# # ChangeLog for molecuilder/src/moleculelist.cpp # # Generated by Trac 1.6 # Sep 23, 2025, 10:50:21 AM Wed, 03 Feb 2010 16:42:06 GMT Tillmann Crueger [8501eb] * molecuilder/src/Patterns/Observer.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/unittests/CacheableTest.cpp (modified) Changed all observed places to new observer structure Tue, 02 Feb 2010 12:21:13 GMT Tillmann Crueger [adcdf8] * molecuilder/src/Actions/small_actions.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) Moved method to rename molecules to a seperate Action Tue, 02 Feb 2010 12:14:54 GMT Tillmann Crueger [795b4d] * molecuilder/src/Actions/Action.hpp (modified) * molecuilder/src/Actions/small_actions.cpp (added) * molecuilder/src/Actions/small_actions.hpp (added) * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) Moved method to rename molecules to a seperate Action Tue, 02 Feb 2010 12:00:19 GMT Tillmann Crueger [6997fa] * molecuilder/src/Makefile.am (modified) * molecuilder/src/Patterns/Observer.hpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/unittests/ObserverTest.cpp (modified) * molecuilder/src/unittests/ObserverTest.hpp (modified) Added a view that displays all molecules using a QTableWidget Wed, 27 Jan 2010 14:36:09 GMT Tillmann Crueger [d34341] * .gitignore (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/gslmatrix.cpp (added) * molecuilder/src/gslmatrix.hpp (added) * molecuilder/src/gslvector.cpp (added) * molecuilder/src/gslvector.hpp (added) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linearsystemofequations.cpp (added) * molecuilder/src/linearsystemofequations.hpp (added) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_pointcloud.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/gslmatrixsymmetricunittest.cpp (added) * molecuilder/src/unittests/gslmatrixsymmetricunittest.hpp (added) * molecuilder/src/unittests/gslmatrixunittest.cpp (added) * molecuilder/src/unittests/gslmatrixunittest.hpp (added) * molecuilder/src/unittests/gslvectorunittest.cpp (added) * molecuilder/src/unittests/gslvectorunittest.hpp (added) * molecuilder/src/unittests/linearsystemofequationsunittest.cpp (added) * molecuilder/src/unittests/linearsystemofequationsunittest.hpp (added) * molecuilder/src/unittests/listofbondsunittest.cpp (modified) * molecuilder/src/unittests/tesselation_boundarytriangleunittest.cpp (added) * molecuilder/src/unittests/tesselation_boundarytriangleunittest.hpp (added) * molecuilder/src/unittests/tesselation_insideoutsideunittest.cpp (added) * molecuilder/src/unittests/tesselation_insideoutsideunittest.hpp (added) * molecuilder/src/unittests/tesselationunittest.cpp (modified) * molecuilder/src/unittests/tesselationunittest.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/version.h (added) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified) * pcp/src/version.h (added) * util/src/Makefile.am (modified) * util/src/version.h (added) Merge commit 'heber/Analysis_PairCorrelation' into MenuRefactoring ... Tue, 26 Jan 2010 12:52:31 GMT Frederik Heber [478683] * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) GetDistanceToSurface() separated, filling now with water instead of ... Tue, 26 Jan 2010 12:45:41 GMT Tillmann Crueger [41182a] * .gitignore (modified) * Makefile.am (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/info.cpp (added) * molecuilder/src/info.hpp (added) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_pointcloud.