# # ChangeLog for molecuilder/src/molecules.cpp # # Generated by Trac 1.6 # Dec 10, 2025, 2:04:52 AM Mon, 28 Sep 2009 18:41:52 GMT Frederik Heber [606dfb] * molecuilder/src/builder.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Implemenation of embedding merge, untested. LinearInterpolation now ... Fri, 21 Aug 2009 12:17:25 GMT Frederik Heber [5f4960] * molecuilder/src/molecules.cpp (modified) formula typo in molecule::PrincipalAxisSystem() fixed Tue, 18 Aug 2009 08:48:06 GMT Frederik Heber [da84d6] * molecuilder/configure.ac (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/leastsquaremin.cpp (added) * molecuilder/src/leastsquaremin.hpp (added) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vectorunittest.cpp (added) * molecuilder/src/vectorunittest.hpp (added) Incorporation of Unit test on class Vector. - new file ... Fri, 07 Aug 2009 12:46:27 GMT Frederik Heber [ef5521] * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) BUGFIX: PointCloud implementation in molecule stopped one before ... Fri, 07 Aug 2009 09:13:21 GMT Frederik Heber [0fc0b5] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Test case of filling a simulation domain with water included. Tue, 04 Aug 2009 13:47:05 GMT Frederik Heber [04dcc0] * molecuilder/src/molecules.cpp (modified) Smaller FIXES to molecule class - new pointer TesselStruct was not ... Mon, 03 Aug 2009 14:58:43 GMT Frederik Heber [e78824] * molecuilder/src/Makefile.am (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) class config definitions moved to their own header file. NOTE: ... Mon, 03 Aug 2009 14:48:42 GMT Frederik Heber [834ff3] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (added) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (added) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (added) * molecuilder/src/tesselation.hpp (added) * molecuilder/src/tesselationhelpers.cpp (added) * molecuilder/src/tesselationhelpers.hpp (added) * molecuilder/src/vector.hpp (modified) Huge refactoring of Tesselation routines, but not finished yet. - ... Mon, 03 Aug 2009 08:10:09 GMT Frederik Heber [4e4940] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) We are one step further in fixing the convex hull: There are two ... Mon, 27 Jul 2009 14:53:57 GMT Frederik Heber [dd69cc] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/molecules.cpp (modified) FIX: DetermineCenterOfAll() did point in wrong direction, convex ... Mon, 27 Jul 2009 14:07:25 GMT Frederik Heber [0ac84df] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/vector.cpp (modified) BUGFIX: molecule::ReturnFullMatrixforSymmetric had it still all ... Fri, 24 Jul 2009 10:38:32 GMT Frederik Heber [c3a303] * .gitignore (modified) * Makefile.am (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (added) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * pcp/Makefile.am (modified) * util/src/CalculateDensity.sh.in (modified) * util/src/CalculateMass.sh.in (modified) * util/src/average.cpp (modified) * util/src/dynamicANOVA.sh.in (modified) Merge branch 'master' into ConcaveHull Conflicts: ... Thu, 23 Jul 2009 14:21:57 GMT Frederik Heber [a048fa] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) fixed indentation from tabs to two spaces. Thu, 23 Jul 2009 14:04:47 GMT Frederik Heber [47548d] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * util/src/CalculateDensity.sh.in (modified) * util/src/CalculateMass.sh.in (modified) Merge branch 'AtomRemoval' Conflicts: ... Thu, 23 Jul 2009 13:53:01 GMT Frederik Heber [1f6efb] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) fixed indentation from tabs to two spaces. Thu, 23 Jul 2009 13:45:24 GMT Frederik Heber [f39735] * .gitignore (modified) * molecuilder/src/#border.cpp# (deleted) * molecuilder/src/#makefile# (deleted) * molecuilder/src/#molecules.hpp# (deleted) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/ellipsoid.cpp (added) * molecuilder/src/ellipsoid.hpp (added) * molecuilder/src/graph.