--- trunk/OOPSE-3.0/ChangeLog 2004/09/24 04:16:43 1490 +++ trunk/OOPSE-3.0/ChangeLog 2004/10/25 22:46:19 1644 @@ -1,647 +1,1272 @@ -2004-07-23 15:31 tim +2004-10-25 12:03 tim - * samples/lipid/5x5.bass: modify 5x5.bass + * 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. -2004-07-23 15:25 tim +2004-10-24 23:08 tim - * samples/water/tip3p_ice/: 200.in, tp3.bass: [no log message] + * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, + brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, + brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes + get reconstructed -2004-07-23 15:18 tim +2004-10-24 02:55 tim - * samples/: water/ssde/ssde.bass, argon/500.bass, - argon/argonNVT.bass: [no log message] + * src/utils/GenericFactory.hpp: GenericFactory pass unit test -2004-07-23 15:12 tim +2004-10-23 18:09 tim - * samples/water/: dimer/two.in, spce/spce.in, ssd/ssd.in, - ssde/ssde.in, tip3p_ice/tp3.in, tip4p/tp4.in: add init files + * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, + StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, + RigidBody.cpp: Refactoring in progress -2004-07-23 15:10 tim +2004-10-22 18:09 tim - * samples/minimizer/: ssdEM.in, tip4p_two.in: add init file + * 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 -2004-07-23 15:09 tim +2004-10-22 17:59 chrisfen - * samples/argon/: NVT.bass, argonNVT.bass, argonNVT.in: rename - NVT.bass to argonNVT.bass + * src/: UseTheForce/LJFF.cpp, + UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear + god! It runs and conserves energy! -2004-07-23 15:07 tim +2004-10-22 17:54 chrisfen - * samples/lipid/5x5.in: add 5x5.in + * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY -2004-07-23 15:06 tim +2004-10-22 17:53 chrisfen - * samples/alkane/: butane.in, init_butane.eor: add butane.in + * 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 -2004-07-23 14:57 gezelter +2004-10-22 17:53 chrisfen - * libBASS/Globals.cpp, samples/minimizer/ssdEM.bass, - samples/minimizer/tip4p_two.bass: changed minimizer keywords + * make/Makefile.in: compiler flags -2004-07-23 14:34 gezelter +2004-10-22 16:20 gezelter - * configure, ac-tools/configure.in: fixed typo + * 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 -2004-07-23 14:32 gezelter +2004-10-22 15:22 gezelter - * samples/minimizer/Makefile.in: fixed sample makefile + * 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 -2004-07-23 14:31 gezelter +2004-10-22 15:21 gezelter - * configure, ac-tools/configure.in, samples/minimizer/Makefile.in, - samples/minimizer/WATER.frc, samples/minimizer/ssdEM.bass, - samples/minimizer/tip4p_two.bass, samples/minimizer/water.mdl: - minimizer sample changes + * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, + DirectionalAtomType.hpp, Makefile: More on AtomType and + DirectionalAtomType -2004-07-23 14:15 gezelter +2004-10-22 09:47 gezelter - * configure, ac-tools/configure.in: removed beadLipid + * src/types/AtomType.hpp: Adding AtomType -2004-07-23 14:08 tim +2004-10-21 16:31 tim - * samples/Makefile.in: remove beadLipid + * 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 -2004-07-23 14:03 chuckv +2004-10-21 16:30 tim - * samples/metals/: Au_nanoparticle.eor, - Au_nanoparticle_coreshell_12-20.bass, - Au_nanoparticle_coreshell_12-20.in: Added core-shell nanoparticle - files. + * test/brains/: BrainsTest.cpp, Makefile, + SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, + SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for + Snapshot and snapshotManager. -2004-07-23 13:51 tim +2004-10-21 15:15 gezelter - * samples/water/tip4p/TP4init.in: remove TP4init.in + * 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. -2004-07-23 13:50 tim +2004-10-21 11:32 tim - * samples/water/tip4p/: Makefile.in, tp4.bass: change init file - name for tip4p and tip3p_ice + * src/utils/GenericData.cpp, src/utils/Makefile, + test/utils/Makefile, test/utils/UtilTest: remove some junk files -2004-07-23 13:48 tim +2004-10-21 11:24 tim - * samples/water/ssde/: Makefile.in, SSDEinit.in: [no log message] + * test/utils/GenericData.hpp: remove backup of GenericData.hpp -2004-07-23 13:48 tim +2004-10-21 11:22 tim - * samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass: change - init file name for ssd + * 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 -2004-07-23 13:46 tim +2004-10-21 10:25 chuckv - * samples/water/spce/: Makefile.in, SPCEinit.in, spce.bass: remove - SPCEInit.in + * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj + module. -2004-07-23 13:45 tim +2004-10-21 10:24 chuckv - * samples/water/dimer/: Makefile.in, two.bass, two.init: change - names for init file + * src/UseTheForce/DarkSide/lj_interface.h: Added interface for + fortran lj module. -2004-07-23 13:40 tim +2004-10-20 17:54 tim - * samples/lipid/: 5x5.bass, 5x5.eor, Makefile.in, init_5x5.eor: - change init file name in lipid directory + * 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. -2004-07-23 13:36 tim +2004-10-20 16:52 gezelter - * samples/argon/init_argon.eor: remove init_argon.eor + * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, + DarkSide/sticky_interface.h: fixed a fortran name problem -2004-07-23 13:34 tim +2004-10-20 16:38 tim - * samples/: alkane/Makefile.in, alkane/butane.bass, - alkane/butane.eor, argon/500.eor, argon/ar864.eor: [no log message] + * test/utils/: GenericData.hpp, GenericDataTestCase.cpp, + GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, + UtilTest, UtilTest.cpp: adding