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/infounittest.cpp (added) * molecuilder/src/unittests/infounittest.hpp (added) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * molecuilder/tests/Tesselations/1_2-dimethoxyethane/NonConvexEnvelope-1_2-dimethoxyethane.dat (modified) * molecuilder/tests/Tesselations/1_2-dimethylbenzene/NonConvexEnvelope-1_2-dimethylbenzene.dat (modified) * molecuilder/tests/Tesselations/2-methylcyclohexanone/NonConvexEnvelope-2-methylcyclohexanone.dat (modified) * molecuilder/tests/Tesselations/C16_0-Torus/NonConvexEnvelope-C16_0-Torus.dat (modified) * molecuilder/tests/Tesselations/Makefile.am (modified) * molecuilder/tests/Tesselations/N_N-dimethylacetamide/NonConvexEnvelope-N_N-dimethylacetamide.dat (modified) * molecuilder/tests/Tesselations/benzene.test (added) * molecuilder/tests/Tesselations/benzene/NonConvexEnvelope-benzene.dat (added) * molecuilder/tests/Tesselations/benzene/benzene.xyz (added) * molecuilder/tests/Tesselations/cholesterol/NonConvexEnvelope-cholesterol.dat (modified) * molecuilder/tests/Tesselations/cluster/NonConvexEnvelope-cluster.dat (modified) * molecuilder/tests/Tesselations/cycloheptane/NonConvexEnvelope-cycloheptane.dat (modified) * molecuilder/tests/Tesselations/defs.in (modified) * molecuilder/tests/Tesselations/dimethyl_bromomalonate/NonConvexEnvelope-dimethyl_bromomalonate.dat (modified) * molecuilder/tests/Tesselations/glucose/NonConvexEnvelope-glucose.dat (modified) * molecuilder/tests/Tesselations/heptan/NonConvexEnvelope-heptan.dat (modified) * molecuilder/tests/Tesselations/isoleucine/NonConvexEnvelope-isoleucine.dat (modified) * molecuilder/tests/Tesselations/neohexane/NonConvexEnvelope-neohexane.dat (modified) * molecuilder/tests/Tesselations/proline/NonConvexEnvelope-proline.dat (modified) * molecuilder/tests/Tesselations/putrescine/NonConvexEnvelope-putrescine.dat (modified) * molecuilder/tests/Tesselations/round_cluster/NonConvexEnvelope-round_cluster.dat (modified) * molecuilder/tests/Tesselations/tartaric_acid/NonConvexEnvelope-tartaric_acid.dat (modified) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/testsuite.at (modified) * pcp/src/Makefile.am (modified) * pcp/src/pcp.c (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/ReadSrcIon.c (modified) * util/src/VibrAlyzer.c (modified) * util/src/average.cpp (modified) * util/src/diagonalize.c (modified) * util/src/stochastik.cpp (modified) Merge commit 'heber/Analysis_PairCorrelation' into MenuRefactoring ... Sun, 10 Jan 2010 19:05:34 GMT Frederik Heber [e6fe8a] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * molecuilder/src/unittests/analysisbondsunittest.cpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (modified) * molecuilder/src/unittests/tesselation_insideoutsideunittest.cpp (modified) * molecuilder/src/unittests/tesselationunittest.cpp (modified) cstring header was missing in files, supplying definition of strlen, ... Sat, 02 Jan 2010 15:49:40 GMT Tillmann Crueger [f48622] * molecuilder/src/menu.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) Moved several Methods from Menu to MoleculeListClass Tue, 29 Dec 2009 11:57:09 GMT Tillmann Crueger [fab853] * molecuilder/src/menu.cpp (modified) * molecuilder/src/menu.hpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) Moved flipChosen method from oldmenu to MoleculeListClass Wed, 16 Dec 2009 16:18:46 GMT Frederik Heber [281324] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/testsuite.at (modified) Merge branch 'FixTestSuite' into FixDegeneratedTesselation Wed, 16 Dec 2009 16:17:50 GMT Frederik Heber [16f34d] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) * molecuilder/tests/testsuite.at (modified) Fixing the testsuite. - Putting performCriticalExit() everywhere ... Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber [2309fa] * molecuilder/src/Menu/DisplayMenuItem.cpp (modified) * molecuilder/src/Menu/DisplayMenuItem.hpp (modified) * molecuilder/src/menu.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) Added Title to DisplayMenuItems. Signed-off-by: Tillmann Crueger ... Tue, 24 Nov 2009 15:34:49 GMT Frederik Heber [cc9225] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_pointcloud.