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (added) * molecuilder/src/linkedcell.hpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * util/src/NanoCreator.c (modified) * util/src/NanoCreator.h (modified) Merge branch 'MultipleMolecules' Conflicts: ... Thu, 23 Jul 2009 12:32:48 GMT Frederik Heber [560995] * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/verbose.cpp (modified) Fix indentation from tabs to two spaces to prepare merging with ... Thu, 23 Jul 2009 12:14:13 GMT Frederik Heber [1b2aa1] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) Fix indentation from tab to two spaces. The trouble was caused at ... Thu, 23 Jul 2009 11:46:57 GMT Frederik Heber [307290] * molecuilder/src/molecules.cpp (modified) Merge branch 'ConstrainedMolecularDynamics' Conflicts: ... Thu, 23 Jul 2009 11:23:59 GMT Frederik Heber [3b470f] * .gitignore (modified) * Makefile.am (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * pcp/Makefile.am (modified) * util/src/average.cpp (modified) Merge branch 'Thermostat' Conflicts: .gitignore ... Fri, 10 Jul 2009 21:19:23 GMT Frederik Heber [c95b69] * molecuilder/src/molecules.cpp (modified) BUGFIX: Due to stupid mistake, first atom was overlooked in periodic ... Fri, 10 Jul 2009 21:01:40 GMT Frederik Heber [88b936] * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) new class ConfigFileBuffer and new overloaded function ... Fri, 10 Jul 2009 20:20:09 GMT Frederik Heber [598f76] * molecuilder/src/molecules.cpp (modified) BUGFIX: molecule::Output...() routines wrote elements beginning with ... Fri, 10 Jul 2009 14:29:56 GMT Frederik Heber [22f587] * molecuilder/src/molecules.cpp (modified) XYZ and config files now store the atoms in the same order as they ... Fri, 10 Jul 2009 12:48:05 GMT Frederik Heber [6fb785] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) molecule::CenterInBox puts atoms now periodically into the given box, ... Wed, 03 Jun 2009 16:16:37 GMT Frederik Heber [378e87] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) BUGFIX: RemoveAtom() would remove the iterator, ... Wed, 08 Apr 2009 11:27:50 GMT Frederik Heber [d618b5] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Lots of bugfixes, some name changes and new functions BUGFIX: - ... Thu, 02 Apr 2009 16:12:54 GMT Frederik Heber [c830e8e] * molecuilder/src/atom.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Basic implementation of Multiple molecules. builder.cpp: - ... Mon, 09 Feb 2009 17:24:10 GMT Frederik Heber [e08f45] * .gitignore (modified) * ChangeLog (modified) * Makefile.am (modified) * configure.ac (modified) * m4/ac_doxygen.m4 (modified) * m4/acx_compilerflags.m4 (modified) * molecuilder/ChangeLog (modified) * molecuilder/Makefile.am (modified) * molecuilder/configure.ac (modified) * molecuilder/doc/Doxyfile (modified) * molecuilder/doc/Makefile.am (modified) * molecuilder/m4/ac_doxygen.m4 (modified) * molecuilder/m4/acx_compilerflags.m4 (modified) * molecuilder/src/.#border.cpp (deleted) * molecuilder/src/.#molecules.hpp (deleted) * molecuilder/src/Hbondangle.db (modified) * molecuilder/src/Hbonddistance.db (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/elements.db (modified) * molecuilder/src/ellipsoid.cpp (added) * molecuilder/src/ellipsoid.hpp (added) * molecuilder/src/graph.