# # ChangeLog for molecuilder/src # # Generated by Trac 1.6 # Dec 7, 2025, 7:28:31 PM 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 11:31:00 GMT Frederik Heber [59a745] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/joiner.cpp (modified) Merge branch 'test' 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 ... Thu, 23 Jul 2009 09:14:18 GMT Frederik Heber [09f4dc] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * util/src/AdaptiveANOVA.sh.in (modified) * util/src/CalculateDensity.sh.in (modified) * util/src/CalculateMass.sh.in (modified) * util/src/CreateFromXYZ.sh.in (modified) * util/src/SortByRings.sh.in (modified) Merge branch 'HessianMatrix' Thu, 23 Jul 2009 09:11:01 GMT Frederik Heber [2218dca] * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (added) Merge branch 'GraphRefactoring' Fri, 10 Apr 2009 23:28:39 GMT Frederik Heber [a41b50] * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.hpp (modified) return type of MoleculeListClass::insert is now void instead of bool ... Fri, 10 Apr 2009 23:28:02 GMT Frederik Heber [bb12e7] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) removed lots of warnings due to unused variables This arose due to ... Wed, 08 Apr 2009 11:35:42 GMT Frederik Heber [37a050] * molecuilder/src/builder.cpp (modified) fixes due to changes in molecule structure (Center...()) and merge ... 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: - ... Wed, 08 Apr 2009 11:25:03 GMT Frederik Heber [8b05c6] * molecuilder/src/moleculelist.cpp (modified) MoleculeListClass::Enumerate() lists center and size of molecule, fix ... Thu, 02 Apr 2009 16:42:53 GMT Frederik Heber [899029f] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.hpp (modified) Framework for embedding one molecule into another, now the embedding ... Thu, 02 Apr 2009 16:42:36 GMT Frederik Heber [3021d93] * molecuilder/src/builder.cpp (modified) simple switched order for edit molecule to be in alphabetical ordering 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: - ... Tue, 10 Feb 2009 12:04:37 GMT Frederik Heber [451d7a] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.hpp (modified) Gaussian basis for MPQC input files can now be specified with -B ... Mon, 09 Feb 2009 23:17:38 GMT Frederik Heber [f23d7d] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.hpp (modified) Basis for MPQC can now be specified via command line switch * -B ... Mon, 09 Feb 2009 23:17:28 GMT Frederik Heber [97c751] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/joiner.cpp (modified) Chi integration had some copy&paste error 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 (modified) * pcp/pseudopot/pseudo.14 (modified) * pcp/pseudopot/pseudo.15 (modified) * pcp/pseudopot/pseudo.16 (modified) * pcp/pseudopot/pseudo.17 (modified) * pcp/pseudopot/pseudo.18 (modified) * pcp/pseudopot/pseudo.19 (modified) * pcp/pseudopot/pseudo.20 (modified) * pcp/pseudopot/pseudo.21 (modified) * pcp/pseudopot/pseudo.22 (modified) * pcp/pseudopot/pseudo.23 (modified) * pcp/pseudopot/pseudo.24 (modified) * pcp/pseudopot/pseudo.25 (modified) * pcp/pseudopot/pseudo.26 (modified) * pcp/pseudopot/pseudo.27 (modified) * pcp/pseudopot/pseudo.28 (modified) * pcp/pseudopot/pseudo.29 (modified) * pcp/pseudopot/pseudo.30 (modified) * pcp/pseudopot/pseudo.31 (modified) * pcp/pseudopot/pseudo.32 (modified) * pcp/pseudopot/pseudo.33 (modified) * pcp/pseudopot/pseudo.34 (modified) * pcp/pseudopot/pseudo.35 (modified) * pcp/pseudopot/pseudo.36 (modified) * pcp/pseudopot/pseudo.37 (modified) * pcp/pseudopot/pseudo.38 (modified) * pcp/pseudopot/pseudo.39 (modified) * pcp/pseudopot/pseudo.40 (modified) * pcp/pseudopot/pseudo.41 (modified) * pcp/pseudopot/pseudo.42 (modified) * pcp/pseudopot/pseudo.43 (modified) * pcp/pseudopot/pseudo.44 (modified) * 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) Merge branch 'ConcaveHull' of ../espack2 into ConcaveHull ... Mon, 09 Feb 2009 14:18:13 GMT Frederik Heber [dafe43] * .