--- trunk/OOPSE-2.0/ChangeLog 2004/10/06 21:27:02 1536 +++ trunk/OOPSE-2.0/ChangeLog 2004/10/18 23:13:23 1594 @@ -1,48 +1,885 @@ +2004-10-16 20:19 tim + + * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, + SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in + progress + +2004-10-15 20:31 tim + + * src/math/Quaternion.hpp: add quaternion class + +2004-10-15 16:11 tim + + * test/io/: DUFF.frc, IfstrstreamTestCase.cpp, + IfstrstreamTestCase.hpp: adding test file + +2004-10-15 16:10 tim + + * src/io/basic_ifstrstream.hpp: fix a bunch of bugs + +2004-10-15 15:42 tim + + * src/io/basic_ifstrstream.hpp: change const_cast to statc_const + +2004-10-15 15:35 tim + + * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp + +2004-10-15 15:34 tim + + * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use + namespace oopse + +2004-10-15 14:38 chuckv + + * configure, ac-tools/aclocal.m4: Changed optimization flags for + XLF and XLC. + +2004-10-15 13:28 tim + + * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: + adding ifstrstream test case + +2004-10-15 13:20 tim + + * src/io/basic_ifstrstream.hpp: fix include + +2004-10-15 13:18 tim + + * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi + +2004-10-15 13:17 tim + + * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile + +2004-10-15 13:16 tim + + * test/io/: Makefile, ifstrstreamTestCase.cpp, + ifstrstreamTestCase.hpp: adding test case for ifstrstream + +2004-10-15 10:37 tim + + * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, + ifstrstreamTestCase.hpp: add ifstrstreamTestCase + +2004-10-15 10:20 tim + + * src/io/basic_ifstrstream.hpp: add checkFilename Option + +2004-10-15 10:19 tim + + * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, + SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add + SquareMatrixTestCase class + +2004-10-15 02:52 tim + + * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream + +2004-10-14 18:28 tim + + * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, + Vector.hpp: math library in progress + +2004-10-14 18:27 tim + + * src/io/FileReader.hpp: FileReader in progress + +2004-10-13 18:53 tim + + * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, + test in isOrthogonal of SquareMatrix is failed by some reasons + +2004-10-13 17:28 tim + + * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap + class + +2004-10-13 17:27 tim + + * test/math/: MainTest.cpp, RectMatrixTestCase.cpp, + RectMatrixTestCase.hpp: adding testing unit + +2004-10-13 17:24 tim + + * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix + +2004-10-13 01:51 tim + + * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, + Vector3.hpp: refactory vector and matrix classes + +2004-10-13 01:50 tim + + * src/math/Vector3d.hpp: Remove some Makefile.in + +2004-10-12 18:57 tim + + * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and + Matrix3x3d.hpp + +2004-10-12 14:08 tim + + * doc/: cppstyle.html, style.css: adding c++ coding style + +2004-10-11 17:15 tim + + * src/: constraints/AbstractClasses.hpp, + integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: + change #include "mpi.h" to #include in AbstractClasses.hpp + +2004-10-11 16:54 tim + + * scripts/filepp: fix a bug in filepp + +2004-10-11 16:13 tim + + * make/Makefile.in: using filepp to generate dependencies instead + of compilers + +2004-10-11 16:10 tim + + * scripts/filepp: filepp can be used to generate dependencies for + c/c++ now + +2004-10-11 13:40 tim + + * make/Makefile.in: remove -module from F90Options + +2004-10-11 13:01 tim + + * make/Makefile.in: adding rules to move fortran 90 module to + target directory + +2004-10-11 10:43 gezelter + + * make/Makefile.in: fixed makefile.in + +2004-10-11 09:51 tim + + * scripts/filepp: remove "use bytes" which causes problem in sgi + machine + +2004-10-11 09:26 tim + + * forceFields/Makefile: add Makefile + +2004-10-11 09:23 tim + + * samples/: water/dimer/Makefile, water/spce/Makefile, + water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, + water/tip4p/Makefile, zcons/Makefile: fix Makefile under water + directory + +2004-10-11 09:23 tim + + * samples/argon/Makefile: remove argon.dump and argon.eor from + Makefile + +2004-10-09 01:01 tim + + * samples/: alkane/Makefile.in, argon/Makefile.in, + lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: + Remove some Makefile.in + +2004-10-08 18:15 tim + + * make/Makefile.in: [no log message] + +2004-10-08 17:51 tim + + * make/Makefile.in: fix make install + +2004-10-08 17:10 tim + + * make/Makefile.in: adding make install + +2004-10-08 17:04 tim + + * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, + metals/Makefile, minimizer/Makefile, water/Makefile.in, + water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, + water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, + water/ssde/Makefile, water/ssde/Makefile.in, + water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, + water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, + zcons/Makefile.in: add Makefile to sample directory + +2004-10-06 