--- trunk/OOPSE-4/ChangeLog 2004/10/20 22:54:30 1622 +++ trunk/OOPSE-4/ChangeLog 2006/04/21 19:32:07 2727 @@ -1,1048 +1,8607 @@ -2004-10-20 16:52 gezelter - - * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, - DarkSide/sticky_interface.h: fixed a fortran name problem - -2004-10-20 16:38 tim - - * test/utils/: GenericData.hpp, GenericDataTestCase.cpp, - GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, - UtilTest, UtilTest.cpp: adding generic data test case - -2004-10-20 16:16 chuckv - - * configure, ac-tools/aclocal.m4, - src/UseTheForce/DarkSide/Makefile, - src/UseTheForce/DarkSide/mpiSimulation.F90, - src/UseTheForce/DarkSide/mpiSimulation_interface.h, - src/UseTheForce/DarkSide/simParallel.F90, - src/UseTheForce/DarkSide/simParallel_interface.h, - src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: - Fortran/C++ interface de-obfuscation project appears to be - complete! Woo hoo! - -2004-10-20 15:47 chuckv - - * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, - fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project - continues - -2004-10-20 15:46 chuckv - - * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, - UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, - UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, - UseTheForce/doForces_interface.h, - UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, - UseTheForce/DarkSide/atype_interface.h, - UseTheForce/DarkSide/eam_interface.h, - UseTheForce/DarkSide/gb_interface.h, - UseTheForce/DarkSide/mpiSimulation_interface.h, - UseTheForce/DarkSide/shapes_interface.h, - UseTheForce/DarkSide/simulation_interface.h, - UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, - brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface - de-obfuscation project (It is a very long story) - -2004-10-20 13:07 tim - - * ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, - test/math/SquareMatrix3TestCase.cpp, - test/math/SquareMatrixTestCase.cpp, - test/math/SquareMatrixTestCase.hpp: Math library pass the unit test - -2004-10-20 00:52 tim - - * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and - SnapshotManager in design phase - -2004-10-19 23:54 gezelter - - * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace - problem prevented linking - -2004-10-19 23:54 gezelter - - * src/UseTheForce/Shapes_FF.cpp: fixed include - -2004-10-19 23:26 gezelter - - * src/utils/: Makefile, definitions.F90, definitions_module.F90, - oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: - more fortran name mangling - -2004-10-19 23:23 gezelter - - * src/profiling/timing.F90: yet more fortran renaming - -2004-10-19 23:19 gezelter - - * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, - do_Forces.F90, do_Forces.h, notifyCutoffs.F90, - notifyCutoffs_interface.h, notifycutoffs_module_interface.h, - wrappers.F90: Fortran name cleanup continues - -2004-10-19 23:12 gezelter - - * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some - broken fortran stuff - -2004-10-19 23:02 gezelter - - * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, - atype_interface.h, atype_module.F90, atype_module_interface.h, - calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, - calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, - calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, - eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, - gb_interface.h, gb_module_interface.h, mpiSimulation.F90, - mpiSimulation_interface.h, mpiSimulation_module.F90, - mpisimulation_module_interface.h, reactionField.F90, shapes.F90, - shapes_interface.h, shapes_module.h, simulation.F90, - simulation_interface.h, simulation_module.F90, - simulation_module_interface.h, sticky.F90, sticky_interface.h, - sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: - name sanity on the fortran side - -2004-10-19 19:18 tim - - * test/math/SquareMatrix3TestCase.hpp: [no log message] - -2004-10-19 18:01 tim - - * src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, - src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: - except diagonalize(), all of functions in math library pass the - test - -2004-10-19 17:43 chuckv - - * src/UseTheForce/do_Forces.h: Added correct prototypes for - C-fortran interface functions. - -2004-10-19 17:37 chuckv - - * src/UseTheForce/DarkSide/: atype_module_interface.h, - eam_module_inteface.h, gb_module_interface.h, - mpisimulation_module_interface.h, simulation_module_interface.h, - sticky_pair_module_interface.h: Added correct prototypes for - C-fortran interface functions. - -2004-10-19 16:28 tim - - * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, - src/math/SquareMatrix.hpp, src/math/Vector.hpp, - test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, - test/math/RectMatrixTestCase.cpp, - test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, - test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more - bugs get fixed at math library - -2004-10-19 15:43 chuckv - - * src/UseTheForce/: DarkSide/atype_module_interface.h, - DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, - DarkSide/mpisimulation_module_interface.h, - DarkSide/simulation_module_interface.h, - DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, - DarkSide/atype_module.F90, DarkSide/calc_gb.F90, - DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, - DarkSide/simulation_module.F90, do_Forces.F90, - fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, - notifycutoffs_module_interface.h: Added new files for fortran - interface. - -2004-10-19 15:43 gezelter - - * src/UseTheForce/Makefile: regressing - -2004-10-19 15:40 gezelter - - * src/: UseTheForce/DarkSide/calc_shapes.F90, - UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: - working on shapes for portability - -2004-10-19 15:40 gezelter - - * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes - -2004-10-19 13:21 chrisfen - - * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around - findBegin - -2004-10-18 23:34 tim - - * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs - are fixed in Vector class - -2004-10-18 23:28 tim - - * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix - some bugs in RectMatrixTestCase - -2004-10-18 23:21 tim - - * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, - test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, - test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, - test/math/VectorTestCase.hpp: implement more test cases - -2004-10-18 18:13 tim - - * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, - src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, - src/math/SquareMatrix3.hpp, src/math/Vector.hpp, - src/utils/StringTokenizer.hpp, test/math/Makefile, - test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more - tests on math library - -2004-10-18 16:03 tim - - * test/math/: Makefile, QuaternionTestCase.cpp, - QuaternionTestCase.hpp, RectMatrixTestCase.cpp, - SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, - Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding - more testing units - -2004-10-18 12:07 tim - - * src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, - math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, - math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, - utils/GenericFactory.hpp: fix some bugs in Quaternion class - -2004-10-18 11:30 gezelter - - * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: - Your basic run of the mill real-valued versions of Y_l^m(\theta, - \phi) - -2004-10-18 11:29 gezelter - - * src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, - types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, - utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting - Shapes into OOPSE - -2004-10-18 10:21 gezelter - - * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType - -2004-10-18 00:23 tim - - * test/math/VectorTestCase.hpp: adding vector test case - -2004-10-18 00:23 tim - - * src/utils/GenericFactory.hpp: adding generic factory and vector - test case - -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, - 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, 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, 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: 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, 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, 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, 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, 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, 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, samples/Makefile.in, +2006-04-20 23:19 chrisfen + + * samples/water/spce/spce.md, + src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added... + +2006-04-20 17:02 chrisfen + + * samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90, + src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky + +2006-04-20 14:24 gezelter + + * samples/metals/EAM/Au_bulk_voter.md, + samples/metals/Sutton-Chen/Au_bulk_SC.md, + samples/water/ssde/ssde.md, src/UseTheForce/ForceField.cpp, + src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/LJ.F90, + src/UseTheForce/DarkSide/eam.F90, + src/UseTheForce/DarkSide/electrostatic.F90, + src/UseTheForce/DarkSide/suttonchen.F90, + src/UseTheForce/DarkSide/switcheroo.F90, + src/UseTheForce/DarkSide/switcheroo_interface.F90, + src/UseTheForce/DarkSide/switcheroo_interface.h, + src/utils/interpolation.F90: Complete rewrite of spline code and + everything that uses it. + +2006-04-17 17:49 gezelter + + * configure, ac-tools/aclocal.m4, samples/argon/500.md, + samples/metals/EAM/Au_bulk_voter.md, + samples/metals/Sutton-Chen/Au_bulk_SC.md, + samples/water/ssde/ssde.md, src/UseTheForce/doForces.F90, + src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90, + src/UseTheForce/DarkSide/electrostatic.F90, + src/UseTheForce/DarkSide/interpolation.F90, + src/UseTheForce/DarkSide/sticky.F90, + src/UseTheForce/DarkSide/suttonchen.F90, + src/UseTheForce/DarkSide/switcheroo.F90, + src/applications/hydrodynamics/Hydro.ggo, + src/applications/hydrodynamics/HydroCmd.c, + src/applications/hydrodynamics/HydroCmd.h, + src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp, + src/utils/interpolation.F90: Many performance improvements + +2006-04-15 22:51 chrisfen + + * configure, samples/argon/500.md, src/UseTheForce/doForces.F90, + src/UseTheForce/fSwitchingFunction.h, + src/UseTheForce/DarkSide/electrostatic.F90, + src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to + switcheroo + +2006-04-15 17:58 chrisfen + + * src/utils/Makefile.in: Since status.F90 is used by + interpolation.F90, the former needs to be listed above the later in + the Makefile. + +2006-04-14 17:59 gezelter + + * src/utils/interpolation.F90: changed the interface a bit + +2006-04-14 17:49 gezelter + + * src/utils/interpolation.F90: added some logical flags + +2006-04-14 17:06 chrisfen + + * src/utils/interpolation.F90: Wiped the spline with derivatives + and corrected a boundary comparision error by eliminating the + check. This algorithm REQUIRES known first derivatives at the + endpoints. + +2006-04-14 16:04 gezelter + + * src/utils/: Makefile.in, interpolation.F90: bug fixes for + interpolation module + +2006-04-14 15:57 gezelter + + * src/utils/interpolation.F90: Heavily modified interpolation + module, also moved to "utils" + +2006-04-12 17:15 chuckv + + * src/UseTheForce/DarkSide/interpolation.F90: Added interpolation + module. + +2006-04-11 11:33 gezelter + + * src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c, + StaticPropsCmd.h: [no log message] + +2006-04-03 11:37 chuckv + + * configure, ac-tools/aclocal.m4, make/Makefile.in, + src/UseTheForce/DarkSide/simParallel.F90: Added status module to + simParallel for error reporting. + +2006-03-31 13:09 tim + + * src/: integrators/NPrT.cpp, io/Globals.cpp: NPrT might work now + +2006-03-30 16:08 chuckv + + * src/UseTheForce/DarkSide/suttonchen.F90: Fixed memory leak bug + where SCList capacity was not reset to zero on destruction. + +2006-03-30 14:37 chuckv + + * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: + More testing of nanoparticleBuilder. + +2006-03-29 17:24 chuckv + + * src/mdParser/SimplePreprocessor.hpp: Added check to make sure md + file exists. + +2006-03-29 14:17 chuckv + + * src/: applications/nanoparticleBuilder/nanoparticleBuilder.cpp, + lattice/shapedLattice.cpp, lattice/shapedLattice.hpp: Fixed + latticeOrt in shapedlatice and latticebuilder. + +2006-03-29 13:11 tim + + * src/applications/dynamicProps/: DipoleCorrFunc.cpp, + LegendreCorrFunc.cpp, VCorrFunc.cpp: Fix the normalization problem + in calculating correlation functions + +2006-03-29 13:09 tim + + * src/applications/hydrodynamics/: ApproximationModel.cpp, + ApproximationModel.hpp, CompositeShape.cpp, Hydro.cpp, Hydro.ggo, + HydroCmd.c, HydroCmd.h, HydrodynamicsModel.hpp, RoughShell.cpp: (1) + RoughShell Model is working; (20)Adding a new option into Hydro + which allows user to generate the beads only + +2006-03-27 11:21 chuckv + + * src/applications/nanoparticleBuilder/Makefile: Makefile for + nanoparticle builder. + +2006-03-27 11:03 chuckv + + * make/Makefile.in, src/lattice/shapedLattice.cpp, + src/lattice/shapedLattice.hpp: Added nanoparticle builder to + makefile + +2006-03-24 15:46 chuckv + + * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp: + Debugging changes to nanoparticle builder. + +2006-03-24 12:29 tim + + * src/applications/dynamicProps/: DynamicProps.cpp, + DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, + RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: back to previous DynamicProps + +2006-03-24 11:49 tim + + * src/applications/dynamicProps/: DynamicProps.cpp, + DynamicProps.ggo, DynamicPropsCmd.c, DynamicPropsCmd.h, Makefile, + RCorrFunc.cpp, RMSD.cpp, RMSD.hpp: Adding position correlation + function. The command line option for DynamicProps is now changed. + --rcorr is for position correlation and --rmsd is for mean square + displacement. + +2006-03-23 10:03 tim + + * src/applications/hydrodynamics/: AnalyticalModel.cpp, + AnalyticalModel.hpp, ApproximationModel.cpp, + ApproximationModel.hpp, HydrodynamicsModel.hpp: update writeBeads + method + +2006-03-23 10:02 tim + + * src/io/Globals.hpp: remove a unknown method + +2006-03-23 10:00 tim + + * src/math/CholeskyDecomposition.hpp: The off diagnal is not set + +2006-03-23 09:59 tim + + * src/mdParser/SimplePreprocessor.hpp: Throw exception if the file + can not be opened for preprocessing + +2006-03-22 15:57 chuckv + + * src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, + shapedLatticeSpherical.cpp, shapedLatticeSpherical.hpp: Added + shaped lattice. + +2006-03-21 10:33 tim + + * src/applications/hydrodynamics/ApproximationModel.cpp: fix a bug + in calculating hydrodynamics tensor when the radius of beads are + not the same + +2006-03-20 19:26 tim + + * src/: applications/hydrodynamics/AnalyticalModel.cpp, + applications/hydrodynamics/BeadModel.cpp, + applications/hydrodynamics/ShapeBuilder.cpp, + integrators/LDForceManager.cpp: Fix a bug in friction calculation + for ellipsoid + +2006-03-20 14:12 tim + + * src/: applications/hydrodynamics/AnalyticalModel.cpp, + applications/hydrodynamics/Ellipsoid.cpp, + applications/hydrodynamics/Ellipsoid.hpp, + applications/hydrodynamics/ShapeBuilder.cpp, + integrators/LDForceManager.cpp: Verify the correctness of + Ellipsoid's hydrodynamics properties + +2006-03-17 18:51 tim + + * src/applications/hydrodynamics/: Hydro.cpp, ShapeBuilder.cpp: New + version of Hydro is working now. + +2006-03-17 18:20 tim + + * src/: applications/hydrodynamics/AnalyticalModel.cpp, + applications/hydrodynamics/AnalyticalModel.hpp, + applications/hydrodynamics/ApproximationModel.cpp, + applications/hydrodynamics/ApproximationModel.hpp, + applications/hydrodynamics/BeadModel.hpp, + applications/hydrodynamics/CompositeShape.cpp, + applications/hydrodynamics/CompositeShape.hpp, + applications/hydrodynamics/Ellipsoid.cpp, + applications/hydrodynamics/Ellipsoid.hpp, + applications/hydrodynamics/Hydro.cpp, + applications/hydrodynamics/Hydro.ggo, + applications/hydrodynamics/HydroCmd.c, + applications/hydrodynamics/HydroCmd.h, + applications/hydrodynamics/HydrodynamicsModel.cpp, + applications/hydrodynamics/HydrodynamicsModel.hpp, + applications/hydrodynamics/HydrodynamicsModelCreator.hpp, + applications/hydrodynamics/HydrodynamicsModelFactory.cpp, + applications/hydrodynamics/HydrodynamicsModelFactory.hpp, + applications/hydrodynamics/Makefile, + applications/hydrodynamics/RoughShell.cpp, + applications/hydrodynamics/RoughShell.hpp, + applications/hydrodynamics/Shape.hpp, + applications/hydrodynamics/ShapeBuilder.cpp, + applications/hydrodynamics/ShapeBuilder.hpp, + applications/hydrodynamics/Spheric.cpp, + applications/hydrodynamics/Spheric.hpp, + applications/hydrodynamics/StuntDoubleShape.cpp, + applications/hydrodynamics/StuntDoubleShape.hpp, + integrators/LDForceManager.cpp, integrators/LDForceManager.hpp, + io/Globals.cpp, io/Globals.hpp, math/SquareMatrix.hpp, + utils/HydroProps.hpp: refactor Hydrodynamics module. + +2006-03-17 11:10 chuckv + + * src/lattice/: shapedLattice.cpp, shapedLattice.hpp, Makefile: + Generic Shaped Lattice for oopse. Can overload to get spherical or + nanorod. + +2006-03-16 17:50 tim + + * src/: applications/hydrodynamics/HydrodynamicsModel.cpp, + integrators/LDForceManager.cpp, math/MersenneTwister.hpp: + LagevinDynamics is working? + +2006-03-16 16:52 gezelter + + * src/applications/hydrodynamics/RoughShell.hpp: fixed a const + problem + +2006-03-15 17:08 tim + + * src/applications/hydrodynamics/HydrodynamicsModel.cpp: unit + conversion for diffusion tensor is wrong + +2006-03-15 16:28 tim + + * src/: applications/hydrodynamics/HydrodynamicsModel.cpp, + utils/NumericConstant.hpp: change the epsilon of numeric_limit + +2006-03-15 15:58 tim + + * src/applications/hydrodynamics/HydrodynamicsModel.cpp: correcting + the unit in HydrodynamicsModel + +2006-03-15 12:35 tim + + * src/primitives/RigidBody.cpp: using setFrc in + RigidBody::calcForcesAndTorques will discard if there are force and + torque applied in rigid body itself. use addFrc instead. + +2006-03-15 10:51 tim + + * src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp, + RoughShell.cpp, RoughShell.hpp: Adding RoughShell and BeadModel + +2006-03-15 10:50 tim + + * make/Makefile.in, src/applications/hydrodynamics/Makefile: adding + hydrodynamics module into build system + +2006-03-14 18:46 tim + + * src/math/CholeskyDecomposition.hpp: adding Cholesky Decomposition + +2006-03-13 17:42 tim + + * src/: applications/hydrodynamics/HydrodynamicsModel.cpp, + applications/hydrodynamics/HydrodynamicsModel.hpp, + applications/hydrodynamics/StuntDoubleShape.cpp, + applications/hydrodynamics/StuntDoubleShape.hpp, + brains/Register.cpp, integrators/LDForceManager.cpp, + integrators/LDForceManager.hpp, integrators/LangevinDynamics.cpp, + integrators/LangevinDynamics.hpp, integrators/Makefile, + io/Globals.cpp, io/Globals.hpp, math/MersenneTwister.hpp, + math/RandNumGen.hpp, math/SquareMatrix3.hpp: LangevinDynamics in + progress + +2006-03-07 11:43 gezelter + + * src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Fixed a + double/int bug. Surprised no one ever noticed before... + +2006-02-24 16:17 tim + + * src/applications/hydrodynamics/HydrodynamicsModel.cpp: fix bugs + in HydrodynamicsModel; (1) sign issue of Xirr calculation (2) out + product of Rij + +2006-02-23 18:16 tim + + * src/applications/hydrodynamics/: Hydro.cpp, Hydro.ggo, + HydroCmd.c, HydroCmd.h, HydrodynamicsModel.cpp, + HydrodynamicsModel.hpp, HydrodynamicsModelCreator.hpp, + HydrodynamicsModelFactory.cpp, HydrodynamicsModelFactory.hpp, + MoleculeShape.cpp, MoleculeShape.hpp, StuntDoubleShape.cpp, + StuntDoubleShape.hpp: Bead Model is working + +2006-02-22 15:35 tim + + * src/: applications/hydrodynamics/Hydro.cpp, + applications/hydrodynamics/Hydro.ggo, + applications/hydrodynamics/HydroCmd.c, + applications/hydrodynamics/HydroCmd.h, + applications/hydrodynamics/HydrodynamicsModel.cpp, + applications/hydrodynamics/HydrodynamicsModel.hpp, + applications/hydrodynamics/HydrodynamicsModelCreator.hpp, + applications/hydrodynamics/HydrodynamicsModelFactory.cpp, + applications/hydrodynamics/HydrodynamicsModelFactory.hpp, + applications/hydrodynamics/MoleculeShape.cpp, + applications/hydrodynamics/MoleculeShape.hpp, + math/DynamicRectMatrix.hpp, math/DynamicVector.hpp, math/LU.hpp, + math/RectMatrix.hpp, math/SquareMatrix3.hpp: Adding Hydrodynamics + Module + +2006-02-16 17:05 gezelter + + * src/brains/Snapshot.cpp: fixed a spelling error + +2006-02-16 16:40 gezelter + + * src/: UseTheForce/doForces.F90, + UseTheForce/DarkSide/simulation.F90, math/Makefile, + math/linearAlgebra.F90: fixed a problem with cutoff radii being set + larger than 1/2 the length of the shortest box dimension. added a + few fortran utility routines + +2006-02-15 15:46 chuckv + + * src/applications/nanoparticleBuilder/: sphericalNanoparticle.cpp, + sphericalNanoparticle.hpp: Changed Names of class files. + +2006-02-10 10:45 kdaily + + * src/applications/dynamicProps/LegendreCorrFunc.cpp: [no log + message] + +2006-02-10 10:12 tim + + * src/math/: LegendrePolynomial.cpp, Vector.hpp: fix a bug in + converting integer to double + +2006-02-08 13:21 chrisfen + + * forceFields/DUFF2.frc: added DPD molecule type parameters + +2006-02-07 11:39 tim + + * src/applications/dynamicProps/: DipoleCorrFunc.cpp, + LegendreCorrFunc.cpp: Fixing a bug which reads the wrong frame of + trajectory file during analysis + +2006-02-02 12:14 tim + + * src/: math/Polynomial.hpp, math/SquareMatrix3.hpp, + types/AtomStamp.cpp: adding transpose into SquareMatrix3; fix a bug + in AtomStamp where orientation is not set correctly. + +2006-02-02 11:49 gezelter + + * src/primitives/RigidBody.cpp: fixed a bug in rigid bodies that + contain directional atoms + +2006-02-02 10:49 xsun + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Adding visitor + for GBlipid atom type + +2006-02-01 21:57 gezelter + + * make/Makefile.in: added CXXFLAGS to the LinkOptions to allow + compilation with icc9 (skipping the gcc-4 std c++ libraries). + +2006-02-01 16:06 chrisfen + + * src/brains/SimInfo.cpp: Missing brace caused the last commit not + to build + +2006-02-01 15:54 chrisfen + + * samples/water/spce/spce.md, src/brains/SimInfo.cpp: Changes to + cutoff radius setting to a more logical procedure - still may + change... + +2006-02-01 12:26 gezelter + + * src/: math/Polynomial.hpp, utils/GenericData.hpp, utils/any.hpp: + Fixing some compile-time warnings and bugs for icc 9.1 on Mac OS X + +2006-01-30 17:25 tim + + * src/: applications/dynamicProps/DipoleCorrFunc.cpp, + applications/dynamicProps/DynamicProps.cpp, + applications/dynamicProps/DynamicProps.ggo, + applications/dynamicProps/DynamicPropsCmd.c, + applications/dynamicProps/DynamicPropsCmd.h, + applications/dynamicProps/LegendreCorrFunc.cpp, + applications/dynamicProps/LegendreCorrFunc.hpp, + applications/dynamicProps/Makefile, math/LegendrePolynomial.cpp, + math/LegendrePolynomial.hpp, math/Makefile, math/Polynomial.hpp: + Adding :LegendrePolynomial + +2006-01-19 17:54 chuckv + + * src/applications/nanoparticleBuilder/: Makefile, + nanoparticleBuilder.cpp, sphericalNanoparticle.hpp: Changes to + nanoparticle builder + +2006-01-18 16:08 chuckv + + * src/applications/nanoparticleBuilder/Makefile: Added Makefile for + nanoparticle builder. + +2006-01-17 11:16 gezelter + + * AUTHORS, README: Cleaning up for 3.0.1 release + +2006-01-17 10:50 gezelter + + * ChangeLog: Prepping 3.0.1 release + +2006-01-17 10:32 gezelter + + * src/config.h.in: new version number + +2006-01-17 10:32 gezelter + + * doc/: OOPSE.pdf, SelectionExpression.html, cppstyle.html, + definition.jpg, gofr.jpg, gofrtheta.jpg, heirarchy.png, + oopseManual.pdf: Updated Documentation + +2006-01-16 18:10 gezelter + + * ChangeLog, README: Getting ready for release! + +2006-01-16 10:26 gezelter + + * configure: Testing commit + +2006-01-13 16:57 chuckv + + * src/: UseTheForce/SC_FF.cpp, + applications/nanoparticleBuilder/sphericalNanoparticle.cpp, + io/Globals.cpp, io/Globals.hpp: Removed MixingRule from Globals. + Handled by forceField now. + +2006-01-13 14:17 chuckv + + * src/io/Globals.cpp: Added NPAT to Globals integrators. + +2006-01-13 11:33 gezelter + + * Makefile: [no log message] + +2006-01-13 11:26 gezelter + + * Makefile: testing to make sure GNU make is the make that was used + to build OOPSE + +2006-01-13 10:48 gezelter + + * configure, ac-tools/configure.in: changed compiler search order + +2006-01-12 19:09 chuckv + + * forceFields/SuttonChen.QSC.frc, forceFields/SuttonChen.frc, + samples/metals/Sutton-Chen/Au_bulk.in, + samples/metals/Sutton-Chen/Au_bulk_QSC.md, + samples/metals/Sutton-Chen/Au_bulk_SC.md: Changes in Sutton-Chen + units + +2006-01-12 16:16 gezelter + + * LICENSE, configure, src/applications/oopse/oopse.cpp: fixed some + version info and the copyright date + +2006-01-12 15:52 gezelter + + * src/config.h.in: added some missing checks for header files + (particularly zlib.h), used autoheader to help generate config.h.in + +2006-01-12 15:51 gezelter + + * configure, ac-tools/configure.in: added some missing checks for + header files (particularly zlib.h) + +2006-01-12 15:19 gezelter + + * make/Makefile.in: fixed a dependency problem for the Executable + builds + +2006-01-12 15:02 gezelter + + * samples/gbljtest/Makefile: Missing Makefile in this sample + directory + +2006-01-12 15:01 gezelter + + * make/Makefile.in, samples/Makefile.in, samples/cutoff/Makefile: + Old makefile.in no longer required + +2006-01-12 15:01 gezelter + + * forceFields/: Makefile, Makefile.in: All of the OpenBabel stuff + needs to be installed + +2006-01-12 14:56 chuckv + + * src/io/DumpWriter.cpp: Changed formating. + +2006-01-12 11:47 chrisfen + + * samples/water/tip4p/tp4.md, + src/UseTheForce/DarkSide/electrostatic.F90, + src/UseTheForce/DarkSide/electrostatic_interface.F90, + src/UseTheForce/DarkSide/electrostatic_interface.h, + src/brains/SimInfo.cpp: unifying function name in electrostatics + +2006-01-12 11:04 tim + + * samples/metals/: EAM/nanoparticle/Makefile, + EAM/nanorod/Au_nanoparticle.in, EAM/nanorod/Makefile, + Sutton-Chen/Makefile: fix make install problem for metals samples + +2006-01-12 10:22 tim + + * make/Makefile.in: remove samples/metals from install list. + +2006-01-12 09:31 tim + + * src/io/: ForceFieldOptions.cpp, Globals.cpp: filepp can not + handle multiple line macro, just convert multiple line macro into + single line macro. + +2006-01-11 23:13 chrisfen + + * src/: UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/neighborLists.F90, io/Globals.cpp: Made some + changes to electrostatics for shifted-potential and shifted-force + with mono and multipoles + +2006-01-11 18:04 gezelter + + * src/config.h.in, src/UseTheForce/doForces_interface.h, + src/UseTheForce/DarkSide/atype_interface.h, + src/UseTheForce/DarkSide/eam_interface.h, + src/UseTheForce/DarkSide/electrostatic_interface.h, + src/UseTheForce/DarkSide/fForceOptions_interface.h, + src/UseTheForce/DarkSide/gb_interface.h, + src/UseTheForce/DarkSide/lj_interface.h, + src/UseTheForce/DarkSide/shapes_interface.h, + src/UseTheForce/DarkSide/simParallel_interface.h, + src/UseTheForce/DarkSide/simulation_interface.h, + src/UseTheForce/DarkSide/sticky_interface.h, + src/UseTheForce/DarkSide/suttonchen_interface.h, + src/UseTheForce/DarkSide/switcheroo_interface.h, + src/mdParser/MDParser.g, src/profiling/mdProfile.cpp, + src/utils/fError.c, configure, make/Makefile.in: autoconf + modernization and cruft removal + +2006-01-11 18:04 gezelter + + * ac-tools/: aclocal.m4, configure.in, fortran90.m4: autoconf + modernization and cruft-removal + +2006-01-11 17:50 tim + + * src/types/: BendStamp.hpp, BondStamp.hpp, TorsionStamp.hpp: fix + some error messages + +2006-01-11 14:01 tim + + * src/: applications/staticProps/RhoZ.cpp, brains/SimCreator.cpp, + io/Globals.cpp, types/AtomStamp.cpp, types/BendStamp.hpp, + types/BondStamp.hpp, types/DataHolder.hpp, types/MoleculeStamp.cpp, + types/TorsionStamp.hpp, utils/OOPSEException.hpp, + utils/StringUtils.hpp: instead of printing to std::cout, throwing + an exception when error is found. + +2006-01-11 13:41 gezelter + + * src/types/: AtomStamp.hpp, MoleculeStamp.cpp: Fixed a spelling + error + +2006-01-10 17:55 chuckv + + * forceFields/SuttonChen.frc: Changed conversion factor. + +2006-01-10 16:14 chuckv + + * samples/metals/Sutton-Chen/Au_bulk_SC.md, + src/UseTheForce/DarkSide/suttonchen.F90: Sutton and Chen should be + working now. + +2006-01-09 17:22 chuckv + + * src/UseTheForce/doForces.F90: Fixed SC bug with SIM_uses_SC + +2006-01-09 17:14 tim + + * src/applications/staticProps/: Makefile, RhoZ.cpp, RhoZ.hpp, + StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, + StaticPropsCmd.h: fixing RhoZ + +2006-01-09 14:26 chuckv + + * forceFields/SuttonChen.frc, + samples/metals/Sutton-Chen/Au_bulk_SC.md, + src/io/LennardJonesAtomTypesSectionParser.cpp, + src/io/SCAtomTypesSectionParser.cpp: Added energy scaling to + section parsers. + +2006-01-09 14:11 tim + + * src/: io/ForceFieldOptions.hpp, utils/StringUtils.cpp, + utils/StringUtils.hpp: replace isType with isInteger + +2006-01-06 16:15 tim + + * src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: remove extra + forceFieldOptions from SC_FF + +2006-01-06 15:27 chuckv + + * forceFields/SuttonChen.frc: Add force file. + +2005-12-31 17:42 chuckv + + * src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen no longer + segfaults or produces 0 potential, but rather produces Inf for the + potential. Progress.... + +2005-12-30 18:15 chuckv + + * samples/metals/Sutton-Chen/Au_bulk_SC.md, + src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, + src/UseTheForce/DarkSide/suttonchen.F90, src/brains/SimInfo.cpp, + src/io/ForceFieldOptions.cpp, src/io/ForceFieldOptions.hpp: More + Sutton-Chen bug fixes. + +2005-12-30 16:25 tim + + * src/: UseTheForce/doForces.F90, brains/Thermo.cpp: Long range + potential return from fortran is already accumulated, it should not + be accumulated again; nGroupTypesCol is not initialized; + GroupMaxCutoffCol is not allocated; + +2005-12-30 10:32 tim + + * make/Makefile.in, src/brains/SimCreator.cpp: In order to compile + MPI version, we need to cast const char* to void* for + stringstream.str(); Previous Makefile use bjects of single version + to make the MPI library; + +2005-12-29 19:18 chuckv + + * make/Makefile.in, samples/metals/Makefile, + src/UseTheForce/SC_FF.cpp, src/UseTheForce/doForces.F90, + src/UseTheForce/DarkSide/suttonchen.F90: Sutton-Chen bug fixes. + Almost there... + +2005-12-29 15:19 chuckv + + * forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Changes in + forcefield. + +2005-12-29 15:07 chuckv + + * samples/metals/Sutton-Chen/: Au_bulk.in, Au_bulk_SC.md, Makefile, + metals.md: added files for sutton-chen + +2005-12-29 11:37 chuckv + + * samples/metals/EAM/nanorod/: Au_nanoparticle_FCC.md, Makefile, + metals.md: More cvs changing. + +2005-12-29 11:34 chuckv + + * samples/metals/Au_nanoparticle.in: More moving... + +2005-12-29 11:33 chuckv + + * samples/metals/EAM/nanoparticle/: + Au-Core-Ag-Shell_Nanoparticle.in, Au-Core-Ag-Shell_Nanoparticle.md, + Au_nanoparticle.in, Au_nanoparticle.md, Makefile, metals.md: More + changes to directory structure. + +2005-12-29 11:21 chuckv + + * samples/metals/EAM/: Au_bulk.in, Au_bulk_FBD.md, + Au_bulk_voter.md, Makefile, metals.md: More Directory changes... + +2005-12-29 11:17 chuckv + + * samples/metals/: Au-Core-Ag-Shell_Nanoparticle.in, + Au-Core-Ag-Shell_Nanoparticle.md, Au_bulk.in, Au_bulk_FBD.md, + Au_bulk_voter.md, Au_nanoparticle.md, metals.md: More changing of + directory structure + +2005-12-29 11:03 chuckv + + * src/: UseTheForce/DarkSide/fForceOptions_interface.F90, + brains/SimCreator.cpp: Fixed issue with symbol naming and added + call to set force options in SimCreator. + +2005-12-28 16:44 chuckv + + * src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp: More + changes to forcefield options. + +2005-12-28 16:42 chuckv + + * src/UseTheForce/: ForceField.cpp, ForceField.hpp: Force options + passed to fortran. + +2005-12-23 18:04 chuckv + + * src/: UseTheForce/DarkSide/fForceOptions_interface.h, + io/ForceFieldOptions.cpp, io/ForceFieldOptions.hpp: Force option + changes. + +2005-12-16 16:52 tim + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + src/config.h.in, src/UseTheForce/DarkSide/gb.F90, + src/openbabel/bitvec.cpp, src/openbabel/bondtyper.cpp, + src/openbabel/chains.cpp, src/openbabel/chiral.cpp, + src/openbabel/data.cpp, src/openbabel/fingerprint.cpp, + src/openbabel/fingerprintformat.cpp, src/openbabel/generic.cpp, + src/openbabel/gromos96format.hpp, src/openbabel/kekulize.cpp, + src/openbabel/matrix3x3.cpp, src/openbabel/mol.cpp, + src/openbabel/molchrg.cpp, src/openbabel/obatom.cpp, + src/openbabel/obbond.cpp, src/openbabel/oberror.cpp, + src/openbabel/oberror.hpp, src/openbabel/obmolecformat.hpp, + src/openbabel/obutil.cpp, src/openbabel/patty.cpp, + src/openbabel/pdbformat.cpp, src/openbabel/phmodel.cpp, + src/openbabel/povrayformat.hpp, src/openbabel/residue.cpp, + src/openbabel/ring.cpp, src/openbabel/rotor.cpp, + src/openbabel/smilesformat.cpp, src/openbabel/tinkerformat.hpp, + src/openbabel/typer.cpp, src/openbabel/xyzformat.cpp: changed + __FUNCTION__ to __func__ to match C99 standard, and then added an + autoconf test to check for __func__ usability. Changed some + default compile flags for the Sun architecture + +2005-12-16 14:01 gezelter + + * ac-tools/AC_CXX_HAVE_STL.m4: added the STL check + +2005-12-16 13:55 tim + + * src/utils/: CaseConversion.hpp, ParameterManager.hpp: make minor + change to build oopse under solaris + +2005-12-16 13:26 tim + + * src/: brains/SimCreator.cpp, io/Globals.cpp, + types/MoleculeStamp.cpp, utils/Predicate.hpp: the standard library + came with SUN compiler does not have a conforming std::use_facet, + define a macro to handle it. Adding exception handling to + SimCreator. + +2005-12-16 10:53 gezelter + + * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, + GB-Ar-traditional.md, gb-ar.in: Removed one parasitic argon atom + which was living inside the GB particle. No alien-like ripping out + of the stomach was required. + +2005-12-15 21:57 tim + + * src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, + MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, + MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: + replace grammar for numerical parsing + +2005-12-15 16:43 gezelter + + * src/UseTheForce/doForces.F90: fixed a cutoff bug + +2005-12-15 09:48 gezelter + + * src/antlr/: CharScanner.hpp, config.hpp: Removing compiler + dependencies and replacing them with real autoconf checks + +2005-12-15 09:47 gezelter + + * configure, ac-tools/AC_CXX_NAMESPACES.m4, ac-tools/AC_CXX_STD.m4, + ac-tools/configure.in, src/config.h.in: Adding checks for various + features used by ANTLR + +2005-12-14 13:02 tim + + * src/mdParser/: MDLexer.cpp, MDLexer.hpp, MDParser.cpp, + MDParser.g, MDParser.hpp, MDTokenTypes.hpp, MDTreeParser.cpp, + MDTreeParser.g, MDTreeParser.hpp, MDTreeParserTokenTypes.hpp: fix a + nasty negative integer parsing problem by refining the grammar + +2005-12-12 14:32 gezelter + + * src/: UseTheForce/doForces_interface.F90, + UseTheForce/doForces_interface.h, + UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/electrostatic_interface.F90, + UseTheForce/DarkSide/electrostatic_interface.h, + brains/MoleculeCreator.cpp, brains/SimInfo.cpp, + math/ChebyshevPolynomials.hpp, openbabel/obconversion.hpp: made + some minor changes to allow compilation with the portland group + compilers + +2005-12-10 11:54 tim + + * src/: types/MoleculeStamp.cpp, utils/Tuple.hpp: fixed compilation + problem for icc7 + +2005-12-09 16:18 gezelter + + * src/utils/CaseConversion.hpp: added missing include + +2005-12-09 12:11 gezelter + + * configure, ac-tools/aclocal.m4: added some checks for pathscale + compiler + +2005-12-08 17:05 gezelter + + * src/io/ForceFieldOptions.cpp: added copyright + +2005-12-08 17:04 gezelter + + * src/UseTheForce/doForces.F90: added info printout + +2005-12-08 17:04 gezelter + + * configure, ac-tools/configure.in: added pathscale + +2005-12-08 10:38 chuckv + + * src/: UseTheForce/CLAYFF.cpp, UseTheForce/DUFF.cpp, + UseTheForce/EAM_FF.cpp, UseTheForce/SC_FF.cpp, + UseTheForce/SHAPES_FF.cpp, io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.hpp, + io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, + io/GayBerneAtomTypesSectionParser.cpp, + io/GayBerneAtomTypesSectionParser.hpp, + io/MultipoleAtomTypesSectionParser.cpp, + io/MultipoleAtomTypesSectionParser.hpp, + io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, + io/ShapeAtomTypesSectionParser.cpp, + io/ShapeAtomTypesSectionParser.hpp, + io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, + io/StickyPowerAtomTypesSectionParser.cpp, + io/StickyPowerAtomTypesSectionParser.hpp, + io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp: + Wow thats alot o' files. Now passing forceFieldOptions to all of + the parsers. + +2005-12-07 18:10 chuckv + + * src/UseTheForce/: CLAYFF.cpp, DUFF.cpp, EAM_FF.cpp, EAM_FF.hpp, + SHAPES_FF.cpp, SHAPES_FF.hpp: This should really break things.... + Started adding support for ForceOptions to section parsers. + +2005-12-07 18:01 gezelter + + * src/UseTheForce/DarkSide/gb_interface.h: [no log message] + +2005-12-07 18:00 chuckv + + * src/io/: LennardJonesAtomTypesSectionParser.cpp, + LennardJonesAtomTypesSectionParser.hpp: Added forceOptions to + section parser + +2005-12-07 14:58 chuckv + + * src/UseTheForce/DarkSide/: LJ.F90, lj_interface.F90, + lj_interface.h, suttonchen.F90, suttonchen_interface.F90, + suttonchen_interface.h: Removed geometric distance mixing from + individual modules and now use force options to detemine what the + deal is. + +2005-12-07 14:46 chuckv + + * src/UseTheForce/: fForceOptions.h, DarkSide/fForceOptions.F90: + Further fixes for compiler issues. + +2005-12-07 14:44 chuckv + + * src/UseTheForce/fForceOptions.h: Fixed ifc public-private issue. + +2005-12-07 14:38 chuckv + + * src/UseTheForce/DarkSide/: Makefile, fForceOptions.F90, + fForceOptions_interface.F90, fForceOptions_interface.h: Added + support for fortran force options. + +2005-12-06 16:01 tim + + * src/types/MoleculeStamp.cpp: Fixed a bug in checkTorsion + +2005-12-06 14:26 chuckv + + * src/UseTheForce/: SC_FF.cpp, SC_FF.hpp: Changes to SC. + +2005-12-06 12:53 chuckv + + * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, + GeometryBuilder.hpp, nanorodBuilder.cpp: Changes to build twinned + crystal + +2005-12-06 12:52 chuckv + + * src/io/: DumpWriter.cpp, DumpWriter.hpp: Overloaded interface for + dumpwriter. + +2005-12-06 11:49 tim + + * samples/: alkane/alkanes.md, alkane/butane.md, argon/500.md, + argon/ar864.md, argon/argonNVT.md, argon/lj.md, + dipole/splitDipole.md, dipole/splitInWater.md, dipole/split_SSD.md, + dipole/twoSplitDipole.md, dipole/water.md, gbljtest/2gb.md, + gbljtest/gb.md, gbljtest/gb2lj1.md, gbljtest/gbRotRoundX.md, + gbljtest/gbRotRoundY.md, gbljtest/gbRotRoundZ.md, gbljtest/lj.md, + lipid/5x5.md, lipid/lipid.md, lipid/water.md, + metals/Au-Core-Ag-Shell_Nanoparticle.md, metals/Au_bulk_FBD.md, + metals/Au_bulk_voter.md, metals/Au_nanoparticle.md, + metals/metals.md, minimizer/ssdEM.md, minimizer/tip4p_two.md, + minimizer/water.md, shape/linear.md, + thermoIntegration/liquid/ssde.md, + thermoIntegration/liquid/water.md, thermoIntegration/solid/ssde.md, + thermoIntegration/solid/water.md, water/dimer/cl.md, + water/dimer/mix.md, water/dimer/mix2.md, water/dimer/ssd.md, + water/dimer/tap.md, water/dimer/two.md, water/dimer/water.md, + water/spce/spce.md, water/spce/water.md, water/ssd/ssd.md, + water/ssd/water.md, water/ssd-ion/ssdCl.md, water/ssd-ion/water.md, + water/ssde/ssde.md, water/ssde/water.md, water/ssdrf/ssdrf.md, + water/ssdrf/water.md, water/tap/tap.md, water/tap/water.md, + water/tip3p_ice/tp3.md, water/tip3p_ice/water.md, + water/tip4p/tp4.md, water/tip4p/water.md, zcons/water.md, + zcons/zconsFixed.md, zcons/zconsMoving.md: remove deprecated + keywords from samples + +2005-12-05 18:37 tim + + * src/io/: ForceFieldOptions.cpp, ForceFieldOptions.hpp, + Globals.cpp, Makefile: Fix parsing error in OptionSectionParser + +2005-12-05 17:23 gezelter + + * src/: UseTheForce/CLAYFF.cpp, UseTheForce/CLAYFF.hpp, + UseTheForce/Makefile, brains/Register.cpp, + io/ForceFieldOptions.hpp, io/OptionSectionParser.cpp: Adding + handler for CLAY force field + +2005-12-05 16:45 chuckv + + * src/openbabel/: zipstream.hpp, zipstreamimpl.hpp: Fixed build bug + in openbabel. + +2005-12-05 14:10 tim + + * src/types/MoleculeStamp.cpp: reformat error message + +2005-12-05 14:07 gezelter + + * forceFields/CLAYFF.frc: Adding .frc file for CLAYFF + +2005-12-05 13:23 tim + + * src/: types/AtomStamp.cpp, types/AtomStamp.hpp, + types/BendStamp.hpp, types/MoleculeStamp.cpp, + types/MoleculeStamp.hpp, types/TorsionStamp.hpp, utils/Tuple.hpp: + adding more checking for topology + +2005-12-02 17:37 gezelter + + * src/antlr/TokenStreamRewriteEngine.cpp: Spurious semicolon + removal + +2005-12-02 17:37 gezelter + + * src/config.h.in: We've made big changes. This isn't 2.0 anymore. + +2005-12-02 17:37 gezelter + + * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, + GB-Ar-traditional.md, cutoff_test.md, gb.md, lj.md, max.md, mix.md, + traditional.md: removing deprecated nAtoms and nComponents lines + +2005-12-02 15:34 tim + + * src/selection/SelectionToken.cpp: adding SelectionToken.cpp + +2005-12-02 15:18 tim + + * src/types/: FragmentStamp.cpp, FragmentStamp.hpp: Adding + FragmentStamp + +2005-12-02 15:11 gezelter + + * src/openbabel/: matrix3x3.cpp, matrix3x3.hpp: Errors are no + longer thrown with consts (fixes compilation bug on the Mac). + +2005-12-02 15:10 gezelter + + * src/integrators/VelocityVerletIntegrator.cpp: Got rid of spurious + printing out of timestep + +2005-12-02 15:10 gezelter + + * src/brains/ForceManager.cpp: Got rid of spurious printing out of + junk + +2005-12-02 15:10 gezelter + + * make/Makefile.in: Change build process for libOOPSE.a so that the + libraries aren't unpacked. libOOPSE.a is now made directly from + the object files + +2005-12-02 15:09 gezelter + + * configure, ac-tools/configure.in: added check for egrep (grep -E) + needed for new build of libOOPSE.a + +2005-12-02 13:43 tim + + * src/types/DataHolder.hpp: adding DataHolder + +2005-12-02 12:01 gezelter + + * samples/cutoff/: GB-Ar-max.md, GB-Ar-mix.md, + GB-Ar-traditional.md, gb-ar.in, gb.md: Added Gay-Berne / Argon test + case for the cutoff policies + +2005-12-02 10:38 tim + + * make/Makefile.in: update Makefile + +2005-12-02 10:38 tim + + * src/: antlr/ANTLRException.hpp, antlr/ANTLRUtil.cpp, + antlr/ANTLRUtil.hpp, antlr/AST.hpp, antlr/ASTArray.hpp, + antlr/ASTFactory.cpp, antlr/ASTFactory.hpp, antlr/ASTNULLType.cpp, + antlr/ASTNULLType.hpp, antlr/ASTPair.hpp, antlr/ASTRefCount.cpp, + antlr/ASTRefCount.hpp, antlr/BaseAST.cpp, antlr/BaseAST.hpp, + antlr/BitSet.cpp, antlr/BitSet.hpp, antlr/CharBuffer.cpp, + antlr/CharBuffer.hpp, antlr/CharInputBuffer.hpp, + antlr/CharScanner.cpp, antlr/CharScanner.hpp, + antlr/CharStreamException.hpp, antlr/CharStreamIOException.hpp, + antlr/CircularQueue.hpp, antlr/CommonAST.cpp, antlr/CommonAST.hpp, + antlr/CommonASTWithHiddenTokens.cpp, + antlr/CommonASTWithHiddenTokens.hpp, + antlr/CommonHiddenStreamToken.cpp, + antlr/CommonHiddenStreamToken.hpp, antlr/CommonToken.cpp, + antlr/CommonToken.hpp, antlr/IOException.hpp, + antlr/InputBuffer.cpp, antlr/InputBuffer.hpp, antlr/LLkParser.cpp, + antlr/LLkParser.hpp, antlr/LexerSharedInputState.hpp, + antlr/Makefile, antlr/MismatchedCharException.cpp, + antlr/MismatchedCharException.hpp, + antlr/MismatchedTokenException.cpp, + antlr/MismatchedTokenException.hpp, antlr/NoViableAltException.cpp, + antlr/NoViableAltException.hpp, + antlr/NoViableAltForCharException.cpp, + antlr/NoViableAltForCharException.hpp, antlr/Parser.cpp, + antlr/Parser.hpp, antlr/ParserSharedInputState.hpp, + antlr/RecognitionException.cpp, antlr/RecognitionException.hpp, + antlr/RefCount.hpp, antlr/SemanticException.hpp, antlr/String.cpp, + antlr/String.hpp, antlr/Token.cpp, antlr/Token.hpp, + antlr/TokenBuffer.cpp, antlr/TokenBuffer.hpp, + antlr/TokenRefCount.cpp, antlr/TokenRefCount.hpp, + antlr/TokenStream.hpp, antlr/TokenStreamBasicFilter.cpp, + antlr/TokenStreamBasicFilter.hpp, antlr/TokenStreamException.hpp, + antlr/TokenStreamHiddenTokenFilter.cpp, + antlr/TokenStreamHiddenTokenFilter.hpp, + antlr/TokenStreamIOException.hpp, + antlr/TokenStreamRecognitionException.hpp, + antlr/TokenStreamRetryException.hpp, + antlr/TokenStreamRewriteEngine.cpp, + antlr/TokenStreamRewriteEngine.hpp, antlr/TokenStreamSelector.cpp, + antlr/TokenStreamSelector.hpp, antlr/TokenWithIndex.hpp, + antlr/TreeParser.cpp, antlr/TreeParser.hpp, + antlr/TreeParserSharedInputState.hpp, antlr/config.hpp, + applications/oopse/oopse.cpp, brains/ForceManager.cpp, + brains/MoleculeCreator.cpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + constraints/ZconstraintForceManager.cpp, + integrators/VelocityVerletIntegrator.cpp, io/BASS_interface.cpp, + io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, + io/BASSlex.l, io/BASSyacc.y, io/Globals.cpp, io/Globals.hpp, + io/LinkedAssign.cpp, io/LinkedAssign.hpp, io/Makefile, + io/ZConsReader.cpp, io/interface.c, io/make_nodes.c, + io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, + io/parse_interface.h, io/parse_me.h, io/parse_tree.c, + io/parse_tree.h, mdParser/FilenameObserver.cpp, + mdParser/FilenameObserver.hpp, mdParser/MDLexer.cpp, + mdParser/MDLexer.hpp, mdParser/MDParser.cpp, mdParser/MDParser.g, + mdParser/MDParser.hpp, mdParser/MDTokenTypes.hpp, + mdParser/MDTreeParser.cpp, mdParser/MDTreeParser.g, + mdParser/MDTreeParser.hpp, mdParser/MDTreeParserTokenTypes.hpp, + mdParser/Makefile, mdParser/SimplePreprocessor.hpp, + openbabel/obconversion.cpp, openbabel/oopseformat.cpp, + openbabel/xyzformat.cpp, primitives/RigidBody.cpp, + selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, + selection/IndexFinder.cpp, selection/IndexFinder.hpp, + selection/Makefile, selection/NameFinder.cpp, + selection/NameFinder.hpp, selection/SelectionCompiler.hpp, + selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, + selection/SelectionManager.hpp, selection/SelectionToken.hpp, + selection/Token.cpp, selection/Token.hpp, selection/TokenMap.hpp, + types/AtomStamp.cpp, types/AtomStamp.hpp, types/BendStamp.cpp, + types/BendStamp.hpp, types/BondStamp.cpp, types/BondStamp.hpp, + types/Component.cpp, types/Component.hpp, + types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, + types/MakeStamps.cpp, types/MakeStamps.hpp, types/Makefile, + types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, + types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, + types/TorsionStamp.cpp, types/TorsionStamp.hpp, + types/ZconStamp.cpp, types/ZconStamp.hpp, types/ZconsStamp.cpp, + types/ZconsStamp.hpp, utils/BitSet.cpp, utils/BitSet.hpp, + utils/Makefile.in, utils/MoLocator.cpp, utils/OOPSEBitSet.cpp, + utils/OOPSEBitSet.hpp, utils/StringTokenizer.cpp, + utils/StringTokenizer.hpp, visitors/ZconsVisitor.cpp: End of the + Link --> List Return of the Oject-Oriented replace yacc/lex parser + with antlr parser + +2005-11-30 16:00 chuckv + + * src/applications/staticProps/: RhoZ.cpp, RhoZ.hpp: Code to + calculate rho(Z) to calculate density profiles for water slabs. + +2005-11-29 17:54 chuckv + + * configure, ac-tools/configure.in: added checks for some functions + to configure script + +2005-11-22 20:05 chuckv + + * src/openbabel/: Makefile, atom.cpp, bond.cpp, obatom.cpp, + obbond.cpp: Changed file names that conflict w/ oopse file name + object files. + +2005-11-21 17:59 gezelter + + * src/utils/residentMem.c: compilation bug + +2005-11-21 17:59 gezelter + + * src/io/: ForceFieldOptions.hpp, Globals.cpp: parsing by filepp + +2005-11-21 17:59 gezelter + + * src/brains/: SimInfo.cpp, SimInfo.hpp: Cutoff Mixing fixes + +2005-11-21 17:59 gezelter + + * src/applications/atom2mdin/: Makefile, atom2mdin.cpp: compilation + issue + +2005-11-21 17:58 gezelter + + * src/UseTheForce/: ForceField.hpp, Makefile, doForces.F90, + doForces_interface.F90, doForces_interface.h, fForceOptions.h, + notifyCutoffs.F90, notifyCutoffs_interface.F90, + notifyCutoffs_interface.h, DarkSide/LJ.F90, + DarkSide/electrostatic.F90, DarkSide/gb.F90, + DarkSide/suttonchen.F90: Cutoff mixing fixes have been made. + +2005-11-21 11:22 tim + + * src/io/ParamConstraint.cpp: Adding ParamConstraint.cpp + +2005-11-21 09:59 tim + + * forceFields/: SMARTS_InteLigand_051110.txt, aromatic.txt, + atomtyp.txt, bondtyp.txt, element.txt, extable.txt, + isotope-small.txt, isotope.txt, patterns.txt, phmodel.txt, + resdata.txt, torlib.txt, types.txt: adding openbabel data files + +2005-11-18 15:17 tim + + * src/: applications/atom2mdin/Makefile, openbabel/oopseformat.cpp: + adding support for soft linking + +2005-11-18 15:17 tim + + * make/Makefile.in: Adding support for soft linking + +2005-11-18 12:50 gezelter + + * make/Makefile.in: Adding linking stuff + +2005-11-18 11:38 tim + + * make/Makefile.in, src/applications/atom2mdin/Makefile, + src/applications/atom2mdin/atom2mdin.cpp, + src/applications/mdinConverter/Makefile, + src/applications/mdinConverter/mdinConverter.cpp, + src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp: + rename mdinConverter to atom2mdin + +2005-11-17 15:44 gezelter + + * src/openbabel/obconversion.cpp: fixed a bug + +2005-11-17 15:39 gezelter + + * configure: Adding some config checks for OpenBabel codes we are + using + +2005-11-17 15:39 gezelter + + * ac-tools/configure.in: Adding some checks for OpenBabel code + +2005-11-17 15:39 gezelter + + * src/config.h.in: Unifying config.h stuff from OOPSE and OpenBabel + +2005-11-17 15:38 gezelter + + * src/openbabel/: babelconfig.hpp, base.cpp, base.hpp, bitvec.hpp, + bondtyper.cpp, config.h.in, config.hpp, data.cpp, data.hpp, + fingerprint.cpp, generic.hpp, grid.hpp, matrix.hpp, mol.hpp, + obconversion.hpp, oberror.cpp, oberror.hpp, obutil.cpp, obutil.hpp, + patty.cpp, pdbformat.hpp, phmodel.cpp, povrayformat.hpp, + residue.cpp, rotor.cpp, smilesformat.cpp, tokenst.cpp, typer.cpp: + Unifying config.h stuff and making sure the OpenBabel codes can + find our default (and environment variable) Force Field + directories. + +2005-11-17 13:35 tim + + * src/io/ForceFieldOptions.hpp: adding ForceFieldOptions + +2005-11-16 18:10 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, + brains/Exclude.cpp, brains/Exclude.hpp, brains/ForceManager.cpp, + brains/ForceManager.hpp, brains/SimCreator.cpp, brains/SimInfo.cpp, + integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, + io/Globals.hpp, io/Makefile, io/OptionSectionParser.cpp, + io/OptionSectionParser.hpp, io/ParamConstraint.hpp, + io/SectionParser.hpp, io/SectionParserManager.cpp, + io/TorsionTypesSectionParser.cpp, math/ChebyshevPolynomials.hpp, + math/Makefile, math/Polynomial.hpp, primitives/Bend.cpp, + primitives/Bend.hpp, primitives/GhostBend.cpp, + primitives/GhostBend.hpp, primitives/GhostTorsion.cpp, + primitives/GhostTorsion.hpp, primitives/Torsion.cpp, + primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, + primitives/UreyBradleyBend.hpp, types/CharmmTorsionType.cpp, + types/CharmmTorsionType.hpp, types/CubicTorsionType.hpp, + types/PolynomialTorsionType.hpp, types/QuarticTorsionType.hpp, + types/TorsionType.hpp, utils/StringUtils.hpp: OptionSectionParser + get compiled + +2005-11-16 16:37 chuckv + + * src/: io/Globals.cpp, io/Globals.hpp, io/OptionSectionParser.cpp, + io/OptionSectionParser.hpp, io/SCAtomTypesSectionParser.cpp, + UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField + optional parameters.... + +2005-11-16 16:24 tim + + * src/applications/mdinConverter/: Makefile, mdinConverter.cpp: + adding mdinConverter + +2005-11-16 16:22 tim + + * src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp, + fingerprint.hpp, fingerprintformat.cpp, fingerprintformat.hpp, + gromos96format.cpp, gromos96format.hpp, oopseformat.cpp, + oopseformat.hpp, pdbformat.cpp, pdbformat.hpp, povrayformat.cpp, + povrayformat.hpp, smilesformat.cpp, smilesformat.hpp, + tinkerformat.cpp, tinkerformat.hpp, xyzformat.cpp, xyzformat.hpp: + adding more readers/writers + +2005-11-16 16:20 tim + + * make/Makefile.in: adding openbabel + +2005-11-16 16:20 tim + + * src/brains/: Register.cpp, Register.hpp: register openbabel + readers/writers + +2005-11-16 14:57 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: included shifted + potential self term + +2005-11-16 14:57 chrisfen + + * samples/water/spce/spce.md: just some parameters + +2005-11-16 14:42 tim + + * src/openbabel/: Makefile, aromatic.hpp, atom.cpp, atomtyp.hpp, + babelconfig.hpp, base.cpp, base.hpp, bitvec.cpp, bitvec.hpp, + bond.cpp, bondtyp.hpp, bondtyper.cpp, bondtyper.hpp, chains.cpp, + chains.hpp, chiral.cpp, chiral.hpp, config.h.in, config.hpp, + data.cpp, data.hpp, element.hpp, extable.hpp, fingerprint.cpp, + fingerprint.hpp, generic.cpp, generic.hpp, grid.cpp, grid.hpp, + isotope.hpp, kekulize.cpp, matrix.cpp, matrix.hpp, matrix3x3.cpp, + matrix3x3.hpp, mol.cpp, mol.hpp, molchrg.cpp, molchrg.hpp, + obconversion.cpp, obconversion.hpp, obconversion.lo, oberror.cpp, + oberror.hpp, obiter.cpp, obiter.hpp, obmolecformat.hpp, obutil.cpp, + obutil.hpp, oopseformat.cpp, parsmart.cpp, parsmart.hpp, patty.cpp, + patty.hpp, pdbformat.cpp, phmodel.cpp, phmodel.hpp, + phmodeldata.hpp, rand.cpp, reaction.hpp, resdata.hpp, residue.cpp, + ring.cpp, ring.hpp, rotamer.cpp, rotamer.hpp, rotor.cpp, rotor.hpp, + snprintf.c, snprintf.h, strncasecmp.c, tinkerformat.cpp, + tokenst.cpp, torlib.hpp, transform.cpp, typer.cpp, typer.hpp, + types.hpp, vector3.cpp, vector3.hpp, xyzformat.cpp, zipstream.hpp, + zipstreamimpl.hpp: adding openbabel + +2005-11-15 14:42 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: removed unnecessary + commented code + +2005-11-15 14:04 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: cleaned up the + charge-charge interactions a bit... + +2005-11-15 14:03 chrisfen + + * samples/water/spce/: spce.md, water.md: just playing + +2005-11-15 11:38 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: fixed a bug in the + shifted_potential case + +2005-11-15 11:37 chrisfen + + * samples/: argon/500.md, water/spce/spce.md, water/spce/water.md: + just playing around - we need to refresh all the samples sometime + soon... + +2005-11-15 11:18 chuckv + + * src/UseTheForce/: SC_FF.cpp, DarkSide/suttonchen.F90: Made + preforce calc public in suttonchen. + +2005-11-15 11:05 chuckv + + * src/brains/: SimInfo.cpp, fSimulation.h: Sutton-Chen added to + SimInfo + +2005-11-15 11:01 chuckv + + * src/UseTheForce/: doForces.F90, DarkSide/fInteractionMap.h, + DarkSide/simulation.F90: Added Sutton-Chen to force loop... + +2005-11-15 10:34 chuckv + + * forceFields/Makefile: Added sutton-chen to makefile. + +2005-11-14 17:20 chuckv + + * src/UseTheForce/DarkSide/: suttonchen.F90, + suttonchen_interface.h: Build Fixes for sutton-chen. + +2005-11-14 17:03 chuckv + + * src/io/Makefile: Missed makefile for sutton-chen. + +2005-11-14 17:03 chuckv + + * src/UseTheForce/: Makefile, DarkSide/Makefile, + DarkSide/atype.F90, DarkSide/atype_interface.F90: Sutton-chen stuff + +2005-11-14 16:29 chuckv + + * src/: UseTheForce/SC_FF.cpp, UseTheForce/SC_FF.hpp, + io/SCAtomTypesSectionParser.cpp, io/SCAtomTypesSectionParser.hpp, + UseTheForce/DarkSide/suttonchen.F90, + UseTheForce/DarkSide/suttonchen_interface.F90, + UseTheForce/DarkSide/suttonchen_interface.h, brains/Register.cpp, + brains/fSimulation.h, types/AtomType.cpp, types/AtomType.hpp, + types/AtomTypeProperties.h: Sutton-Chen almost done. Just need to + fix do_forces to use Sutton-Chen. + +2005-11-11 12:21 chrisfen + + * src/UseTheForce/DarkSide/: fSwitchingFunctionType.h, + switcheroo_interface.F90, switcheroo_interface.h: Forgot to add + some files + +2005-11-11 10:22 chrisfen + + * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/DumpWriter.cpp, + io/Globals.cpp, io/Globals.hpp: added in a 5th order polynomial + switching function option + +2005-11-11 10:21 chrisfen + + * src/UseTheForce/DarkSide/: Makefile, switcheroo.F90: added in a + 5th order polynomial switching function + +2005-11-11 10:21 chrisfen + + * samples/water/ssd/ssd.md: playing with switching functions again + +2005-11-11 10:21 chrisfen + + * samples/argon/500.md: playing with switching functions + +2005-11-08 19:11 chuckv + + * forceFields/: SuttonChen.QSC.frc, SuttonChen.SC.frc: Added force + files for Sutton-Chen and Quantum Sutton-Chen + +2005-11-08 08:32 chrisfen + + * src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp, + DumpWriter.hpp, Globals.cpp, Globals.hpp: Added a keyword and + ability to output forces and torques + +2005-11-08 08:32 chrisfen + + * src/brains/: SimInfo.cpp, fSimulation.h: Added a keyword for + output of forces and torques + +2005-11-08 08:31 chrisfen + + * src/UseTheForce/DarkSide/: electrostatic.F90, simulation.F90: + Working on shifted_force... + +2005-11-08 08:31 chrisfen + + * samples/water/: spce/spce.md, ssde/ssde.md: Just testing... + +2005-11-03 18:22 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: removed a poorly + commented section + +2005-11-03 18:12 chrisfen + + * src/: UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/fElectrostaticScreeningMethod.h, + UseTheForce/DarkSide/fScreeningMethod.h, brains/SimInfo.cpp, + io/Globals.cpp, io/Globals.hpp: improvements in shifted-force + +2005-11-03 18:11 chrisfen + + * samples/water/spce/spce.md: mmm... damped shifted force... + +2005-11-03 18:06 chuckv + + * src/UseTheForce/DarkSide/suttonchen.F90: More work on SC. + +2005-11-02 18:50 chuckv + + * src/UseTheForce/DarkSide/suttonchen.F90: More work on suttonchen. + +2005-11-02 16:01 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: + removed some test code + +2005-11-02 15:45 chrisfen + + * src/UseTheForce/DarkSide/fScreeningMethod.h: forgot to add the + screening method header + +2005-11-02 15:36 chrisfen + + * src/brains/SimInfo.cpp: again, changing how we deal with + summation and screening methods + +2005-11-02 15:36 chrisfen + + * src/: UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/electrostatic_interface.F90, + UseTheForce/DarkSide/electrostatic_interface.h, + UseTheForce/DarkSide/fElectrostaticSummationMethod.h, + io/Globals.cpp, io/Globals.hpp: changing how we deal with summation + and screening methods + +2005-11-02 15:35 chrisfen + + * src/UseTheForce/doForces.F90: debug stuff for rf removed + +2005-11-01 18:32 chuckv + + * src/: UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/atype_interface.F90, + UseTheForce/DarkSide/suttonchen.F90, types/AtomType.cpp, + types/AtomTypeProperties.h: Added suppport to atypes for MEAM and + sutton-chen + +2005-11-01 14:24 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: + removed some testing code... + +2005-11-01 14:14 chrisfen + + * src/: brains/Register.cpp, brains/SimInfo.cpp, + brains/fSimulation.h, integrators/IntegratorFactory.hpp, + io/Globals.cpp: fixed a capitalization problem with NPT integrator + initialization + +2005-11-01 14:13 chrisfen + + * src/applications/oopse/oopse.cpp: nothing + +2005-11-01 14:09 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, + DarkSide/simulation.F90: still fixing up wolf... + +2005-11-01 13:29 chuckv + + * src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In + process of adding sutton-chen forcefield. + +2005-10-26 18:32 chrisfen + + * src/brains/SimInfo.cpp: changed the default switching radius to + 85% of rcut + +2005-10-26 18:31 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks + to be working now - for charges and dipoles alike + +2005-10-26 18:31 chrisfen + + * src/UseTheForce/doForces.F90: reaction field looks to be working + now + +2005-10-26 18:30 chrisfen + + * samples/water/ssdrf/water.md: added a test molecule + +2005-10-26 18:30 chrisfen + + * forceFields/DUFF2.frc: added a test atom type + +2005-10-24 09:06 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole + reaction field - don't know if it works... + +2005-10-23 16:08 chrisfen + + * src/: UseTheForce/doForces.F90, + UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp: + streamlined reaction field for dipoles (now a good bit faster) and + added reaction field for charges - still need to do charge-dipole + RF + +2005-10-23 16:07 chrisfen + + * samples/water/ssdrf/ssdrf.md: minor changes when testing reaction + field + +2005-10-23 16:06 chrisfen + + * samples/water/spce/spce.md: reaction field now works for charges + +2005-10-20 15:27 tim + + * src/primitives/Torsion.cpp: Fix the other branch of force + calculation in Torision.cpp + +2005-10-19 14:24 chrisfen + + * src/: UseTheForce/doForces.F90, + UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/simulation.F90, applications/oopse/oopse.cpp, + brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals + toUpper problems - these changes should fix those... + +2005-10-19 14:23 chrisfen + + * samples/water/ssdrf/ssdrf.md: nothing + +2005-10-19 12:03 gezelter + + * src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in + GayBerne + +2005-10-19 11:49 tim + + * src/: UseTheForce/DarkSide/fInteractionMap.h, + brains/ForceManager.cpp: fix an index mismathcing between c and + fortran + +2005-10-18 18:03 gezelter + + * samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added + samples for the cutoff methods that Yang Zheng has been working on + +2005-10-18 16:13 gezelter + + * src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques + and a rotation matrix bug + +2005-10-18 16:13 gezelter + + * samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md, + gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: + added a few GB test cases + +2005-10-18 16:13 gezelter + + * forceFields/DUFF2.frc: Fixing GB parameters + +2005-10-18 13:36 kdaily + + * forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne + type + +2005-10-18 10:01 chrisfen + + * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, + UseTheForce/DarkSide/Makefile, + UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/electrostatic_interface.F90, + UseTheForce/DarkSide/electrostatic_interface.h, + UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged + reaction field with electrostatics.F90 + +2005-10-17 18:13 tim + + * src/: brains/ForceManager.cpp, brains/Stats.cpp, + brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp, + io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp, + io/StatWriter.hpp: Customized StatWriter is working + +2005-10-17 17:42 kdaily + + * src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver + paper + +2005-10-17 16:47 gezelter + + * src/UseTheForce/DarkSide/gb.F90: bugtracking gb + +2005-10-17 14:24 tim + + * src/io/ParamConstraint.hpp: Another bug fix + +2005-10-17 14:22 tim + + * src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace + issues in Globals + +2005-10-17 14:12 