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# (added) * molecuilder/src/#makefile# (added) * molecuilder/src/#molecules.hpp# (added) * molecuilder/src/Hbondangle.db (modified) * molecuilder/src/Hbonddistance.db (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/ReMapDBondFileFromXYZ.py (added) * molecuilder/src/TAGS (added) * 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) * pcp/pseudopot/pseudo.18 (modified) * pcp/pseudopot/pseudo.19 (modified) * pcp/pseudopot/pseudo.20 (modified) * pcp/pseudopot/pseudo.21 (modified) * pcp/pseudopot/pseudo.22 (modified) * pcp/pseudopot/pseudo.23 (modified) * pcp/pseudopot/pseudo.24 (modified) * pcp/pseudopot/pseudo.25 (modified) * pcp/pseudopot/pseudo.26 (modified) * pcp/pseudopot/pseudo.27 (modified) * pcp/pseudopot/pseudo.28 (modified) * pcp/pseudopot/pseudo.29 (modified) * pcp/pseudopot/pseudo.30 (modified) * pcp/pseudopot/pseudo.31 (modified) * pcp/pseudopot/pseudo.32 (modified) * pcp/pseudopot/pseudo.33 (modified) * pcp/pseudopot/pseudo.34 (modified) * pcp/pseudopot/pseudo.35 (modified) * pcp/pseudopot/pseudo.36 (modified) * pcp/pseudopot/pseudo.37 (modified) * pcp/pseudopot/pseudo.38 (modified) * pcp/pseudopot/pseudo.39 (modified) * pcp/pseudopot/pseudo.40 (modified) * pcp/pseudopot/pseudo.41 (modified) * pcp/pseudopot/pseudo.42 (modified) * pcp/pseudopot/pseudo.43 (modified) * pcp/pseudopot/pseudo.44 (modified) * 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) Merge ../espack3 Fri, 06 Feb 2009 09:48:09 GMT Frederik Heber [d3d15c] * molecuilder/src/boundary.cpp (modified) Find_non_convex_border(): calls CreateAdjacencyList() to fill bond list Fri, 06 Feb 2009 09:44:15 GMT Frederik Heber [95183e] * molecuilder/src/linkedcell.cpp (added) * molecuilder/src/linkedcell.hpp (added) New file and class LinkedCell that contains the linked cell ... 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 Mon, 29 Dec 2008 12:29:21 GMT Frederik Heber [3d9045] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Merge branch 'ConcaveHull' of ... Mon, 29 Dec 2008 12:25:04 GMT Frederik Heber [eec6c8] * molecuilder/src/#border.cpp# (deleted) * molecuilder/src/#makefile# (deleted) * molecuilder/src/#molecules.hpp# (deleted) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) Now we also produce Raster3D output files additionally to TecPlot ... Tue, 23 Dec 2008 13:28:05 GMT Christian Neuen [2ac928] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) fancy commit Tue, 23 Dec 2008 13:06:36 GMT Frederik Heber [fe3c9a] * molecuilder/src/boundary.cpp (modified) Merge branch 'ConcaveHull' of ... Tue, 23 Dec 2008 11:22:57 GMT Frederik Heber [07c050] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Cleaned up all debugging output Tue, 23 Dec 2008 11:21:29 GMT Christian Neuen [56a489] * molecuilder/src/boundary.cpp (modified) BallAngel enhanced, added new alternative direction for issues with ... Fri, 19 Dec 2008 16:21:11 GMT Christian Neuen [edf4a0] * molecuilder/src/boundary.cpp (modified) Switched choice process to Ball angle completely. Problem remains. ... Thu, 18 Dec 2008 17:21:34 GMT Christian Neuen [2b7a1a] * molecuilder/src/boundary.cpp (modified) First change to Ball angle as criteria, however, change sucks. Wed, 17 Dec 2008 15:56:07 GMT Christian Neuen [87c8e7] * molecuilder/src/boundary.cpp (modified) Solved possible problem with Second quadrant overhaul Tue, 16 Dec 2008 18:39:28 GMT Christian Neuen [313dff] * molecuilder/configure.ac (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * pcp/configure.ac (modified) * util/configure.ac (modified) Tesselation starts to look good, minor discrepancies are still there ... 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 ... Thu, 04 Dec 2008 15:15:00 GMT Christian Neuen [db177a] * molecuilder/src/border.cpp (deleted) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) several changes, now output is created, quality unknown Wed, 03 Dec 2008 14:18:10 GMT Christian Neuen [3e20fe] * molecuilder/src/ReMapDBondFileFromXYZ.py (added) Parses a pdb and xyz file and decideds which atoms are in both and ... 