in |
1471 |
> |
a position where it will compile and run first runs. |
1472 |
> |
|
1473 |
> |
2003-10-04 13:46 chuckv |
1474 |
> |
|
1475 |
> |
* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
1476 |
> |
samples/metals/Au.bass: Fixed bug in calc_eam. |
1477 |
> |
|
1478 |
> |
2003-10-04 13:08 chuckv |
1479 |
> |
|
1480 |
> |
* samples/metals/init_au.in: added Au init file for eam. |
1481 |
> |
|
1482 |
> |
2003-10-03 17:11 mmeineke |
1483 |
> |
|
1484 |
> |
* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
1485 |
> |
entahlpy from the statwriter and thermo. |
1486 |
> |
|
1487 |
> |
2003-10-03 17:02 mmeineke |
1488 |
> |
|
1489 |
> |
* libmdtools/SimInfo.hpp: changed the formating ogf the error |
1490 |
> |
statements in simError |
1491 |
> |
|
1492 |
> |
added a function to get the maxCutoff |
1493 |
> |
|
1494 |
> |
2003-10-03 17:01 mmeineke |
1495 |
> |
|
1496 |
> |
* libBASS/simError.c: changed the formating ogf the error |
1497 |
> |
statements in simError |
1498 |
> |
|
1499 |
> |
2003-09-30 11:00 mmeineke |
1500 |
> |
|
1501 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
1502 |
> |
f90Flags so they are no longer overwritten by the compiler. |
1503 |
> |
|
1504 |
> |
2003-09-29 17:06 mmeineke |
1505 |
> |
|
1506 |
> |
* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
1507 |
> |
for conifig.in |
1508 |
> |
|
1509 |
> |
fixed wrappers to extern "C" |
1510 |
> |
|
1511 |
> |
2003-09-29 17:06 mmeineke |
1512 |
> |
|
1513 |
> |
* ac-tools/configure.in: added mpif90 mod check back same for |
1514 |
> |
conifig.in |
1515 |
> |
|
1516 |
> |
2003-09-29 17:05 mmeineke |
1517 |
> |
|
1518 |
> |
* configure: added mpif90 mod check back |
1519 |
> |
|
1520 |
> |
2003-09-29 16:16 mmeineke |
1521 |
> |
|
1522 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
1523 |
> |
libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
1524 |
> |
libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
1525 |
> |
libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
1526 |
> |
libBASS/ZconStamp.cpp, libBASS/simError.c, |
1527 |
> |
libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
1528 |
> |
libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
1529 |
> |
libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
1530 |
> |
found with SUN's SUNWspro.s1s7 |
1531 |
> |
|
1532 |
> |
2003-09-29 12:38 mmeineke |
1533 |
> |
|
1534 |
> |
* libmdtools/GenericData.hpp: light change in syntax. no |
1535 |
> |
signifigant change. |
1536 |
> |
|
1537 |
> |
2003-09-25 16:17 mmeineke |
1538 |
> |
|
1539 |
> |
* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
1540 |
> |
additional remarks from icc -w3 (extra verbose output) |
1541 |
> |
|
1542 |
> |
2003-09-25 14:27 mmeineke |
1543 |
> |
|
1544 |
> |
* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1545 |
> |
libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
1546 |
> |
libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
1547 |
> |
libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
1548 |
> |
libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
1549 |
> |
libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
1550 |
> |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1551 |
> |
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1552 |
> |
libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
1553 |
> |
libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
1554 |
> |
gcc -Wall and g++ -Wall |
1555 |
|
|
1556 |
+ |
2003-09-25 13:54 gezelter |
1557 |
+ |
|
1558 |
+ |
* configure, ac-tools/configure.in: fixed a bug in configure |
1559 |
+ |
|
1560 |
+ |
2003-09-25 11:42 gezelter |
1561 |
+ |
|
1562 |
+ |
* Makefile.in, configure, ac-tools/aclocal.m4, |
1563 |
+ |
ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
1564 |
+ |
src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
1565 |
+ |
fixes for configure |
1566 |
+ |
|
1567 |
+ |
2003-09-24 14:34 mmeineke |
1568 |
+ |
|
1569 |
+ |
* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
1570 |
+ |
that it is called before the first Statistics are written. |
1571 |
+ |
|
1572 |
+ |
2003-09-23 15:36 gezelter |
1573 |
+ |
|
1574 |
+ |
* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
1575 |
+ |
bunch of Make.dep files to CVS |
1576 |
+ |
|
1577 |
+ |
2003-09-23 15:34 mmeineke |
1578 |
+ |
|
1579 |
+ |
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
1580 |
+ |
SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
1581 |
+ |
|
1582 |
+ |
Some small syntax cleaning in NPTfm and SimSetup |
1583 |
+ |
|
1584 |
+ |
2003-09-22 18:07 tim |
1585 |
+ |
|
1586 |
+ |
* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
1587 |
+ |
SimInfo.hpp: fix bug in calculating maxCutoff |
1588 |
+ |
|
1589 |
+ |
2003-09-22 16:23 mmeineke |
1590 |
+ |