generic data test case -2004-07-23 13:33 tim +2004-10-20 16:16 chuckv - * samples/argon/Makefile.in: remove eor file + * 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! -2004-07-23 13:31 tim +2004-10-20 15:47 chuckv - * samples/argon/: Makefile.in, argon.bass, argon.eor, argonEM.bass: - change names for argon + * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, + fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project + continues -2004-07-23 11:47 tim +2004-10-20 15:46 chuckv - * samples/water/ssde/SSDEinit.in: [no log message] + * 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) -2004-07-23 11:45 tim +2004-10-20 13:07 tim - * samples/water/ssde/SSDEinit.in: add init file for ssde + * 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 -2004-07-23 11:43 chuckv +2004-10-20 00:52 tim - * libmdtools/calc_eam.F90: Fixed bug in calc_eam with mixtures and - cutoffs associated with mixture. + * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and + SnapshotManager in design phase -2004-07-23 10:35 tim +2004-10-19 23:54 gezelter - * libmdtools/: AtomVisitor.cpp, AtomVisitor.hpp: support SSD_E - SSD_RF SSD1 + * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace + problem prevented linking -2004-07-23 09:53 tim +2004-10-19 23:54 gezelter - * libmdtools/AtomVisitor.cpp: SSDVisitor support SSD_RF, SSD_E, - SSD1 now + * src/UseTheForce/Shapes_FF.cpp: fixed include -2004-07-23 09:19 tim +2004-10-19 23:26 gezelter - * libmdtools/ZConsReader.cpp: remove ^M from ZConsReader.cpp + * src/utils/: Makefile, definitions.F90, definitions_module.F90, + oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: + more fortran name mangling -2004-07-23 09:18 tim +2004-10-19 23:23 gezelter - * samples/lipid/5x5.bass: remove unsupport keyword + * src/profiling/timing.F90: yet more fortran renaming -2004-07-22 16:01 chuckv +2004-10-19 23:19 gezelter - * samples/metals/: init_Au_bulk.in, init_Au_nanoparticle.in: - Changed init files to be more OOPSE like... - -2004-07-22 10:11 gezelter - - * configure, ac-tools/configure.in: added sample directory + * 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 -2004-07-22 10:06 chrisfen +2004-10-19 23:12 gezelter - * src/Makefile.in: fixed icc7 incompatibility in linking + * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some + broken fortran stuff -2004-07-21 17:03 chrisfen +2004-10-19 23:02 gezelter - * samples/water/: Makefile.in, tip3p_ice/200.in, - tip3p_ice/Makefile.in, tip3p_ice/tp3.bass, tip3p_ice/water.mdl: - Added tip3p_ice to Makefile + * 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 -2004-07-21 16:46 chuckv +2004-10-19 19:18 tim - * samples/metals/: Au.bass, Au.eor, Au_bulk_FBD.bass, - Au_bulk_voter.bass, Au_nanoparticle.bass, Au_nanoparticle.eor, - init_Au_bulk.in, init_Au_nanoparticle.in, init_au.in: Added sample - files for bulk metals and a bass file for both voter and FBD - formulations of EAM. + * test/math/SquareMatrix3TestCase.hpp: [no log message] -2004-07-21 14:53 gezelter +2004-10-19 18:01 tim - * samples/water/dimer/two.bass: Checked a bug where eor file wasn't - being written at the end of the run + * 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 -2004-07-21 14:53 gezelter +2004-10-19 17:43 chuckv - * libmdtools/Integrator.cpp: Fixed a bug where eor file wasn't - being written at the end of the run + * src/UseTheForce/do_Forces.h: Added correct prototypes for + C-fortran interface functions. -2004-07-21 09:11 gezelter +2004-10-19 17:37 chuckv - * README: [no log message] + * 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. -2004-07-21 09:08 gezelter +2004-10-19 16:28 tim - * samples/argon/machines: cleaning up for export + * 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 -2004-07-21 09:04 gezelter +2004-10-19 15:43 chuckv - * NEWS, README: cleaning up for export + * 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. -2004-07-21 08:45 gezelter +2004-10-19 15:43 gezelter - * configure, ac-tools/configure.in: removing staticProps from cvs - tree + * src/UseTheForce/Makefile: regressing -2004-07-20 12:07 gezelter +2004-10-19 15:40 gezelter - * configure, ac-tools/aclocal.m4, utils/Makefile.in, - utils/quickLate.c, utils/sysbuilder/Makefile.in: [no log message] + * src/: UseTheForce/DarkSide/calc_shapes.F90, + UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: + working on shapes for portability -2004-07-20 10:17 gezelter +2004-10-19 15:40 gezelter - * configure, ac-tools/aclocal.m4, ac-tools/configure.in, - third-party/gnugetopt.h, utils/getopt.c, utils/getopt1.c, - utils/gnugetopt.h: fixing getopt_long + * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes -2004-07-19 16:58 gezelter +2004-10-19 13:21 chrisfen - * configure, ac-tools/configure.in, libmdtools/ReadWrite.hpp, - libmdtools/ZConsWriter.hpp, src/Makefile.in, - third-party/gnugetopt.h, utils/Dump2XYZCmd.c, utils/Make.dep, - utils/Makefile.in, utils/sysbuilder/Makefile.in, - utils/sysbuilder/latticeBuilder.cpp: [no log message] + * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around + findBegin -2004-07-19 16:52 tim +2004-10-18 23:34 tim - * utils/quickLate.c: minor fix of format string in quicklate.c + * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs + are fixed in Vector class -2004-07-19 16:30 tim +2004-10-18 23:28 tim - * utils/zsub: remove zsub from cvs tree + * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix + some bugs in RectMatrixTestCase -2004-07-19 16:25 tim +2004-10-18 