18:03 gezelter + + * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt + stuff + +2004-10-06 18:03 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + make/Doxyfile, src/applications/getopt.c, + src/applications/getopt1.c, src/applications/gnugetopt.h: more + build fixes + +2004-10-06 17:20 tim + + * make/: Doxyfile, Makefile.in: adding doxygen configuration file + +2004-10-06 17:19 tim + + * scripts/filepp: filepp can handle different fortran module case + and suffix + +2004-10-06 16:27 gezelter + + * src/restraints/Restraints.cpp: Chris doesn't know about the + OOPSE-2.0 directory structure yet + +2004-10-06 16:27 gezelter + + * ChangeLog: Yeah yeah, we'lll get around to it later + 2004-10-06 16:22 gezelter - * configure, ac-tools/configure.in, ac-tools/fortran90.m4: cleaning - up build process + * configure, ac-tools/configure.in, ac-tools/fortran90.m4, + make/Makefile.in: cleaning up build process +2004-10-06 15:01 chrisfen + + * src/restraints/Restraints.cpp: made the file reading in + restraints more intelligent - no longer gives uninformative seg + faults + +2004-10-06 14:55 gezelter + + * src/applications/simpleBuilder/Make.ftemp.old: cleaning up + 2004-10-06 14:51 gezelter - * LICENSE, MPIobj/dummy: Cleaning up a bit + * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, + scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit +2004-10-06 13:53 tim + + * make/: Makefile, Makefile.in: fix make statistics + +2004-10-06 13:18 tim + + * make/: Makefile, Makefile.in: adding GNU make functions to + combine all of the static libraries to a big library + +2004-10-05 17:57 tim + + * make/: Makefile, Makefile.in: adding shared library flag + +2004-10-05 14:37 tim + + * src/: Makefile, UseTheForce/Makefile, + UseTheForce/mpiSimulation_module.F90, + UseTheForce/DarkSide/Makefile, + UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move + mpiSimulation_module to DarkSide + +2004-10-05 14:35 tim + + * make/: Makefile, Makefile.in: building MPI version;using static + library instead of shared library + +2004-10-05 09:14 tim + + * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 + to filepp + +2004-10-04 15:56 tim + + * make/: Makefile, Makefile.in: add make cvslog + +2004-10-04 11:24 gezelter + + * make/: Makefile, Makefile.in: more work on the parallel build + +2004-10-04 11:06 gezelter + + * make/: Makefile, Makefile.in: changes to backport declare flags + +2004-10-04 10:27 gezelter + + * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, + DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging + shapes + +2004-10-01 23:40 tim + + * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree + +2004-10-01 23:22 tim + + * make/: Makefile, Makefile.in: add oopse_ as library prefix + +2004-10-01 16:59 tim + + * make/: Makefile, Makefile.in: fix a space trimming bug in filepp + 2004-10-01 16:22 gezelter - * Makefile, ac-tools/aclocal.m4: A few minor build changes + * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A + few minor build changes +2004-10-01 16:11 tim + + * scripts/filepp: adding fortran90 make dependency tool + +2004-09-30 10:41 tim + + * make/: Makefile, Makefile.in: make clean is smart enough to only + remove object files belong to current package. turn off silent + mode + +2004-09-29 16:55 tim + + * src/: Makefile, UseTheForce/Makefile, + UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, + applications/oopse/Makefile, applications/simpleBuilder/Makefile, + brains/Makedepend, brains/Makefile, constraints/Makefile, + integrators/Makefile, io/Makefile, math/Makefile, + minimizers/Makefile, primitives/Makefile, profiling/Makefile, + restraints/Makefile, types/Makefile, utils/Makefile, + visitors/Makefile: define DEV_ROOT as relative path + +2004-09-29 16:54 tim + + * make/: Makefile, Makefile.in: get the relative path by shell + script + +2004-09-29 16:32 tim + + * make/Makefile: eliminate DEV_ROOT by relative path + +2004-09-29 13:37 tim + + * make/Makefile.in: add PackageLibs; fix dependency rule + 2004-09-29 12:57 gezelter * configure, ac-tools/configure.in: updates +2004-09-29 12:56 gezelter + + * make/: Make.conf.in, Makefile.in, _files/style.css: Working on + make stuff + 2004-09-29 12:46 tim * Makefile: If makefile does not exist, print error message +2004-09-29 12:12 tim + + * make/: Make.conf.in, Makefile: fix dependencies rule + 2004-09-29 10:58 gezelter - * Makefile: still working on build process + * Makefile, make/Makefile: still working on build process +2004-09-29 10:00 tim + + * make/Makefile: add print statment to rules + +2004-09-29 09:59 tim + + * src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, + applications/dump2Xyz/Makefile, applications/oopse/Makefile, + applications/simpleBuilder/Makefile, brains/Makefile, + constraints/Makefile, integrators/Makefile, io/Makefile, + math/Makefile, minimizers/Makefile, primitives/Makefile, + profiling/Makefile, restraints/Makefile, types/Makefile, + utils/Makefile, visitors/Makefile: change Makefile to relative path + +2004-09-28 21:55 tim + + * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c + which cause headache in bulding libutils + +2004-09-28 18:24 tim + + * src/applications/: BaseLattice.cpp, BaseLattice.hpp, + Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, + Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, + LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, + MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, + nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, + simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, + dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, + dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, + oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, + simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, + simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, + simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, + simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, + simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, + simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, + simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, + simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: + change directory structure of application. Every executable file is + replaced in seperate directory + +2004-09-28 17:15 gezelter + + * lib/dummy: Keep that lib around, please. + 2004-09-28 17:14 gezelter - * Makefile, configure, ac-tools/configure.in: starting a configure - version + * Makefile, configure, ac-tools/configure.in, make/Make.conf.in: + starting a configure version +2004-09-28 16:08 tim + + * src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, + UseTheForce/DarkSide/Makefile, + UseTheForce/DarkSide/notifyCutoffs.F90, + UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, + brains/Makefile, brains/simulation_module.F90: move fortran files + around to solve dependency problem + 2004-09-28 15:43 tim - * Makefile: [no log message] + * Makefile, src/UseTheForce/ForceFields.hpp, + src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, + src/applications/Makedepend, src/applications/Makefile, + src/brains/Makedepend, src/brains/simulation_module.F90, + src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, + src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, + src/utils/Makefile: [no log message] +2004-09-28 15:41 tim + + * make/Makefile, scripts/sfmakedepend: fix fortran dependency + problem + +2004-09-28 11:13 tim + + * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, + src/io/Makefile: add yacc and lex rules + +2004-09-27 15:24 tim + + * make/Makefile: adding include path to F90Options + +2004-09-27 15:13 tim + + * make/Makefile: change suffix from .cc to .cpp + +2004-09-24 11:27 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, + UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, + UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, + UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, + UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, + UseTheForce/DarkSide/calc_LJ_FF.F90, + UseTheForce/DarkSide/notifyCutoffs.F90, + UseTheForce/DarkSide/switch_module.F90, + applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, + applications/Dump2XYZCmd.c, applications/Lattice.cpp, + applications/Lattice.hpp, applications/LatticeCreator.cpp, + applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, + applications/MoLocator.cpp, applications/MoLocator.hpp, + applications/cmdline.c, applications/nanoBuilder.cpp, + applications/oopse.cpp, applications/simpleBuilder.cpp, + applications/simpleBuilderCmd.c, brains/Exclude.cpp, + brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, + brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, + brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, + constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, + integrators/AbstractClasses.hpp, integrators/Integrator.cpp, + integrators/Integrator.hpp, integrators/NPT.cpp, + integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, + integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, + io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, + io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, + io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, + io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, + io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, + io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, + io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, + math/MatVec3.h, math/randomSPRNG.cpp, + minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, + minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, + minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, + primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, + primitives/BendExtensions.cpp, primitives/Bond.cpp, + primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, + primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, + primitives/GhostBend.cpp, primitives/Molecule.cpp, + primitives/Molecule.hpp, primitives/RigidBody.cpp, + primitives/RigidBody.hpp, primitives/SRI.hpp, + primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, + primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, + profiling/mdProfile.cpp, restraints/Restraints.cpp, + restraints/Restraints.hpp, types/AtomStamp.cpp, + types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, + types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, + types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, + types/MakeStamps.cpp, types/MakeStamps.hpp, + types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, + types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, + types/TorsionStamp.cpp, types/TorsionStamp.hpp, + types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, + utils/StreamTokenizer.cpp, utils/StringUtils.c, + utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, + utils/simError.c, visitors/AtomVisitor.cpp, + visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, + visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, + visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, + visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, + visitors/ZconsVisitor.hpp: change the #include in source files + 2004-09-23 23:16 gezelter * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, + src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, + src/constraints/Makefile, src/constraints/ZConstraint.cpp, + src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, + src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, + src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, + src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, + src/UseTheForce/fForceField.h, + src/UseTheForce/fSwitchingFunction.h, + src/UseTheForce/fortranWrapDefines.hpp, + src/UseTheForce/fortranWrappers.cpp, + src/UseTheForce/fortranWrappers.hpp, + src/UseTheForce/mpiComponentPlan.h, + src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, + src/UseTheForce/mpiSimulation_module.F90, + src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, + src/UseTheForce/DarkSide/atype_module.F90, + src/UseTheForce/DarkSide/calc_LJ_FF.F90, + src/UseTheForce/DarkSide/calc_charge_charge.F90, + src/UseTheForce/DarkSide/calc_dipole_dipole.F90, + src/UseTheForce/DarkSide/calc_eam.F90, + src/UseTheForce/DarkSide/calc_gb.F90, + src/UseTheForce/DarkSide/calc_reaction_field.F90, + src/UseTheForce/DarkSide/calc_sticky_pair.F90, + src/UseTheForce/DarkSide/force_globals.F90, + src/UseTheForce/DarkSide/neighborLists.F90, + src/UseTheForce/DarkSide/notifyCutoffs.F90, + src/UseTheForce/DarkSide/switch_module.F90, + src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, + src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, + src/io/DumpWriter.cpp, src/io/Globals.cpp, + src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, + src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, + src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, + src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, + src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, + src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, + src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, + src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, + src/types/AtomStamp.hpp, src/types/BendStamp.cpp, + src/types/BendStamp.hpp, src/types/BondStamp.cpp, + src/types/BondStamp.hpp, src/types/Component.cpp, + src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, + src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, + src/types/MakeStamps.hpp, src/types/Makefile, + src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, + src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, + src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, + src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, + src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, + src/brains/Exclude.hpp, src/brains/ForceFields.cpp, + src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, + src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, + src/brains/SimSetup.hpp, src/brains/SimState.cpp, + src/brains/SimState.hpp, src/brains/SkipList.cpp, + src/brains/SkipList.hpp, src/brains/Thermo.cpp, + src/brains/Thermo.hpp, src/brains/fSimulation.h, + src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, + src/brains/simulation_module.F90, src/io/BASS_interface.cpp, + src/io/Globals.hpp, src/io/LinkedAssign.cpp, + src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, + src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, + src/math/mt19937ar.c, src/math/randomSPRNG.cpp, + src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, + src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, + src/minimizers/OOPSEMinimizer.cpp, + src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, + src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, + src/primitives/Atom.cpp, src/primitives/Atom.hpp, + src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, + src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, + src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