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/tests/Tesselations/1_2-dimethoxyethane/NonConvexEnvelope-1_2-dimethoxyethane.dat (modified) * molecuilder/tests/Tesselations/1_2-dimethylbenzene/NonConvexEnvelope-1_2-dimethylbenzene.dat (modified) * molecuilder/tests/Tesselations/2-methylcyclohexanone/NonConvexEnvelope-2-methylcyclohexanone.dat (modified) * molecuilder/tests/Tesselations/C16_0-Torus/NonConvexEnvelope-C16_0-Torus.dat (modified) * molecuilder/tests/Tesselations/Makefile.am (modified) * molecuilder/tests/Tesselations/N_N-dimethylacetamide/NonConvexEnvelope-N_N-dimethylacetamide.dat (modified) * molecuilder/tests/Tesselations/benzene.test (added) * molecuilder/tests/Tesselations/benzene/NonConvexEnvelope-benzene.dat (added) * molecuilder/tests/Tesselations/benzene/benzene.xyz (added) * molecuilder/tests/Tesselations/cholesterol/NonConvexEnvelope-cholesterol.dat (modified) * molecuilder/tests/Tesselations/cluster/NonConvexEnvelope-cluster.dat (modified) * molecuilder/tests/Tesselations/cycloheptane/NonConvexEnvelope-cycloheptane.dat (modified) * molecuilder/tests/Tesselations/dimethyl_bromomalonate/NonConvexEnvelope-dimethyl_bromomalonate.dat (modified) * molecuilder/tests/Tesselations/glucose/NonConvexEnvelope-glucose.dat (modified) * molecuilder/tests/Tesselations/heptan/NonConvexEnvelope-heptan.dat (modified) * molecuilder/tests/Tesselations/isoleucine/NonConvexEnvelope-isoleucine.dat (modified) * molecuilder/tests/Tesselations/neohexane/NonConvexEnvelope-neohexane.dat (modified) * molecuilder/tests/Tesselations/proline/NonConvexEnvelope-proline.dat (modified) * molecuilder/tests/Tesselations/putrescine/NonConvexEnvelope-putrescine.dat (modified) * molecuilder/tests/Tesselations/round_cluster/NonConvexEnvelope-round_cluster.dat (modified) * molecuilder/tests/Tesselations/tartaric_acid/NonConvexEnvelope-tartaric_acid.dat (modified) Fixes and naming of final Tecplot output file is now molecule name. ... Mon, 23 Nov 2009 18:51:50 GMT Frederik Heber [3d4969] * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) Fixing ticket #18. - each eLog() << Verbose(0) is now followed by ... Mon, 23 Nov 2009 18:22:33 GMT Frederik Heber [418117a] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_graphnode.cpp (modified) * molecuilder/src/atom_trajectoryparticle.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/vector.cpp (modified) Verbosity corrected for ERROR and WARNING - present ERROR and ... Sat, 07 Nov 2009 12:16:57 GMT Frederik Heber [486aa5] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) Added config::SavePDB() and config::SaveMPQC(). - note: for CODICE ... Wed, 04 Nov 2009 19:56:04 GMT Frederik Heber [543ce4] * molecuilder/src/Makefile.am (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_bondedparticle.hpp (modified) * molecuilder/src/atom_graphnode.cpp (modified) * molecuilder/src/atom_graphnode.hpp (modified) * molecuilder/src/atom_trajectoryparticle.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/bondgraph.hpp (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/element.cpp (modified) * molecuilder/src/element.hpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/errorlogger.cpp (moved) * molecuilder/src/errorlogger.hpp (moved) * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/log.cpp (modified) * molecuilder/src/log.hpp (modified) * molecuilder/src/logger.cpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_pointcloud.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) * molecuilder/src/test/ActOnAlltest.hpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) * molecuilder/src/unittests/logunittest.cpp (modified) * molecuilder/src/unittests/memoryallocatorunittest.cpp (modified) * molecuilder/src/unittests/stackclassunittest.cpp (modified) * molecuilder/src/unittests/tesselationunittest.cpp (modified) * molecuilder/src/unittests/vectorunittest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) Huge change from ofstream * (const) out --> Log(). - first shift ... Wed, 04 Nov 2009 15:08:11 GMT Frederik Heber [c1b76e] * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) config::Load() refactored: Dissection into connected subgraphs -> ... Tue, 03 Nov 2009 14:34:02 GMT Frederik Heber [08b88b] * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/bondgraph.