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90, + UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90, + UseTheForce/DarkSide/gb_interface.F90, + UseTheForce/DarkSide/gb_interface.h, + io/GayBerneAtomTypesSectionParser.cpp, + types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: + changing GB architecture + +2005-10-17 14:12 gezelter + + * samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in, + gbRotRoundZ.in: Adding samples for gb tests + +2005-10-16 22:06 tim + + * src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy + a string to event's err_msg, there are still tons of memory + leaking problem in Globals + +2005-10-16 19:51 tim + + * src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change + error message in Globals + +2005-10-14 16:43 tim + + * src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for + parameters are working now + +2005-10-14 11:43 gezelter + + * samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests + +2005-10-14 11:05 gezelter + + * samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md, + gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md: + Adding some Gay Berne tests + +2005-10-14 11:05 gezelter + + * samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some + cutoff tests + +2005-10-14 10:44 kdaily + + * forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp, + src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90, + src/UseTheForce/DarkSide/gb_interface.F90, + src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne + LJ + +2005-10-14 09:48 tim + + * src/io/ParamConstraint.hpp: Adding Parameter Constraint class + +2005-10-14 09:18 chrisfen + + * samples/thermoIntegration/liquid/ssde.md, + samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp, + src/restraints/Restraints.cpp: added default restraint spring + constants into Globals + +2005-10-13 17:26 tim + + * src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp, + brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp, + constraints/ZconstraintForceManager.cpp, + integrators/Integrator.cpp, integrators/NPT.cpp, + integrators/NVT.cpp, integrators/Velocitizer.cpp, io/Globals.cpp, + io/Globals.hpp, io/ZConsReader.cpp, minimizers/Minimizer.cpp, + minimizers/MinimizerParameterSet.cpp, restraints/Restraints.cpp, + restraints/ThermoIntegrationForceManager.cpp, + visitors/ZconsVisitor.cpp: rewrite Globals + +2005-10-12 16:57 chuckv + + * src/brains/ForceManager.cpp: Fix to forceManager to pass + potential array to fortran. + +2005-10-12 16:00 gezelter + + * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't + remember what we did + +2005-10-12 16:00 gezelter + + * src/UseTheForce/: doForces.F90, doForces_interface.F90, + DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h, + DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90, + DarkSide/sticky.F90: simplifying long range potential array + +2005-10-12 16:00 gezelter + + * samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new + cutoff methods + +2005-10-12 16:00 gezelter + + * forceFields/DUFF2.frc: Messing with 2-point water models + +2005-10-12 15:22 chuckv + + * src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran + interface now expects an array for pot. + +2005-10-12 15:18 chuckv + + * src/UseTheForce/: doForces.F90, DarkSide/gb.F90, + DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for + calculation of potential. + +2005-10-12 14:55 chuckv + + * src/UseTheForce/doForces.F90: More changes to MPI potential + calculations. + +2005-10-12 13:59 chuckv + + * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90, + DarkSide/eam.F90, DarkSide/electrostatic.F90, + DarkSide/fInteractionMap.h, DarkSide/force_globals.F90, + DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky + Breaky: Add Support for seperating potential contributions. + +2005-10-11 17:00 chuckv + + * src/UseTheForce/doForces.F90: Free some variables that weren't + freed before. + +2005-10-11 16:59 chuckv + + * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, + GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod + builder --twinned. + +2005-10-11 16:57 chuckv + + * src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp, + nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c, + nanoparticleBuilderCmd.h, sphericalNanoparticle.cpp, + sphericalNanoparticle.hpp: Added code for nanoparticle builder to + cvs. + +2005-10-10 16:34 chuckv + + * src/UseTheForce/doForces.F90: Bug fix, undeclared local variable + in MPI. + +2005-10-10 16:20 chuckv + + * src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column + indexing of groupToGtype. We now have two seperate maps + groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer + that is set to groupToGtypeRow in the single processor version. + +2005-10-06 13:44 chrisfen + + * samples/water/: dimer/water.md, spce/water.md, ssd/water.md, + ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md, + tip3p_ice/water.md, tip4p/water.md: fixing up the samples + +2005-10-05 16:12 tim + + * src/primitives/RigidBody.cpp: There is still something wrong with + inertia tensor projection + +2005-10-05 14:35 tim + + * src/primitives/RigidBody.cpp: erase output of inertia tensor. + There is still something wrong with current implementation. + +2005-10-05 14:34 tim + + * src/brains/MoleculeCreator.cpp: fix a bug in creating + cutoffGroup. When cutoffGroup is turned off, there is a mismatch + between group and center of mass array + +2005-10-05 14:12 tim + + * src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup. + When cutoffGroup is turned off, there is a mismatch between group + and center of mass array + +2005-10-04 14:34 chrisfen + + * src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying + mass ratio bug that results in simulation failure with massless + particles + +2005-10-04 14:33 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on + wolf + +2005-10-04 14:32 chrisfen + + * samples/water/dimer/two.md, samples/water/dimer/water.md, + samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md, + samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some + random changes when testing + +2005-10-03 10:54 tim + + * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in + projecting the inertia tensor of directional atom in rigibody into + rigidbody's body frame (previous commit is wrong) + +2005-10-03 09:31 tim + + * src/primitives/RigidBody.cpp: fix a bug in projecting the inertia + tensor of directional atom in rigibody into rigidbody's body frame + +2005-09-28 13:47 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: working on wolf + +2005-09-28 13:46 chrisfen + + * samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md, + dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md, + ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md, + tip4p/tp4.md: fixed some samples + +2005-09-28 13:46 chrisfen + + * ChangeLog: updated + +2005-09-28 11:55 tim + + * src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid + divergence in rotation matrix to quaternion transformation + +2005-09-28 11:32 gezelter + + * src/primitives/RigidBody.cpp: Rotation matrix multiplication + order error + +2005-09-28 11:32 gezelter + + * src/io/DumpReader.cpp: tracking down quaternion bug + +2005-09-28 11:32 gezelter + + * forceFields/DUFF2.frc: Added DIP atom types for 2-point water + model + +2005-09-27 15:02 tim + + * src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix + to quaternion + +2005-09-26 13:38 chuckv + + * src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc + 7 so derfc is external. Other compilers should treat erfc as + intrinsic. + +2005-09-26 12:07 chuckv + + * src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc + and declared it to be external to fix issure with ifc7. Hopefully + this will not cause a problem with other compilers where derfc is + an intrinsic function. + +2005-09-26 11:42 chuckv + + * src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype + in simulation module. We needed a seperate receive buffer. + +2005-09-26 10:58 chuckv + + * src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added + support for skinThickness keyword to Globals. + +2005-09-26 10:56 tim + + * src/io/DumpReader.cpp: fix a typo in DumpReader + +2005-09-26 09:27 chrisfen + + * samples/: minimizer/tip4p_two.md, + thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md, + water/dimer/cl.md, water/dimer/mix.md, water/dimer/mix2.md, + water/dimer/ssd.md, water/dimer/tap.md, water/dimer/two.md, + water/spce/spce.md, water/ssd/ssd.md, water/ssd-ion/ssdCl.md, + water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md, + water/tip4p/tp4.md: fixing up some samples + +2005-09-24 12:39 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now + roughly the same speed as the old version when using dipoles + + energies are now exactly the same between the old version of OOPSE + and this version + +2005-09-24 12:38 chrisfen + + * samples/water/ssdrf/ssdrf.md: turned rf on + +2005-09-23 15:31 chuckv + + * src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the + skin thickness and hardcode listSkin to be 1.0. We now get listskin + from skin. This will get fixed to where we can manually set skin + thickness. + +2005-09-22 13:50 gezelter + + * src/math/derfc.F90: added error function + +2005-09-21 19:08 chuckv + + * src/integrators/Velocitizer.cpp: Removed print statement for + angular momentum and inertia tensor from velocitizer. + +2005-09-21 19:04 chuckv + + * src/integrators/Velocitizer.cpp: Removed print statements for + remove angular momentum. + +2005-09-21 18:45 chuckv + + * src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ + (say we are using EAM), we probably shouldn't rebuild the LJ mixing + map. + +2005-09-21 15:59 tim + + * src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp: + DumpReader using pure c++ io + +2005-09-21 12:20 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a + defaultCutoff bug (HEMES!) + +2005-09-20 17:13 gezelter + + * make/Makefile.in: libz additions + +2005-09-20 17:03 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + src/config.h.in: added check for zlib in configure + +2005-09-20 16:22 tim + + * src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp, + gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter + +2005-09-20 11:22 tim + + * test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding + testcase for zipstream + +2005-09-20 10:41 tim + + * src/io/zipstream.hpp: adding zipstream.hpp + +2005-09-20 10:34 chrisfen + + * samples/: dipole/splitInWater.md, dipole/split_SSD.md, + dipole/twoSplitDipole.md, minimizer/ssdEM.md, + minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md, + zcons/zconsMoving.md: fixed up some sample md files + +2005-09-19 18:21 chrisfen + + * ChangeLog, samples/water/ssdrf/ssdrf.md, + src/UseTheForce/doForces.F90, + src/UseTheForce/DarkSide/electrostatic.F90, + src/UseTheForce/DarkSide/simulation.F90, src/brains/SimInfo.cpp, + src/brains/fSimulation.h: Fixed bugs in reaction field, now it + appears as though it really is working... + +2005-09-18 15:45 chrisfen + + * ChangeLog, samples/water/ssdrf/ssdrf.md, + src/UseTheForce/doForces.F90, + src/UseTheForce/doForces_interface.F90, + src/UseTheForce/doForces_interface.h, + src/UseTheForce/DarkSide/electrostatic.F90, + src/UseTheForce/DarkSide/electrostatic_interface.h, + src/brains/SimInfo.cpp: reaction field seems to work now, still + need to do some testing... + +2005-09-16 18:04 chuckv + + * src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed + dump files. + +2005-09-16 16:07 chrisfen + + * src/: UseTheForce/doForces_interface.F90, + UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a + bug that ifc missed... + +2005-09-16 15:36 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90: + fixing some summation method issues + +2005-09-16 14:35 chrisfen + + * src/brains/SimInfo.cpp: fixed a capitalization error + +2005-09-16 14:34 chrisfen + + * src/UseTheForce/: fElectrostaticSummationMethod.h, + DarkSide/fElectrostaticSummationMethod.h: moved a header file + around + +2005-09-16 14:00 chrisfen + + * src/: UseTheForce/DarkSide/electrostatic_interface.F90, + brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there + are known issues - particularly with reaction field... + +2005-09-16 11:07 chrisfen + + * src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp, + io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking + (cutting out the old way to do reaction field) + +2005-09-15 17:05 gezelter + + * src/UseTheForce/: doForces.F90, fCoulombicCorrection.h, + fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90, + DarkSide/electrostatic_interface.F90, + DarkSide/electrostatic_interface.h: Working on adding WOLF + +2005-09-15 14:17 tim + + * src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame + is called without calling getNFrames + +2005-09-15 08:47 chrisfen + + * src/UseTheForce/fCoulombicCorrection.h: forgot to add a header + +2005-09-14 21:48 chuckv + + * src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was + not initialized after creation. When maxval(gtypeMaxCutoff) was + called, the largest random garbage value was returned from the + array. + +2005-09-14 19:14 chrisfen + + * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp, + io/Globals.hpp: changes to include the coulombicCorrection selector + +2005-09-14 19:13 chrisfen + + * src/UseTheForce/DarkSide/: Makefile, electrostatic.F90, + reactionField.F90: added in the undamped wolf, in the process of + doing the damped wolf + +2005-09-14 19:13 chrisfen + + * src/UseTheForce/: doForces.F90, doForces_interface.F90, + doForces_interface.h, notifyCutoffs.F90: some changes to activate + the coulombicCorrection selector + +2005-09-14 19:11 chrisfen + + * samples/water/dimer/: cl.in, cl.md, water.md: just some testing + +2005-09-14 19:11 chrisfen + + * samples/argon/: 500.in, 500.md: Equilibrated the sample + +2005-09-14 19:10 chrisfen + + * forceFields/DUFF2.frc: re-added Cl- and Na+ + +2005-09-14 15:31 chuckv + + * src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup + eamAtypes instead of assuming a 1-1 correspondence to atypes. + +2005-09-14 15:28 gezelter + + * src/UseTheForce/doForces.F90: fix to put back calculation of r in + do_prepair + +2005-09-14 14:02 gezelter + + * src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the + createMixingMap routine. It should now set doShift correctly + +2005-09-07 17:44 chuckv + + * src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build. + +2005-09-07 17:23 chuckv + + * src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi + logical variables + +2005-09-07 17:08 gezelter + + * src/UseTheForce/doForces.F90: bugfix on the grouptype finding + algorithm + +2005-09-07 15:46 gezelter + + * src/: UseTheForce/doForces.F90, + UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90, + UseTheForce/notifyCutoffs_interface.F90, + UseTheForce/notifyCutoffs_interface.h, brains/SimInfo.cpp, + io/Globals.cpp, io/Globals.hpp: adding c-side interface to change + cutoff Policy + +2005-09-07 14:18 gezelter + + * src/UseTheForce/doForces.F90: Some bug hunting + +2005-09-07 14:18 gezelter + + * samples/argon/argonNVT.md: Just a longer test + +2005-09-06 12:32 chuckv + + * src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap + etc.. + +2005-09-01 17:56 gezelter + + * src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to + zero + +2005-09-01 15:17 gezelter + + * src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote + createGtypeCutoffMap + +2005-08-30 13:23 chrisfen + + * src/: UseTheForce/doForces.F90, + UseTheForce/doForces_interface.F90, + UseTheForce/doForces_interface.h, + UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/gb.F90, brains/SimInfo.cpp, + brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some + changes for implementing the wolf potential + +2005-08-26 17:39 chrisfen + + * src/UseTheForce/DarkSide/eam.F90: updated getEAMCut + +2005-08-26 16:30 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/eam.F90, + DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added + some probably nonfunctional get*cut routines + +2005-08-26 15:34 chuckv + + * src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map. + +2005-08-26 11:36 gezelter + + * src/UseTheForce/doForces.F90: fixing some of the problems in the + interactionHash and gtypeCutoff routines + +2005-08-17 10:26 gezelter + + * src/UseTheForce/: doForces.F90, fCutoffPolicy.h, + DarkSide/simulation.F90: added fCutoffPolicy.h + +2005-08-11 16:04 gezelter + + * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in + progress + +2005-08-10 14:17 gezelter + + * src/primitives/StuntDouble.hpp: putting spaceballs back where + they belong + +2005-08-09 17:33 gezelter + + * src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard + Jones module + +2005-08-09 17:33 gezelter + + * src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky + +2005-08-09 14:40 chuckv + + * src/UseTheForce/doForces.F90: In process of re-write for group + based cutoff.... + +2005-07-29 14:38 gezelter + + * src/UseTheForce/doForces.F90: fixes in progress + +2005-07-29 12:34 tim + + * src/UseTheForce/doForces.F90: fix a bug which does not update + me_i and me_j correctly + +2005-07-28 17:12 chuckv + + * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed + cutoffs... Segfaults nicely now... + +2005-07-20 12:04 gezelter + + * configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text + error messages from pathscale compiler + +2005-07-13 11:48 tim + + * src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in + + +2005-07-13 10:54 tim + + * src/: UseTheForce/fSwitchingFunction.h, + UseTheForce/mpiComponentPlan.h, + UseTheForce/DarkSide/fInteractionMap.h, brains/fSimulation.h, + io/BASS_interface.h, io/BASS_parse.c, io/BASS_parse.h, + io/BASSlex.l, io/BASSyacc.y, io/interface.c, io/make_nodes.c, + io/mpiBASS.c, io/mpiBASS.h, io/node_list.h, io/parse_tree.c, + io/parse_tree.h, math/MatVec3.c, utils/residentMem.c, + utils/simError.c, utils/simError.h: replace c++ style comment in c + files + +2005-07-03 15:53 chuckv + + * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90, + UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added + subroutine to set cuttoff for Interaction map and function in + simulation.F90 to determine if a particular atype is present in a + simulation. + +2005-06-28 08:58 gezelter + + * src/UseTheForce/doForces.F90: [no log message] + +2005-06-27 17:21 chuckv + + * src/UseTheForce/doForces.F90: More breaking and destruction of + force code. Does not build at this point... + +2005-06-27 16:01 gezelter + + * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/fInteractionMap.h, + UseTheForce/DarkSide/interactions.F90, utils/definitions.F90: + Breaky breaky! + +2005-06-20 11:03 gezelter + + * samples/water/ssd/ssd.md, + src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a + simulation + +2005-06-13 13:25 tim + + * src/: applications/staticProps/DensityPlot.cpp, + applications/staticProps/DensityPlot.hpp, + applications/staticProps/SCDOrderParameter.cpp, + applications/staticProps/StaticProps.cpp, + io/AtomTypesSectionParser.cpp: working version of DensityPlot + +2005-05-31 17:31 chuckv + + * src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to + remove angular momentum. + +2005-05-31 12:34 chuckv + + * src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in + typo in nanorodBuilder. + +2005-05-30 09:01 chuckv + + * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, + brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp, + brains/Stats.hpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp: Added method to remove system angular + momentum to velocitizer and added method to calculate system + angular momentum to siminfo. + +2005-05-29 16:16 chrisfen + + * src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed + balance from the Darkside (files) + +2005-05-29 16:15 chrisfen + + * src/UseTheForce/doForces.F90: Removed balance from doForces + +2005-05-29 16:15 chrisfen + + * samples/water/tap/: tap.in, tap.md: Updated tap sample + +2005-05-29 16:15 chrisfen + + * samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap + dimer for testing purposes + +2005-05-29 16:14 chrisfen + + * forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It + was apparently wiped earlier this month... + +2005-05-29 16:13 chrisfen + + * ChangeLog: ran make cvslog + +2005-05-28 19:16 tim + + * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding + AtomNameVisitor + +2005-05-28 19:09 tim + + * src/integrators/Integrator.cpp: dding resetIntegrator + +2005-05-28 19:06 tim + + * src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp, + NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp, + VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding + resetIntegrator + +2005-05-27 16:11 tim + + * src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp, + Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp, + SCDOrderParameter.hpp, StaticProps.cpp, StaticProps.ggo, + StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into + StaticProps + +2005-05-26 23:41 tim + + * src/: applications/staticProps/Makefile, + applications/staticProps/P2OrderParameter.cpp, + applications/staticProps/P2OrderParameter.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticProps.ggo, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp, + utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps + +2005-05-26 17:45 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, + applications/staticProps/Makefile, + applications/staticProps/P2OrderParameter.cpp, + applications/staticProps/P2OrderParameter.hpp, + applications/staticProps/RadialDistrFunc.cpp, + applications/staticProps/RadialDistrFunc.hpp, + applications/staticProps/StaticAnalyser.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticProps.ggo, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, visitors/Makefile, + visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp: adding + AtomNameVisitor to convert atom name to its base name; + wrappingvisitor now wrap back to the center of the mass; adding + P2OrderParameter into StaticProps + +2005-05-22 16:36 chuckv + + * src/: applications/nanoRodBuilder/Geometry.cpp, + applications/nanoRodBuilder/GeometryBuilder.cpp, + applications/nanoRodBuilder/GeometryFactory.cpp, + applications/nanoRodBuilder/GeometryFactory.hpp, + applications/nanoRodBuilder/nanorodBuilder.cpp, + integrators/VelocityVerletIntegrator.cpp: Fix to print pressure + tensor. + +2005-05-22 16:05 tim + + * src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, + integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp, + io/Globals.hpp, io/SectionParserManager.cpp: adding keyword + printPressureTensor + +2005-05-20 14:27 tim + + * src/integrators/NPrT.cpp: NPrT in progress + +2005-05-20 11:01 tim + + * src/: integrators/NPrT.cpp, io/Globals.cpp, + utils/OOPSEConstant.hpp: NPrT in progress + +2005-05-19 16:31 tim + + * src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp, + integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp, + io/Globals.hpp: NPAT is working + +2005-05-19 10:49 tim + + * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile, + integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT + +2005-05-18 23:28 tim + + * src/: brains/Register.cpp, integrators/NPAT.cpp, + integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp, + io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators + +2005-05-18 14:06 chrisfen + + * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just + some tap changes + +2005-05-18 13:31 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, + DarkSide/sticky.F90: Modifications to temper the dipolar strength + in the first solvation shell for tap + +2005-05-18 07:35 chrisfen + + * samples/water/tap/: tap.in, tap.md, water.md: added a tap example + for testing purposes + +2005-05-17 17:35 chrisfen + + * ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md, + samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp, + src/UseTheForce/doForces.F90, + src/UseTheForce/DarkSide/electrostatic.F90, + src/UseTheForce/DarkSide/electrostatic_interface.F90, + src/UseTheForce/DarkSide/sticky.F90: Modifications to tap. Also + correcting changes to the previous merge that were not caught + +2005-05-16 23:20 chuckv + + * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp: + Fixed merge issues between Kyle and Chris so OOPSE will actually + build. + +2005-05-16 22:46 kdaily + + * src/io/: GayBerneAtomTypesSectionParser.cpp, + GayBerneAtomTypesSectionParser.hpp, Makefile: help + +2005-05-16 21:08 kdaily + + * forceFields/DUFF2.frc, src/UseTheForce/doForces.F90, + src/UseTheForce/DarkSide/gb.F90, src/io/Makefile, + src/types/DirectionalAtomType.cpp, + src/types/DirectionalAtomType.hpp: added gb + +2005-05-13 15:36 chrisfen + + * forceFields/DUFF2.frc: Better tap + +2005-05-12 14:43 chrisfen + + * forceFields/DUFF2.frc, samples/water/dimer/ssd.in, + samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90, + src/applications/dump2Xyz/Dump2XYZ.cpp, + src/visitors/AtomVisitor.hpp: Couple of changes for TAP water. + Need to parametrize. + +2005-05-11 18:15 chuckv + + * src/: io/ShapeAtomTypesSectionParser.cpp, + math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed + build issues under ifc7. + +2005-05-09 17:07 chuckv + + * src/applications/nanoRodBuilder/Geometry.hpp: More geometry + builder changes. + +2005-05-05 10:06 chrisfen + + * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED + to TAP + +2005-05-05 09:47 chrisfen + + * forceFields/DUFF2.frc, samples/water/ssde/ssde.md, + samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp, + src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/Makefile, + src/UseTheForce/DarkSide/atype.F90, + src/UseTheForce/DarkSide/atype_interface.F90, + src/UseTheForce/DarkSide/simulation.F90, + src/UseTheForce/DarkSide/sticky.F90, src/brains/SimInfo.cpp, + src/brains/fSimulation.h, src/io/Makefile, + src/io/StickyAtomTypesSectionParser.cpp, + src/io/StickyPowerAtomTypesSectionParser.cpp, + src/io/StickyPowerAtomTypesSectionParser.hpp, + src/types/AtomType.cpp, src/types/AtomType.hpp, + src/types/AtomTypeProperties.h, src/types/DirectionalAtomType.cpp, + src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water. It's + not parametrized, but OOPSE will now let me run it... + +2005-05-03 17:55 chuckv + + * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp, + GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp: + Adding support for generic geometry to nanorodbuilder. + +2005-05-03 12:55 chuckv + + * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, + nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c, + nanorodBuilderCmd.h: More changes to nanoRodBuilder.... + +2005-04-29 14:16 gezelter + + * make/Makefile.in: [no log message] + +2005-04-29 11:26 chrisfen + + * forceFields/DUFF2.frc, samples/water/spce/water.md, + samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md, + samples/water/ssd-ion/water.md, samples/water/ssde/water.md, + samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md, + samples/water/tip4p/water.md: Added TIP4P-Ew + +2005-04-27 19:24 chuckv + + * src/applications/nanoRodBuilder/: GeometryBuilder.cpp, + GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo, + nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with + nanoRodBuilder.... + +2005-04-27 15:13 chrisfen + + * samples/shape/Shapes.frc, samples/shape/linear.shape, + src/UseTheForce/DarkSide/atype.F90, + src/UseTheForce/DarkSide/shapes.F90, + src/UseTheForce/DarkSide/shapes_interface.F90, + src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of + write statements and am closer to a working shapes + +2005-04-22 16:57 chuckv + + * src/utils/Predicate.hpp: Fixed gcc4 bug... + +2005-04-22 16:52 tim + + * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp, + Trim.hpp: adding CharClassificationFunctor to fix the locale + problem of c++ + +2005-04-21 09:12 chrisfen + + * samples/shape/Shapes.frc, samples/shape/linear.in, + samples/shape/linear.md, src/UseTheForce/ForceField.hpp, + src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/Makefile, + src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp, + src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/atype.F90, + src/UseTheForce/DarkSide/shapes.F90, + src/UseTheForce/DarkSide/shapes_interface.F90, + src/UseTheForce/DarkSide/shapes_interface.h, + src/brains/Register.cpp, src/brains/SimCreator.cpp, + src/io/Makefile, src/io/SectionParser.cpp, + src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, + src/io/ShapeAtomTypesSectionParser.cpp, + src/io/ShapeAtomTypesSectionParser.hpp, src/math/Makefile, + src/types/AtomType.cpp, src/types/ShapeAtomType.cpp, + src/types/ShapeAtomType.hpp: Shapes is limping along with a array + bounds overwrite (I think...). At least the parser loads the + forcefield fine... + +2005-04-18 10:44 chrisfen + + * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on + Mac (capitalization confusion of filenames) + +2005-04-17 22:50 chrisfen + + * src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp, + UseTheForce/Shapes_FF.cpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/ShapeAtomTypesSectionParser.cpp, + io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser... + +2005-04-15 17:43 gezelter + + * README: gmake in case people forget + +2005-04-15 17:40 gezelter + + * src/applications/oopse/oopse.cpp: fixed the spacing on the + banner. Vanity. + +2005-04-15 17:22 gezelter + + * src/: config.h.in, applications/oopse/oopse.cpp: Version string + in banner (and version numbers in config.h) + +2005-04-15 17:22 gezelter + + * ChangeLog, LICENSE, README: Documentation changes + +2005-04-15 17:03 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp, + UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + UseTheForce/ForceFieldCreator.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, + UseTheForce/doForces.F90, UseTheForce/doForces_interface.F90, + UseTheForce/doForces_interface.h, UseTheForce/mpiComponentPlan.h, + UseTheForce/notifyCutoffs.F90, + UseTheForce/notifyCutoffs_interface.F90, + UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, + UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/atype_interface.F90, + UseTheForce/DarkSide/eam.F90, + UseTheForce/DarkSide/eam_interface.F90, + UseTheForce/DarkSide/eam_interface.h, + UseTheForce/DarkSide/electrostatic.F90, + UseTheForce/DarkSide/electrostatic_interface.F90, + UseTheForce/DarkSide/electrostatic_interface.h, + UseTheForce/DarkSide/force_globals.F90, + UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, + UseTheForce/DarkSide/lj_interface.F90, + UseTheForce/DarkSide/lj_interface.h, + UseTheForce/DarkSide/neighborLists.F90, + UseTheForce/DarkSide/reactionField.F90, + UseTheForce/DarkSide/shapes.F90, + UseTheForce/DarkSide/shapes_interface.F90, + UseTheForce/DarkSide/shapes_interface.h, + UseTheForce/DarkSide/simParallel.F90, + UseTheForce/DarkSide/simParallel_interface.F90, + UseTheForce/DarkSide/simParallel_interface.h, + UseTheForce/DarkSide/simulation.F90, + UseTheForce/DarkSide/simulation_interface.F90, + UseTheForce/DarkSide/simulation_interface.h, + UseTheForce/DarkSide/sticky.F90, + UseTheForce/DarkSide/sticky_interface.F90, + UseTheForce/DarkSide/sticky_interface.h, + UseTheForce/DarkSide/switcheroo.F90, + applications/dump2Xyz/Dump2XYZ.cpp, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, + applications/dynamicProps/CrossTimeCorrFunc.cpp, + applications/dynamicProps/CrossTimeCorrFunc.hpp, + applications/dynamicProps/DipoleCorrFunc.cpp, + applications/dynamicProps/DipoleCorrFunc.hpp, + applications/dynamicProps/DynamicProps.cpp, + applications/dynamicProps/DynamicPropsCmd.c, + applications/dynamicProps/DynamicPropsCmd.h, + applications/dynamicProps/FrameTimeCorrFunc.hpp, + applications/dynamicProps/ParticleTimeCorrFunc.cpp, + applications/dynamicProps/ParticleTimeCorrFunc.hpp, + applications/dynamicProps/RCorrFunc.cpp, + applications/dynamicProps/RCorrFunc.hpp, + applications/dynamicProps/TimeCorrFunc.cpp, + applications/dynamicProps/TimeCorrFunc.hpp, + applications/dynamicProps/VCorrFunc.cpp, + applications/dynamicProps/VCorrFunc.hpp, + applications/nanoRodBuilder/GeometryBuilder.cpp, + applications/nanoRodBuilder/GeometryBuilder.hpp, + applications/nanoRodBuilder/nanorodBuilder.cpp, + applications/nanoRodBuilder/nanorodBuilderCmd.c, + applications/nanoRodBuilder/nanorodBuilderCmd.h, + applications/oopse/oopse.cpp, + applications/simpleBuilder/simpleBuilder.cpp, + applications/simpleBuilder/simpleBuilderCmd.c, + applications/simpleBuilder/simpleBuilderCmd.h, + applications/staticProps/GofAngle2.cpp, + applications/staticProps/GofAngle2.hpp, + applications/staticProps/GofR.cpp, + applications/staticProps/GofR.hpp, + applications/staticProps/GofRAngle.cpp, + applications/staticProps/GofRAngle.hpp, + applications/staticProps/GofXyz.cpp, + applications/staticProps/GofXyz.hpp, + applications/staticProps/RadialDistrFunc.cpp, + applications/staticProps/RadialDistrFunc.