, + src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, + src/primitives/Makefile, src/primitives/Molecule.cpp, + src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, + src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, + src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, + src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, + src/restraints/Makefile, src/restraints/Restraints.cpp, + src/restraints/Restraints.hpp, src/utils/GenericData.cpp, + src/utils/GenericData.hpp, src/utils/Makefile, + src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, + src/utils/StringUtils.c, src/utils/StringUtils.cpp, + src/utils/StringUtils.h, src/utils/StringUtils.hpp, + src/utils/TypeInfo.hpp, src/utils/Utility.cpp, + src/utils/Utility.hpp, src/utils/definitions_module.F90, + src/utils/fError.c, src/utils/oopseMPI_module.F90, + src/utils/simError.c, src/utils/simError.h, + src/utils/status_module.F90, src/utils/vector_class.F90, + src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, + src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, + src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, + src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, + src/visitors/RigidBodyVisitor.cpp, + src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, + src/visitors/ZconsVisitor.hpp, make/Makefile, + make/_files/style.css, samples/Makefile.in, + samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, + samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, + samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, + samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, + samples/zcons/Makefile.in, samples/zcons/water.md, + samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, + samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, + src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, + src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, + src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, + src/applications/Lattice.cpp, src/applications/Lattice.hpp, + src/applications/LatticeCreator.cpp, + src/applications/LatticeCreator.hpp, + src/applications/LatticeFactory.cpp, + src/applications/LatticeFactory.hpp, src/applications/Makedepend, + src/applications/Makefile, src/applications/MoLocator.cpp, + src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, + src/applications/cmdline.c, src/applications/cmdline.h, + src/applications/getopt.c, src/applications/getopt1.c, + src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, + src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, + src/applications/quickLate.c, src/applications/simpleBuilder.cpp, + src/applications/simpleBuilder.ggo, + src/applications/simpleBuilderCmd.c, + src/integrators/AbstractClasses.hpp, + src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, + src/integrators/Integrator.hpp, src/integrators/Makefile, + src/integrators/NPT.cpp, src/integrators/NPTf.cpp, + src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, + src/integrators/NVT.cpp, src/profiling/Makefile, + src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, + src/profiling/timing.F90, samples/metals/Au_bulk.in, + samples/metals/Au_nanoparticle.in, samples/metals/metals.md, + samples/water/Makefile.in, samples/water/dimer/Makefile.in, + samples/water/dimer/two.in, samples/water/dimer/two.md, + samples/water/dimer/water.md, samples/water/spce/Makefile.in, + samples/water/spce/spce.in, samples/water/spce/spce.md, + samples/water/spce/water.md, samples/water/ssde/Makefile.in, + samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, + samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, + samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, + samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, + samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, + samples/water/ssd/water.md, samples/water/tip4p/tp4.in, + samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, + samples/alkane/Makefile.in, samples/alkane/alkanes.md, + samples/alkane/butane.in, samples/alkane/butane.md, + samples/argon/500.in, samples/argon/500.md, + samples/argon/Makefile.in, samples/argon/ar864.in, + samples/argon/ar864.md, samples/argon/argonNVT.in, + samples/argon/argonNVT.md, samples/argon/lj.md, + samples/lipid/5x5.in, samples/lipid/5x5.md, + samples/lipid/Makefile.in, samples/lipid/lipid.md, + samples/lipid/water.md, samples/minimizer/Makefile.in, + samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, + samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, + samples/minimizer/tip4p_two.md, samples/minimizer/water.md, + samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, + forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, + forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, + forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, + forceFields/DUFF.frc, forceFields/DipoleTest.frc, + forceFields/EAM.VC.frc, forceFields/EAM.frc, + forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, + forceFields/Makefile.in, forceFields/Ni.u3.funcfl, + forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, + forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, + forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, + scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, - ac-tools/install-sh, ac-tools/shtool: Import of OOPSE v. 2.0 + ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, + forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, + forceFields/Au.u3.funcfl, forceFields/LJFF.frc, + forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, + forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 2004-09-23 23:16 gezelter * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, + src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, + src/constraints/Makefile, src/constraints/ZConstraint.cpp, + src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, + src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, + src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, + src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, + src/UseTheForce/fForceField.h, + src/UseTheForce/fSwitchingFunction.h, + src/UseTheForce/fortranWrapDefines.hpp, + src/UseTheForce/fortranWrappers.cpp, + src/UseTheForce/fortranWrappers.hpp, + src/UseTheForce/mpiComponentPlan.h, + src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, + src/UseTheForce/mpiSimulation_module.F90, + src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, + src/UseTheForce/DarkSide/atype_module.F90, + src/UseTheForce/DarkSide/calc_LJ_FF.F90, + src/UseTheForce/DarkSide/calc_charge_charge.F90, + src/UseTheForce/DarkSide/calc_dipole_dipole.F90, + src/UseTheForce/DarkSide/calc_eam.F90, + src/UseTheForce/DarkSide/calc_gb.F90, + src/UseTheForce/DarkSide/calc_reaction_field.F90, + src/UseTheForce/DarkSide/calc_sticky_pair.F90, + src/UseTheForce/DarkSide/force_globals.F90, + src/UseTheForce/DarkSide/neighborLists.F90, + src/UseTheForce/DarkSide/notifyCutoffs.F90, + src/UseTheForce/DarkSide/switch_module.F90, + src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, + src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, + src/io/DumpWriter.cpp, src/io/Globals.cpp, + src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, + src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, + src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, + src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, + src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, + src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, + src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, + src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, + src/types/AtomStamp.hpp, src/types/BendStamp.cpp, + src/types/BendStamp.hpp, src/types/BondStamp.cpp, + src/types/BondStamp.hpp, src/types/Component.cpp, + src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, + src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, + src/types/MakeStamps.hpp, src/types/Makefile, + src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, + src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, + src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, + src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, + src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, + src/brains/Exclude.hpp, src/brains/ForceFields.cpp, + src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, + src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, + src/brains/SimSetup.hpp, src/brains/SimState.cpp, + src/brains/SimState.hpp, src/brains/SkipList.cpp, + src/brains/SkipList.hpp, src/brains/Thermo.cpp, + src/brains/Thermo.hpp, src/brains/fSimulation.h, + src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, + src/brains/simulation_module.F90, src/io/BASS_interface.cpp, + src/io/Globals.hpp, src/io/LinkedAssign.cpp, + src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, + src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, + src/math/mt19937ar.c, src/math/randomSPRNG.cpp, + src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, + src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, + src/minimizers/OOPSEMinimizer.cpp, + src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, + src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, + src/primitives/Atom.cpp, src/primitives/Atom.hpp, + src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, + src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, + src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, + src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, + src/primitives/Makefile, src/primitives/Molecule.cpp, + src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, + src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, + src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, + src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, + src/restraints/Makefile, src/restraints/Restraints.cpp, + src/restraints/Restraints.hpp, src/utils/GenericData.cpp, + src/utils/GenericData.hpp, src/utils/Makefile, + src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