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) Fixing not created adjacency list, partially fixing subgraph ... Tue, 03 Nov 2009 12:37:55 GMT Frederik Heber [8bc524] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/unittests/memoryallocatorunittest.cpp (modified) Several memory bugfixes (thx valgrind). - main() - shortened case ... Mon, 02 Nov 2009 12:50:57 GMT Frederik Heber [df0520] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) Small changes. - VolumeOfConvexEnvelope() - setprecision corrected ... Tue, 27 Oct 2009 16:11:22 GMT Frederik Heber [a9b2a0a] * molecuilder/configure.ac (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/leastsquaremin.cpp (modified) * molecuilder/src/leastsquaremin.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_pointcloud.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Huge refactoring to make const what is const (ticket #38), continued. ... Sun, 18 Oct 2009 14:51:38 GMT Frederik Heber [872b51] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/lists.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/listofbondsunittest.cpp (added) * molecuilder/src/unittests/listofbondsunittest.hpp (added) Huge refactoring: molecule::ListOfBondsPerAtom and ... Fri, 09 Oct 2009 10:54:52 GMT Frederik Heber [17b3a5c] * molecuilder/src/ActOnAllUnitTest.cpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/element.hpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/leastsquaremin.cpp (modified) * molecuilder/src/leastsquaremin.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/lists.hpp (added) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_pointcloud.cpp (modified) * molecuilder/src/molecule_template.hpp (modified) * molecuilder/src/moleculelist.cpp (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/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) * molecuilder/src/tesselationunittest.hpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * molecuilder/src/verbose.hpp (modified) forward declarations used to untangle interdependet classes. - ... Mon, 05 Oct 2009 22:10:53 GMT Frederik Heber [f92d00] * molecuilder/src/Makefile.am (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/graph.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (added) * molecuilder/src/molecule_fragmentation.cpp (added) * molecuilder/src/molecule_geometry.cpp (added) * molecuilder/src/molecule_graph.cpp (added) * molecuilder/src/molecule_pointcloud.cpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/verbose.cpp (modified) class molecule implementation split up into six separate parts. - ... Mon, 05 Oct 2009 16:05:53 GMT Frederik Heber [8afe31] * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/memoryallocator.hpp (added) * molecuilder/src/memoryallocatorunittest.cpp (added) * molecuilder/src/memoryallocatorunittest.hpp (added) * molecuilder/src/memoryusageobserver.cpp (added) * molecuilder/src/memoryusageobserver.hpp (added) * molecuilder/src/memoryusageobserverunittest.cpp (added) * molecuilder/src/memoryusageobserverunittest.hpp (added) * 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/tesselation.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vectorunittest.cpp (modified) * molecuilder/src/vectorunittest.hpp (modified) Merge branch 'ConcaveHull' into ConvexHull Conflicts: ... 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 ... Mon, 21 Sep 2009 11:48:42 GMT Saskia Metzler [390a2b] * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/memoryallocator.hpp (added) * molecuilder/src/memoryallocatorunittest.cpp (added) * molecuilder/src/memoryallocatorunittest.hpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/vector.cpp (modified) Ticket 11: use templates and/or traits to fix Malloc/ReAlloc-Free ... 