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, + brains/Exclude.hpp, brains/ForceManager.cpp, + brains/ForceManager.hpp, brains/MoleculeCreator.cpp, + brains/MoleculeCreator.hpp, brains/Register.cpp, + brains/Register.hpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, + brains/SimSnapshotManager.hpp, brains/Snapshot.cpp, + brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Stats.cpp, + brains/Stats.hpp, brains/Thermo.cpp, brains/Thermo.hpp, + brains/fSimulation.h, constraints/ConstraintElem.hpp, + constraints/ConstraintPair.hpp, constraints/Rattle.cpp, + constraints/Rattle.hpp, constraints/ZconsStruct.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, + integrators/DLM.hpp, integrators/Integrator.cpp, + integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/NPT.cpp, + integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, + integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, + integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, + integrators/NVT.cpp, integrators/NVT.hpp, + integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, + io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, + io/BASS_parse.h, io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, + io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, + io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, + io/Globals.cpp, io/Globals.hpp, + io/LennardJonesAtomTypesSectionParser.cpp, + io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, + io/LinkedAssign.hpp, io/MultipoleAtomTypesSectionParser.cpp, + io/MultipoleAtomTypesSectionParser.hpp, io/RestReader.cpp, + io/RestReader.hpp, io/RestWriter.cpp, io/RestWriter.hpp, + io/SectionParser.cpp, io/SectionParser.hpp, + io/SectionParserManager.cpp, io/SectionParserManager.hpp, + io/StatWriter.cpp, io/StatWriter.hpp, + io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, + io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, + io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, + io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/basic_teebuf.hpp, + io/interface.c, io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, + io/mpiBASS.h, io/node_list.h, io/parse_interface.h, io/parse_me.h, + io/parse_tree.c, io/parse_tree.h, lattice/CubicLattice.cpp, + lattice/CubicLattice.hpp, lattice/FCCLattice.cpp, + lattice/FCCLattice.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, + lattice/LatticeCreator.hpp, lattice/LatticeFactory.cpp, + lattice/LatticeFactory.hpp, math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, + math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, + math/ParallelRandNumGen.hpp, math/Polynomial.hpp, + math/Quaternion.hpp, math/RandNumGen.hpp, + math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, + math/RectMatrix.hpp, math/SeqRandNumGen.cpp, + math/SeqRandNumGen.hpp, math/SquareMatrix.hpp, + math/SquareMatrix3.hpp, math/Vector.hpp, math/Vector3.hpp, + minimizers/CGFamilyMinimizer.cpp, minimizers/CGFamilyMinimizer.hpp, + minimizers/Minimizer.cpp, minimizers/Minimizer.hpp, + minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, + minimizers/MinimizerFactory.hpp, + minimizers/MinimizerParameterSet.cpp, + minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, + minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, + minimizers/SDMinimizer.hpp, primitives/Atom.cpp, + primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, + primitives/Bond.hpp, primitives/CutoffGroup.hpp, + primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, + primitives/GhostBend.cpp, primitives/GhostBend.hpp, + primitives/GhostTorsion.cpp, primitives/GhostTorsion.hpp, + primitives/Molecule.cpp, primitives/Molecule.hpp, + primitives/RigidBody.cpp, primitives/RigidBody.hpp, + primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, + primitives/Torsion.cpp, primitives/Torsion.hpp, + primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, + profiling/mdProfile.cpp, profiling/mdProfile.hpp, + profiling/timing.F90, restraints/Restraints.cpp, + restraints/Restraints.hpp, + restraints/ThermoIntegrationForceManager.cpp, + restraints/ThermoIntegrationForceManager.hpp, + selection/DistanceFinder.cpp, selection/DistanceFinder.hpp, + selection/IndexFinder.cpp, selection/IndexFinder.hpp, + selection/NameFinder.cpp, selection/NameFinder.hpp, + selection/SelectionCompiler.cpp, selection/SelectionCompiler.hpp, + selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, + selection/SelectionManager.cpp, selection/SelectionManager.hpp, + selection/Token.cpp, selection/Token.hpp, selection/TokenMap.cpp, + selection/TokenMap.hpp, types/AtomStamp.cpp, types/AtomStamp.hpp, + types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, + types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, + types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, + types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, + types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, + types/CubicBondType.hpp, types/CubicTorsionType.hpp, + types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, + types/DirectionalAtomType.hpp, types/FixedBondType.hpp, + types/HarmonicBendType.hpp, types/HarmonicBondType.hpp, + types/MakeStamps.cpp, types/MakeStamps.hpp, + types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, + types/MorseBondType.hpp, types/OplsTorsionType.hpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp, types/QuarticBendType.hpp, + types/QuarticBondType.hpp, types/QuarticTorsionType.hpp, + types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, + types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, + types/TorsionStamp.cpp, types/TorsionStamp.hpp, + types/TorsionType.hpp, types/UreyBradleyBendType.hpp, + types/ZconStamp.cpp, types/ZconStamp.hpp, utils/Algorithm.hpp, + utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, + utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, + utils/MemoryUtils.hpp, utils/MoLocator.cpp, utils/MoLocator.hpp, + utils/NumericConstant.hpp, utils/OOPSEConstant.hpp, + utils/PropertyMap.cpp, utils/PropertyMap.hpp, + utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, + utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, + utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, + utils/TypeInfo.hpp, utils/Utility.cpp, utils/Utility.hpp, + utils/any.hpp, utils/definitions.F90, utils/fError.c, + utils/getopt.c, utils/getopt1.c, utils/gnugetopt.h, + utils/next_combination.hpp, utils/oopseMPI.F90, utils/physmem.h, + utils/residentMem.h, utils/simError.c, utils/simError.h, + utils/status.F90, utils/vector_class.F90, utils/wildcards.hpp, + visitors/AtomData.hpp, visitors/AtomVisitor.cpp, + visitors/AtomVisitor.hpp, visitors/BaseVisitor.hpp, + visitors/CompositeVisitor.cpp, visitors/CompositeVisitor.hpp, + visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, + visitors/OtherVisitor.cpp, visitors/OtherVisitor.hpp, + visitors/RigidBodyVisitor.cpp, visitors/RigidBodyVisitor.hpp, + visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has + been drafted to perform our indentation services + +2005-04-15 17:03 gezelter + + * configure, ac-tools/configure.in: Jedi mind-trick warning + messages have been added to make users ignore CGAL. + +2005-04-15 13:41 tim + + * make/Makefile.in: fix make install + +2005-04-15 13:41 tim + + * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile: + add Makefile of samples + +2005-04-15 13:33 tim + + * samples/: lipid/Makefile, water/dimer/Makefile, + water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not + installed correctly + +2005-04-14 16:41 gezelter + + * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in, + make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl, + scripts/filepp, scripts/filepp.in: configure now searches for perl + to use with filepp + +2005-04-14 16:20 gezelter + + * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of + MoLocator + +2005-04-14 14:12 gezelter + + * LICENSE: [no log message] + +2005-04-14 11:10 chuckv + + * src/applications/nanoRodBuilder/nanorodBuilder.cpp: + nanorodbuilder now exit's when libCGAL is not present. + +2005-04-14 10:20 tim + + * src/io/make_nodes.h: fix one more warning message in make_nodes + +2005-04-13 18:36 chuckv + + * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed + interface name for SGI Compiler + +2005-04-13 18:29 chrisfen + + * samples/water/ssde/ssde.md: oops... bad sample + +2005-04-13 18:00 chuckv + + * src/config.h.in: Change typo in CGAL. + +2005-04-13 17:43 tim + + * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, + selection/SelectionCompiler.hpp: fix some warning messages + +2005-04-13 17:30 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in, + make/Makefile.in, src/config.h.in, + src/applications/nanoRodBuilder/Makefile, + src/applications/nanoRodBuilder/Makefile.in, + src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL + checks + +2005-04-13 15:36 chuckv + + * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, + DarkSide/LJ.F90, DarkSide/electrostatic.F90, + DarkSide/electrostatic_interface.F90, + DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, + DarkSide/lj_interface.h, DarkSide/sticky.F90, + DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added + destroy methods for Fortran modules. + +2005-04-13 15:17 chuckv + + * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, + shapes_interface.h: Added destroy method to clean up memory + +2005-04-13 13:41 tim + + * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, + brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, + primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, + types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are + fixed + +2005-04-12 17:44 chuckv + + * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed + for nanoRodBuilder. + +2005-04-12 17:42 tim + + * src/applications/: nanoRodBuilder/nanorodBuilder.cpp, + simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder + and simpleBuilder(forget to delete lattice) + +2005-04-12 17:33 tim + + * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: + refactory lattice + +2005-04-12 17:07 tim + + * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, + CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, + Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory + LatticeFactory and LatticeCreator + +2005-04-12 16:58 tim + + * src/: applications/nanoRodBuilder/nanorodBuilder.cpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, + brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, + lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, + lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, + lattice/Makefile: refactory LatticeFactory and LatticeCreator + +2005-04-12 16:28 gezelter + + * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, + vector_class.F90: cleaned up vector_class memory leak fix by + deallocating in reverse order of how we allocated. Also migrated + MoLocator into utils directory + +2005-04-12 16:27 gezelter + + * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, + Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, + LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice + directory + +2005-04-12 16:27 gezelter + + * src/applications/: nanoRodBuilder/BaseLattice.cpp, + nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, + nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, + nanoRodBuilder/LatticeCreator.hpp, + nanoRodBuilder/LatticeFactory.cpp, + nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, + nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, + nanoRodBuilder/nanorodBuilder.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/Makefile, + simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, + simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of + these files are now redundant + +2005-04-12 16:27 gezelter + + * src/UseTheForce/DarkSide/: atype_interface.F90, + atype_interface.h: cleaned up memory leak fix + +2005-04-12 16:26 gezelter + + * make/Makefile.in: added lattice subdirectory + +2005-04-12 15:57 chrisfen + + * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added + a space by accident + +2005-04-12 15:56 chrisfen + + * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added + quadrupole sample + +2005-04-12 15:56 chrisfen + + * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating + samples + +2005-04-12 13:30 tim + + * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom + type in fortran side + +2005-04-12 12:45 chuckv + + * src/utils/vector_class.F90: Further changes to vector_class + destroy function. + +2005-04-12 12:39 chuckv + + * src/utils/vector_class.F90: Fixed pointer memory leak in + vector_class. + +2005-04-12 12:12 chuckv + + * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, + DarkSide/atype_interface.F90, DarkSide/atype_interface.h, + DarkSide/eam.F90, DarkSide/eam_interface.F90, + DarkSide/eam_interface.h: Updates to deallocate object in fortran. + +2005-04-12 09:24 chrisfen + + * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI + output + +2005-04-11 19:29 chuckv + + * src/: UseTheForce/DarkSide/atype.F90, + applications/nanoRodBuilder/Makefile: Changes to delete atypes... + +2005-04-11 19:28 chuckv + + * src/utils/vector_class.F90: Added code to delete vector. + +2005-04-11 16:58 tim + + * src/io/basic_ifstrstream.hpp: avoid multiple inherit in + basic_ifstrstream + +2005-04-11 16:37 chuckv + + * make/Makefile.in, + src/applications/nanoRodBuilder/BaseLattice.cpp, + src/applications/nanoRodBuilder/BaseLattice.hpp, + src/applications/nanoRodBuilder/GeometryBuilder.cpp, + src/applications/nanoRodBuilder/GeometryBuilder.hpp, + src/applications/nanoRodBuilder/Lattice.cpp, + src/applications/nanoRodBuilder/Lattice.hpp, + src/applications/nanoRodBuilder/LatticeCreator.cpp, + src/applications/nanoRodBuilder/LatticeCreator.hpp, + src/applications/nanoRodBuilder/LatticeFactory.cpp, + src/applications/nanoRodBuilder/LatticeFactory.hpp, + src/applications/nanoRodBuilder/Makefile, + src/applications/nanoRodBuilder/MoLocator.cpp, + src/applications/nanoRodBuilder/MoLocator.hpp, + src/applications/nanoRodBuilder/nanoBuilder.ggo, + src/applications/nanoRodBuilder/nanorodBuilder.cpp, + src/applications/nanoRodBuilder/nanorodBuilder.ggo, + src/applications/nanoRodBuilder/nanorodBuilderCmd.c, + src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing + nanoRodBuilder application (may not work yet). ((Doesn't work + yet.)) (((May never work....))) + +2005-04-11 15:54 tim + + * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete + prepareVisitor in Dump2XYZ + +2005-04-11 15:19 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the + quadrupoles. look! it's divide by 3 like stone says! + +2005-04-11 15:18 chrisfen + + * forceFields/DUFF2.frc: fixing of the quadrupoles + +2005-04-11 15:16 tim + + * src/selection/Token.hpp: change the parameter name in + constructors + +2005-04-11 14:49 gezelter + + * make/Makefile.in: One more bug fix for GNU make versions < 3.80 + +2005-04-11 14:06 gezelter + + * make/Makefile.in: Fixed the uc and lc functions for GNU make + versions < 3.80 + +2005-04-11 11:13 gezelter + + * make/Makefile.in, src/UseTheForce/Makefile, + src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added + some stuff to clean out module files during "make clean" + +2005-04-08 17:13 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole + interactions should be working with a remaining question of + interaction magnitude + +2005-04-08 17:12 chrisfen + + * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with + samples + +2005-04-08 13:48 chrisfen + + * samples/water/ssd/ssd.md: oops... messed up a sample + +2005-04-08 09:43 chrisfen + + * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix + charge-dipole interactions + +2005-04-08 09:42 chrisfen + + * samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, + ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole + +2005-04-08 09:41 chrisfen + + * forceFields/DUFF2.frc: added Cl- and Na+ + +2005-04-06 18:59 tim + + * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser + +2005-04-05 18:09 tim + + * src/selection/: NameFinder.cpp, SelectionCompiler.cpp, + SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' + in atom type name;clean the code a little bit + +2005-03-29 16:00 tim + + * src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug + in converting rotation matrix to quaternion + +2005-03-28 17:41 tim + + * src/visitors/LipidTransVisitor.cpp: fixed the wrapping + +2005-03-28 17:30 tim + + * src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do + the wrapping + +2005-03-28 10:54 tim + + * src/applications/staticProps/GofXyz.cpp: fix a bug in getting the + dimension of histogram + +2005-03-22 11:38 tim + + * make/Makefile.in, src/applications/dump2Xyz/Makefile, + src/applications/dynamicProps/Makefile, + src/applications/oopse/Makefile, + src/applications/simpleBuilder/Makefile, + src/applications/staticProps/Makefile: avoid building parallel + executable for dump2XYZ, simpleBuilder, staticProps and + dynamicProps + +2005-03-21 17:34 chrisfen + + * forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the + forcefield files + +2005-03-21 15:51 chrisfen + + * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, + DarkSide/reactionField.F90: Make sure electrostatic_module provides + data for reaction_field + +2005-03-21 15:50 chrisfen + + * forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE + WILL CHANGE THIS BACK, RIGHT? + +2005-03-21 14:23 gezelter + + * src/UseTheForce/DarkSide/electrostatic.F90: constant back to + correct value + +2005-03-21 14:22 gezelter + + * make/Makefile.in: fixed an install-related bug. + $(InstallCommand) had been set to $(InstallData) + +2005-03-15 09:21 gezelter + + * src/integrators/Integrator.cpp: VelocityVerletIntegrator already + deletes and Nullifies restWriter, so Integrator shouldn't do it. + +2005-03-15 09:20 gezelter + + * src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos + +2005-03-13 02:39 gezelter + + * src/UseTheForce/DarkSide/electrostatic.F90: first run at + charge-quadrupole interactions + +2005-03-12 14:12 chrisfen + + * samples/: Makefile.in, thermoIntegration/liquid/Makefile, + thermoIntegration/solid/Makefile: forgot a couple of makefiles + +2005-03-12 14:05 chrisfen + + * samples/thermoIntegration/liquid/ssde.in, + samples/thermoIntegration/liquid/ssde.md, + samples/thermoIntegration/liquid/water.md, + samples/thermoIntegration/solid/idealCrystal.in, + samples/thermoIntegration/solid/ssde.in, + samples/thermoIntegration/solid/ssde.md, + samples/thermoIntegration/solid/ssde.zang0, + samples/thermoIntegration/solid/water.md, + samples/water/tip3p_ice/tp3.md, + src/UseTheForce/DarkSide/sticky.F90, + src/restraints/ThermoIntegrationForceManager.cpp: added some + samples + +2005-03-11 12:50 tim + + * src/: brains/SimCreator.cpp, + io/MultipoleAtomTypesSectionParser.cpp: fix a typo in + MultipoleAtomTypesSectionParser + +2005-03-11 10:55 tim + + * src/brains/SimInfo.cpp: pairs inside cutoff group should not be + excluded + +2005-03-11 10:53 gezelter + + * src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for + quadrupoles + +2005-03-11 10:52 gezelter + + * forceFields/DUFF2.frc: quadrupoles for SSD models + +2005-03-11 10:00 tim + + * ChangeLog, doc/SelectionExpression.html, + doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, + doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png, + src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp, + src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp, + src/selection/TokenMap.cpp: clean up SimInfo; modify the images of + SelectionExpression.html + +2005-03-10 19:43 chrisfen + + * samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, + src/io/RestReader.cpp, src/restraints/Restraints.cpp, + src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in + MPI restraints + +2005-03-10 18:56 tim + + * doc/SelectionExpression.html, src/brains/SimInfo.cpp, + src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody + and cutoff group + +2005-03-10 17:06 gezelter + + * src/types/MorseBondType.hpp: fixed a doxygen problem + +2005-03-10 16:51 gezelter + + * samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with + the split dipole test cases + +2005-03-10 16:51 gezelter + + * doc/SelectionExpression.html: updated some documentation + +2005-03-10 15:40 gezelter + + * src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, + Makefile: LinkedList removal project starts now + +2005-03-10 15:28 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: + using map to replace link list + +2005-03-10 14:11 tim + + * samples/dipole/: splitInWater.in, splitInWater.md: adding test + case of split dipole + +2005-03-10 14:10 chrisfen + + * samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, + src/io/RestWriter.cpp, + src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now + builds... + +2005-03-10 13:44 tim + + * samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, + split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: + adding test case for split dipole + +2005-03-10 12:54 gezelter + + * src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side + support for split dipoles + +2005-03-10 11:27 chrisfen + + * samples/water/tip3p_ice/tp3.md, + src/restraints/ThermoIntegrationForceManager.cpp: fixes to + restraints + +2005-03-10 11:15 chrisfen + + * samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, + src/UseTheForce/ForceFields.hpp, + src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints + +2005-03-10 11:14 tim + + * ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, + src/io/MultipoleAtomTypesSectionParser.cpp, + src/selection/SelectionEvaluator.cpp: minor change + +2005-03-10 10:10 chrisfen + + * make/Makefile.in, samples/water/tip3p_ice/tp3.md, + src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, + src/integrators/Integrator.cpp, src/integrators/Integrator.hpp, + src/integrators/VelocityVerletIntegrator.cpp, + src/integrators/VelocityVerletIntegrator.hpp, + src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp, + src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp, + src/io/RestReader.hpp, src/io/RestWriter.cpp, + src/io/RestWriter.hpp, src/io/RestraintReader.cpp, + src/io/RestraintWriter.cpp, src/restraints/Makefile, + src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, + src/restraints/ThermoIntegrationForceManager.cpp, + src/restraints/ThermoIntegrationForceManager.hpp: First commit of + the new restraints code + +2005-03-09 13:48 tim + + * src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding + IndexFinder + +2005-03-09 13:46 tim + + * src/: applications/dump2Xyz/Dump2XYZ.ggo, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, + selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: + fix compilation issue + +2005-03-09 12:58 tim + + * forceFields/DUFF2.frc, scripts/filepp, + src/UseTheForce/EAM_FF.cpp, + src/io/MultipoleAtomTypesSectionParser.cpp, + src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug + in SectionParser (lineNo is not updated) + +2005-03-09 12:30 tim + + * src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, + applications/dump2Xyz/Dump2XYZ.ggo, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp, + brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile, + io/MultipoleAtomTypesSectionParser.cpp, + io/MultipoleAtomTypesSectionParser.hpp, + io/SectionParserManager.cpp, selection/Makefile, + selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, + types/AtomType.cpp, types/DirectionalAtomType.cpp, + visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp, + visitors/OtherVisitor.hpp: adding IndexFinder which is used to + select the molecules; Seperate ElectrostaticAtomTypesSectionParser + into ChargeAtomTypesSectionParser and + MultipoleAtomTypesSectionParser;remove print dipole option from + Dump2XYZ; + +2005-03-09 12:28 tim + + * forceFields/DUFF2.frc: change the format of DUFF2 + +2005-03-09 10:44 gezelter + + * src/UseTheForce/DarkSide/: electrostatic.F90, + electrostatic_interface.F90, electrostatic_interface.h: new + electrostatic module + +2005-03-09 09:26 gezelter + + * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, + DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole + and fixed quadrupole stuff + +2005-03-09 09:25 gezelter + + * src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines + for outdated charge and dipole interfaces + +2005-03-08 16:08 gezelter + + * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, + mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun + charge-dipole test cases + +2005-03-08 16:07 gezelter + + * src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, + OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a + strange icc8 bug (we think). + +2005-03-08 16:07 gezelter + + * src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! + +2005-03-08 16:07 gezelter + + * src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic + Unification Project + +2005-03-08 16:07 gezelter + + * src/io/Globals.cpp: Dunno + +2005-03-08 16:06 gezelter + + * src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using + OOPSE_itoa and checking a NULL left over from the LinkedList days + +2005-03-08 16:06 gezelter + + * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, + atype_interface.F90, atype_interface.h, charge.F90, + charge_interface.F90, charge_interface.h, dipole.F90, + dipole_interface.F90, dipole_interface.h: electrostatic unification + project fixed an uninitialized variable in Lennard Jones mixing map + +2005-03-08 16:05 gezelter + + * src/UseTheForce/doForces.F90: electrostatic unification project + +2005-03-08 16:05 gezelter + + * samples/water/dimer/: two.md, water.md: making some cool test + cases + +2005-03-08 16:05 gezelter + + * forceFields/DUFF2.frc: Added a charge for Chlorine + +2005-03-07 17:39 tim + + * src/: brains/SimInfo.cpp, io/DumpReader.cpp, + math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, + primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: + Fixing a bug in BitSet.cpp + +2005-03-04 10:28 gezelter + + * src/config.h.in: Cleaning up config.h.in by adding comments + +2005-03-04 10:28 gezelter + + * configure, ac-tools/configure.in, make/Makefile.in, + src/brains/SimCreator.cpp: SPRNG eradication project + +2005-03-03 09:40 tim + + * src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the + missing atom type problem) + +2005-03-02 11:29 tim + + * src/math/RandNumGen.hpp: adding base class of Random Number + generator + +2005-03-02 11:28 tim + + * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, + math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in + Velocitizer is not initialized which causes a seg fault + +2005-03-02 10:36 tim + + * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp, math/Makefile, + math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, + math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp, + math/SeqRandNumGen.hpp: remove default parameter from + MersenneTwister.hpp which causes all kinds of trouble. Refactory + random number generator + +2005-03-02 02:32 tim + + * test/math/testRandNumGen.cpp: Adding unit test for random number + generator + +2005-03-01 18:17 tim + + * src/brains/Thermo.hpp: fixed a file inclusion problem + +2005-03-01 18:17 tim + + * test/math/: Makefile, OOPSERandNumGenTestCase.cpp, + OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, + ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, + RandNumGenTestCase.hpp: fixed compilation problem + +2005-03-01 18:02 tim + + * src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp, math/Makefile, + math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp, + math/ParallelRandNumGen.hpp, math/mt19937ar.c, + math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand + +2005-03-01 18:00 tim + + * test/math/: Makefile, ParallelandNumGenTestCase.cpp, + ParallelandNumGenTestCase.hpp: Change the name of test case + +2005-03-01 16:00 tim + + * test/math/: Makefile, OOPSERandNumGenTestCase.cpp, + OOPSERandNumGenTestCase.hpp: adding testcase for random number + generator + +2005-03-01 15:10 tim + + * src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, + integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, + math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp, + math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp, + math/Vector3.hpp, minimizers/MinimizerCreator.hpp, + utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, + utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, + visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 + +2005-03-01 14:11 tim + + * src/: brains/SimCreator.cpp, brains/SimInfo.hpp, + integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, + math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding + OOPSERandNumGen + +2005-03-01 10:44 gezelter + + * make/Makefile.in: Fixed the damned build problem with the + libraries not being removed in make clean and make distclean (at + least we think it is fixed). + +2005-03-01 10:26 gezelter + + * src/math/MersenneTwister.hpp: Making small modifications to allow + for use on MPI machines + +2005-03-01 09:45 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, + integrators/Velocitizer.cpp, io/DumpReader.cpp, + math/MersenneTwister.hpp: adding MersenneTwister random number + generator + +2005-02-28 22:55 tim + + * src/math/MersenneTwister.hpp: Adding a modified version of + MersenneTwister.hpp + +2005-02-28 12:24 tim + + * doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, + definition.jpg: selection expression + +2005-02-25 16:22 tim + + * src/: UseTheForce/DarkSide/LJ.F90, + UseTheForce/DarkSide/lj_interface.F90, + UseTheForce/DarkSide/lj_interface.h, + io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, + types/AtomType.hpp: adding soft potential to LJ Module + +2005-02-25 11:38 tim + + * doc/SelectionExpression.html: adding documentation for selection + expression + +2005-02-24 15:55 tim + + * src/: applications/simpleBuilder/simpleBuilder.cpp, + integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, + io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp: + adding basic_teebuf which can operate on multiple stream + simutaneously. + +2005-02-22 14:26 chrisfen + + * samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf + sample + +2005-02-22 13:56 tim + + * src/: UseTheForce/DarkSide/reactionField.F90, + primitives/RigidBody.cpp: reactionfield get fixed + +2005-02-21 11:57 tim + + * src/: applications/staticProps/GofRAngle.cpp, + visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix + a bug in GofRAngle + +2005-02-21 10:28 tim + + * src/primitives/Molecule.cpp: Fix for compilation on the Sun + +2005-02-21 10:22 tim + + * src/utils/next_combination.hpp: fix for compilation on the Sun + +2005-02-21 10:21 tim + + * src/utils/GenericData.hpp: fix problem in sun + +2005-02-18 18:07 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + applications/dump2Xyz/Dump2XYZ.ggo, + applications/dump2Xyz/Dump2XYZCmd.c, + applications/dump2Xyz/Dump2XYZCmd.h, + applications/dynamicProps/RCorrFunc.cpp, + applications/staticProps/GofXyz.cpp, + applications/staticProps/GofXyz.