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/orbitals.db (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/valence.db (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * molecuilder/tests/Makefile.am (modified) * molecuilder/tests/atlocal.in (modified) * molecuilder/tests/molecuilder.in (modified) * molecuilder/tests/testsuite.at (modified) * pcp/ChangeLog (modified) * pcp/Makefile.am (modified) * pcp/configure.ac (modified) * pcp/doc/Doxyfile (modified) * pcp/doc/Makefile.am (modified) * pcp/m4/ac_doxygen.m4 (modified) * pcp/m4/acx_compilerflags.m4 (modified) * pcp/m4/acx_mpi.m4 (modified) * pcp/pseudopot/pseudo.01 (modified) * pcp/pseudopot/pseudo.02 (modified) * pcp/pseudopot/pseudo.03 (modified) * pcp/pseudopot/pseudo.04 (modified) * pcp/pseudopot/pseudo.05 (modified) * pcp/pseudopot/pseudo.06 (modified) * pcp/pseudopot/pseudo.07 (modified) * pcp/pseudopot/pseudo.08 (modified) * pcp/pseudopot/pseudo.09 (modified) * pcp/pseudopot/pseudo.10 (modified) * pcp/pseudopot/pseudo.11 (modified) * pcp/pseudopot/pseudo.12 (modified) * pcp/pseudopot/pseudo.13 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pcp/src/defs.h (modified) * pcp/src/density.c (modified) * pcp/src/density.h (modified) * pcp/src/energy.c (modified) * pcp/src/energy.h (modified) * pcp/src/errors.c (modified) * pcp/src/errors.h (modified) * pcp/src/excor.c (modified) * pcp/src/excor.h (modified) * pcp/src/grad.c (modified) * pcp/src/grad.h (modified) * pcp/src/gramsch.c (modified) * pcp/src/gramsch.h (modified) * pcp/src/helpers.c (modified) * pcp/src/helpers.h (modified) * pcp/src/init.c (modified) * pcp/src/init.h (modified) * pcp/src/ions.c (modified) * pcp/src/ions.h (modified) * pcp/src/mergesort2.c (modified) * pcp/src/mergesort2.h (modified) * pcp/src/myfft.c (modified) * pcp/src/myfft.h (modified) * pcp/src/mymath.c (modified) * pcp/src/mymath.h (modified) * pcp/src/opt.c (modified) * pcp/src/opt.h (modified) * pcp/src/output.c (modified) * pcp/src/output.h (modified) * pcp/src/parsetest.c (modified) * pcp/src/pcp.c (modified) * pcp/src/pcp.h (modified) * pcp/src/pdbformat.c (modified) * pcp/src/pdbformat.h (modified) * pcp/src/perturbed.c (modified) * pcp/src/perturbed.h (modified) * pcp/src/pseudo.c (modified) * pcp/src/pseudo.h (modified) * pcp/src/riemann.c (modified) * pcp/src/riemann.h (modified) * pcp/src/run.c (modified) * pcp/src/run.h (modified) * pcp/src/test.c (modified) * pcp/src/wannier.c (modified) * pcp/src/wannier.h (modified) * pcp/tests/Makefile.am (modified) * pcp/tests/atlocal.in (modified) * pcp/tests/pcp.in (modified) * pcp/tests/testsuite.at (modified) * util/ChangeLog (modified) * util/Makefile.am (modified) * util/configure.ac (modified) * util/doc/Doxyfile (modified) * util/doc/Makefile.am (modified) * util/m4/ac_doxygen.m4 (modified) * util/m4/acx_compilerflags.m4 (modified) * util/specvisual.cfg (modified) * util/specvisual.net (modified) * util/specvisualOnly.net (modified) * util/src/CreateGaAs.c (modified) * util/src/CreateH2.c (modified) * util/src/GetPdb.c (modified) * util/src/Makefile.am (modified) * util/src/NanoCreator.c (modified) * util/src/NanoCreator.h (modified) * util/src/ReadSrcIon.c (modified) * util/src/VibrAlyzer.c (modified) * util/src/average.cpp (modified) * util/src/diagonalize.c (modified) * util/src/mergesort.c (modified) * util/src/mergesort.h (modified) * util/src/stochastik.cpp (modified) * util/suffix (modified) * util/tests/Makefile.am (modified) * util/tests/NanoCreator.in (modified) * util/tests/atlocal.in (modified) * util/tests/testsuite.at (modified) * util/visual.cfg (modified) * util/visual.net (modified) * util/visualOnly.net (modified) Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull ... Mon, 29 Dec 2008 21:46:58 GMT Frederik Heber [848729] * .gitignore (modified) * ChangeLog (modified) * Makefile.am (modified) * configure.ac (modified) * m4/ac_doxygen.m4 (modified) * m4/acx_compilerflags.m4 (modified) * molecuilder/ChangeLog (modified) * molecuilder/Makefile.am (modified) * molecuilder/configure.ac (modified) * molecuilder/doc/Doxyfile (modified) * molecuilder/doc/Makefile.am (modified) * molecuilder/m4/ac_doxygen.m4 (modified) * molecuilder/m4/acx_compilerflags.m4 (modified) * molecuilder/src/.#border.cpp (deleted) * molecuilder/src/.#molecules.hpp (deleted) * molecuilder/src/Hbondangle.db (modified) * molecuilder/src/Hbonddistance.db (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/elements.db (modified) * molecuilder/src/graph.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/orbitals.db (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/valence.db (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * molecuilder/tests/Makefile.am (modified) * molecuilder/tests/atlocal.in (modified) * molecuilder/tests/molecuilder.in (modified) * molecuilder/tests/testsuite.at (modified) * pcp/ChangeLog (modified) * pcp/Makefile.am (modified) * pcp/configure.ac (modified) * pcp/doc/Doxyfile (modified) * pcp/doc/Makefile.am (modified) * pcp/m4/ac_doxygen.m4 (modified) * pcp/m4/acx_compilerflags.m4 (modified) * pcp/m4/acx_mpi.m4 (modified) * pcp/pseudopot/pseudo.01 (modified) * pcp/pseudopot/pseudo.02 (modified) * pcp/pseudopot/pseudo.03 (modified) * pcp/pseudopot/pseudo.04 (modified) * pcp/pseudopot/pseudo.05 (modified) * pcp/pseudopot/pseudo.06 (modified) * pcp/pseudopot/pseudo.07 (modified) * pcp/pseudopot/pseudo.08 (modified) * pcp/pseudopot/pseudo.09 (modified) * pcp/pseudopot/pseudo.10 (modified) * pcp/pseudopot/pseudo.11 (modified) * pcp/pseudopot/pseudo.12 (modified) * pcp/pseudopot/pseudo.13 (modified) * pcp/pseudopot/pseudo.14 (modified) * pcp/pseudopot/pseudo.15 (modified) * pcp/pseudopot/pseudo.16 (modified) * pcp/pseudopot/pseudo.17 (modified) * 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pcp/pseudopot/pseudo.45 (modified) * pcp/pseudopot/pseudo.46 (modified) * pcp/pseudopot/pseudo.47 (modified) * pcp/pseudopot/pseudo.48 (modified) * pcp/pseudopot/pseudo.49 (modified) * pcp/pseudopot/pseudo.50 (modified) * pcp/pseudopot/pseudo.51 (modified) * pcp/pseudopot/pseudo.52 (modified) * pcp/pseudopot/pseudo.53 (modified) * pcp/pseudopot/pseudo.54 (modified) * pcp/pseudopot/pseudo.55 (modified) * pcp/pseudopot/pseudo.56 (modified) * pcp/pseudopot/pseudo.72 (modified) * pcp/pseudopot/pseudo.73 (modified) * pcp/pseudopot/pseudo.74 (modified) * pcp/pseudopot/pseudo.75 (modified) * pcp/pseudopot/pseudo.76 (modified) * pcp/pseudopot/pseudo.77 (modified) * pcp/pseudopot/pseudo.78 (modified) * pcp/pseudopot/pseudo.79 (modified) * pcp/pseudopot/pseudo.80 (modified) * pcp/src/Makefile.am (modified) * pcp/src/data.h (modified) * pcp/src/defs.h (modified) * pcp/src/density.c (modified) * pcp/src/density.h (modified) * pcp/src/energy.c (modified) * pcp/src/energy.h (modified) * pcp/src/errors.c (modified) * pcp/src/errors.h (modified) * pcp/src/excor.c (modified) * pcp/src/excor.h (modified) * pcp/src/grad.c (modified) * pcp/src/grad.h (modified) * pcp/src/gramsch.c (modified) * pcp/src/gramsch.h (modified) * pcp/src/helpers.c (modified) * pcp/src/helpers.h (modified) * pcp/src/init.c (modified) * pcp/src/init.h (modified) * pcp/src/ions.c (modified) * pcp/src/ions.h (modified) * pcp/src/mergesort2.c (modified) * pcp/src/mergesort2.h (modified) * pcp/src/myfft.c (modified) * pcp/src/myfft.h (modified) * pcp/src/mymath.c (modified) * pcp/src/mymath.h (modified) * pcp/src/opt.c (modified) * pcp/src/opt.h (modified) * pcp/src/output.c (modified) * pcp/src/output.h (modified) * pcp/src/parsetest.c (modified) * pcp/src/pcp.c (modified) * pcp/src/pcp.h (modified) * pcp/src/pdbformat.c (modified) * pcp/src/pdbformat.h (modified) * pcp/src/perturbed.c (modified) * pcp/src/perturbed.h (modified) * pcp/src/pseudo.c (modified) * pcp/src/pseudo.h (modified) * pcp/src/riemann.c (modified) * pcp/src/riemann.h (modified) * pcp/src/run.c (modified) * pcp/src/run.h (modified) * pcp/src/test.c (modified) * pcp/src/wannier.c (modified) * pcp/src/wannier.h (modified) * pcp/tests/Makefile.am (modified) * pcp/tests/atlocal.in (modified) * pcp/tests/pcp.in (modified) * pcp/tests/testsuite.at (modified) * util/ChangeLog (modified) * util/Makefile.am (modified) * util/configure.ac (modified) * util/doc/Doxyfile (modified) * util/doc/Makefile.am (modified) * util/m4/ac_doxygen.m4 (modified) * util/m4/acx_compilerflags.m4 (modified) * util/specvisual.cfg (modified) * util/specvisual.net (modified) * util/specvisualOnly.net (modified) * util/src/CreateGaAs.c (modified) * util/src/CreateH2.c (modified) * util/src/GetPdb.c (modified) * util/src/Makefile.am (modified) * util/src/NanoCreator.c (modified) * util/src/NanoCreator.h (modified) * util/src/ReadSrcIon.c (modified) * util/src/VibrAlyzer.c (modified) * util/src/average.cpp (modified) * util/src/diagonalize.c (modified) * util/src/mergesort.c (modified) * util/src/mergesort.h (modified) * util/src/stochastik.cpp (modified) * util/suffix (modified) * util/tests/Makefile.am (modified) * util/tests/NanoCreator.in (modified) * util/tests/atlocal.in (modified) * util/tests/testsuite.at (modified) * util/visual.cfg (modified) * util/visual.net (modified) * util/visualOnly.net (modified) Just a temporary commit Thu, 11 Dec 2008 15:23:01 GMT Christian Neuen [5a447f] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecules.cpp (modified) Atom indices are now correctly processed. Mon, 08 Dec 2008 14:16:34 GMT Christian Neuen [735468] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) Another update w.r.t. the Tesselation. Some signs switched, but atom ... Wed, 03 Dec 2008 14:12:05 GMT Christian Neuen [e0c5b1] * molecuilder/src/#border.cpp# (added) * molecuilder/src/#makefile# (added) * molecuilder/src/#molecules.hpp# (added) * molecuilder/src/.#border.cpp (added) * molecuilder/src/.#molecules.hpp (added) * molecuilder/src/TAGS (added) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) Multiple changes to boundary, currently not fully operational. ... Fri, 17 Oct 2008 13:24:10 GMT Frederik Heber [f5d7e1] * molecuilder/src/molecules.cpp (modified) molecule::PickLocalBackEdges(): BUGFIX: if Walker as not in subgraph, ... Wed, 15 Oct 2008 17:16:43 GMT Frederik Heber [a7e452] * molecuilder/src/molecules.cpp (modified) molecule::VerletForceIntegration() different code, same algorithm ... Sat, 11 Oct 2008 16:07:28 GMT Frederik Heber [1e5e16] * molecuilder/src/molecules.cpp (modified) molecule::AddHydrogenReplacementAtom() returns false on missing ... Fri, 10 Oct 2008 13:39:54 GMT Frederik Heber [4959f1] * molecuilder/src/molecules.cpp (modified) BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in ... Fri, 10 Oct 2008 13:38:41 GMT Frederik Heber [31ed7d] * molecuilder/src/molecules.cpp (modified) BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in ... Fri, 10 Oct 2008 13:32:33 GMT Frederik Heber [d01f4d] * molecuilder/src/molecules.cpp (modified) BUGFIX: molecule::CreateAdjacencyList() used CandidateBondNo in ... Thu, 09 Oct 2008 18:29:34 GMT Frederik Heber [1bd619] * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected ... Thu, 09 Oct 2008 18:29:03 GMT Frederik Heber [5a78f5] * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected ... Thu, 09 Oct 2008 18:27:56 GMT Frederik Heber [b86de7] * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) BUGFIXES: CyclicStructureAnalysis() now compatible to disconnected ... Sun, 28 Sep 2008 17:55:04 GMT Frederik Heber [68cfd1] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.cpp (modified) corrected molecule::VerletForceIntegration() and analyzer creates ... Thu, 25 Sep 2008 17:57:19 GMT Frederik Heber [556157] * .gitignore (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) thermostats enumerator, necessary variables included in class config, ... Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber [4a434c] * molecuilder/src/molecules.cpp (modified) molecule::MinimiseConstrainedPotential(): Extension of search and ... Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber [9070650] * molecuilder/src/molecules.cpp (modified) molecule::MinimiseConstrainedPotential() : Minimisation is fixed ... Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber [63b5c31] * molecuilder/src/builder.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Implemented molecule::LinearInterpolationBetweenConfiguration(). ... Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber [909610] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Basic implementation of Constrained MD is done, missing testing. Thu, 11 Sep 2008 13:28:25 GMT Frederik Heber [c99adf] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Constrained Molecular Dynamics: two new functions ... Tue, 09 Sep 2008 08:37:07 GMT Frederik Heber [79cd79] * molecuilder/src/builder.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) new function: molecule::OutputTemperatureFromTrajectories() stores ... Sat, 06 Sep 2008 16:21:31 GMT Frederik Heber [b21e1f] * molecuilder/src/molecules.cpp (modified) BUGFIX: molecule::...Scale(),Translate(),Mirror() and Align() did ... Sat, 06 Sep 2008 15:08:32 GMT Frederik Heber [d473c3] * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) BUGFIX: config::SaveMPQC() used molecule::DetermineCenter() which ... Fri, 29 Aug 2008 10:39:59 GMT Frederik Heber [830971] * molecuilder/src/molecules.cpp (modified) molecule::ScanForPeriodicCorrection() two printfs were commented out Mon, 18 Aug 2008 09:02:34 GMT Frederik Heber [04c868] * molecuilder/src/molecules.cpp (modified) tiny comments and docu update for FragmentMolecule() Mon, 18 Aug 2008 08:57:58 GMT Frederik Heber [644ba1] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Adaptivity fixes, MD by VerletForceIntegration introduced, MD ... Wed, 06 Aug 2008 12:00:18 GMT Frederik Heber [67f102] * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) config::Save() and config::Load() parse MD steps into and out of ... Wed, 06 Aug 2008 09:02:01 GMT Frederik Heber [8f8621] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Rename of class vector to Vector to avoid conflict with vector from STL. Wed, 06 Aug 2008 08:59:06 GMT Frederik Heber [0a08df] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Scaffold of new function: VerletForceIntegration() - does MD step by ... Thu, 31 Jul 2008 14:05:37 GMT Frederik Heber [7670cab] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) new test function CheckForConnectedSubgraph() and bigger rewrite of ... Wed, 30 Jul 2008 14:16:21 GMT Frederik Heber [ec947b] * molecuilder/src/molecules.cpp (modified) CyclicStructureAnalysis(): BUGFIX - BFSStack may be empty if we can't ... Wed, 30 Jul 2008 13:11:30 GMT Frederik Heber [d49416] * molecuilder/src/molecules.cpp (modified) 2 BUGFIXES: CreateAdjacencyList() and CyclicStructureAnalysis() ... Mon, 28 Jul 2008 14:41:22 GMT Frederik Heber [126934] * molecuilder/src/atom.