, + src/utils/StringUtils.c, src/utils/StringUtils.cpp, + src/utils/StringUtils.h, src/utils/StringUtils.hpp, + src/utils/TypeInfo.hpp, src/utils/Utility.cpp, + src/utils/Utility.hpp, src/utils/definitions_module.F90, + src/utils/fError.c, src/utils/oopseMPI_module.F90, + src/utils/simError.c, src/utils/simError.h, + src/utils/status_module.F90, src/utils/vector_class.F90, + src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, + src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, + src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, + src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, + src/visitors/RigidBodyVisitor.cpp, + src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, + src/visitors/ZconsVisitor.hpp, make/Makefile, + make/_files/style.css, samples/Makefile.in, + samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, + samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, + samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, + samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, + samples/zcons/Makefile.in, samples/zcons/water.md, + samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, + samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, + src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, + src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, + src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, + src/applications/Lattice.cpp, src/applications/Lattice.hpp, + src/applications/LatticeCreator.cpp, + src/applications/LatticeCreator.hpp, + src/applications/LatticeFactory.cpp, + src/applications/LatticeFactory.hpp, src/applications/Makedepend, + src/applications/Makefile, src/applications/MoLocator.cpp, + src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, + src/applications/cmdline.c, src/applications/cmdline.h, + src/applications/getopt.c, src/applications/getopt1.c, + src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, + src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, + src/applications/quickLate.c, src/applications/simpleBuilder.cpp, + src/applications/simpleBuilder.ggo, + src/applications/simpleBuilderCmd.c, + src/integrators/AbstractClasses.hpp, + src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, + src/integrators/Integrator.hpp, src/integrators/Makefile, + src/integrators/NPT.cpp, src/integrators/NPTf.cpp, + src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, + src/integrators/NVT.cpp, src/profiling/Makefile, + src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, + src/profiling/timing.F90, samples/metals/Au_bulk.in, + samples/metals/Au_nanoparticle.in, samples/metals/metals.md, + samples/water/Makefile.in, samples/water/dimer/Makefile.in, + samples/water/dimer/two.in, samples/water/dimer/two.md, + samples/water/dimer/water.md, samples/water/spce/Makefile.in, + samples/water/spce/spce.in, samples/water/spce/spce.md, + samples/water/spce/water.md, samples/water/ssde/Makefile.in, + samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, + samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, + samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, + samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, + samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, + samples/water/ssd/water.md, samples/water/tip4p/tp4.in, + samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, + samples/alkane/Makefile.in, samples/alkane/alkanes.md, + samples/alkane/butane.in, samples/alkane/butane.md, + samples/argon/500.in, samples/argon/500.md, + samples/argon/Makefile.in, samples/argon/ar864.in, + samples/argon/ar864.md, samples/argon/argonNVT.in, + samples/argon/argonNVT.md, samples/argon/lj.md, + samples/lipid/5x5.in, samples/lipid/5x5.md, + samples/lipid/Makefile.in, samples/lipid/lipid.md, + samples/lipid/water.md, samples/minimizer/Makefile.in, + samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, + samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, + samples/minimizer/tip4p_two.md, samples/minimizer/water.md, + samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, + forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, + forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, + forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, + forceFields/DUFF.frc, forceFields/DipoleTest.frc, + forceFields/EAM.VC.frc, forceFields/EAM.frc, + forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, + forceFields/Makefile.in, forceFields/Ni.u3.funcfl, + forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, + forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, + forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, + scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, - ac-tools/install-sh, ac-tools/shtool: Initial revision + ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, + forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, + forceFields/Au.u3.funcfl, forceFields/LJFF.frc, + forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, + forceFields/Pt.VC.funcfl: Initial revision