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: ... 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 12:14:13 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 11:23:59 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 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 ... 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 16:12:54 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 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 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, 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 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, ... 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 13:36:06 GMT Frederik Heber [14178b] * molecuilder/src/moleculelist.cpp (modified) BUGFIX: AssignKeySetsToFragment() had FragmentCounter-- at wrong ... 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, 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(). ... Fri, 29 Aug 2008 10:39:17 GMT Frederik Heber [ff74f7] * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.hpp (modified) config::SaveMPQC() included in headers and used in ... 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 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. 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) ... Fri, 20 Jun 2008 07:08:31 GMT Frederik Heber [b73d28] * molecuilder/src/moleculelist.cpp (modified) OutputConfigForListOfFragments(): boundary is now 2.5 Angstroem ... 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 ... Fri, 30 May 2008 13:51:53 GMT Frederik Heber [eefb8e] * molecuilder/src/moleculelist.cpp (modified) OutputConfigForListOfFragments(): return of ... Mon, 26 May 2008 13:22:10 GMT Frederik Heber [5063f1] * molecuilder/src/moleculelist.cpp (modified) bit more verbosity on the FragmentNumber 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 ... Fri, 09 May 2008 13:49:57 GMT Frederik Heber [2700f5e] * molecuilder/src/moleculelist.cpp (modified) TranslateIndicesToGlobalIDs() did not check whether FragmentList[..] ... 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 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 15:22:41 GMT Frederik Heber [84e88a] * molecuilder/src/moleculelist.cpp (modified) new function FillListOfLocalAtoms() checks whether List needs filling ... Thu, 08 May 2008 12:41:47 GMT Frederik Heber [255d13] * molecuilder/src/moleculelist.cpp (modified) FillBondStructureFromReference: previous == NULL was bad idea, new ... Thu, 08 May 2008 12:02:43 GMT Frederik Heber [b8eb3a] * molecuilder/src/moleculelist.cpp (modified) new function MoleculeLeafClass::FillBondStructureFromReference that ... 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 13:25:48 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 07:04:59 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 13:46:05 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 11:36:11 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 07:16:42 GMT Frederik Heber [23409a] * molecuilder/src/moleculelist.cpp (modified) OutputConfigForListOfFragments(): various ofstream gathered into a ... Fri, 18 Apr 2008 11:26:42 GMT Frederik Heber [a0bcf1] * AUTHORS (added) * COPYING (added) * ChangeLog (added) * Makefile.am (added) * NEWS (added) * README (added) * autogen.sh (added) * configure.ac (added) * molecuilder/AUTHORS (added) * molecuilder/ChangeLog (added) * molecuilder/Makefile.am (added) * molecuilder/NEWS (added) * molecuilder/README (added) * molecuilder/autogen.sh (added) * molecuilder/configure.ac (added) * molecuilder/doc/Doxyfile (added) * molecuilder/doc/Makefile.am (added) * molecuilder/m4/ac_doxygen.m4 (added) * molecuilder/src/Hbondangle.db (added) * molecuilder/src/Hbonddistance.db (added) * molecuilder/src/Makefile.am (added) * molecuilder/src/analyzer.cpp (added) * molecuilder/src/atom.cpp (added) * molecuilder/src/bond.cpp (added) * molecuilder/src/builder.cpp (added) * molecuilder/src/config.cpp (added) * molecuilder/src/datacreator.cpp (added) * molecuilder/src/datacreator.hpp (added) * molecuilder/src/defs.hpp (added) * molecuilder/src/element.cpp (added) * molecuilder/src/elements.db (added) * molecuilder/src/graph.cpp (added) * molecuilder/src/helpers.cpp (added) * molecuilder/src/helpers.hpp (added) * molecuilder/src/joiner.cpp (added) * molecuilder/src/moleculelist.cpp (added) * molecuilder/src/molecules.cpp (added) * molecuilder/src/molecules.hpp (added) * molecuilder/src/orbitals.db (added) * molecuilder/src/parser.cpp (added) * molecuilder/src/parser.hpp (added) * molecuilder/src/periodentafel.cpp (added) * molecuilder/src/valence.db (added) * molecuilder/src/vector.cpp (added) * molecuilder/src/verbose.cpp (added) * pcp/AUTHORS (added) * pcp/CHANGES (added) * pcp/ChangeLog (added) * pcp/Makefile.am (added) * pcp/NEWS (added) * pcp/README (added) * pcp/autogen.sh (added) * pcp/configure.ac (added) * pcp/doc/Doxyfile (added) * pcp/doc/Makefile.am (added) * pcp/m4/ac_doxygen.m4 (added) * pcp/m4/acx_mpi.m4 (added) * pcp/src/Makefile.am (added) * pcp/src/Makefile.in (added) * pcp/src/data.h (added) * pcp/src/defs.h (added) * pcp/src/density.c (added) * pcp/src/density.h (added) * pcp/src/energy.c (added) * pcp/src/energy.h (added) * pcp/src/errors.c (added) * pcp/src/errors.h (added) * pcp/src/excor.c (added) * pcp/src/excor.h (added) * pcp/src/grad.c (added) * pcp/src/grad.h (added) * pcp/src/gramsch.c (added) * pcp/src/gramsch.h (added) * pcp/src/helpers.c (added) * pcp/src/helpers.h (added) * pcp/src/init.c (added) * pcp/src/init.h (added) * pcp/src/ions.c (added) * pcp/src/ions.h (added) * pcp/src/mergesort2.c (added) * pcp/src/mergesort2.h (added) * pcp/src/myfft.c (added) * pcp/src/myfft.h (added) * pcp/src/mymath.c (added) * pcp/src/mymath.h (added) * pcp/src/opt.c (added) * pcp/src/opt.h (added) * pcp/src/output.c (added) * pcp/src/output.h (added) * pcp/src/parsetest.c (added) * pcp/src/pcp.c (added) * pcp/src/pcp.h (added) * pcp/src/pdbformat.c (added) * pcp/src/pdbformat.h (added) * pcp/src/perturbed.c (added) * pcp/src/perturbed.h (added) * pcp/src/pseudo.c (added) * pcp/src/pseudo.h (added) * pcp/src/riemann.c (added) * pcp/src/riemann.h (added) * pcp/src/run.c (added) * pcp/src/run.h (added) * pcp/src/test.c (added) * pcp/src/wannier.c (added) * pcp/src/wannier.h (added) * util/AUTHORS (added) * util/BOSSEvaluate.pl.in (added) * util/ChangeLog (added) * util/CreateFromXYZ.sh (added) * util/CreateGaAs.c (added) * util/CreateH2.c (added) * util/GetPdb.c (added) * util/Makefile.am (added) * util/NEWS (added) * util/NanoCreator.c (added) * util/NanoCreator.h (added) * util/Nanotubes.pl.in (added) * util/README (added) * util/ReSequenceDX.pl.in (added) * util/ReadSrcIon.c (added) * util/VibrAlyzer.c (added) * util/autogen.sh (added) * util/average.cpp (added) * util/average_result.sh (added) * util/compile (added) * util/config2xyz.sh (added) * util/configure.ac (added) * util/convert2old.sh (added) * util/convertpdb.sh (added) * util/depcomp (added) * util/doc/Doxyfile (added) * util/doc/Makefile.am (added) * util/gather_all_results.sh (added) * util/gather_averaged_results.sh (added) * util/gather_result.sh (added) * util/grep_shielding.sh (added) * util/install-sh (added) * util/m4/ac_doxygen.m4 (added) * util/meas2pdb.sh (added) * util/mergesort.c (added) * util/mergesort.h (added) * util/specvisual.cfg (added) * util/specvisual.net (added) * util/specvisualOnly.net (added) * util/stochastik.cpp (added) * util/suffix (added) * util/visual.cfg (added) * util/visual.net (added) * util/visualOnly.net (added) -initial commit -Minimum set of files needed from ESPACK SVN ...