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticProps.ggo, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, + io/ElectrostaticAtomTypesSectionParser.cpp, + visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, + visitors/Makefile: adding LipidTransVisitor, GofXyz is working now + +2005-02-18 10:58 gezelter + + * src/brains/Register.cpp: Corrected filename collision for EAM on + Mac OS X + +2005-02-18 10:58 gezelter + + * src/applications/oopse/oopse.cpp: Updated copyright information + +2005-02-18 10:58 gezelter + + * src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, + Makefile: corrected filename collision for EAM on operating systems + which are not case sensitive (aka Mac OS X) + +2005-02-17 15:15 tim + + * src/applications/staticProps/GofXyz.cpp: more bug get fixed + +2005-02-17 14:50 tim + + * src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug + in GofXyz + +2005-02-17 14:09 tim + + * src/applications/staticProps/RadialDistrFunc.hpp: make + processHistogram non-abstrct function + +2005-02-17 13:41 tim + + * src/applications/staticProps/GofXyz.cpp: [no log message] + +2005-02-17 13:30 tim + + * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, + GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: + finish GofXyz + +2005-02-17 11:21 tim + + * src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, + GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial + distribution function + +2005-02-17 10:23 tim + + * src/utils/BitSet.hpp: forget the const correctness for BitSet + +2005-02-17 10:18 tim + + * src/: brains/BlockSnapshotManager.cpp, + selection/DistanceFinder.cpp: The change of interface of BitSet + cause a bug in SelectionEvaluation + +2005-02-16 16:13 tim + + * src/utils/residentMem.c: return residentMem in byte + +2005-02-16 16:00 tim + + * src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix + a bug in writing out the value of cosang + +2005-02-16 15:43 tim + + * src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to + estimate avaliable memory + +2005-02-16 15:30 tim + + * src/: applications/staticProps/GofAngle2.cpp, + applications/staticProps/GofAngle2.hpp, + applications/staticProps/GofR.cpp, + applications/staticProps/GofR.hpp, + applications/staticProps/GofRAngle.cpp, + applications/staticProps/GofRAngle.hpp, + applications/staticProps/GofXyz.cpp, + applications/staticProps/GofXyz.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticProps.ggo, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, + brains/BlockSnapshotManager.cpp: change the default bin number + +2005-02-16 14:36 tim + + * src/: applications/dynamicProps/DipoleCorrFunc.cpp, + applications/dynamicProps/RCorrFunc.cpp, + applications/dynamicProps/TimeCorrFunc.cpp, + applications/dynamicProps/VCorrFunc.cpp, + applications/staticProps/GofAngle2.cpp, + applications/staticProps/GofR.cpp, + applications/staticProps/GofR.hpp, + applications/staticProps/GofRAngle.cpp, + applications/staticProps/GofRAngle.hpp, + applications/staticProps/RadialDistrFunc.cpp, + applications/staticProps/RadialDistrFunc.hpp, + selection/SelectionManager.cpp, selection/SelectionManager.hpp, + utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output + files;fix the problem of counting in staticProps + +2005-02-15 14:39 tim + + * src/brains/BlockSnapshotManager.cpp: fix a bug in + BlockSnapshotManager + +2005-02-15 14:36 tim + + * src/: applications/dynamicProps/TimeCorrFunc.cpp, + applications/staticProps/RadialDistrFunc.cpp, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + selection/SelectionEvaluator.cpp: BlockSnapshotManager is using + reference counting now + +2005-02-15 12:49 tim + + * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: + replace std::make_pair by VariablesType::value_type to make Sun + Compiler happy + +2005-02-15 12:35 tim + + * src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to + TokenMap, using TokenMapType::value_type instead of std::make_pair + to make Sun compiler happy + +2005-02-15 12:24 tim + + * src/applications/staticProps/: GofRAngle.cpp, + RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps + +2005-02-15 12:11 tim + + * src/: applications/staticProps/GofR.cpp, + applications/staticProps/RadialDistrFunc.cpp, + applications/staticProps/RadialDistrFunc.hpp, + brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding + #ifdef __RWSTD to make sun compiler happy (2) fix pair density + calculation problem when two selections intersect with each other + +2005-02-15 10:24 gezelter + + * src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy + xlc++ + +2005-02-15 10:17 gezelter + + * configure, ac-tools/configure.in, src/config.h.in, + src/utils/residentMem.c: [no log message] + +2005-02-15 01:17 gezelter + + * src/utils/residentMem.c: bug fix for null termination + +2005-02-15 01:11 gezelter + + * configure, ac-tools/configure.in, src/utils/residentMem.c: + bugfixing residentMem + +2005-02-15 00:59 gezelter + + * configure, ac-tools/configure.in, src/config.h.in, + src/utils/residentMem.c: bugfixes for residentMem on LINUX + +2005-02-15 00:08 gezelter + + * src/utils/Makefile.in: added residentMem + +2005-02-15 00:05 gezelter + + * configure, ac-tools/configure.in, make/Makefile.in, + src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, + src/utils/residentMem.h: modifications to estimate memory in use by + other processes autoconf fixes ps syntax checking config.h file + cleaning + +2005-02-14 18:26 gezelter + + * configure, ac-tools/configure.in, make/Makefile.in: ps niceness + +2005-02-14 18:16 gezelter + + * configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps + strangeness + +2005-02-14 14:42 tim + + * src/brains/BlockSnapshotManager.cpp: fix a bug in + BlockSnapshotManager.hpp + +2005-02-14 13:51 tim + + * src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, + StaticPropsCmd.c: default length for staticProps is 1/2 smallest + length of first frame + +2005-02-14 13:12 tim + + * src/integrators/VelocityVerletIntegrator.cpp: fix a bug in + VelocityVerletIntegrator : last frame is written twice + +2005-02-14 12:57 tim + + * src/: applications/dynamicProps/TimeCorrFunc.cpp, + brains/SimInfo.cpp, primitives/RigidBody.cpp, + primitives/StuntDouble.hpp: begin bug fix + +2005-02-14 12:35 tim + + * src/applications/dynamicProps/: CorrelationFunction.cpp, + CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, + CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp, + DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile, + ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp, + RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, + VCorrFunc.hpp: refactory CorrelationFunction + +2005-02-14 10:18 gezelter + + * src/applications/dynamicProps/CorrelationFunction.cpp: bug fix + and start of switch for type of correlation function + +2005-02-13 16:18 tim + + * src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in + calculating bytes per stuntdouble + +2005-02-13 16:03 tim + + * src/applications/dynamicProps/CorrelationFunction.cpp: more fix + +2005-02-13 15:57 tim + + * src/applications/dynamicProps/CorrelationFunction.cpp: fixed a + bug in CorrelationFunction + +2005-02-13 15:36 tim + + * src/: applications/staticProps/GofR.cpp, + applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a + bug in SimInfo::getCutoff() + +2005-02-13 15:08 tim + + * make/Makefile.in: adding staticProps and dynamicProps into + Makefile.in + +2005-02-13 15:05 tim + + * src/: applications/dynamicProps/CorrelationFunction.cpp, + applications/dynamicProps/CorrelationFunction.hpp, + applications/staticProps/StaticProps.cpp, + applications/staticProps/StaticProps.ggo, + applications/staticProps/StaticPropsCmd.c, + applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp, + brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length + defaults to the cutoff radius + +2005-02-13 14:14 tim + + * src/utils/Algorithm.hpp: adding Algorithm.hpp + +2005-02-13 14:10 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + applications/dynamicProps/CorrelationFunction.cpp, + applications/dynamicProps/CorrelationFunction.hpp, + applications/dynamicProps/DynamicProps.cpp, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + integrators/Integrator.cpp, integrators/Integrator.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp, + io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp, + utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, + visitors/OtherVisitor.cpp: dynamicProps get built + +2005-02-13 10:56 tim + + * src/: applications/dynamicProps/CorrelationFunction.cpp, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in + progress + +2005-02-13 03:04 tim + + * src/: applications/dynamicProps/CorrelationFunction.hpp, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, + brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more + work in dynamicProps + +2005-02-13 02:25 tim + + * src/applications/dynamicProps/DynamicProps.cpp: adding + dynamicProps + +2005-02-13 02:14 tim + + * src/applications/dynamicProps/: DynamicPropsCmd.c, + DynamicPropsCmd.h: adding command line option to DynamicProps + +2005-02-13 02:13 tim + + * src/applications/dynamicProps/: DynamicProps.ggo, Makefile: + adding command line option for DynamicProps + +2005-02-13 01:57 tim + + * src/: applications/dynamicProps/CorrelationFunction.cpp, + applications/dynamicProps/CorrelationFunction.hpp, + applications/dynamicProps/DipoleCorrFunc.cpp, + applications/dynamicProps/DipoleCorrFunc.hpp, + applications/dynamicProps/RCorrFunc.cpp, + applications/dynamicProps/RCorrFunc.hpp, + applications/dynamicProps/VCorrFunc.cpp, + applications/dynamicProps/VCorrFunc.hpp, + applications/staticProps/RadialDistrFunc.cpp, + brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, + brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, + brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp, + primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding + dynamicProps + +2005-02-12 15:09 tim + + * src/selection/SelectionManager.cpp: adding SelectionManager.cpp + +2005-02-11 17:41 tim + + * src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one + more constructor to Snapshot to create customized DataStorage + +2005-02-11 17:39 tim + + * src/selection/: DistanceFinder.hpp, Makefile, + SelectionManager.hpp: adding beginSelected, nextSelected method to + SelectionManager + +2005-02-11 17:36 tim + + * src/config.h.in, configure: adding support for physmem + +2005-02-11 17:35 tim + + * ac-tools/configure.in: adding supprot for physmem + +2005-02-11 17:35 tim + + * src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding + physmem + +2005-02-10 17:37 tim + + * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, + GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, + GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, + StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, + StaticPropsCmd.h: more work in StaticProps + +2005-02-10 13:14 tim + + * src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, + GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, + GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp, + Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, + StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, + StaticPropsCmd.h: change the filenames + +2005-02-10 09:15 tim + + * src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, + GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, + RadialDistrFunc.hpp: adding GofRAngle + +2005-02-09 13:21 tim + + * src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some + useless files + +2005-02-09 13:12 tim + + * src/applications/staticProps/: GofR.cpp, Makefile, + RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress + +2005-02-09 12:08 tim + + * src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, + GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, + RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR + +2005-02-07 17:39 tim + + * src/primitives/Molecule.hpp: add getRigidBodyAt function into + Molecule class + +2005-02-07 17:38 tim + + * src/applications/dump2Xyz/Dump2XYZCmd.c: update help info + +2005-02-07 17:36 tim + + * src/selection/: NameFinder.cpp, NameFinder.hpp, + SelectionCompiler.cpp: support select internal index selection, for + example, select DMPC.3 + +2005-02-07 16:11 tim + + * src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update + help info for Dump2XYZ + +2005-02-07 15:39 chrisfen + + * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: + selection librarys added + +2005-02-07 15:31 tim + + * src/selection/Makefile, make/Makefile.in: adding Makefile + +2005-02-07 15:20 chrisfen + + * src/utils/wildcards.hpp: issue commented out in wildcards + +2005-02-07 15:06 tim + + * src/selection/SelectionEvaluator.cpp: forget to reset the pc + which cause reevaluate return NULL + +2005-02-07 14:14 tim + + * src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, + SimSnapshotManager.hpp: fix a bug in determing the global index for + rigidbodies + +2005-02-07 14:13 tim + + * src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change + in Bitset + +2005-02-07 14:13 tim + + * src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, + SelectionCompiler.cpp, SelectionCompiler.hpp, + SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, + TokenMap.cpp: selection library is working + +2005-02-04 17:46 tim + + * src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor + +2005-02-04 17:45 tim + + * src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor + and XYZVisitor now use selection library + +2005-02-04 17:44 tim + + * src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: + adding SelectionManager into SimInfo + +2005-02-04 17:43 tim + + * src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, + Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of + selection library + +2005-02-04 17:42 tim + + * src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change + in BitSet + +2005-02-04 17:41 tim + + * src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing + implementation + +2005-02-04 17:39 tim + + * src/selection/: NameFinder.cpp, NameFinder.hpp, + SelectionCompiler.cpp, SelectionCompiler.hpp, + SelectionEvaluator.cpp, SelectionEvaluator.hpp, + SelectionManager.hpp, Token.hpp: half of the selection utility is + working need to debug within keyword and atomproperty keyword + +2005-02-04 00:42 tim + + * src/selection/: NameFinder.cpp, NameFinder.hpp: selection library + get built + +2005-02-04 00:42 tim + + * src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet + +2005-02-04 00:26 tim + + * src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: + remove some useless files + +2005-02-03 23:57 tim + + * src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, + selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: + adding wildcard class; NameFinder is finished + +2005-02-03 18:14 tim + + * src/selection/: NameFinder.cpp, NameFinder.hpp, + SelectionCompiler.cpp, SelectionCompiler.hpp, + SelectionEvaluator.cpp, SelectionEvaluator.hpp, + SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in + selection library + +2005-02-03 09:04 tim + + * src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: + selection in progress + +2005-02-02 18:13 tim + + * src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, + SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, + Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in + progress, except SelectionEvaluator, other files are compiled + +2005-02-02 18:12 tim + + * src/utils/: Makefile.in, any.hpp: adding boost::any + +2005-02-02 07:51 tim + + * src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp + +2005-02-01 17:49 tim + + * src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, + selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, + selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, + selection/Token.hpp: Selection in progress + +2005-02-01 01:55 tim + + * src/: selection/SelectionCompiler.hpp, + selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, + selection/SelectionManager.hpp, selection/Token.hpp, + utils/BitSet.cpp, utils/BitSet.hpp: adding selection library + +2005-01-26 10:26 tim + + * src/integrators/: Integrator.cpp, Integrator.hpp, + VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget + to add eorWriter + +2005-01-26 10:15 tim + + * src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: + (1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the + wrong column of electroframe + +2005-01-25 16:59 tim + + * src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in + SimInfo, use number of cutoff stamp as counter to loop over + rigidbody stamp + +2005-01-25 12:45 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + brains/MoleculeCreator.cpp, brains/SimCreator.cpp, + integrators/DLM.cpp, io/AtomTypesSectionParser.cpp, + io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp, + io/EAMAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp, + io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.cpp, + io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, + math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp, + primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp, + primitives/GhostTorsion.hpp, primitives/Makefile, + primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete + section parser's error message (2) add GhostTorsion (3) accumulate + inertial tensor from the directional atoms before calculate + rigidbody's inertial tensor + +2005-01-17 17:17 tim + + * forceFields/DUFF2.frc: forget to set dipole for lipid head group + +2005-01-17 11:58 tim + + * src/integrators/NVT.cpp: fix a bug in loading initial extended + system parameters + +2005-01-17 11:05 tim + + * src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT + +2005-01-14 17:02 tim + + * src/UseTheForce/WATER.cpp: remove WATER.cpp + +2005-01-14 16:37 tim + + * forceFields/Makefile: sync Makefile + +2005-01-14 16:13 gezelter + + * make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, + src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, + src/applications/dump2Xyz/Makefile, + src/applications/oopse/Makefile, + src/applications/simpleBuilder/Makefile, src/brains/Makefile, + src/constraints/Makefile, src/integrators/Makefile, + src/io/Makefile, src/math/Makefile, src/minimizers/Makefile, + src/primitives/Makefile, src/profiling/Makefile, + src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in, + src/visitors/Makefile: moved Package variable into subdirectory + makefiles to speed up the building process + +2005-01-14 15:48 gezelter + + * src/applications/oopse/oopse.cpp: Fixed publication details in + banner + +2005-01-14 15:48 gezelter + + * src/UseTheForce/DarkSide/: simParallel_interface.F90, + simParallel_interface.h: added dummy subroutine to avoid empty + unit, synchronized this dummy routine between C and fortran + +2005-01-14 15:31 gezelter + + * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, + notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, + DarkSide/Makefile, DarkSide/atype.F90, + DarkSide/atype_interface.F90, DarkSide/charge.F90, + DarkSide/charge_interface.F90, DarkSide/dipole.F90, + DarkSide/dipole_interface.F90, DarkSide/eam.F90, + DarkSide/eam_interface.F90, DarkSide/gb.F90, + DarkSide/gb_interface.F90, DarkSide/lj_interface.F90, + DarkSide/shapes.F90, DarkSide/shapes_interface.F90, + DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90, + DarkSide/simulation.F90, DarkSide/simulation_interface.F90, + DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating + modules and C/Fortran interface subroutines + +2005-01-14 15:15 gezelter + + * configure, ac-tools/aclocal.m4: more fixes for gnugetopt + +2005-01-14 15:09 gezelter + + * configure, ac-tools/configure.in, src/config.h.in, + src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt + +2005-01-14 11:49 tim + + * src/: io/EAMAtomTypesSectionParser.cpp, + utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, + utils/StringUtils.hpp: using c library to do conversion instead of + using iostream due to a bug in libstdc++(GCC 3.2) + +2005-01-13 21:40 tim + + * src/brains/SimSetup.cpp: no message + +2005-01-13 20:56 tim + + * src/primitives/Molecule.hpp: fix a bug in global index + +2005-01-13 20:04 tim + + * src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include + Integrator.hpp in Minimizer + +2005-01-13 17:14 gezelter + + * src/utils/Makefile: compile getopt and getopt1 if we need to + +2005-01-13 16:56 gezelter + + * make/Makefile.in: template flags + +2005-01-13 16:48 gezelter + + * src/applications/oopse/Makefile: formatting + +2005-01-13 16:48 gezelter + + * make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir + target + +2005-01-13 14:40 tim + + * src/: UseTheForce/fSwitchingFunction.h, + UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, + math/Makefile, math/RectMatrix.hpp, math/Vector.hpp, + primitives/RigidBody.cpp, types/AtomTypeProperties.h, + types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform + +2005-01-13 13:26 tim + + * make/Makefile.in: change the order of linking (object file comes + first and then follow by user built library) + +2005-01-12 18:24 tim + + * src/io/DumpWriter.cpp: remove useless debug info + +2005-01-12 18:21 tim + + * src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix + +2005-01-12 18:17 tim + + * make/: Makefile.in, Makefile.in: missing tab + +2005-01-12 18:15 tim + + * src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor + get fixed + +2005-01-12 17:40 gezelter + + * make/Makefile.in, src/UseTheForce/DUFF.cpp, + src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, + src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp, + src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, + src/UseTheForce/ForceFieldCreator.hpp, + src/UseTheForce/ForceFieldFactory.cpp, + src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp, + src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp, + src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h, + src/UseTheForce/fSwitchingFunction.h, + src/UseTheForce/mpiComponentPlan.h, + src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, + src/UseTheForce/notifyCutoffs.F90, + src/UseTheForce/notifyCutoffs_interface.h, + src/UseTheForce/DarkSide/LJ.F90, + src/UseTheForce/DarkSide/atype.F90, + src/UseTheForce/DarkSide/atype_interface.h, + src/UseTheForce/DarkSide/charge.F90, + src/UseTheForce/DarkSide/charge_interface.h, + src/UseTheForce/DarkSide/dipole.F90, + src/UseTheForce/DarkSide/dipole_interface.h, + src/UseTheForce/DarkSide/eam.F90, + src/UseTheForce/DarkSide/eam_interface.h, + src/UseTheForce/DarkSide/force_globals.F90, + src/UseTheForce/DarkSide/gb.F90, + src/UseTheForce/DarkSide/gb_interface.h, + src/UseTheForce/DarkSide/lj_interface.h, + src/UseTheForce/DarkSide/neighborLists.F90, + src/UseTheForce/DarkSide/reactionField.F90, + src/UseTheForce/DarkSide/shapes.F90, + src/UseTheForce/DarkSide/shapes_interface.h, + src/UseTheForce/DarkSide/simParallel.F90, + src/UseTheForce/DarkSide/simParallel_interface.h, + src/UseTheForce/DarkSide/simulation.F90, + src/UseTheForce/DarkSide/simulation_interface.h, + src/UseTheForce/DarkSide/sticky.F90, + src/UseTheForce/DarkSide/sticky_interface.h, + src/UseTheForce/DarkSide/switcheroo.F90, + src/applications/Makedepend, src/applications/quickLate.c, + src/applications/dump2Xyz/Dump2XYZ.cpp, + src/applications/oopse/oopse.cpp, + src/applications/simpleBuilder/BaseLattice.cpp, + src/applications/simpleBuilder/BaseLattice.hpp, + src/applications/simpleBuilder/Lattice.cpp, + src/applications/simpleBuilder/Lattice.hpp, + src/applications/simpleBuilder/LatticeCreator.cpp, + src/applications/simpleBuilder/LatticeCreator.hpp, + src/applications/simpleBuilder/LatticeFactory.cpp, + src/applications/simpleBuilder/LatticeFactory.hpp, + src/applications/simpleBuilder/MoLocator.cpp, + src/applications/simpleBuilder/MoLocator.hpp, + src/applications/simpleBuilder/simpleBuilder.cpp, + src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, + src/brains/Exclude.cpp, src/brains/Exclude.hpp, + src/brains/ForceManager.cpp, src/brains/ForceManager.hpp, + src/brains/Makefile, src/brains/Migrator.hpp, + src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp, + src/brains/Register.cpp, src/brains/Register.hpp, + src/brains/SimCreator.cpp, src/brains/SimCreator.hpp, + src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, + src/brains/SimModel.hpp, src/brains/SimSetup.hpp, + src/brains/SimSnapshotManager.cpp, + src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp, + src/brains/SimState.hpp, src/brains/SkipList.cpp, + src/brains/SkipList.hpp, src/brains/Snapshot.cpp, + src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, + src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp, + src/brains/Thermo.hpp, src/brains/fSimulation.h, + src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, + src/constraints/AbstractClasses.hpp, + src/constraints/ConstraintElem.hpp, + src/constraints/ConstraintPair.hpp, src/constraints/Makefile, + src/constraints/Rattle.cpp, src/constraints/Rattle.hpp, + src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, + src/constraints/ZconsStruct.hpp, + src/constraints/ZconstraintForceManager.cpp, + src/constraints/ZconstraintForceManager.hpp, + src/integrators/AbstractClasses.hpp, + src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp, + src/integrators/DLM.hpp, src/integrators/Integrator.cpp, + src/integrators/Integrator.hpp, + src/integrators/IntegratorCreator.hpp, + src/integrators/IntegratorFactory.cpp, + src/integrators/IntegratorFactory.hpp, src/integrators/Makefile, + src/integrators/NPT.cpp, src/integrators/NPT.hpp, + src/integrators/NPTf.cpp, src/integrators/NPTf.hpp, + src/integrators/NPTi.cpp, src/integrators/NPTi.hpp, + src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp, + src/integrators/NVE.cpp, src/integrators/NVE.hpp, + src/integrators/NVT.cpp, src/integrators/NVT.hpp, + src/integrators/RotationAlgorithm.hpp, + src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, + src/integrators/VelocityVerletIntegrator.cpp, + src/integrators/VelocityVerletIntegrator.hpp, + src/io/AtomTypesSectionParser.cpp, + src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp, + src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, + src/io/BendTypesSectionParser.cpp, + src/io/BendTypesSectionParser.hpp, + src/io/BondTypesSectionParser.cpp, + src/io/BondTypesSectionParser.hpp, + src/io/DirectionalAtomTypesSectionParser.cpp, + src/io/DirectionalAtomTypesSectionParser.hpp, + src/io/DumpReader.cpp, src/io/DumpReader.hpp, + src/io/DumpWriter.cpp, src/io/DumpWriter.hpp, + src/io/EAMAtomTypesSectionParser.cpp, + src/io/EAMAtomTypesSectionParser.hpp, + src/io/ElectrostaticAtomTypesSectionParser.cpp, + src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp, + src/io/Globals.hpp, src/io/InitializeFromFile.cpp, + src/io/LennardJonesAtomTypesSectionParser.cpp, + src/io/LennardJonesAtomTypesSectionParser.hpp, + src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp, + src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, + src/io/Makefile, src/io/SectionParser.cpp, + src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, + src/io/SectionParserManager.hpp, src/io/StatWriter.cpp, + src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp, + src/io/StickyAtomTypesSectionParser.hpp, + src/io/TorsionTypesSectionParser.cpp, + src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp, + src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, + src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.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/math/ChebyshevPolynomials.cpp, + src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c, + src/math/MatVec3.h, src/math/Polynomial.hpp, + src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp, + src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp, + src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, + src/math/Vector.hpp, src/math/Vector3.hpp, + src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp, + src/minimizers/CGFamilyMinimizer.cpp, + src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile, + src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp, + src/minimizers/MinimizerCreator.hpp, + src/minimizers/MinimizerFactory.cpp, + src/minimizers/MinimizerFactory.hpp, + src/minimizers/MinimizerParameterSet.cpp, + src/minimizers/MinimizerParameterSet.hpp, + src/minimizers/OOPSEMinimizer.cpp, + src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, + src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp, + src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp, + src/primitives/Atom.cpp, src/primitives/Atom.hpp, + src/primitives/Bend.cpp, src/primitives/Bend.hpp, + src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp, + src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp, + src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, + src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, + src/primitives/GhostBend.hpp, 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/Torsion.hpp, src/primitives/TorsionExtensions.cpp, + src/primitives/UreyBradleyBend.cpp, + src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, + src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp, + src/types/AtomStamp.hpp, src/types/AtomType.cpp, + src/types/AtomType.hpp, src/types/AtomTypeProperties.h, + src/types/BendStamp.cpp, src/types/BendStamp.hpp, + src/types/BendType.hpp, src/types/BondStamp.cpp, + src/types/BondStamp.hpp, src/types/BondType.hpp, + src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp, + src/types/Component.cpp, src/types/Component.hpp, + src/types/CubicBendType.hpp, src/types/CubicBondType.hpp, + src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp, + src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp, + src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, + src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, + src/types/MakeStamps.cpp, src/types/MakeStamps.hpp, + src/types/Makefile, src/types/MoleculeStamp.cpp, + src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp, + src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp, + src/types/PolynomialBondType.hpp, + src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, + src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, + src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, + src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, + src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, + src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, + src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, + src/utils/GenericData.hpp, src/utils/GenericFactory.hpp, + src/utils/LocalIndexManager.hpp, src/utils/Makefile, + src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp, + src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp, + src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp, + src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp, + src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp, + src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp, + src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp, + src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp, + src/utils/Utility.cpp, src/utils/Utility.hpp, + src/utils/definitions.F90, src/utils/fError.c, + src/utils/next_combination.hpp, src/utils/oopseMPI.F90, + src/utils/simError.c, src/utils/simError.h, src/utils/status.F90, + src/utils/vector_class.F90, src/visitors/AtomData.hpp, + src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, + src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, + src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, + src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, + src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, + src/visitors/ZconsVisitor.hpp: merging new_design branch into + OOPSE-2.0 + +2005-01-12 13:13 tim + + * src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, + utils/TypeContainer.hpp: forget to include + +2005-01-12 12:25 tim + + * forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, + newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force + fields + +2005-01-12 12:14 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, + UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + UseTheForce/ForceFieldCreator.