23:21 tim - * libmdtools/ZConstraint.cpp, utils/Dump2XYZ.cpp: remove some - comment lines + * 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 -2004-07-19 16:00 tim +2004-10-18 18:13 tim - * libmdtools/OOPSEMinimizer.hpp: remove an extra semicolon from - OOPSEMinimizer.hpp + * 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 -2004-07-19 13:55 gezelter +2004-10-18 16:03 tim - * libBASS/y.tab.h: Shouldn't have been in CVS + * test/math/: Makefile, QuaternionTestCase.cpp, + QuaternionTestCase.hpp, RectMatrixTestCase.cpp, + SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, + Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding + more testing units -2004-07-19 13:54 gezelter +2004-10-18 12:07 tim - * libBASS/y.tab.h, libmdtools/ForceFields.cpp: Fix for - thermodynamic integration of rigid bodies + * 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 -2004-07-19 12:00 gezelter +2004-10-18 11:30 gezelter - * libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: These can be - generated via lex and yacc at compile time + * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: + Your basic run of the mill real-valued versions of Y_l^m(\theta, + \phi) -2004-07-19 11:47 gezelter +2004-10-18 11:29 gezelter - * libBASS/BASSlex.c, libBASS/BASSyacc.c, libBASS/BASSyacc.h, - libBASS/make_nodes.c, libBASS/y.tab.h, libmdtools/Makefile.in, - libmdtools/MatVec3.c, src/Makefile.in: [no log message] + * 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 -2004-07-19 11:32 gezelter +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 - * configure, ac-tools/aclocal.m4, ac-tools/configure.in, - third-party/gnugetopt.h, utils/Makefile.in, - utils/sysbuilder/Makefile.in: changes for gnu getopt and fixed - SPRNG configure script + * src/utils/GenericFactory.hpp: adding generic factory and vector + test case -2004-07-16 16:49 gezelter +2004-10-16 20:19 tim - * libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: fixing for machines - that don't have lex and yacc + * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, + SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in + progress -2004-07-16 15:55 gezelter +2004-10-15 20:31 tim - * Makefile: Makefiles don't belong in cvs repository + * src/math/Quaternion.hpp: add quaternion class -2004-07-16 15:54 gezelter +2004-10-15 16:11 tim - * Makefile, forceFields/Makefile, libBASS/Makefile, - libmdtools/Makefile, samples/Makefile, src/Makefile, - third-party/Makefile, utils/Makefile, utils/sysbuilder/Makefile: - Makefiles don't belong in repository + * test/io/: DUFF.frc, IfstrstreamTestCase.cpp, + IfstrstreamTestCase.hpp: adding test file -2004-07-16 15:49 gezelter +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: Makefiles don't belong in repository + 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 -2004-07-16 15:20 chrisfen +2004-10-06 18:03 gezelter - * Makefile, configure, ac-tools/configure.in, forceFields/Makefile, - libBASS/Makefile, libmdtools/Makefile, samples/alkane/Makefile, - samples/argon/Makefile, samples/lipid/Makefile, - samples/metals/Makefile, src/Makefile, utils/Makefile, - utils/sysbuilder/Makefile: Updated configure for new samples + * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt + stuff -2004-07-16 14:57 chrisfen +2004-10-06 18:03 gezelter - * samples/water/tip4p/Makefile.in: tip4p makefile.in added + * 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 -2004-07-16 14:57 chrisfen +2004-10-06 17:20 tim - * samples/water/ssde/: 256init.in, Makefile.in, ssde.bass: ssde - makefile.in added + * make/: Doxyfile, Makefile.in: adding doxygen configuration file -2004-07-16 14:57 chrisfen +2004-10-06 17:19 tim - * samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass, - water.mdl: ssd files sorted added + * scripts/filepp: filepp can handle different fortran module case + and suffix -2004-07-16 14:57 chrisfen +2004-10-06 16:27 gezelter - * samples/water/spce/Makefile.in: spce makefile.in added + * src/restraints/Restraints.cpp: Chris doesn't know about the + OOPSE-2.0 directory structure yet -2004-07-16 14:56 chrisfen +2004-10-06 16:27 gezelter - * samples/water/dimer/: Makefile.in, two.bass, two.init, water.mdl: - dimer files added + * ChangeLog: Yeah yeah, we'lll get around to it later -2004-07-16 14:56 chrisfen +2004-10-06 16:22 gezelter - * samples/water/: 200.in, Makefile, Makefile.in, init_ssd.eor, - spce.bass, spce.eor, ssd.bass, ssd.eor, tim.bass, tim.eor, - tim.init, tim.xyz, tip3p.bass, tip3p.eor, tip3p.init, two.bass, - two.eor, two.init, two.xyz, water.mdl: Cleaned up this file - considerably + * configure, ac-tools/configure.in, ac-tools/fortran90.m4, + make/Makefile.in: cleaning up build process -2004-07-16 13:57 gezelter +2004-10-06 15:01 chrisfen - * AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README, - configure, 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, - forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl, - forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl, - forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl, + * 