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. ... Thu, 27 Nov 2008 09:59:27 GMT Christian Neuen [f5b58e] * molecuilder/src/border.cpp (modified) The border.cpp contains the same functions as the changes in ... Thu, 27 Nov 2008 09:55:08 GMT Christian Neuen [6b3826] * molecuilder/src/border.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) In vector a function for calculation of the vector-(cross-)product ... Tue, 25 Nov 2008 15:05:07 GMT Christian Neuen [a709c4] * molecuilder/src/border.cpp (added) Construction of border triangles of non convex point set Thu, 30 Oct 2008 16:17:23 GMT Frederik Heber [6ce722] * molecuilder/src/analyzer.cpp (modified) Analyzer now produces data file with Frobenius norm of hessian matrix. Thu, 30 Oct 2008 16:17:23 GMT Frederik Heber [ab64f4] * molecuilder/src/parser.cpp (modified) Added some commentary to HessianMatrix::SumSubHessians to ease debugging Thu, 30 Oct 2008 16:17:23 GMT Frederik Heber [95628a] * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) Implemented Frobenius norm calculation for class HessianMatrix ... Thu, 30 Oct 2008 16:17:23 GMT Frederik Heber [f98e5a] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) HessianMatrix implemented fully, but not yet working, probably due to ... Thu, 30 Oct 2008 16:13:32 GMT Frederik Heber [002351] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/parser.hpp (modified) Implemented analysis of magnetic susceptibilites. This is very ... Thu, 30 Oct 2008 16:12:57 GMT Frederik Heber [650212] * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (added) Begin of implementing classes Graph, SubGraph, Node and Edge. So ... Thu, 30 Oct 2008 01:01:04 GMT Frederik Heber [d40e32] * molecuilder/src/analyzer.cpp (modified) Analyzer now produces data file with Frobenius norm of hessian matrix. Thu, 30 Oct 2008 00:59:40 GMT Frederik Heber [5f5df2] * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (added) Begin of implementing classes Graph, SubGraph, Node and Edge. So ... Thu, 30 Oct 2008 00:56:02 GMT Frederik Heber [25f5089] * molecuilder/src/parser.cpp (modified) Added some commentary to HessianMatrix::SumSubHessians to ease debugging Thu, 30 Oct 2008 00:55:19 GMT Frederik Heber [348b6a] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/parser.hpp (modified) Implemented analysis of magnetic susceptibilites. This is very ... Wed, 29 Oct 2008 14:54:54 GMT Frederik Heber [5fd79e] * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) Implemented Frobenius norm calculation for class HessianMatrix ... Sun, 19 Oct 2008 13:57:23 GMT Frederik Heber [aa2e37] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) HessianMatrix implemented fully, but not yet working, probably due to ... Sat, 18 Oct 2008 15:05:54 GMT Frederik Heber [b4c71a] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) ColumnCounter -> *ColumnCounter columns of the MatrixContainer ... Sat, 18 Oct 2008 14:06:51 GMT Frederik Heber [d87482] * molecuilder/src/joiner.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) Introduced new class HessianMatrix derived from MatrixContainer, ... Sat, 18 Oct 2008 14:03:57 GMT Frederik Heber [59f86c] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) VolumeOfConvexEnvelope() has new parameter with tecplot ofstream and ... 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, ... Fri, 17 Oct 2008 13:22:38 GMT Frederik Heber [fa2d7d] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/datacreator.cpp (modified) Analyzer now writes usable plot and data files for shielding ... Fri, 17 Oct 2008 13:20:42 GMT Frederik Heber [f89a9e] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.hpp (modified) config::Save() and config::SaveMPQC() now take string for filename, ... Thu, 16 Oct 2008 09:27:17 GMT Frederik Heber [136e89] * molecuilder/src/builder.cpp (modified) ParseCommandLineOptions(): All cases now make thorough checks ... Thu, 16 Oct 2008 09:26:48 GMT Frederik Heber [88e31c] * molecuilder/src/periodentafel.cpp (modified) periodentafel::LoadPeriodentafel(): if other dbs fail, we just give a ... Thu, 16 Oct 2008 09:25:56 GMT