|
1591 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
1592 |
+ |
Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
1593 |
+ |
Converted NPTf to work with the NPT base class. |
1594 |
+ |
|
1595 |
+ |
Removed NPTfm and NPTim from cvs |
1596 |
+ |
|
1597 |
+ |
2003-09-19 15:00 mmeineke |
1598 |
+ |
|
1599 |
+ |
* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
1600 |
+ |
NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
1601 |
+ |
class. NPTi is up to date. NPTf is not. |
1602 |
+ |
|
1603 |
+ |
2003-09-19 11:03 mmeineke |
1604 |
+ |
|
1605 |
+ |
* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
1606 |
+ |
makefile |
1607 |
+ |
|
1608 |
+ |
2003-09-19 11:01 gezelter |
1609 |
+ |
|
1610 |
+ |
* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
1611 |
+ |
|
1612 |
+ |
2003-09-19 11:01 gezelter |
1613 |
+ |
|
1614 |
+ |
* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
1615 |
+ |
(nearly) conserved quantities for both NPTi and NPTf |
1616 |
+ |
|
1617 |
+ |
2003-09-19 10:20 mmeineke |
1618 |
+ |
|
1619 |
+ |
* utils/Makefile.in: fixed a typo in the makefile. |
1620 |
+ |
|
1621 |
+ |
2003-09-19 09:55 gezelter |
1622 |
+ |
|
1623 |
+ |
* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
1624 |
+ |
samples/water/ssd.bass: [no log message] |
1625 |
+ |
|
1626 |
+ |
2003-09-19 09:22 tim |
1627 |
+ |
|
1628 |
+ |
* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
1629 |
+ |
|
1630 |
+ |
2003-09-17 09:22 mmeineke |
1631 |
+ |
|
1632 |
+ |
* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
1633 |
+ |
work with constraints. |
1634 |
+ |
|
1635 |
+ |
2003-09-16 15:02 tim |
1636 |
+ |
|
1637 |
+ |
* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
1638 |
+ |
SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
1639 |
+ |
|
1640 |
+ |
fixed conserved quantity in NPT (Still some small bug) |
1641 |
+ |
|
1642 |
+ |
NPTi appears very stable. |
1643 |
+ |
|
1644 |
+ |
2003-09-15 11:52 tim |
1645 |
+ |
|
1646 |
+ |
* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
1647 |
+ |
libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
1648 |
+ |
libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
1649 |
+ |
libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1650 |
+ |
libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
1651 |
+ |
libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
1652 |
+ |
utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
1653 |
+ |
statWriter fix bug of vector wrapping at NPTi |
1654 |
+ |
|
1655 |
+ |
2003-09-12 11:20 gezelter |
1656 |
+ |
|
1657 |
+ |
* libmdtools/: Make.dep, Makefile.in: Added integrators to |
1658 |
+ |
Makefile.in |
1659 |
+ |
|
1660 |
+ |
2003-09-12 11:20 gezelter |
1661 |
+ |
|
1662 |
+ |
* ChangeLog: Entered changes for configure into ChangeLog |
1663 |
+ |
|
1664 |
|
2003-09-09 15:35 mmeineke |
1665 |
|
|
1666 |
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
1701 |
|
samples/Makefile.in, samples/alkane/Makefile, |
1702 |
|
samples/alkane/Makefile.in, samples/argon/Makefile, |
1703 |
|
samples/argon/Makefile.in, samples/argon/argon.bass, |
1704 |
< |
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
1705 |
< |
samples/lipid/Makefile, samples/lipid/Makefile.in, |
1706 |
< |
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
1707 |
< |
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
1708 |
< |
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
1709 |
< |
autoconf / configure method of configuring OOPSE |
1704 |
> |
samples/minimizer/argon/Makefile, |
1705 |
> |
samples/minimizer/argon/Makefile.in, |
1706 |
> |
samples/minimizer/argon/argon.bass, samples/beadLipid/Makefile, |
1707 |
> |
samples/beadLipid/Makefile.in, samples/lipid/Makefile, |
1708 |
> |
samples/lipid/Makefile.in, samples/water/Makefile, |
1709 |
> |
samples/water/Makefile.in, src/Makefile, src/Makefile.in, |
1710 |
> |
utils/Makefile, utils/Makefile.in, utils/sysbuilder/Makefile, |
1711 |
> |
utils/sysbuilder/Makefile.in: Changes to autoconf / configure |
1712 |
> |
method of configuring OOPSE |
1713 |
|
|
1714 |
|
2003-09-04 16:48 mmeineke |
1715 |
|
|
1737 |
|
* ChangeLog, libmdtools/GenericData.cpp, |
1738 |
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
1739 |
|
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. |
1740 |
|
|
1741 |
|
2003-08-27 14:23 tim |
1742 |
|
|
2008 |
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
2009 |
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
2010 |
|
works..... |
363 |
– |
|
364 |
– |
2003-08-08 13:32 mmeineke |
2011 |
|
|
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 |
– |
|
2012 |
|
2003-08-08 12:48 mmeineke |
2013 |
|
|
2014 |
|
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
2065 |
|
2003-07-29 11:32 mmeineke |
2066 |
|
|
