--- trunk/OOPSE/ChangeLog 2004/01/05 21:00:05 894 +++ trunk/OOPSE/ChangeLog 2004/02/17 19:23:44 1057 @@ -1,3 +1,475 @@ +2004-02-10 16:33 tim + + * ChangeLog, libmdtools/ConjugateMinimizer.cpp, + libmdtools/DirectionalAtom.cpp, libmdtools/OOPSEMinimizerBase.cpp: + single version of energy minimization is working. + +2004-02-09 15:38 mmeineke + + * staticProps/: AllCorr.cpp, staticProps.cpp: started a bug fix on + the massive memory overusage by OOPSE + +2004-02-09 09:48 chrisfen + + * libmdtools/: SimSetup.cpp, calc_LJ_FF.F90: Stripped out the + hardwired LJ_rcut + +2004-02-06 19:14 tim + + * libmdtools/: SymMatrix.hpp, Utility.cpp, Utility.hpp: [no log + message] + +2004-02-06 16:37 tim + + * ChangeLog, libBASS/Globals.cpp, + libmdtools/ConjugateMinimizer.cpp, libmdtools/Integrator.cpp, + libmdtools/Integrator.hpp, libmdtools/OOPSEMinimizerBase.cpp, + libmdtools/SimSetup.cpp, samples/water/ssd.bass: Single version of + energy minimization for argon is working, need to add constraint + +2004-02-06 14:05 tim + + * libmdtools/: AllIntegrator.hpp, Makefile.in, SimSetup.cpp: Add + one more file into Makefile.in + +2004-02-06 13:58 tim + + * ChangeLog, libBASS/Globals.cpp, libBASS/Globals.hpp, + libmdtools/AllIntegrator.hpp, libmdtools/ConjugateMinimizer.cpp, + libmdtools/ConjugateMinimizer.hpp, libmdtools/Functor.hpp, + libmdtools/Integrator.hpp, libmdtools/Makefile.in, + libmdtools/Minimizer.hpp, libmdtools/Minimizer1D.cpp, + libmdtools/Minimizer1D.hpp, libmdtools/MinimizerBase.hpp, + libmdtools/MinimizerParameterSet.hpp, libmdtools/NLModel.hpp, + libmdtools/NLModel1.cpp, libmdtools/OOPSEMinimizerBase.cpp, + libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, + libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, src/oose.cpp: Add + some lines into global.cpp to make it work with energy minimization + +2004-02-04 17:26 tim + + * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, + Constraint.hpp, Functor.hpp, Minimizer.hpp, Minimizer1D.cpp, + Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp, + NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Fix a bunch of bugs :-) + Single version of conjugate gradient with golden search linesearch + pass a couple of functions test. Brent's algorithm is still broken + +2004-02-03 17:54 tim + + * libmdtools/: ConjugateMinimizer.cpp, ConjugateMinimizer.hpp, + Minimizer1D.cpp, Minimizer1D.hpp, MinimizerParameterSet.hpp, + NLModel.hpp, NLModel0.cpp, NLModel1.cpp, SteepestDescent.cpp, + SteepestDescent.hpp: NLModel0, NLModel1 pass uit test + +2004-02-03 15:47 tim + + * libmdtools/: ConjugateMinimizer.cpp, ConstraintList.cpp, + ConstraintList.hpp, LinearCons.cpp, LinearCons.hpp, Minimizer.hpp, + NonlinearCons.cpp, NonlinearCons.hpp, OOPSEMinimizerBase.cpp, + SimpleBoundCons.cpp, SimpleBoundCons.hpp, SteepestDescent.cpp, + SteepestDescent.hpp: [no log message] + +2004-02-03 15:43 tim + + * libmdtools/: ConjugateMinimizer.hpp, Constraint.cpp, + Constraint.hpp, Integrator.hpp, Minimizer1D.cpp, Minimizer1D.hpp, + MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, + NLModel0.cpp, NLModel1.cpp: to avoid cyclic depency, refactory + constraint class + +2004-02-03 12:10 tim + + * libmdtools/Functor.hpp: Functor.hpp pass unit test + +2004-02-03 10:21 tim + + * ChangeLog, libmdtools/Minimizer1D.cpp, + libmdtools/Minimizer1D.hpp: begin unit test of minimizer + +2004-02-02 15:29 tim + + * libmdtools/: ConjugateMinimizer.hpp, Minimizer1D.cpp, + Minimizer1D.hpp, MinimizerBase.hpp, MinimizerParameterSet.hpp: + Adding GoldenSection and Brent LineSearch Method + +2004-01-30 16:47 tim + + * libmdtools/: ConjugateMinimizer.hpp, DumpWriter.cpp, + MinimizerBase.hpp, MinimizerParameterSet.hpp, NLModel.hpp, + NLModel0.cpp, NLModel1.cpp: using class Minimizer1D derived from + MinimizerBase instead of a functor to do line seach + +2004-01-30 10:00 chrisfen + + * forceFields/Makefile.in, libmdtools/Atom.cpp, + libmdtools/Atom.hpp, libmdtools/ForceFields.hpp, + libmdtools/Integrator.cpp, libmdtools/Makefile.in, + libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, + libmdtools/WATER.cpp, libmdtools/calc_LJ_FF.F90, + libmdtools/calc_reaction_field.F90, libmdtools/do_Forces.F90, + libmdtools/fortranWrapDefines.hpp: Substantial changes. OOPSE now + has a working WATER.cpp forcefield and parser. This involved + changes to WATER.cpp and ForceFields amoung other files. One + important note: a hardwiring of LJ_rcut was made in calc_LJ_FF.F90. + This will be removed on the next commit... + +2004-01-29 18:00 gezelter + + * libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, + libBASS/BASS_parse.c, libBASS/BASSlex.l, libBASS/BASSyacc.y, + libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, + libBASS/Makefile.in, libBASS/RigidBodyStamp.cpp, + libBASS/RigidBodyStamp.hpp, libBASS/interface.c, + libBASS/make_nodes.c, libBASS/make_nodes.h, libBASS/mpiBASS.c, + libBASS/mpiBASS.h, libBASS/node_list.h, libBASS/parse_interface.h, + libBASS/parse_tree.c, libmdtools/Make.dep, samples/water/water.mdl: + member list fixes for rigid bodies + +2004-01-29 16:44 tim + + * libmdtools/MinimizerParameterSet.hpp: Adding + MinimizerParameterSet class. + +2004-01-28 17:44 tim + + * libmdtools/: NLModel.hpp, NLModel0.cpp, NLModel1.cpp: Revision of + NLModel0 and NLModel1 + +2004-01-28 15:40 tim + + * libmdtools/: Constraint.hpp, NLModel.hpp, NLOPModel.hpp: revision + of NLModel + +2004-01-27 15:34 gezelter + + * samples/water/: ssd.bass, water.mdl: Added point-charge models to + water.mdl file, updated ssd.bass to use new SSD name + +2004-01-27 15:34 gezelter + + * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, + MemberStamp.cpp, MemberStamp.hpp, node_list.h: Fix to new RigidBody + stuff + +2004-01-27 14:39 gezelter + + * samples/water/ssd.bass: Longer run time to test SSD water in MPI + +2004-01-27 14:39 gezelter + + * samples/metals/Au.bass: Longer run time to test gold in MPI + +2004-01-27 14:38 gezelter + + * samples/argon/argon.bass: Longer run time to test argon + +2004-01-27 14:38 gezelter + + * libmdtools/: Make.dep, WATER.cpp, mpiSimulation.cpp: More BASS + changes to do new rigidBody scheme a copy of WATER.cpp from this + morning + +2004-01-27 14:37 gezelter + + * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, + BASSyacc.y, MakeStamps.cpp, MakeStamps.hpp, Makefile.in, + MemberStamp.cpp, MemberStamp.hpp, MoleculeStamp.cpp, + MoleculeStamp.hpp, RigidBodyStamp.cpp, RigidBodyStamp.hpp, + interface.c, make_nodes.c, make_nodes.h, mpiBASS.c, mpiBASS.h, + node_list.h, parse_interface.h, parse_tree.c: More BASS changes to + do new rigidBody scheme + +2004-01-27 14:15 tim + + * libmdtools/: AbstractClasses.hpp, ConjugateMinimizer.hpp, + Constraint.cpp, Constraint.hpp, Functor.hpp, Integrator.hpp, + MinimizerBase.hpp, NLOPConstraint.hpp, NLOPModel.hpp: revision of + constraint for Nonlinear Optimization Model + +2004-01-26 17:01 gezelter + + * utils/sysbuilder/MoLocator.cpp: Changes to BASS reader to use + Euler angles for orientation instead of unit vectors required + changes in MoLocator + +2004-01-26 16:53 gezelter + + * samples/: alkane/alkanes.mdl, beadLipid/beadLipid.mdl, + beadLipid/water.mdl, lipid/lipid.mdl, lipid/water.mdl, + water/water.mdl: Changed orientation lines from unit vectors to + euler angles + +2004-01-26 16:52 gezelter + + * libmdtools/SimSetup.cpp: Convert Eulers in degrees into radians + +2004-01-26 16:45 gezelter + + * libmdtools/SimSetup.cpp: Changed default orientation in BASS to + use Euler angles in the following order: phi, theta, psi Removed + the ability to set orientation using a unit vector + +2004-01-26 16:26 gezelter + + * libBASS/: AtomStamp.cpp, AtomStamp.hpp, RigidBodyStamp.cpp, + RigidBodyStamp.hpp: Changed default orientation in BASS to use + Euler angles in the following order: phi, theta, psi Removed