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) CyclicStructureAnalysis: BUGFIX - MinimumRingSize of non-loop atoms ... Mon, 28 Jul 2008 14:18:25 GMT Frederik Heber [3f805d] * molecuilder/src/molecules.cpp (modified) CyclicStructureAnalysis: BUGFIX - MinimumRingSize was not set ... Mon, 28 Jul 2008 13:45:43 GMT Frederik Heber [747b10] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) CheckOrderAtSite: BUGFIX - Added MinimumRingSize to parameter list, ... Thu, 24 Jul 2008 14:00:19 GMT Frederik Heber [db3ea3] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) BIG change: Hcorrection included and bugfix of analyzer (wrt forces) ... Wed, 09 Jul 2008 13:24:20 GMT Frederik Heber [23b4aa] * molecuilder/src/molecules.cpp (modified) StoreKeySetFile(): removed unncessary iterator "ende" storing Tue, 08 Jul 2008 13:12:55 GMT Frederik Heber [6beb99] * molecuilder/src/molecules.cpp (modified) * pcp/src/ions.c (modified) changed verbosity a bit Mon, 23 Jun 2008 11:23:50 GMT Frederik Heber [329d0f] * molecuilder/src/molecules.cpp (modified) StoreFragmentFromKeySet(): BUGFIX - commented out the Leaf->AddBond ... Mon, 16 Jun 2008 14:09:27 GMT Frederik Heber [1f9f1b] * molecuilder/src/builder.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/periodentafel.cpp (modified) BUGFIX: If other databases could not be loaded, no error was ... Thu, 12 Jun 2008 19:14:46 GMT Frederik Heber [e292c10] * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) VolumeOfConvexEnvelope: Works! VolumeOfConvexEnvelope has been ... Tue, 10 Jun 2008 11:21:32 GMT Frederik Heber [2259f4] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) VolumeOfConvexEnvelope() finished and tested with SiOH4, ... Sat, 07 Jun 2008 13:21:53 GMT Frederik Heber [32b6dc] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Working version of PAS transformation (tested on C-S-H cluster) and ... Mon, 26 May 2008 13:20:10 GMT Frederik Heber [94b458] * molecuilder/src/molecules.cpp (modified) BUGFIX: line.erase() threw exception with illegal line end Found by ... Mon, 26 May 2008 10:52:00 GMT Frederik Heber [5eb05a] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) molecule::CreateAdjacencyList() now needs IsAngstroem as parameter ... Fri, 23 May 2008 09:17:19 GMT Frederik Heber [f75030] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/verbose.cpp (modified) Lots of for loops now count in reverse order where it does not ... Wed, 21 May 2008 11:14:06 GMT Frederik Heber [927aba] * molecuilder/src/molecules.cpp (modified) new function CenterInBox, some char* converted to string ... Fri, 09 May 2008 14:38:27 GMT Frederik Heber [cc6dfb] * molecuilder/src/molecules.cpp (modified) CyclicStructureAnalysis(): forget to check whether we actually have ... Fri, 09 May 2008 14:20:08 GMT Frederik Heber [0716ff4] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) MinimumRingSize is now an array over all atoms Each entry in ... Thu, 08 May 2008 17:31:04 GMT Frederik Heber [a3ff7b2] * molecuilder/src/defs.