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, + UseTheForce/doForces.F90, UseTheForce/doForces_interface.h, + UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, + UseTheForce/notifyCutoffs.F90, + UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, + UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/atype_interface.h, + UseTheForce/DarkSide/charge.F90, + UseTheForce/DarkSide/charge_interface.h, + UseTheForce/DarkSide/dipole.F90, + UseTheForce/DarkSide/dipole_interface.h, + UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h, + UseTheForce/DarkSide/force_globals.F90, + UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, + UseTheForce/DarkSide/lj_interface.h, + UseTheForce/DarkSide/neighborLists.F90, + UseTheForce/DarkSide/reactionField.F90, + UseTheForce/DarkSide/shapes.F90, + UseTheForce/DarkSide/shapes_interface.h, + UseTheForce/DarkSide/simParallel.F90, + UseTheForce/DarkSide/simParallel_interface.h, + UseTheForce/DarkSide/simulation.F90, + UseTheForce/DarkSide/simulation_interface.h, + UseTheForce/DarkSide/sticky.F90, + UseTheForce/DarkSide/sticky_interface.h, + UseTheForce/DarkSide/switcheroo.F90, + applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, + applications/simpleBuilder/BaseLattice.cpp, + applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.cpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeCreator.cpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/MoLocator.cpp, + applications/simpleBuilder/MoLocator.hpp, + applications/simpleBuilder/simpleBuilder.cpp, + brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, + brains/Exclude.hpp, brains/ForceManager.cpp, + brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp, + brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, + brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp, + brains/Snapshot.cpp, brains/Snapshot.hpp, + brains/SnapshotManager.hpp, brains/Stats.cpp, brains/Stats.hpp, + brains/Thermo.cpp, brains/Thermo.hpp, brains/fSimulation.h, + constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp, + constraints/Rattle.cpp, constraints/Rattle.hpp, + constraints/ZconsStruct.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, + integrators/DLM.hpp, integrators/Integrator.cpp, + integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/NPT.cpp, + integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, + integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, + integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, + integrators/NVT.cpp, integrators/NVT.hpp, + integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, + integrators/Velocitizer.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, + io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, + io/BASS_parse.h, io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, + io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, + io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp, + io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, + io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, + io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.hpp, + io/SectionParser.cpp, io/SectionParser.hpp, + io/SectionParserManager.cpp, io/SectionParserManager.hpp, + io/StatWriter.cpp, io/StatWriter.hpp, + io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, + io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, + io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, + io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/interface.c, + io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, + io/node_list.h, io/parse_interface.h, io/parse_me.h, + io/parse_tree.c, io/parse_tree.h, math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, + math/Polynomial.hpp, math/Quaternion.hpp, + math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, + math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp, + math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp, + math/randomSPRNG.hpp, minimizers/CGFamilyMinimizer.cpp, + minimizers/CGFamilyMinimizer.hpp, minimizers/Minimizer.cpp, + minimizers/Minimizer.hpp, minimizers/MinimizerCreator.hpp, + minimizers/MinimizerFactory.cpp, minimizers/MinimizerFactory.hpp, + minimizers/MinimizerParameterSet.cpp, + minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, + minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, + minimizers/SDMinimizer.hpp, primitives/Atom.cpp, + primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, + primitives/Bond.hpp, primitives/CutoffGroup.hpp, + primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, + primitives/GhostBend.cpp, primitives/GhostBend.hpp, + primitives/Molecule.cpp, primitives/Molecule.hpp, + primitives/RigidBody.cpp, primitives/RigidBody.hpp, + primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, + primitives/Torsion.cpp, primitives/Torsion.hpp, + primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, + profiling/mdProfile.cpp, profiling/mdProfile.hpp, + restraints/Restraints.cpp, restraints/Restraints.hpp, + types/AtomStamp.cpp, types/AtomStamp.hpp, types/AtomType.cpp, + types/AtomType.hpp, types/AtomTypeProperties.h, + types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, + types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, + types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, + types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, + types/CubicBondType.hpp, types/CubicTorsionType.hpp, + types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, + types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp, + types/FixedBondType.hpp, types/HarmonicBendType.hpp, + types/HarmonicBondType.hpp, types/MakeStamps.cpp, + types/MakeStamps.hpp, types/MoleculeStamp.cpp, + types/MoleculeStamp.hpp, types/MorseBondType.hpp, + types/OplsTorsionType.hpp, types/PolynomialBendType.hpp, + types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, + types/QuarticBendType.hpp, types/QuarticBondType.hpp, + types/QuarticTorsionType.hpp, types/RigidBodyStamp.cpp, + types/RigidBodyStamp.hpp, types/ShapeAtomType.cpp, + types/ShapeAtomType.hpp, types/TorsionStamp.cpp, + types/TorsionStamp.hpp, types/TorsionType.hpp, + types/UreyBradleyBendType.hpp, types/ZconStamp.cpp, + types/ZconStamp.hpp, utils/GenericData.hpp, + utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, + utils/MemoryUtils.hpp, utils/NumericConstant.hpp, + utils/OOPSEConstant.hpp, utils/PropertyMap.cpp, + utils/PropertyMap.hpp, utils/StringTokenizer.cpp, + utils/StringTokenizer.hpp, utils/StringUtils.cpp, + utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, + utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, + utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90, + utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90, + utils/simError.c, utils/simError.h, utils/status.F90, + utils/vector_class.F90, visitors/AtomData.hpp, + visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp, + visitors/BaseVisitor.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 license + +2005-01-12 12:14 tim + + * src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on + branch new_design. + +2005-01-11 16:03 tim + + * src/: constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, + minimizers/MinimizerParameterSet.cpp, + minimizers/MinimizerParameterSet.hpp: change const static double + data member to const double + +2005-01-11 15:50 tim + + * src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: + +2005-01-11 15:39 tim + + * src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: + change data type from logical to integer in AtomTypeProperties.h + +2005-01-11 11:36 tim + + * forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding + new format of EAM force field + +2005-01-11 11:24 tim + + * src/UseTheForce/DUFF.cpp: change default name of DUFF force field + to DUFF2.frc + +2005-01-11 11:23 tim + + * forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to + DUFF2.frc + +2005-01-11 11:09 tim + + * make/Makefile.in: adding constraints and minimizers into + Makefile.in + +2005-01-11 11:03 tim + + * src/io/: ChargeAtomTypesSectionParser.cpp, + ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, + DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless + files + +2005-01-11 10:59 tim + + * src/io/ZConsWriter.cpp: [no log message] + +2005-01-11 10:53 tim + + * src/UseTheForce/EAM.cpp: minor fix + +2005-01-11 10:52 tim + + * src/constraints/Rattle.hpp: file Rattle.hpp was initially added + on branch new_design. + +2005-01-11 10:52 tim + + * src/constraints/Rattle.cpp: file Rattle.cpp was initially added + on branch new_design. + +2005-01-11 10:52 tim + + * src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm + +2005-01-11 10:47 tim + + * make/Makefile.in: forget a '$' sign + +2005-01-11 10:46 tim + + * make/Makefile.in: missing tab in rules + +2005-01-10 17:04 tim + + * src/: UseTheForce/ForceFieldCreator.cpp, + UseTheForce/ForceFieldCreator.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, + applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile, + brains/Register.cpp, brains/Register.hpp, + integrators/IntegratorCreator.cpp, + integrators/IntegratorCreator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/Makefile, + integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp, + minimizers/Makefile, minimizers/MinimizerCreator.cpp, + minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, + minimizers/MinimizerFactory.hpp: create a register module to + register force fields, integrators and minimizers + +2005-01-10 17:04 tim + + * src/brains/Register.cpp: file Register.cpp was initially added on + branch new_design. + +2005-01-10 17:04 tim + + * src/brains/Register.hpp: file Register.hpp was initially added on + branch new_design. + +2005-01-10 15:52 tim + + * src/: UseTheForce/ForceFieldFactory.cpp, + applications/oopse/oopse.cpp, brains/ForceManager.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, + integrators/IntegratorFactory.cpp, + integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp, + io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp, + visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint + method is working now + +2005-01-10 13:05 tim + + * src/: constraints/ConstraintElem.hpp, + constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp, + io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp, + visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in + zconstraint + +2005-01-10 13:05 tim + + * src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was + initially added on branch new_design. + +2005-01-07 16:50 tim + + * src/constraints/ZconstraintForceManager.cpp: file + ZconstraintForceManager.cpp was initially added on branch + new_design. + +2005-01-07 16:50 tim + + * src/constraints/ZconstraintForceManager.hpp: file + ZconstraintForceManager.hpp was initially added on branch + new_design. + +2005-01-07 16:50 tim + + * src/: applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp, + constraints/ConstraintElem.hpp, constraints/Makefile, + constraints/ZConstraint.cpp, constraints/ZconsData.hpp, + constraints/ZconstraintForceManager.cpp, + constraints/ZconstraintForceManager.hpp, + integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, + utils/NumericConstant.hpp: ZConstraintForceManager in progress + +2005-01-07 16:50 tim + + * src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was + initially added on branch new_design. + +2005-01-06 17:31 tim + + * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + constraints/ConstraintPair.hpp, integrators/Integrator.cpp, + integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp, + io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: + constraint is almost working + +2005-01-05 19:36 tim + + * src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is + working + +2005-01-05 19:16 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + applications/oopse/oopse.cpp, + applications/simpleBuilder/BaseLattice.cpp, + applications/simpleBuilder/Lattice.cpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/MoLocator.cpp, + applications/simpleBuilder/MoLocator.hpp, + applications/simpleBuilder/simpleBuilder.cpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp, + minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder + in progress + +2005-01-05 12:35 tim + + * src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp + was initially added on branch new_design. + +2005-01-05 12:35 tim + + * src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially + added on branch new_design. + +2005-01-05 12:35 tim + + * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, + Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, + MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp, + OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, + SDMinimizer.hpp: minimizer in progress + +2005-01-05 12:35 tim + + * src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp + was initially added on branch new_design. + +2005-01-05 12:35 tim + + * src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp + was initially added on branch new_design. + +2005-01-05 12:35 tim + + * src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp + was initially added on branch new_design. + +2005-01-05 12:35 tim + + * src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially + added on branch new_design. + +2005-01-04 17:18 tim + + * src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, + brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, + brains/Thermo.cpp, constraints/ConstraintPair.hpp, + constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp, + integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp, + primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in + progress + +2005-01-04 17:18 tim + + * src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was + initially added on branch new_design. + +2005-01-04 17:18 tim + + * src/minimizers/MinimizerParameterSet.cpp: file + MinimizerParameterSet.cpp was initially added on branch new_design. + +2005-01-04 17:18 tim + + * src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was + initially added on branch new_design. + +2005-01-04 17:18 tim + + * src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp + was initially added on branch new_design. + +2005-01-04 17:18 tim + + * src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, + Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, + OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, + SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress + +2005-01-04 17:18 tim + + * src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on + branch new_design. + +2004-12-20 15:50 chuckv + + * make/Makefile.in: Fixed Makefile test bug under OSX and possibly + other BSD's, replaced test -f *.mod with ls function since BSD test + apparently doesn't support wildcards. + +2004-12-20 15:36 tim + + * make/Makefile.in: fix a test command incompatiable problem + +2004-12-20 14:49 tim + + * src/integrators/NPTi.cpp: NPT is working now + +2004-12-16 14:20 tim + + * src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the + invalid stamp id + +2004-12-16 14:00 tim + + * forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, + newEAM.u6.frc: adding new EAM force field files + +2004-12-16 13:55 tim + + * src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays + in EAM parameter file is incorrect + +2004-12-16 12:27 tim + + * src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, + brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, + utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM + +2004-12-15 17:34 tim + + * src/: applications/simpleBuilder/BaseLattice.cpp, + applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.cpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeCreator.cpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/simpleBuilder.cpp, + io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream + +2004-12-15 16:07 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, + applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: + add EAM Force Field + +2004-12-15 14:40 tim + + * src/applications/oopse/oopse.cpp: add more force fields + +2004-12-15 11:44 tim + + * src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget + to call All_reduce in MPI version) + +2004-12-15 11:13 tim + + * src/: brains/SimCreator.cpp, brains/SimInfo.cpp, + io/DumpReader.cpp: MPI in NVE is working + +2004-12-14 16:57 tim + + * src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. + Master nodes does not brocast the total number of frames + +2004-12-14 14:08 tim + + * src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, + integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, + minimizers/CGFamilyMinimizer.cpp, + minimizers/MinimizerParameterSet.hpp, + minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, + minimizers/SDMinimizer.cpp: more fix in MPI version + +2004-12-13 17:30 tim + + * src/: UseTheForce/DarkSide/simParallel.F90, + applications/oopse/oopse.cpp, brains/SimCreator.cpp, + brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp, + integrators/DLM.cpp, integrators/Integrator.cpp, + integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, + integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp, + io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp, + io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, + math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp, + primitives/RigidBody.cpp, primitives/StuntDouble.cpp, + primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp, + utils/LocalIndexManager.hpp, utils/PropertyMap.cpp, + utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version + is built + +2004-12-10 13:41 tim + + * src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp + +2004-12-10 11:14 tim + + * src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, + primitives/StuntDouble.hpp: forget to zero out the torque. Sticky + and Dipole is working now + +2004-12-09 18:15 tim + + * src/: UseTheForce/DarkSide/dipole.F90, + UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: + fix an index problem in eFrame matrix + +2004-12-09 18:09 tim + + * src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when + initializing the new Charge AtomType + +2004-12-09 16:15 tim + + * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, + types/DirectionalAtomType.cpp: sticky module get compiled + +2004-12-09 15:43 gezelter + + * src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, + reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for + GB + +2004-12-09 15:42 gezelter + + * src/UseTheForce/doForces.F90: u_l -> eFrame + +2004-12-09 15:27 gezelter + + * src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky + module now has the option for multiple sticky types + +2004-12-09 15:27 gezelter + + * src/UseTheForce/doForces.F90: sticky + +2004-12-09 11:22 tim + + * src/integrators/: NPT.cpp, NVT.cpp: fix an interface + inconsistency in lab2Bidy + +2004-12-09 10:45 tim + + * src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug + in calculating torque in rigid body + +2004-12-08 15:37 tim + + * src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, + brains/SnapShot.cpp, brains/Snapshot.hpp, + integrators/Integrator.cpp, + io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: + fix a parsing bug in ElectroStaticAtomTypesSectionParser + +2004-12-08 12:03 tim + + * src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane + in NVT is working + +2004-12-07 18:08 tim + + * src/: UseTheForce/Makefile, brains/SimInfo.hpp, + integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, + integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, + io/DumpWriter.cpp: NPT in progress + +2004-12-07 09:43 tim + + * test/utils/: Makefile, NextCombinationTestCase.hpp: [no log + message] + +2004-12-07 00:12 tim + + * src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in + UseInitXSstate + +2004-12-07 00:00 tim + + * src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message + +2004-12-06 23:47 tim + + * src/types/DirectionalAtomType.cpp: [no log message] + +2004-12-06 21:18 tim + + * forceFields/newDUFF.frc: merge WATER force field into DUFF + +2004-12-06 20:33 tim + + * forceFields/newDUFF.frc: change the force constant of bonds + +2004-12-06 18:29 tim + + * src/: UseTheForce/DarkSide/charge.F90, + UseTheForce/DarkSide/charge_interface.h, + UseTheForce/DarkSide/dipole.F90, + UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: + fix atom type ident in Charge and Dipole Module + +2004-12-06 17:56 tim + + * src/primitives/Torsion.cpp: butane is working now + +2004-12-06 15:15 tim + + * src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, + primitives/Bond.hpp, primitives/Torsion.cpp: short range + interaction for butane is correct.Still something wrong with long + range one + +2004-12-05 23:49 tim + + * src/: brains/Exclude.cpp, brains/Exclude.hpp, + brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + io/BendTypesSectionParser.cpp, math/Polynomial.hpp, + primitives/Atom.hpp, utils/NumericConstant.hpp, + utils/TypeContainer.hpp: fix a bug in Exclude List + +2004-12-05 17:21 tim + + * forceFields/newDUFF.frc: minor fix in DUFF + +2004-12-05 17:02 tim + + * src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, + utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: + fix a bug in filling MolMembership + +2004-12-05 12:12 tim + + * forceFields/newDUFF.frc: minor fix in force field file + +2004-12-05 12:09 tim + + * src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, + integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp + +2004-12-04 15:09 tim + + * src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, + math/Vector3.hpp: NVE is working now, get the same result as + OOPSE-1.0 + +2004-12-04 14:29 tim + + * src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy + +2004-12-04 14:24 gezelter + + * src/primitives/: Bend.cpp, Torsion.cpp: What? + +2004-12-04 14:24 gezelter + + * src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion + +2004-12-04 00:24 tim + + * src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, + integrators/Integrator.hpp, + integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp, + utils/TypeContainer.hpp: NVE conserved energy, however, potential + is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf + and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, + dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step + 4 EAM Step 5 Shape Step 6 Constraint & Restraint + +2004-12-03 19:01 tim + + * src/: UseTheForce/DarkSide/LJ.F90, + applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, + io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, + energy of NVE is not conserved + +2004-12-03 17:36 tim + + * src/: brains/DataStorage.hpp, brains/Snapshot.hpp, + primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running + +2004-12-03 16:30 tim + + * src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, + integrators/NVE.cpp, primitives/Molecule.cpp, + primitives/Molecule.hpp, primitives/StuntDouble.hpp, + primitives/Torsion.hpp: more missing function get implemented + +2004-12-03 15:30 tim + + * src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, + SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo + +2004-12-03 12:59 tim + + * src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp, + io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp, + io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, + utils/TypeContainer.hpp: begin to fix bugs + +2004-12-02 19:26 tim + + * src/utils/Trim.cpp: file Trim.cpp was initially added on branch + new_design. + +2004-12-02 19:26 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/ForceFieldCreator.cpp, + UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, + integrators/IntegratorCreator.cpp, + integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp, + io/SectionParserManager.hpp, utils/Makefile, + utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a + bug in countTokens in StringTokenizer + +2004-12-02 19:06 tim + + * forceFields/newDUFF.frc: minor fix + +2004-12-02 18:15 tim + + * forceFields/newDUFF.frc: new ForceField format + +2004-12-02 17:15 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/ForceFieldCreator.cpp, + UseTheForce/ForceFieldCreator.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, + applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp, + integrators/IntegratorCreator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/Makefile, + integrators/NPTf.cpp, integrators/NPTf.hpp, integrators/NPTi.cpp, + integrators/NPTi.hpp, integrators/NPTxyz.cpp, + integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, + integrators/NVT.cpp, integrators/NVT.hpp, + types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, + types/Makefile: refine factory pattern to make it initialized + correctly + +2004-12-02 17:15 tim + + * src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp + was initially added on branch new_design. + +2004-12-02 17:15 tim + + * src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp + was initially added on branch new_design. + +2004-12-02 17:15 tim + + * src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp + was initially added on branch new_design. + +2004-12-02 17:15 tim + + * src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp + was initially added on branch new_design. + +2004-12-02 11:53 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, + types/DirectionalAtomType.cpp, types/Makefile: oopse get built + +2004-12-02 11:04 tim + + * src/: applications/simpleBuilder/LatticeCreator.cpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp, + brains/MoleculeCreator.cpp, brains/SimCreator.cpp, + brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, + brains/SnapshotManager.hpp, brains/Stats.cpp, + constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp, + io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp, + io/basic_ifstrstream.hpp, primitives/Bend.hpp, + primitives/GhostBend.cpp, primitives/GhostBend.hpp, + types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, + types/OplsTorsionType.hpp, types/ShapeAtomType.hpp, + utils/PropertyMap.hpp, utils/TypeContainer.hpp, + visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp, + visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, + visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, + visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still + have two linking problem + +2004-12-02 00:17 tim + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + applications/simpleBuilder/Lattice.cpp, + applications/simpleBuilder/simpleBuilder.cpp, + constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp, + io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp, + minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp, + restraints/Restraints.cpp, visitors/AtomVisitor.cpp, + visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, + visitors/ZconsVisitor.cpp: change endl to std::endl + +2004-12-02 00:14 tim + + * src/: UseTheForce/Shapes_FF.cpp, + applications/dump2Xyz/Dump2XYZ.cpp, + applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, + io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, + minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, + utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, + visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, + visitors/RigidBodyVisitor.hpp: minor fix + +2004-12-02 00:09 tim + + * src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: + remove StreamTokenizer + +2004-12-02 00:06 tim + + * src/: UseTheForce/Shapes_FF.cpp, + applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, + applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp, + io/ZConsWriter.cpp, math/randomSPRNG.cpp, + restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using + namespace std in .cpp file + +2004-12-02 00:04 tim + + * src/: UseTheForce/Shapes_FF.cpp, + applications/dump2Xyz/Dump2XYZ.cpp, + applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.cpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/MoLocator.cpp, + applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp, + brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp, + io/ZConsWriter.cpp, io/ZConsWriter.hpp, + minimizers/MinimizerParameterSet.hpp, + minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, + minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp, + restraints/Restraints.cpp, restraints/Restraints.hpp, + types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, + types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, + utils/GenericData.hpp, visitors/CompositeVisitor.cpp, + visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, + visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding + qulified name prefix std + +2004-12-01 23:55 tim + + * src/: UseTheForce/Shapes_FF.cpp, + applications/dump2Xyz/Dump2XYZ.cpp, + applications/simpleBuilder/BaseLattice.hpp, + applications/simpleBuilder/Lattice.hpp, + applications/simpleBuilder/LatticeCreator.hpp, + applications/simpleBuilder/LatticeFactory.cpp, + applications/simpleBuilder/LatticeFactory.hpp, + applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, + io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, + minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, + utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, + visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, + visitors/RigidBodyVisitor.hpp: replace string by std::string + +2004-12-01 22:12 tim + + * make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, + src/applications/simpleBuilder/BaseLattice.hpp, + src/applications/simpleBuilder/Lattice.hpp, + src/applications/simpleBuilder/LatticeCreator.hpp, + src/applications/simpleBuilder/LatticeFactory.hpp, + src/applications/simpleBuilder/MoLocator.hpp, + src/brains/SimInfo.cpp, src/brains/SkipList.hpp, + src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp, + src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp, + src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, + src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp, + src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp, + src/utils/Makefile, src/utils/StringUtils.cpp, + src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp, + src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp, + src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp, + test/brains/RigidBody.cpp: replace misuse of using namespace std in + header files + +2004-12-01 21:23 tim + + * src/: primitives/Atom.hpp, primitives/RigidBody.hpp, + primitives/StuntDouble.hpp, utils/TypeContainer.hpp, + utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: + begin to fix linking problem + +2004-12-01 21:08 tim + + * src/: applications/oopse/oopse.cpp, brains/Stats.cpp, + brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, + integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, + integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, + integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp, + math/SquareMatrix3.hpp, primitives/Atom.hpp, + primitives/RigidBody.hpp, primitives/StuntDouble.hpp, + utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, + still has some linking problem + +2004-12-01 19:26 tim + + * src/: integrators/NVT.cpp, integrators/NVT.hpp, + utils/OOPSEConstant.hpp: NVT get built + +2004-12-01 19:09 tim + + * src/integrators/DLM.cpp: file DLM.cpp was initially added on + branch new_design. + +2004-12-01 19:09 tim + + * src/integrators/DLM.hpp: file DLM.hpp was initially added on + branch new_design. + +2004-12-01 19:09 tim + + * src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, + brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, + brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp, + integrators/Integrator.hpp, integrators/Makefile, + integrators/NVE.cpp, integrators/NVE.hpp, + integrators/RotationAlgorithm.