the + ability to set orientation using a unit vector + +2004-01-26 13:52 gezelter + + * libBASS/: BASS_interface.cpp, MakeStamps.cpp, MakeStamps.hpp, + MoleculeStamp.cpp: Fix broken atom assignment for rigid bodies + +2004-01-22 12:34 chrisfen + + * libmdtools/: DUFF.cpp, EAM_FF.cpp, ForceFields.hpp, LJFF.cpp, + TraPPE_ExFF.cpp, WATER.cpp, mpiForceField.c, mpiForceField.h: + Corrected spelling in several directories, and stated WATER.cpp + +2004-01-21 17:16 tim + + * libmdtools/: MinimizerBase.hpp, NLOPConstraint.hpp, + NLOPModel.hpp: constraint class in energy minimization + +2004-01-20 15:34 tim + + * libmdtools/MinimizerBase.hpp: Adding energy minimization + +2004-01-20 15:32 tim + + * libmdtools/: ConjugateMinimizer.hpp, Integrator.hpp, + NLOPConstraint.hpp, NLOPModel.hpp: Energy Minimizer + +2004-01-19 16:17 gezelter + + * libmdtools/: SimInfo.cpp, SimSetup.cpp: Made some error messages + more user-friendly + +2004-01-19 13:51 chrisfen + + * forceFields/DUFF.frc: Updated the default water to SSD/E + +2004-01-19 13:36 tim + + * libmdtools/: Functor.hpp, SimSetup.cpp: Adding warning if sample + time, status time, thermal time and reset time are not divisible by + dt + +2004-01-19 11:10 gezelter + + * third-party/Makefile.in: Added a bunch of dummy targets so make + won't complain + +2004-01-19 11:10 gezelter + + * samples/lipid/5x5.bass: Fixed old bass file + +2004-01-19 11:09 gezelter + + * libmdtools/mpiSimulation.cpp: BASS changes to add RigidBodies + required a change in how the MoleculeStamps are used by divideLabor + in mpiSimulation.cpp + +2004-01-19 11:08 gezelter + + * libBASS/: BASS_interface.cpp, BASS_interface.h, BASS_parse.c, + BASSyacc.y, Globals.cpp, Globals.hpp, MakeStamps.cpp, + MakeStamps.hpp, Makefile.in, MoleculeStamp.cpp, MoleculeStamp.hpp, + RigidBodyStamp.cpp, RigidBodyStamp.hpp, interface.c, make_nodes.c, + make_nodes.h, mpiBASS.c, mpiBASS.h, node_list.h, parse_interface.h, + parse_tree.c: BASS changes to add RigidBodies and LJrcut + +2004-01-16 16:55 tim + + * libmdtools/: DumpWriter.cpp, EAM_FF.cpp: fix a bug in creating + eor file + +2004-01-16 16:51 mmeineke + + * libmdtools/DumpWriter.cpp: fixed a bug where only MPI jobs could + write eor files + +2004-01-16 10:01 mmeineke + + * libmdtools/DUFF.cpp: fixed an struct mismatch error in the mpi + initialization of the AtomStruct + +2004-01-15 16:57 chuckv + + * configure, libmdtools/DumpWriter.cpp: Fixes for Dumps + +2004-01-15 10:51 gezelter + + * ac-tools/aclocal.m4: Changes for altivec + +2004-01-15 09:22 gezelter + + * libmdtools/DumpWriter.cpp: Documented the Spud Toss + +2004-01-14 23:33 gezelter + + * libmdtools/do_Forces.F90: changes for charge charge interactions + +2004-01-14 20:14 gezelter + + * libmdtools/: calc_charge_charge.F90, calc_dipole_dipole.F90, + notifyCutoffs.F90: More work for adding charges + +2004-01-14 17:41 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + src/Makefile.in: autoconf fixes + +2004-01-14 11:28 mmeineke + + * utils/sysbuilder/latticeBilayer.cpp: fixed a periodic box bug + +2004-01-14 10:48 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + src/Makefile.in, third-party/Makefile.in: autoconf compatibility + changes for icc8 + +2004-01-13 18:01 gezelter + + * libmdtools/: DUFF.cpp, EAM_FF.cpp, LJFF.cpp, SimInfo.cpp, + SimInfo.hpp, TraPPE_ExFF.cpp, atype_module.F90, do_Forces.F90, + fSimulation.h, fortranWrapDefines.hpp, simulation_module.F90: + Changes for adding direct charge-charge interactions (with + switching function) + +2004-01-13 17:34 gezelter + + * libmdtools/: Make.dep, Makefile.in, calc_charge_charge.F90, + oopseMPI_module.F90: Some changes for new MPI organization and + direct charge-charge interactions + +2004-01-13 17:11 tim + + * Functor.hpp, libmdtools/Functor.hpp: [no log message] + +2004-01-13 16:22 tim + + * Functor.hpp, samples/water/ssd.bass: Energy Minimization method + +2004-01-13 