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) molecule::CheckOrderAtSite() now interprets negative Orders as ... Thu, 08 May 2008 16:18:07 GMT Frederik Heber [461e93] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) molecule::CheckOrderAtSite() returns bool and used as threshold ... Thu, 08 May 2008 15:52:11 GMT Frederik Heber [d88597] * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) new function molecule::CreateMappingLabelsToConfigSequence() creates ... Thu, 08 May 2008 15:39:36 GMT Frederik Heber [2b79c3] * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) new function MoleculeLeafClass::TranslateIndicesToGlobalIDs() used in ... Thu, 08 May 2008 15:25:00 GMT Frederik Heber [ea84ed] * molecuilder/src/molecules.cpp (modified) FragmentMolecule(): abstractized AssignKeySetsToFragments() and ... Thu, 08 May 2008 12:45:52 GMT Frederik Heber [08fd83] * molecuilder/src/molecules.cpp (modified) MoleculeLeafClass::FillRootStackForSubgraphs used to remove filling ... Thu, 08 May 2008 12:04:42 GMT Frederik Heber [9c3496] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) new function molecule::CheckOrderAtSite and ... Wed, 07 May 2008 14:46:33 GMT Frederik Heber [a01955] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) rewritten CyclicStructureAnalysis(): uses DFS spanning tree and ... Wed, 07 May 2008 13:38:13 GMT Frederik Heber [d50d2a] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/stackclass.hpp (added) AtomStackClass -> template StackClass change in new ... Tue, 06 May 2008 09:45:31 GMT Frederik Heber [0e8321] * molecuilder/src/molecules.cpp (modified) KeySetFile is stored without an additional last tab on each line Mon, 05 May 2008 16:19:05 GMT Frederik Heber [115bf4] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) ForcesFile and TEFactors are _needed_, reincorporated. ... Fri, 02 May 2008 13:35:10 GMT Frederik Heber [30fda2] * molecuilder/src/molecules.cpp (modified) commenting in header changed for the four main functions that ... Fri, 02 May 2008 13:25:48 GMT Frederik Heber [c75363] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/vector.cpp (modified) HUGE REWRITE to allow for adaptive increase of the bond order, first ... Tue, 29 Apr 2008 12:19:51 GMT Frederik Heber [c510a7] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * pcp/src/defs.h (modified) * pcp/src/helpers.c (modified) * pcp/src/init.c (modified) * pcp/src/ions.c (modified) * pcp/src/opt.c (modified) * pcp/src/output.c (modified) * pcp/src/perturbed.c (modified) * pcp/src/pseudo.c (modified) * pcp/src/wannier.c (modified) char lengths of 255 and MAXDUMMYSTRING replaced with define ... Tue, 29 Apr 2008 07:55:34 GMT Frederik Heber [307fd1] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Store/CheckAdj...() now also incorporate bond order to check against. Tue, 29 Apr 2008 07:04:59 GMT Frederik Heber [7b1cea] * molecuilder/src/config.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) configname is also stored in config structure, GetDefaultPath by ... Mon, 28 Apr 2008 13:53:54 GMT Frederik Heber [661288] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Atoms in the fragments in the configs are again ordered as first ... Mon, 28 Apr 2008 13:46:05 GMT Frederik Heber [e565a8] * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) removed some output lines (commented-out) mostly in ... Mon, 28 Apr 2008 11:39:07 GMT Frederik Heber [8efbfc] * molecuilder/src/molecules.cpp (modified) FragmentMolecule(): status variable used when checking adjacency file ... Mon, 28 Apr 2008 11:36:11 GMT Frederik Heber [d982bb] * molecuilder/src/defs.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) All filenames (const char *) have been transferred to defs.hpp ... Mon, 28 Apr 2008 10:41:40 GMT Frederik Heber [34d37c] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) storing and comparing Adjacency outsourced into two new functions. ... Mon, 28 Apr 2008 09:22:38 GMT Frederik Heber [2614f83] * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) FragmentMolecule(): Adjacency store/check and parsing of KeySetFile ...