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE + get built + +2004-12-01 19:09 tim + + * src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp + was initially added on branch new_design. + +2004-12-01 17:45 tim + + * src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/Makefile, + integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp, + io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, + io/StatWriter.hpp: rename DumpWrite to DumpWriter + +2004-12-01 17:45 tim + + * src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on + branch new_design. + +2004-12-01 15:05 tim + + * src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, + io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, + utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp, + visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp, + visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, + visitors/ZconsVisitor.hpp: visitors get built + +2004-12-01 14:32 chrisfen + + * samples/water/tip3p_ice/tp3.md: fixed a sample + +2004-12-01 14:10 tim + + * src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, + src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, + src/types/AtomType.hpp, src/utils/Utility.hpp, + src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, + src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: + spell check + +2004-12-01 13:42 tim + + * src/: UseTheForce/DarkSide/atype.F90, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp, + primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp, + primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator + and constraint, other directories get built + +2004-12-01 12:38 tim + + * src/: brains/DataStorage.cpp, brains/DataStorage.hpp, + brains/ForceManager.cpp, brains/MoleculeCreator.cpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, + primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, + primitives/GhostBend.cpp, primitives/RigidBody.cpp, + primitives/RigidBody.hpp, primitives/StuntDouble.hpp, + types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, + types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: + refactory AtomType + +2004-11-30 22:11 tim + + * src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change + +2004-11-30 21:30 tim + + * src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change + NumericConstant + +2004-11-30 21:24 tim + + * src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, + primitives/RigidBody.cpp: minor fix + +2004-11-30 18:14 tim + + * src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, + io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, + io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io + get built, next is integrator + +2004-11-30 17:43 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/ForceField.hpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + io/BASS_interface.cpp, primitives/StuntDouble.hpp, + utils/StringUtils.hpp: brains get built + +2004-11-30 15:50 tim + + * src/: brains/ForceManager.cpp, brains/Makefile, + brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + primitives/RigidBody.cpp, primitives/RigidBody.hpp, + utils/StringUtils.hpp: brains get built, io is next + +2004-11-30 14:58 tim + + * src/: brains/Exclude.cpp, brains/Exclude.hpp, + brains/ForceManager.cpp, brains/ForceManager.hpp, + brains/MoleculeCreator.cpp, brains/SimCreator.hpp, + brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, + brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp, + brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, + math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo + +2004-11-30 14:58 tim + + * src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially + added on branch new_design. + +2004-11-30 12:54 tim + + * src/: primitives/Bend.hpp, primitives/Bond.hpp, + primitives/StuntDouble.hpp, primitives/Torsion.hpp, + utils/LocalIndexManager.hpp: more get fixed + +2004-11-30 00:03 tim + + * src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was + initially added on branch new_design. + +2004-11-30 00:03 tim + + * src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename + LocalndexManager.hpp to LocalIndexManager.hpp + +2004-11-29 23:43 tim + + * src/: io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp, + io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp: Section Parsers get compiled + +2004-11-29 23:14 tim + + * src/: io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor + fixed + +2004-11-29 22:49 tim + + * src/: io/TorsionTypesSectionParser.cpp, + io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, + types/CubicTorsionType.hpp, types/PolynomialBendType.hpp, + types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, + types/QuarticTorsionType.hpp: minor fixed + +2004-11-29 22:32 tim + + * src/: io/TorsionTypesSectionParser.cpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp: #inlcude statement can not be + embedded + +2004-11-29 16:42 tim + + * test/math/: Makefile, PolynomialTestCase.cpp, + PolynomialTestCase.hpp: add PolynomialTestCase + +2004-11-29 16:42 tim + + * src/math/Polynomial.hpp: Polynomial passes unit test + +2004-11-29 15:03 tim + + * src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename + QuarticTorsion.hpp to QuarticTorsionType.hpp + +2004-11-29 15:03 tim + + * src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was + initially added on branch new_design. + +2004-11-29 14:56 tim + + * src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was + initially added on branch new_design. + +2004-11-29 14:56 tim + + * src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add + CubicTorsionType and QuarticTorsionType + +2004-11-29 14:56 tim + + * src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was + initially added on branch new_design. + +2004-11-29 13:00 tim + + * src/: brains/DataStorage.hpp, brains/Snapshot.hpp, + types/CubicBendType.hpp, types/CubicBondType.hpp, + types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get + fixed + +2004-11-29 12:59 tim + + * src/utils/Trim.hpp: file Trim.hpp was initially added on branch + new_design. + +2004-11-29 12:59 tim + + * src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim + Algorithm for std::string + +2004-11-29 10:52 tim + + * src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove + some useless files + +2004-11-29 10:50 tim + + * src/io/: BondTypesSectionParser.cpp, + ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, + ElectrostaticAtomTypesSectionParser.cpp, + HarmonicBondTypesSectionParser.cpp, + HarmonicBondTypesSectionParser.hpp, + LennardJonesAtomTypesSectionParser.cpp, Makefile, + SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, + StickyAtomTypesSectionParser.hpp: more files get fixed + +2004-11-29 10:27 tim + + * src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, + DirectionalAtomTypesSectionParser.cpp, + EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp, + Makefile, SectionParser.cpp, SectionParser.hpp, + SectionParserManager.cpp, SectionParserManager.hpp: part of io get + built + +2004-11-29 09:49 tim + + * src/types/UreyBradleyBendType.hpp: types get built + +2004-11-29 09:40 tim + + * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: + types get built + +2004-11-25 21:13 tim + + * src/: UseTheForce/ForceField.hpp, + io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, + types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some + files + +2004-11-25 15:18 tim + + * src/types/QuarticBondType.hpp: file QuarticBondType.hpp was + initially added on branch new_design. + +2004-11-25 15:18 tim + + * src/: io/AtomTypesSectionParser.cpp, + io/BondTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.cpp, + types/QuadraticBendType.hpp, types/QuadraticBondType.hpp, + types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some + files + +2004-11-25 15:18 tim + + * src/types/QuarticBendType.hpp: file QuarticBendType.hpp was + initially added on branch new_design. + +2004-11-24 17:12 tim + + * src/: io/AtomTypesSectionParser.cpp, + io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, + io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, + io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/DipoleAtomTypesSectionParser.cpp, + io/DipoleAtomTypesSectionParser.hpp, + io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, + io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp, + io/EAMAtomTypesSectionParser.hpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, + io/HarmonicBondTypesSectionParser.hpp, + io/LennardJonesAtomTypesSectionParser.cpp, + io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile, + io/SectionParser.hpp, io/SectionParserManager.hpp, + io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, + io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, + utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built + +2004-11-24 16:33 tim + + * src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, + ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, + LJFF.cpp, Makefile: UseTheForce get built + +2004-11-24 15:55 tim + + * src/: math/RectMatrix.hpp, primitives/Bend.cpp, + primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, + primitives/Makefile, primitives/Molecule.cpp, + primitives/Molecule.hpp, primitives/RigidBody.cpp, + primitives/StuntDouble.hpp, primitives/Torsion.cpp, + primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, + primitives/UreyBradleyBend.hpp: types and primitives get built + +2004-11-24 14:49 tim + + * test/utils/: Makefile, NextCombinationTestCase.cpp, + StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint + StringTokenizerTestCase + +2004-11-24 14:49 tim + + * src/utils/: GenericData.hpp, StringTokenizer.cpp, + StringTokenizer.hpp: StringTokenizer passes unit test + +2004-11-24 13:20 tim + + * ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, + src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: + change Makefile + +2004-11-24 13:06 chrisfen + + * src/io/RestraintReader.cpp: improved restraints - mpi should work + fine + +2004-11-24 13:06 chrisfen + + * src/integrators/Integrator.cpp: improved restraints + +2004-11-24 13:05 chrisfen + + * samples/water/tip3p_ice/tp3.md: oops... + +2004-11-24 12:42 tim + + * src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, + brains/DataStorage.hpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, integrators/Integrator.hpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + primitives/DirectionalAtom.cpp: add SetForceManager method to + integrator + +2004-11-23 18:12 tim + + * src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, + integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, + integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, + integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, + integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, + integrators/NVT.hpp, integrators/Velocitizer.cpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + types/UreyBradleyBendType.hpp: refactory NPT integrator + +2004-11-23 17:50 chrisfen + + * samples/water/tip3p_ice/tp3.md: Back to normal... Oh... + Restraints should work in parallel now + +2004-11-23 17:48 chrisfen + + * src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, + brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, + integrators/Integrator.cpp, integrators/Integrator.hpp, + io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, + io/RestraintReader.cpp, io/RestraintWriter.cpp, + restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements + to restraints + +2004-11-23 17:47 chrisfen + + * samples/water/tip3p_ice/tp3.md: just some testing changes, I'll + return to the original on next commit + +2004-11-23 12:53 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + applications/simpleBuilder/simpleBuilder.cpp, + io/ChargeAtomTypesSectionParser.cpp, + io/DirectionalAtomTypesSectionParser.hpp, + io/EAMAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.cpp, + io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, + io/SectionParser.hpp, types/DirectionalAtomType.cpp, + utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser + +2004-11-23 12:53 tim + + * src/io/ElectrostaticAtomTypesSectionParser.hpp: file + ElectrostaticAtomTypesSectionParser.hpp was initially added on + branch new_design. + +2004-11-23 12:53 tim + + * src/io/ElectrostaticAtomTypesSectionParser.cpp: file + ElectrostaticAtomTypesSectionParser.cpp was initially added on + branch new_design. + +2004-11-23 01:03 tim + + * src/: io/EAMAtomTypesSectionParser.cpp, + io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, + types/AtomType.hpp, types/DirectionalAtomType.cpp, + types/DirectionalAtomType.hpp: add EAM AtomType Section Parser + +2004-11-23 01:03 tim + + * src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp + was initially added on branch new_design. + +2004-11-23 01:03 tim + + * src/io/EAMAtomTypesSectionParser.hpp: file + EAMAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-23 01:03 tim + + * src/io/EAMAtomTypesSectionParser.cpp: file + EAMAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/TorsionTypesSectionParser.hpp: file + TorsionTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/BendTypesSectionParser.hpp: file + BendTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/BondTypesSectionParser.hpp: file + BondTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/BondTypesSectionParser.cpp: file + BondTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/TorsionTypesSectionParser.cpp: file + TorsionTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 23:35 tim + + * src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, + BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, + TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add + BondTypesSectionParser, BendTypesSectionParser and + TorsionTypeSectionParser + +2004-11-22 23:35 tim + + * src/io/BendTypesSectionParser.cpp: file + BendTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 18:04 tim + + * src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in + DUFF and EAM + +2004-11-22 18:02 tim + + * src/io/: DirectionalAtomTypesParser.hpp, + DirectionalAtomTypesSectionParser.hpp: adding section parsers + +2004-11-22 18:02 tim + + * src/io/DirectionalAtomTypesSectionParser.hpp: file + DirectionalAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/DipoleAtomTypesSectionParser.hpp: file + DipoleAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/AtomTypesSectionParser.hpp: file + AtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/HarmonicBondTypesSectionParser.hpp: file + HarmonicBondTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/StickyAtomTypesSectionParser.cpp: file + StickyAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/LennardJonesAtomTypesSectionParser.hpp: file + LennardJonesAtomTypesSectionParser.hpp was initially added on + branch new_design. + +2004-11-22 15:55 tim + + * src/io/HarmonicBondTypesSectionParser.cpp: file + HarmonicBondTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/DirectionalAtomTypesSectionParser.cpp: file + DirectionalAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/SectionParserManager.cpp: file SectionParserManager.cpp + was initially added on branch new_design. + +2004-11-22 15:55 tim + + * src/io/AtomTypesSectionParser.cpp: file + AtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/ChargeAtomTypesSectionParser.cpp: file + ChargeAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/DipoleAtomTypesSectionParser.cpp: file + DipoleAtomTypesSectionParser.cpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/LennardJonesAtomTypesSectionParser.cpp: file + LennardJonesAtomTypesSectionParser.cpp was initially added on + branch new_design. + +2004-11-22 15:55 tim + + * src/io/ChargeAtomTypesSectionParser.hpp: file + ChargeAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/StickyAtomTypesSectionParser.hpp: file + StickyAtomTypesSectionParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/SectionParser.hpp: file SectionParser.hpp was initially + added on branch new_design. + +2004-11-22 15:55 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, + brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, + brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, + integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, + io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, + io/ChargeAtomTypesSectionParser.hpp, + io/DipoleAtomTypesSectionParser.cpp, + io/DipoleAtomTypesSectionParser.hpp, + io/DirectionalAtomTypesParser.hpp, + io/DirectionalAtomTypesSectionParser.cpp, + io/HarmonicBondTypesSectionParser.cpp, + io/HarmonicBondTypesSectionParser.hpp, + io/LennardJonesAtomTypesSectionParser.cpp, + io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, + io/SectionParser.hpp, io/SectionParserManager.cpp, + io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, + io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, + types/AtomType.hpp, types/DirectionalAtomType.hpp, + utils/GenericData.hpp: adding section parsers + +2004-11-22 15:55 tim + + * src/io/DirectionalAtomTypesParser.hpp: file + DirectionalAtomTypesParser.hpp was initially added on branch + new_design. + +2004-11-22 15:55 tim + + * src/io/SectionParserManager.hpp: file SectionParserManager.hpp + was initially added on branch new_design. + +2004-11-22 15:55 tim + + * src/io/SectionParser.cpp: file SectionParser.cpp was initially + added on branch new_design. + +2004-11-19 17:12 tim + + * src/types/FixedBondType.hpp: file FixedBondType.hpp was initially + added on branch new_design. + +2004-11-19 17:12 tim + + * src/: brains/SimState.cpp, brains/SimState.hpp, + io/InitializeFromFile.cpp, types/FixBondType.hpp, + types/FixedBondType.hpp: remove more useless files + +2004-11-19 16:47 tim + + * src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, + integrators/Integrator.cpp, applications/Makedepend: remove more + useless files + +2004-11-19 16:38 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, + integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, + integrators/NVT.hpp: refactory integrator + +2004-11-19 16:38 tim + + * src/integrators/NPTi.hpp: file NPTi.hpp was initially added on + branch new_design. + +2004-11-19 16:38 tim + + * src/integrators/NPTf.hpp: file NPTf.hpp was initially added on + branch new_design. + +2004-11-19 16:38 tim + + * src/integrators/NPT.hpp: file NPT.hpp was initially added on + branch new_design. + +2004-11-19 16:38 tim + + * src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added + on branch new_design. + +2004-11-19 16:38 tim + + * src/integrators/NVT.hpp: file NVT.hpp was initially added on + branch new_design. + +2004-11-19 15:37 tim + + * forceFields/newDUFF.frc: new DUFF forcefield + +2004-11-19 15:23 tim + + * src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on + branch new_design. + +2004-11-19 15:23 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, + UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, + utils/TypeContainer.hpp: add EAM + +2004-11-19 15:23 tim + + * src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on + branch new_design. + +2004-11-19 13:02 tim + + * src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except + error checking + +2004-11-19 12:56 tim + + * src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp + was initially added on branch new_design. + +2004-11-19 12:56 tim + + * src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp + was initially added on branch new_design. + +2004-11-19 12:56 tim + + * src/types/FixBondType.hpp: file FixBondType.hpp was initially + added on branch new_design. + +2004-11-19 12:56 tim + + * src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, + UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, + UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, + integrators/IntegratorFactory.cpp, + integrators/IntegratorFactory.hpp, integrators/NVE.hpp, + integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, + utils/StringTokenizer.cpp: DUFF is almost done except error + checking + +2004-11-18 19:11 tim + + * src/UseTheForce/DUFF.cpp: adding DUFF parser + +2004-11-18 18:26 tim + + * src/integrators/Velocitizer.cpp: file Velocitizer.cpp was + initially added on branch new_design. + +2004-11-18 18:26 tim + + * src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, + integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, + integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, + types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, + types/CubicBendType.hpp, types/CubicBondType.hpp, + types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, + types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding + DUFF parser + +2004-11-18 16:42 tim + + * forceFields/newDUFF.frc: adding new format DUFF force field + +2004-11-18 10:57 chrisfen + + * src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that + slowed down the force loop + +2004-11-18 00:42 tim + + * src/utils/NumericConstant.cpp: file NumericConstant.cpp was + initially added on branch new_design. + +2004-11-18 00:42 tim + + * src/utils/NumericConstant.hpp: file NumericConstant.hpp was + initially added on branch new_design. + +2004-11-18 00:42 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, + primitives/Bend.cpp, utils/NumericConstant.cpp, + utils/NumericConstant.hpp: Adding NumericConstant class + +2004-11-17 23:16 tim + + * src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, + UseTheForce/ForceFields.hpp: remove more junk files + +2004-11-17 23:12 tim + + * src/: brains/ForceFields.cpp, brains/SimSetup.cpp, + brains/SimSetup.hpp, constraints/AbstractClasses.hpp, + integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, + primitives/AbstractClasses.hpp, primitives/Bond.cpp, + primitives/BondExtensions.cpp, primitives/SRI.hpp, + primitives/TorsionExtensions.cpp: remove some junk files + +2004-11-17 23:07 tim + + * src/primitives/BendExtensions.cpp: remove some junk files + +2004-11-17 23:04 tim + + * src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, + QuadraticBondType.hpp: refine QudraticBond + +2004-11-17 22:57 tim + + * src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp + +2004-11-17 22:57 tim + + * src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was + initially added on branch new_design. + +2004-11-17 16:47 tim + + * src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp + was initially added on branch new_design. + +2004-11-17 16:47 tim + + * src/types/CubicBendType.hpp: file CubicBendType.hpp was initially + added on branch new_design. + +2004-11-17 16:47 tim + + * src/primitives/GhostBend.hpp: file GhostBend.hpp was initially + added on branch new_design. + +2004-11-17 16:47 tim + + * src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was + initially added on branch new_design. + +2004-11-17 16:47 tim + + * src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was + initially added on branch new_design. + +2004-11-17 16:47 tim + + * src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was + initially added on branch new_design. + +2004-11-17 16:47 tim + + * src/types/CubicBondType.hpp: file CubicBondType.hpp was initially + added on branch new_design. + +2004-11-17 16:47 tim + + * src/: math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, + primitives/Bend.hpp, primitives/GhostBend.cpp, + primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, + primitives/UreyBradleyBend.hpp, types/BondType.hpp, + types/CubicBendType.hpp, types/CubicBondType.hpp, + types/HarmonicBondType.hpp, types/MorseBondType.hpp, + types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: + UreyBradleyBend and GhostBend + +2004-11-17 13:58 tim + + * src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp + was initially added on branch new_design. + +2004-11-17 13:58 tim + + * src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp + was initially added on branch new_design. + +2004-11-17 13:58 tim + + * src/: math/ChebyshevPolynomials.cpp, + math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, + primitives/Bond.hpp, types/CharmmTorsionType.hpp, + types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types + stuff and Chebyshev Polynomial + +2004-11-17 13:58 tim + + * src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was + initially added on branch new_design. + +2004-11-17 01:37 tim + + * src/types/PolynomialTorsionType.hpp: file + PolynomialTorsionType.hpp was initially added on branch new_design. + +2004-11-17 01:37 tim + + * src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was + initially added on branch new_design. + +2004-11-17 01:37 tim + + * src/: math/Polynomial.hpp, primitives/Bend.cpp, + primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, + types/BondType.hpp, types/CharmmTorsionType.cpp, + types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, + types/HarmonicBondType.hpp, types/MorseBondType.hpp, + types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, + types/PolynomialTorsionType.hpp, types/TorsionType.hpp, + utils/StringTokenizer.hpp: add PolynomialBondType, + PolynomialBendType, PolynomialTorsionType, HarmonicBendType and + CharmmTorsionType. Need to refine the design and add document for + them + +2004-11-17 01:37 tim + + * src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was + initially added on branch new_design. + +2004-11-17 01:37 tim + + * src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was + initially added on branch new_design. + +2004-11-17 01:37 tim + + * src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was + initially added on branch new_design. + +2004-11-16 20:11 tim + + * src/types/: BendType.hpp, PolynomialBondType.hpp, + TorsionType.hpp: add PolynomialBondType + +2004-11-16 20:11 tim + + * src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was + initially added on branch new_design. + +2004-11-16 18:20 tim + + * src/math/Polynomial.hpp: file Polynomial.hpp was initially added + on branch new_design. + +2004-11-16 18:20 tim + + * src/math/Polynomial.hpp: Adding Polynomial class + +2004-11-16 17:04 gezelter + + * src/types/MorseBondType.hpp: file MorseBondType.hpp was initially + added on branch new_design. + +2004-11-16 17:04 gezelter + + * src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was + initially added on branch new_design. + +2004-11-16 17:04 gezelter + + * src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, + MorseBondType.hpp, TorsionType.hpp: added some new stuff + +2004-11-16 15:36 tim + + * src/: primitives/Bend.cpp, primitives/Bend.hpp, + primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, + types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and + TorsionType + +2004-11-15 21:07 tim + + * src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on + branch new_design. + +2004-11-15 21:07 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, + UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, + utils/StringTokenizer.cpp: adding DUFF class; adding checking + statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer + +2004-11-15 18:00 tim + + * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + UseTheForce/ForceFieldFactory.cpp, + UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, + UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, + types/AtomType.hpp: adding ForceFieldFactory and LJFF classes + +2004-11-15 18:00 tim + + * src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp + was initially added on branch new_design. + +2004-11-15 18:00 tim + + * src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp + was initially added on branch new_design. + +2004-11-15 18:00 tim + + * src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on + branch new_design. + +2004-11-15 13:02 tim + + * src/integrators/Velocitizer.hpp: file Velocitizer.hpp was + initially added on branch new_design. + +2004-11-15 13:02 tim + + * src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on + branch new_design. + +2004-11-15 13:02 tim + + * src/io/DumpReader.hpp: file DumpReader.hpp was initially added on + branch new_design. + +2004-11-15 13:02 tim + + * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, + integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, + io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, + DumpWriter.Next Step is LJFF and integrators + +2004-11-13 00:08 tim + + * src/: brains/ForceManager.cpp, brains/ForceManager.