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/LJFF.frc, forceFields/Makefile, - forceFields/Makefile.in, forceFields/Ni.VC.funcfl, - forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl, - forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl, - forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl, - forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl, - forceFields/WATER.frc, libBASS/AtomStamp.cpp, - libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, - libBASS/BASS_interface.h, libBASS/BASS_parse.c, - libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, - libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, - libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, - libBASS/Component.cpp, libBASS/Component.hpp, - libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp, - libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, - libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, - libBASS/LinkedCommand.hpp, libBASS/Make.dep, - libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, - libBASS/Makefile.in, libBASS/MoleculeStamp.cpp, - libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp, - libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp, - libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp, - libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c, - libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, - libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, - libBASS/parse_interface.h, libBASS/parse_me.h, - libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, - libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy, - libBASS/obj/dummy, libmdtools/AbstractClasses.hpp, - libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp, - libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp, - libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp, - libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, - libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, - libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp, - libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp, - libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp, - libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp, - libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp, - libmdtools/Euler3.cpp, libmdtools/Euler3.hpp, - libmdtools/Exclude.cpp, libmdtools/Exclude.hpp, - libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp, - libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, - libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp, - libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, - libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile, - libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h, - libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp, - libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, - libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, - libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, - libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, - libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp, - libmdtools/Restraints.cpp, libmdtools/Restraints.hpp, - libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, - libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, - libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp, - libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, - libmdtools/SimState.cpp, libmdtools/SimState.hpp, - libmdtools/SkipList.cpp, libmdtools/SkipList.hpp, - libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp, - libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c, - libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp, - libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp, - libmdtools/Thermo.hpp, libmdtools/Torsion.cpp, - libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp, - libmdtools/Utility.cpp, libmdtools/Utility.hpp, - libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp, - libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp, - libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp, - libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp, - libmdtools/atype_module.F90, libmdtools/calc_LJ_FF.F90, - libmdtools/calc_charge_charge.F90, - libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, - libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, - libmdtools/calc_sticky_pair.F90, libmdtools/config.h.in, - libmdtools/definitions_module.F90, libmdtools/do_Forces.F90, - libmdtools/fForceField.h, libmdtools/fSimulation.h, - libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp, - libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, - libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, - libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp, - libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, - libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, - libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, - libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90, - libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp, - libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, - libmdtools/status_module.F90, libmdtools/switch_module.F90, - libmdtools/timing.F90, libmdtools/vector_class.F90, - libmdtools/wrappers.F90, libmdtools/MPIobj/dummy, - libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in, - samples/alkane/Makefile, samples/alkane/Makefile.in, - samples/alkane/alkanes.mdl, samples/alkane/butane.bass, - samples/alkane/butane.eor, samples/alkane/init_butane.eor, - samples/argon/500.bass, samples/argon/500.eor, - samples/argon/500.in, samples/argon/Makefile, - samples/argon/Makefile.in, samples/argon/NVT.bass, - samples/argon/ar864.bass, samples/argon/ar864.eor, - samples/argon/ar864.in, samples/argon/argon.bass, - samples/argon/argon.eor, samples/argon/argonEM.bass