15:35 tim + + * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: open and close the + eor file whenever it is used instead of rewinding it + +2004-01-13 15:04 tim + + * libmdtools/: DumpWriter.cpp, ReadWrite.hpp: change the interface + of writeFrame + +2004-01-13 10:46 tim + + * libmdtools/: DumpWriter.cpp, Integrator.cpp, ReadWrite.hpp: + Merge the code of writeFinal and writeDump; + Adding sortingIndex into DumpWriter; + Fix a bug of writing last frame twice in integrator + +2004-01-12 17:54 tim + + * ChangeLog, libmdtools/DumpWriter.cpp, samples/water/ssd.bass: fix + a bug in copying string + +2004-01-12 15:37 tim + + * ChangeLog, libmdtools/DumpWriter.cpp, samples/argon/argon.bass, + samples/water/ssd.bass: Dumpwriter only write out the atoms on + master nodes + +2004-01-10 04:46 tim + + * ChangeLog, libmdtools/DumpWriter.cpp: tagub is not a bug. Just + roll it back fix a bug of copying string to a pointer Still have + Seg fault, it looks like a random MPI seg fault in totalview + +2004-01-09 21:15 tim + + * libmdtools/DumpWriter.cpp: Fix a bug of declaration of tagub + +2004-01-09 15:29 gezelter + + * libmdtools/DumpWriter.cpp: New DumpWriter (Attempt #4) + +2004-01-08 17:25 chuckv + + * libmdtools/DumpWriter.cpp: A work in progress... + +2004-01-08 13:59 gezelter + + * libmdtools/DumpWriter.cpp: null terminate some strings just in + case + +2004-01-08 13:13 mmeineke + + * libmdtools/InitializeFromFile.cpp: refixed the NVT readin XS + state bug. + +2004-01-08 13:05 gezelter + + * libmdtools/DumpWriter.cpp: added strncpy to DumpWriter + +2004-01-08 12:57 mmeineke + + * libmdtools/InitializeFromFile.cpp: fixed the restart from NVT + exstended state bug + +2004-01-08 12:40 gezelter + + * libmdtools/DumpWriter.cpp: First Stab at fixing DumpWriter + +2004-01-08 10:44 mmeineke + + * libmdtools/InitializeFromFile.cpp: added support for the ignore + XS state info flag + +2004-01-07 14:26 tim + + * libmdtools/DumpWriter.cpp, libmdtools/InitializeFromFile.cpp, + samples/argon/argon.bass, samples/water/ssd.bass: Fixed a bug of + sending message from master node to itself in DumpWriter.cpp and + InitializeFromFile.cpp + +2004-01-06 14:49 chuckv + + * libmdtools/: calc_dipole_dipole.F90, calc_reaction_field.F90: + performance fixes in the dipole dipole and reaction field code + +2004-01-06 13:54 chuckv + + * libmdtools/: calc_LJ_FF.F90, do_Forces.F90: Making do_Forces a + little more sane + +2004-01-05 17:49 chuckv + + * libmdtools/: calc_LJ_FF.F90, calc_dipole_dipole.F90, + calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, + calc_sticky_pair.F90, do_Forces.F90: Attempting to increase + performance by reducing spurious function calls + +2004-01-05 17:18 chuckv + + * libmdtools/do_Forces.F90: mangling forces even further + +2004-01-05 17:18 chuckv + + * configure, ac-tools/configure.in: mpich mucking + +2004-01-05 17:12 chuckv + + * libmdtools/do_Forces.F90: mangled do_forces... + +2004-01-05 16:00 chuckv + + * ChangeLog, ac-tools/configure.in, libmdtools/atype_module.F90, + libmdtools/do_Forces.F90: Added bitmask to do_forces property + lookup + 2003-12-29 14:56 chuckv * samples/metals/Au.bass, third-party/mt19937ar.c: Added @@ -2178,7 +2650,7 @@ 2003-03-25 09:29 mmeineke - * libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, + * libBASS/obj/dummy, libmdtools/obj/dummy, libmdtools/MPIobj/dummy, src/MPIobj/dummy, src/obj/dummy: [no log message] 2003-03-25 09:29 mmeineke @@ -2332,8 +2804,8 @@ libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, - libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE - Tree + libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial + revision 2003-03-21 12:42 mmeineke @@ -2390,6 +2862,6 @@ libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, - libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial - revision + libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE + Tree