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, primitives/Molecule.cpp, + primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, + refactory, refactory + +2004-11-12 17:43 tim + + * src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, + StringTokenizer.cpp: bug fix in hasMoreTokens + +2004-11-12 17:28 tim + + * src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was + initially added on branch new_design. + +2004-11-12 17:28 tim + + * src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding + StringUtils, a c-style strtok like class, need unit test + +2004-11-12 12:40 tim + + * src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test + +2004-11-12 02:05 tim + + * src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + primitives/CutoffGroup.hpp, primitives/Molecule.cpp: + MoleculeCreator forget to create CutoffGroups for free atoms + +2004-11-12 01:19 tim + + * src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, + brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, + io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: + OOPSE = Object-Obfuscated Parallel Simulation Engine + +2004-11-11 16:48 chrisfen + + * samples/water/tip3p_ice/tp3.md: working sample + +2004-11-11 16:47 chrisfen + + * src/restraints/Restraints.cpp: working towards parallel + restraints + +2004-11-11 16:47 chrisfen + + * src/integrators/Integrator.cpp: Commented out some write + statements + +2004-11-11 16:46 chrisfen + + * src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some + write statements + +2004-11-11 16:46 chrisfen + + * samples/water/tip3p_ice/tp3.md: Fun with ice + +2004-11-11 11:41 tim + + * src/: brains/Exclude.cpp, brains/Exclude.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, + brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, + io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove + useless mpiSimulation + +2004-11-11 11:41 tim + + * src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on + branch new_design. + +2004-11-10 17:50 tim + + * src/: brains/ForceManager.cpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, + integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo + +2004-11-10 17:01 tim + + * src/: brains/SimCreator.cpp, brains/SimCreator.hpp, + brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, + brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, + brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, + io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, + visitors/AtomVisitor.cpp: another painful day (1) SimCreator, + SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom + File will be removed) (3) ForceField (at least LJ) and BondType, + BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & + Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint + +2004-11-10 09:52 tim + + * src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a + configurable StatWriter + +2004-11-10 09:52 tim + + * src/io/StatWriter.hpp: file StatWriter.hpp was initially added on + branch new_design. + +2004-11-09 21:58 tim + + * src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation + in progress + +2004-11-09 18:11 tim + + * src/brains/ForceManager.cpp: file ForceManager.cpp was initially + added on branch new_design. + +2004-11-09 18:11 tim + + * src/integrators/VelocityVerletIntegrator.cpp: file + VelocityVerletIntegrator.cpp was initially added on branch + new_design. + +2004-11-09 18:11 tim + + * src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, + brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, + brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, + brains/mpiSimulation.hpp, integrators/Integrator.hpp, + integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, + integrators/VelocityVerletIntegrator.hpp: adding ForceManager + +2004-11-09 18:11 tim + + * src/brains/ForceManager.hpp: file ForceManager.hpp was initially + added on branch new_design. + +2004-11-09 18:11 tim + + * src/integrators/NVE.cpp: file NVE.cpp was initially added on + branch new_design. + +2004-11-08 20:08 tim + + * src/integrators/VelocityVerletIntegrator.hpp: file + VelocityVerletIntegrator.hpp was initially added on branch + new_design. + +2004-11-08 20:08 tim + + * src/integrators/NVE.hpp: file NVE.hpp was initially added on + branch new_design. + +2004-11-08 20:08 tim + + * src/: brains/Exclude.hpp, brains/Stats.hpp, + integrators/Integrator.hpp, integrators/NVE.hpp, + integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, + utils/TypeContainer.hpp: More to break + +2004-11-06 00:21 tim + + * src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially + added on branch new_design. + +2004-11-06 00:21 tim + + * src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, + UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, + utils/TypeContainer.hpp, utils/next_combination.hpp: adding + ForceField and TypeContainer classes + +2004-11-05 18:38 tim + + * src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was + initially added on branch new_design. + +2004-11-05 18:38 tim + + * src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was + initially added on branch new_design. + +2004-11-05 18:38 tim + + * src/: brains/Exclude.cpp, brains/Exclude.hpp, + brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, + brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, + brains/SimInfo.hpp, primitives/Molecule.hpp, + utils/LocalndexManager.hpp: Fix Exclude class etc. + +2004-11-05 16:45 chrisfen + + * src/: applications/dump2Xyz/Dump2XYZ.cpp, + visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the + linear visitor + +2004-11-05 16:04 chrisfen + + * src/UseTheForce/DarkSide/shapes.F90: current status of the + debugging process + +2004-11-05 16:04 chrisfen + + * make/Makefile.in: included visitors and minimizer + +2004-11-05 16:03 chrisfen + + * ChangeLog: new changes + +2004-11-04 21:56 tim + + * src/: brains/SimCreator.cpp, brains/SimCreator.hpp, + primitives/Molecule.hpp: Pain...... + +2004-11-04 15:55 tim + + * ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, + src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, + src/brains/Stats.hpp: time to break SimSetup + +2004-11-04 15:51 gezelter + + * src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new + classes in progress + +2004-11-04 14:48 tim + + * src/brains/Stats.cpp: file Stats.cpp was initially added on + branch new_design. + +2004-11-04 14:48 tim + + * src/brains/Stats.hpp: file Stats.hpp was initially added on + branch new_design. + +2004-11-04 14:48 tim + + * src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, + SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats + class + +2004-11-04 11:22 gezelter + + * src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, + RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and + linearAxis are virtual in StuntDouble, but are implemented by + DirectionalAtom and RigidBody In StuntDouble, they should return + false and "-1" but there should be logic to figure them out in the + other two classes + +2004-11-04 11:20 gezelter + + * src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't + remember what I did + +2004-11-04 11:20 gezelter + + * src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky + +2004-11-04 11:20 gezelter + + * src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX + in the entry_plug so that it only is set if the atoms really are in + the simulation + +2004-11-04 11:20 gezelter + + * samples/water/ssd/ssd.md: testing force fields + +2004-11-04 11:19 gezelter + + * samples/shape/linear.in: testing shapes + +2004-11-03 14:56 tim + + * src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator + class(similar as SimSetup) + +2004-11-03 14:56 tim + + * src/brains/SimCreator.hpp: file SimCreator.hpp was initially + added on branch new_design. + +2004-11-03 14:56 tim + + * src/brains/SimCreator.cpp: file SimCreator.cpp was initially + added on branch new_design. + +2004-11-03 13:00 tim + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, + UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, + brains/DataStorage.hpp, primitives/Atom.hpp, + primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, + visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get + compiled. Still a long way to go ...... + +2004-11-03 11:08 tim + + * ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, + src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, + src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, + src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, + src/io/ZConsReader.cpp, src/primitives/Bend.cpp, + src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, + src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, + src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, + src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, + src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, + src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, + src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... + +2004-11-02 17:41 tim + + * src/: brains/Migrator.hpp, brains/SimModel.cpp, + utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. + Need unit test + +2004-11-02 17:41 tim + + * src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was + initially added on branch new_design. + +2004-11-02 17:41 tim + + * src/brains/Migrator.hpp: file Migrator.hpp was initially added on + branch new_design. + +2004-11-02 11:59 tim + + * src/brains/SimModel.cpp: file SimModel.cpp was initially added on + branch new_design. + +2004-11-02 11:59 tim + + * src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, + SimSnapshotManager.hpp: SimModel in progress + +2004-11-02 10:28 chrisfen + + * src/: UseTheForce/DarkSide/shapes.F90, + primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes + looks like it's working + +2004-11-02 10:27 tim + + * src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some + functions for dealing with memory issue + +2004-11-02 10:27 tim + + * src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially + added on branch new_design. + +2004-11-02 10:23 tim + + * src/: brains/SimModel.hpp, brains/Snapshot.hpp, + brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding + SimModel(something similar as SimInfo) + +2004-11-01 17:52 tim + + * src/: applications/simpleBuilder/MoLocator.hpp, + applications/simpleBuilder/simpleBuilder.cpp, + brains/DataStorage.hpp, brains/ForceFields.cpp, + brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, + constraints/ZConstraint.cpp, integrators/Integrator.cpp, + integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, + math/SquareMatrix3.hpp, math/Vector3.hpp, + minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, + primitives/Bond.hpp, primitives/CutoffGroup.hpp, + primitives/Molecule.cpp, primitives/Molecule.hpp, + primitives/RigidBody.hpp, primitives/Torsion.hpp, + restraints/Restraints.cpp, types/TorsionType.hpp, + utils/PropertyMap.hpp, utils/StringTokenizer.hpp, + visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, + visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, + RigidBody and StuntDouble classes get compiled + +2004-11-01 16:40 tim + + * src/primitives/Torsion.hpp: file Torsion.hpp was initially added + on branch new_design. + +2004-11-01 16:40 tim + + * src/primitives/Bend.hpp: file Bend.hpp was initially added on + branch new_design. + +2004-11-01 16:40 tim + + * src/primitives/Bond.hpp: file Bond.hpp was initially added on + branch new_design. + +2004-11-01 16:40 tim + + * src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial + version of Bond, Bend and Torsion. + +2004-11-01 16:37 tim + + * src/types/BendType.hpp: file BendType.hpp was initially added on + branch new_design. + +2004-11-01 16:37 tim + + * src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding + BondType, BendType, TorsionType + +2004-11-01 16:37 tim + + * src/types/TorsionType.hpp: file TorsionType.hpp was initially + added on branch new_design. + +2004-11-01 16:37 tim + + * src/types/BondType.hpp: file BondType.hpp was initially added on + branch new_design. + +2004-11-01 15:15 tim + + * src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, + CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, + GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, + RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: + break, break and break..... + +2004-11-01 14:57 tim + + * test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, + DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, + StuntDouble.hpp: these core classes get compiled + +2004-10-29 17:37 tim + + * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule + class + +2004-10-29 17:28 chrisfen + + * src/: UseTheForce/DarkSide/atype.F90, + UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, + types/ShapeAtomType.cpp: still debugging + +2004-10-29 17:28 chrisfen + + * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: + shapes rcut calculator added + +2004-10-29 17:27 chrisfen + + * samples/shape/linear.md: shorter run + +2004-10-29 15:54 tim + + * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. + +2004-10-29 11:22 tim + + * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, + ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove + some deprecated files + +2004-10-29 11:20 tim + + * test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, + DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: + More painful reconstruction is coming !!! + +2004-10-28 17:34 tim + + * src/brains/DataStorage.hpp, src/utils/next_combination.hpp, + test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, + test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, + test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, + DirectionalAtom and RigidBody + +2004-10-28 17:26 tim + + * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, + src/applications/simpleBuilder/MoLocator.cpp, + src/applications/simpleBuilder/Vector3d.hpp, + src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: + remove old Vector3d.hpp from application/simpleBuilder + +2004-10-28 16:42 tim + + * src/utils/next_combination.hpp: Minor change in next_combination + +2004-10-28 16:28 tim + + * src/utils/next_combination.hpp, + test/utils/NextCombinationTestCase.cpp, + test/utils/ReplaceWildCardTestCase.cpp: Done with combination + +2004-10-28 16:11 tim + + * src/utils/next_combination.hpp: change documentation of + next_combination.hpp + +2004-10-28 15:41 tim + + * ChangeLog, src/utils/next_combination.hpp, + test/utils/NextCombinationTestCase.cpp, + test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working + +2004-10-28 15:01 tim + + * src/utils/next_combination.hpp: adding replace wildcard function + +2004-10-28 14:33 tim + + * src/utils/next_combination.hpp: Minor change + +2004-10-28 14:06 tim + + * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, + src/applications/simpleBuilder/simpleBuilder.cpp, + src/utils/next_combination.hpp, test/utils/Makefile, + test/utils/NextCombinationTestCase.cpp, + test/utils/ReplaceWildCardTestCase.cpp, + test/utils/next_combination.hpp: STL next_permutation like + next_combination is working + +2004-10-28 12:22 chrisfen + + * src/UseTheForce/WATER.cpp: fix of setDipoles + +2004-10-28 12:20 gezelter + + * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the + shapeFile + +2004-10-28 12:20 gezelter + + * samples/shape/linear.md: forgot the orientation line + +2004-10-28 11:56 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, + UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate + declaration foo + +2004-10-28 11:55 gezelter + + * samples/lipid/5x5.md: uncommented .in line + +2004-10-28 10:42 tim + + * test/utils/: Makefile, NextCombinationTestCase.cpp, + NextCombinationTestCase.hpp, next_combination.hpp: next_combination + in progress + +2004-10-28 10:15 tim + + * test/utils/: NextCombinationTestCase.cpp, + NextCombinationTestCase.hpp: adding next_combination test case + +2004-10-28 10:02 tim + + * test/utils/next_combination.hpp: STL Compatible combination + sequence generator + +2004-10-28 01:23 tim + + * test/utils/: GenerateCombination.hpp, + ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp + +2004-10-28 01:16 tim + + * test/utils/GenerateCombination.hpp: a STL next_permutaion like + next_combination function. + +2004-10-27 22:27 tim + + * test/utils/ReplaceWildCard.hpp: no message + +2004-10-27 22:14 tim + + * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: + ReplaceWildCard(recursive version) is working, need refactoring. An + iterative version is on the way + +2004-10-27 21:28 tim + + * test/utils/: Makefile, ReplaceWildCard.hpp, + ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress + +2004-10-27 21:08 tim + + * test/utils/: ReplaceWildCardTestCase.cpp, + ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard + +2004-10-27 18:17 tim + + * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need + test + +2004-10-27 01:25 tim + + * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild + char matching is on the way + +2004-10-27 01:07 tim + + * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 + +2004-10-26 22:00 gezelter + + * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix + +2004-10-26 21:20 gezelter + + * src/UseTheForce/ForceFields.hpp: subclass foo + +2004-10-26 21:16 gezelter + + * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> + string conversion + +2004-10-26 19:01 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, + brains/SimSetup.hpp: char* -> string + +2004-10-26 17:25 gezelter + + * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, + Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, + ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some + isXXX + +2004-10-26 17:25 gezelter + + * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: + define name collision + +2004-10-26 17:24 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, + UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, + UseTheForce/WATER.cpp, UseTheForce/doForces.F90, + UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: + forcefield refactoring for shapes + +2004-10-26 17:24 gezelter + + * samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, + Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, + linear.md, linear.shape, toluene.shape: adding sample shape + directory + +2004-10-26 17:19 tim + + * ChangeLog, src/brains/DataStorage.cpp, + src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, + test/brains/DataStorageTestCase.cpp, + test/brains/DataStorageTestCase.hpp, test/brains/Makefile: + DataStorage passes unit test + +2004-10-26 13:03 chrisfen + + * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: + Changes to help advance shapes + +2004-10-26 13:02 chrisfen + + * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to + Shapes force field reader + +2004-10-26 12:28 tim + + * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and + SnapshotTestCase in progress + +2004-10-25 17:46 tim + + * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, + src/math/SquareMatrix3.hpp, src/math/Vector.hpp, + src/math/Vector3.hpp, test/brains/StuntDouble.hpp, + test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, + test/math/VectorTestCase.cpp: add getArray function to RectMatrix + and Vector classes + +2004-10-25 12:03 tim + + * ChangeLog, src/utils/GenericFactory.hpp, + test/utils/GenericFactoryTestCase.cpp, + test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding + GenericFactory Test Case. GenericFactory now can bed used to creat + ForcefieldFactory and IntegratorFactory etc. + +2004-10-24 23:08 tim + + * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, + brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, + brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes + get reconstructed + +2004-10-24 02:55 tim + + * src/utils/GenericFactory.hpp: GenericFactory pass unit test + +2004-10-23 18:09 tim + + * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, + StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, + RigidBody.cpp: Refactoring in progress + +2004-10-22 18:09 tim + + * ChangeLog, src/brains/Snapshot.hpp, + src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, + test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, + test/brains/StuntDouble.hpp: more work in Snapshot + +2004-10-22 17:59 chrisfen + + * src/: UseTheForce/LJFF.cpp, + UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear + god! It runs and conserves energy! + +2004-10-22 17:54 chrisfen + + * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY + +2004-10-22 17:53 chrisfen + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, + UseTheForce/WATER.cpp, UseTheForce/doForces.F90, + brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey + breakey + +2004-10-22 17:53 chrisfen + + * make/Makefile.in: compiler flags + +2004-10-22 16:20 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, + brains/fSimulation.h, types/AtomType.hpp, + types/DirectionalAtomType.hpp: fixey fixey + +2004-10-22 15:22 gezelter + + * src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, + charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, + lj_interface.h, shapes.F90, simulation.F90: Added un-busticated + fortran files and c/Fortran interfaces + +2004-10-22 15:21 gezelter + + * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, + DirectionalAtomType.hpp, Makefile: More on AtomType and + DirectionalAtomType + +2004-10-22 09:47 gezelter + + * src/types/AtomType.hpp: Adding AtomType + +2004-10-21 16:31 tim + + * ChangeLog, src/brains/Snapshot.hpp, + src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, + src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, + src/math/Vector.hpp, src/math/Vector3.hpp, + test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: + Snapshot and SnapshotManager in progress + +2004-10-21 16:30 tim + + * test/brains/: BrainsTest.cpp, Makefile, + SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, + SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for + Snapshot and snapshotManager. + +2004-10-21 15:15 gezelter + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, + UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, + UseTheForce/WATER.cpp, UseTheForce/doForces.F90, + UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, + UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, + brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. + Fixey Fixey. + +2004-10-21 11:32 tim + + * src/utils/GenericData.cpp, src/utils/Makefile, + test/utils/Makefile, test/utils/UtilTest: remove some junk files + +2004-10-21 11:24 tim + + * test/utils/GenericData.hpp: remove backup of GenericData.hpp + +2004-10-21 11:22 tim + + * ChangeLog, src/brains/SimSetup.cpp, + src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, + src/integrators/NPT.cpp, src/integrators/NPTf.cpp, + src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, + src/integrators/NVT.cpp, src/io/DumpReader.cpp, + src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, + src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, + src/utils/GenericData.cpp, src/utils/GenericData.hpp, + src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, + src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, + src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, + src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, + src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, + src/visitors/ZconsVisitor.hpp: replace old GebericData with new + GenericData + +2004-10-21 10:25 chuckv + + * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj + module. + +2004-10-21 10:24 chuckv + + * src/UseTheForce/DarkSide/lj_interface.h: Added interface for + fortran lj module. + +2004-10-20 17:54 tim + + * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, + test/utils/GenericDataTestCase.cpp, test/utils/Makefile, + test/utils/PropertyMapTestCase.cpp, + test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: + GenericData and PropertyMap pass unit test. + +2004-10-20 16:52 gezelter + + * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, + DarkSide/sticky_interface.h: fixed a fortran name problem + +2004-10-20 16:38 tim + + * test/utils/: GenericData.hpp, GenericDataTestCase.cpp, + GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, + UtilTest, UtilTest.cpp: adding generic data test case + +2004-10-20 16:16 chuckv + + * configure, ac-tools/aclocal.m4, + src/UseTheForce/DarkSide/Makefile, + src/UseTheForce/DarkSide/mpiSimulation.F90, + src/UseTheForce/DarkSide/mpiSimulation_interface.h, + src/UseTheForce/DarkSide/simParallel.F90, + src/UseTheForce/DarkSide/simParallel_interface.h, + src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: + Fortran/C++ interface de-obfuscation project appears to be + complete! Woo hoo! + +2004-10-20 15:47 chuckv + + * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, + fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project + continues + +2004-10-20 15:46 chuckv + + * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, + UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, + UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, + UseTheForce/doForces_interface.h, + UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, + UseTheForce/DarkSide/atype_interface.h, + UseTheForce/DarkSide/eam_interface.h, + UseTheForce/DarkSide/gb_interface.h, + UseTheForce/DarkSide/mpiSimulation_interface.h, + UseTheForce/DarkSide/shapes_interface.h, + UseTheForce/DarkSide/simulation_interface.h, + UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, + brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface + de-obfuscation project (It is a very long story) + +2004-10-20 13:07 tim + + * ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, + test/math/SquareMatrix3TestCase.cpp, + test/math/SquareMatrixTestCase.cpp, + test/math/SquareMatrixTestCase.hpp: Math library pass the unit test + +2004-10-20 00:52 tim + + * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and + SnapshotManager in design phase + +2004-10-19 23:54 gezelter + + * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace + problem prevented linking + +2004-10-19 23:54 gezelter + + * src/UseTheForce/Shapes_FF.cpp: fixed include + +2004-10-19 23:26 gezelter + + * src/utils/: Makefile, definitions.F90, definitions_module.F90, + oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: + more fortran name mangling + +2004-10-19 23:23 gezelter + + * src/profiling/timing.F90: yet more fortran renaming + +2004-10-19 23:19 gezelter + + * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, + do_Forces.F90, do_Forces.h, notifyCutoffs.F90, + notifyCutoffs_interface.h, notifycutoffs_module_interface.h, + wrappers.F90: Fortran name cleanup continues + +2004-10-19 23:12 gezelter + + * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some + broken fortran stuff + +2004-10-19 23:02 gezelter + + * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, + atype_interface.h, atype_module.F90, atype_module_interface.h, + calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, + calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, + calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, + eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, + gb_interface.h, gb_module_interface.h, mpiSimulation.F90, + mpiSimulation_interface.h, mpiSimulation_module.F90, + mpisimulation_module_interface.h, reactionField.F90, shapes.F90, + shapes_interface.h, shapes_module.h, simulation.F90, + simulation_interface.h, simulation_module.F90, + simulation_module_interface.h, sticky.F90, sticky_interface.h, + sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: + name sanity on the fortran side + +2004-10-19 19:18 tim + + * test/math/SquareMatrix3TestCase.hpp: [no log message] + +2004-10-19 18:01 tim + + * src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, + src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: + except diagonalize(), all of functions in math library pass the + test + +2004-10-19 17:43 chuckv + + * src/UseTheForce/do_Forces.h: Added correct prototypes for + C-fortran interface functions. + +2004-10-19 17:37 chuckv + + * src/UseTheForce/DarkSide/: atype_module_interface.h, + eam_module_inteface.h, gb_module_interface.h, + mpisimulation_module_interface.h, simulation_module_interface.h, + sticky_pair_module_interface.h: Added correct prototypes for + C-fortran interface functions. + +2004-10-19 16:28 tim + + * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, + src/math/SquareMatrix.hpp, src/math/Vector.hpp, + test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, + test/math/RectMatrixTestCase.cpp, + test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, + test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more + bugs get fixed at math library + +2004-10-19 15:43 chuckv + + * src/UseTheForce/: DarkSide/atype_module_interface.h, + DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, + DarkSide/mpisimulation_module_interface.h, + DarkSide/simulation_module_interface.h, + DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, + DarkSide/atype_module.F90, DarkSide/calc_gb.F90, + DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, + DarkSide/simulation_module.F90, do_Forces.F90, + fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, + notifycutoffs_module_interface.h: Added new files for fortran + interface. + +2004-10-19 15:43 gezelter + + * src/UseTheForce/Makefile: regressing + +2004-10-19 15:40 gezelter + + * src/: UseTheForce/DarkSide/calc_shapes.F90, + UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: + working on shapes for portability + +2004-10-19 15:40 gezelter + + * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes + +2004-10-19 13:21 chrisfen + + * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around + findBegin + +2004-10-18 23:34 tim + + * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs + are fixed in Vector class + +2004-10-18 23:28 tim + + * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix + some bugs in RectMatrixTestCase + +2004-10-18 23:21 tim + + * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, + test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, + test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, + test/math/VectorTestCase.hpp: implement more test cases + +2004-10-18 18:13 tim + + * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, + src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, + src/math/SquareMatrix3.hpp, src/math/Vector.hpp, + src/utils/StringTokenizer.hpp, test/math/Makefile, + test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more + tests on math library + +2004-10-18 16:03 tim + + * test/math/: Makefile, QuaternionTestCase.cpp, + QuaternionTestCase.hpp, RectMatrixTestCase.cpp, + SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, + Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding + more testing units + +2004-10-18 12:07 tim + + * src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, + math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, + math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, + utils/GenericFactory.hpp: fix some bugs in Quaternion class + +2004-10-18 11:30 gezelter + + * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: + Your basic run of the mill real-valued versions of Y_l^m(\theta, + \phi) + +2004-10-18 11:29 gezelter + + * src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, + types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, + utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting + Shapes into OOPSE + +2004-10-18 10:21 gezelter + + * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType + +2004-10-18 00:23 tim + + * test/math/VectorTestCase.hpp: adding vector test case + +2004-10-18 00:23 tim + + * src/utils/GenericFactory.hpp: adding generic factory and vector + test case + +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, + 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, 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, 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, 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, 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, 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, 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,