, - samples/argon/init_argon.eor, samples/argon/lj.mdl, - samples/argon/machines, samples/lipid/5x5.bass, - samples/lipid/5x5.eor, samples/lipid/Makefile, - samples/lipid/Makefile.in, samples/lipid/init_5x5.eor, - samples/lipid/lipid.mdl, samples/lipid/water.mdl, - samples/metals/Au.bass, samples/metals/Au.eor, - samples/metals/Makefile, samples/metals/Makefile.in, - samples/metals/init_au.in, samples/metals/metals.mdl, - samples/water/200.in, samples/water/Makefile, - samples/water/Makefile.in, samples/water/init_ssd.eor, - samples/water/spce.bass, samples/water/spce.eor, - samples/water/ssd.bass, samples/water/ssd.eor, - samples/water/tim.bass, samples/water/tim.eor, - samples/water/tim.init, samples/water/tim.xyz, - samples/water/tip3p.bass, samples/water/tip3p.eor, - samples/water/tip3p.init, samples/water/two.bass, - samples/water/two.eor, samples/water/two.init, - samples/water/two.xyz, samples/water/water.mdl, - samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass, - samples/water/spce/water.mdl, samples/water/ssde/256init.in, - samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl, - samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass, - samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl, - scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in, - src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy, - third-party/Makefile, third-party/Makefile.in, - third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, - utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep, - utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub, - utils/MPIobj/placeHolder, utils/obj/placeHolder, - utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile, - utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp, - utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c, - utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp, - utils/sysbuilder/latticeBuilder.cpp, - utils/sysbuilder/latticeBuilder.hpp, - utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp, - utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp, - utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp, - utils/sysbuilder/MPIobj/placeHolder, - utils/sysbuilder/obj/placeHolder: Initial import of OOPSE-1.0 - source tree + 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: Initial revision -2004-07-16 13:57 gezelter +2004-09-23 23:16 gezelter - * AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README, - configure, 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, - forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl, - forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl, - forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl, + * 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/LJFF.frc, forceFields/Makefile, - forceFields/Makefile.in, forceFields/Ni.VC.funcfl, - forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl, - forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl, - forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl, - forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl, - forceFields/WATER.frc, libBASS/AtomStamp.cpp, - libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, - libBASS/BASS_interface.h, libBASS/BASS_parse.c, - libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, - libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, - libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, - libBASS/Component.cpp, libBASS/Component.hpp, - libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp, - libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, - libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, - libBASS/LinkedCommand.hpp, libBASS/Make.dep, - libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, - libBASS/Makefile.in, libBASS/MoleculeStamp.cpp, - libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp, - libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp, - libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp, - libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c, - libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, - libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, - libBASS/parse_interface.h, libBASS/parse_me.h, - libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, - libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy, - libBASS/obj/dummy, libmdtools/AbstractClasses.hpp, - libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp, - libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp, - libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp, - libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, - libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, - libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp, - libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp, - libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp, - libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp, - libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp, - libmdtools/Euler3.cpp, libmdtools/Euler3.hpp, - libmdtools/Exclude.cpp, libmdtools/Exclude.hpp, - libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp, - libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, - libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp, - libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, - libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile, - libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h, - libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp, - libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, - libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, - libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, - libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, - libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp, - libmdtools/Restraints.cpp, libmdtools/Restraints.hpp, - libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, - libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, - libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp, - libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, - libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, - libmdtools/SimState.cpp, libmdtools/SimState.hpp, - libmdtools/SkipList.cpp, libmdtools/SkipList.hpp, - libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp, - libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c, - libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp, - libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp, - libmdtools/Thermo.hpp, libmdtools/Torsion.cpp, - libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp, - libmdtools/Utility.cpp, libmdtools/Utility.hpp, - libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp, - libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp, - libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp, - libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp, - libmdtools/atype_module.F90, libmdtools/calc_LJ_FF.F90, - libmdtools/calc_charge_charge.F90, - libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, - libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, - libmdtools/calc_sticky_pair.F90, libmdtools/config.h.in, - libmdtools/definitions_module.F90, libmdtools/do_Forces.F90, - libmdtools/fForceField.h, libmdtools/fSimulation.h, - libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp, - libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, - libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, - libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp, - libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, - libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, - libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, - libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90, - libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp, - libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, - libmdtools/status_module.F90, libmdtools/switch_module.F90, - libmdtools/timing.F90, libmdtools/vector_class.F90, - libmdtools/wrappers.F90, libmdtools/MPIobj/dummy, - libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in, - samples/alkane/Makefile, samples/alkane/Makefile.in, - samples/alkane/alkanes.mdl, samples/alkane/butane.bass, - samples/alkane/butane.eor, samples/alkane/init_butane.eor, - samples/argon/500.bass, samples/argon/500.eor, - samples/argon/500.in, samples/argon/Makefile, - samples/argon/Makefile.in, samples/argon/NVT.bass, - samples/argon/ar864.bass, samples/argon/ar864.eor, - samples/argon/ar864.in, samples/argon/argon.bass, - samples/argon/argon.eor, samples/argon/argonEM.bass, - samples/argon/init_argon.eor, samples/argon/lj.mdl, - samples/argon/machines, samples/lipid/5x5.bass, - samples/lipid/5x5.eor, samples/lipid/Makefile, - samples/lipid/Makefile.in, samples/lipid/init_5x5.eor, - samples/lipid/lipid.mdl, samples/lipid/water.mdl, - samples/metals/Au.bass, samples/metals/Au.eor, - samples/metals/Makefile, samples/metals/Makefile.in, - samples/metals/init_au.in, samples/metals/metals.mdl, - samples/water/200.in, samples/water/Makefile, - samples/water/Makefile.in, samples/water/init_ssd.eor, - samples/water/spce.bass, samples/water/spce.eor, - samples/water/ssd.bass, samples/water/ssd.eor, - samples/water/tim.bass, samples/water/tim.eor, - samples/water/tim.init, samples/water/tim.xyz, - samples/water/tip3p.bass, samples/water/tip3p.eor, - samples/water/tip3p.init, samples/water/two.bass, - samples/water/two.eor, samples/water/two.init, - samples/water/two.xyz, samples/water/water.mdl, - samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass, - samples/water/spce/water.mdl, samples/water/ssde/256init.in, - samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl, - samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass, - samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl, - scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in, - src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy, - third-party/Makefile, third-party/Makefile.in, - third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, - utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep, - utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub, - utils/MPIobj/placeHolder, utils/obj/placeHolder, - utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile, - utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp, - utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c, - utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp, - utils/sysbuilder/latticeBuilder.cpp, - utils/sysbuilder/latticeBuilder.hpp, - utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp, - utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp, - utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp, - utils/sysbuilder/MPIobj/placeHolder, - utils/sysbuilder/obj/placeHolder: Initial revision + 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