2067 |
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
2068 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
2069 |
< |
props/frameCount.c, props/frameCount.h, props/props.cpp, |
429 |
< |
src/Makefile: working on the props code |
2068 |
> |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/Makefile: |
2069 |
> |
working on the props code |
2070 |
|
|
2071 |
|
2003-07-29 11:32 mmeineke |
2072 |
|
|
2298 |
|
2003-07-14 18:06 gezelter |
2299 |
|
|
2300 |
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
2301 |
< |
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
2302 |
< |
for samples |
2301 |
> |
argon/init_argon.eor, minimizer/argon/argon.bass, |
2302 |
> |
minimizer/argon/init_argon.eor, lipid/init_5x5.eor, |
2303 |
> |
water/init_ssd.eor: Fixes for samples |
2304 |
|
|
2305 |
|
2003-07-14 18:06 gezelter |
2306 |
|
|
2973 |
|
|
2974 |
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
2975 |
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
2976 |
< |
samples/argon/argon.bass: more bug fixes.... |
2976 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: more |
2977 |
> |
bug fixes.... |
2978 |
|
|
2979 |
|
2003-04-01 11:49 mmeineke |
2980 |
|
|
3181 |
|
2003-03-26 10:37 chuckv |
3182 |
|
|
3183 |
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
3184 |
< |
samples/argon/argon.bass: Fixes for Parallel thermalization |
3184 |
> |
samples/argon/argon.bass, samples/minimizer/argon/argon.bass: Fixes |
3185 |
> |
for Parallel thermalization |
3186 |
|
|
3187 |
|
2003-03-26 09:55 mmeineke |
3188 |
|
|
3196 |
|
|
3197 |
|
2003-03-25 09:29 mmeineke |
3198 |
|
|
3199 |
< |
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
3199 |
> |
* libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, |
3200 |
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
3201 |
|
|
3202 |
|
2003-03-25 09:29 mmeineke |
3206 |
|
|
3207 |
|
2003-03-24 20:07 gezelter |
3208 |
|
|
3209 |
< |
* samples/Makefile, tests/Makefile: moving tests to samples |
3209 |
> |
* samples/Makefile: moving tests to samples |
3210 |
|
|
3211 |
|
2003-03-24 20:06 gezelter |
3212 |
|
|
3213 |
< |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
3214 |
< |
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
3215 |
< |
samples/argon/Makefile, samples/argon/argon.bass, |
3216 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
3217 |
< |
samples/lipid/5x5.bass, samples/lipid/Makefile, |
3218 |
< |
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
3219 |
< |
samples/lipid/water.mdl, samples/water/Makefile, |
3220 |
< |
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 |
3213 |
> |
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
3214 |
> |
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
3215 |
> |
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
3216 |
> |
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
3217 |
> |
lipid/lipid.mdl, lipid/water.mdl, minimizer/argon/Makefile, |
3218 |
> |
minimizer/argon/argon.bass, minimizer/argon/init_argon.eor, |
3219 |
> |
minimizer/argon/lj.mdl, water/Makefile, water/init_ssd.eor, |
3220 |
> |
water/ssd.bass, water/water.mdl: moved tests to samples |
3221 |
|
|
3222 |
|
2003-03-24 19:51 gezelter |
3223 |
|
|
3225 |
|
|
3226 |
|
2003-03-24 19:46 gezelter |
3227 |
|
|
3228 |
< |
* 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 |
3228 |
> |
* ac-tools/Make.conf.in: Added makefiles in tests directories |
3229 |
|
|
3230 |
|
2003-03-24 16:55 gezelter |
3231 |
|
|
3242 |
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
3243 |
|
do_Forces.F90: little bug fixes here and there |
3244 |
|
|
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 |
– |
|
3245 |
|
2003-03-24 10:26 mmeineke |
3246 |
|
|
3247 |
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
3351 |
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
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libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
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libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
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libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
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libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
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libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
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libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
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libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
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libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
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