Frederik Heber [45105b] * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) New function IsValidNumber(): checks whether a command line argument ... Wed, 15 Oct 2008 18:20:51 GMT Frederik Heber [93d0ee] * molecuilder/src/analyzer.cpp (modified) Analyzer now prints usable ShieldingsPAS data and plot files (so that ... Wed, 15 Oct 2008 18:20:40 GMT Frederik Heber [b248ca] * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) new function AppendOutputFile() for appending to output files whereas ... Wed, 15 Oct 2008 17:16:43 GMT Frederik Heber [a7e452] * molecuilder/src/molecules.cpp (modified) molecule::VerletForceIntegration() different code, same algorithm ... Tue, 14 Oct 2008 19:14:10 GMT Frederik Heber [7a3724] * molecuilder/src/boundary.cpp (modified) new version of Tesselation::GuessStartingTriangle() seems to fix ... Tue, 14 Oct 2008 13:26:02 GMT Frederik Heber [51d33c5] * molecuilder/src/boundary.cpp (modified) BUGFIX: Tesselation::AddPoint() always increased ... Sun, 12 Oct 2008 15:58:48 GMT Frederik Heber [45d5cc] * molecuilder/src/config.cpp (modified) changed basis set for mpqc from STO-3G to 3-21G (more stable with ... Sat, 11 Oct 2008 16:07:45 GMT Frederik Heber [139f8c] * molecuilder/src/Hbondangle.db (modified) * molecuilder/src/Hbonddistance.db (modified) * molecuilder/src/orbitals.db (modified) * molecuilder/src/valence.db (modified) corrected number of valence orbitals for Calcium (2 -> 4) and ... 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 13:39:58 GMT Frederik Heber [2bfaf8] * molecuilder/src/moleculelist.cpp (modified) BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong ... 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 13:38:46 GMT Frederik Heber [372c4cd] * molecuilder/src/moleculelist.cpp (modified) BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong ... 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 13:36:06 GMT Frederik Heber [14178b] * molecuilder/src/moleculelist.cpp (modified) BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong ... 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 ... Thu, 09 Oct 2008 16:19:39 GMT Frederik Heber [a7b3b8] * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/molecules.hpp (modified) Output of atom and bond to stream now is set to const bond/atom 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, 25 Sep 2008 17:57:02 GMT Frederik Heber [c49678] * molecuilder/src/defs.hpp (modified) Lots of conversion factors for various units Were taken from PCP defs.h Thu, 25 Sep 2008 17:50:17 GMT Frederik Heber [bb28e0] * Makefile.am (modified) * molecuilder/src/Makefile.am (modified) * pcp/Makefile.am (modified) Some files were missing in the repository pseudopotentials and the ... 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 ... Thu, 11 Sep 2008 13:25:47 GMT Frederik Heber [4917ddd] * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.hpp (modified) config::DoWannier implemented that is parsed from config file, ... Thu, 11 Sep 2008 13:08:18 GMT Frederik Heber [55ebd0] * molecuilder/src/builder.cpp (modified) ParseCommandLineOptions(): Command line option "-E" for changing an ... Tue, 09 Sep 2008 15:32:16 GMT Frederik Heber [8e52aa] * molecuilder/src/vector.cpp (modified) BUGFIX: Normalize() would try to normalize a zero vector which ended ... 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 ... Sat, 06 Sep 2008 15:06:51 GMT Frederik Heber [f9cd68] * molecuilder/src/builder.cpp (modified) BUGFIX: Moved case 'a' in ParseCommandLineOptions() to the ... Fri, 05 Sep 2008 17:09:39 GMT Frederik Heber [5887ed] * molecuilder/src/builder.cpp (modified) SaveConfig() now also stores an MPQC input file. ... Fri, 05 Sep 2008 17:02:18 GMT Frederik Heber [dfc1c7] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecules.hpp (modified) moved all definitions from boundary.hpp to molecules.hpp, and renamed ... Wed, 03 Sep 2008 17:28:31 GMT Frederik Heber [0f508c] * molecuilder/src/config.cpp (modified) BUGFIX: config::load() parses endlessly if there are no atoms in the ...