# # ChangeLog for molecuilder/src/builder.cpp # # Generated by Trac 1.6 # Sep 22, 2025, 11:39:01 AM Thu, 18 Feb 2010 10:59:29 GMT Tillmann Crueger [b53a7e] * molecuilder/src/Actions/Process.cpp (added) * molecuilder/src/Actions/Process.hpp (added) * molecuilder/src/Actions/small_actions.hpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/World.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.hpp (modified) Added a special class of Actions that take some time. Tue, 16 Feb 2010 17:26:59 GMT Tillmann Crueger [120f8b] * molecuilder/src/World.cpp (modified) * molecuilder/src/World.hpp (modified) * molecuilder/src/builder.cpp (modified) Moved control of molecules and periode to World. Tue, 02 Feb 2010 12:22:06 GMT Tillmann Crueger [4bb871a] * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_bondedparticle.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * util/src/NanoCreator.c (modified) * util/src/NanoCreator.h (modified) Merge commit 'heber/Analysis_PairCorrelation' into MenuRefactoring 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 09:43:52 GMT Frederik Heber [6d0fcaa] * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_bondedparticle.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) Possibility to store all bonds to file added. So far we only could ... Sat, 30 Jan 2010 17:35:48 GMT Frederik Heber [8d0b25] * molecuilder/src/builder.cpp (modified) Added output of surfacemap in ParseCommandLineOptions(), case 'C' again. 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 ... Thu, 14 Jan 2010 17:36:09 GMT Frederik Heber [1aa2a5] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) FillBoxWithMolecule now allows boundary between filler molecules and ... Wed, 13 Jan 2010 10:22:29 GMT Tillmann Crueger [f89c1c] * molecuilder/src/UIElements/Dialog.cpp (modified) * molecuilder/src/UIElements/Dialog.hpp (modified) * molecuilder/src/UIElements/TextDialog.cpp (modified) * molecuilder/src/UIElements/TextDialog.hpp (modified) * molecuilder/src/builder.cpp (modified) Changed dialog structure to use objects for queries. Mon, 11 Jan 2010 09:35:52 GMT Frederik Heber [afa056] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Removed unnecessary epsilon parameter. - epsilon before was used as ... 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, 09 Jan 2010 11:30:49 GMT Tillmann Crueger [d97af9] * molecuilder/src/Actions/ActionRegistry.cpp (modified) * molecuilder/src/UIElements/MainWindow.hpp (modified) * molecuilder/src/UIElements/TextUIFactory.cpp (modified) * molecuilder/src/UIElements/TextUIFactory.hpp (modified) * molecuilder/src/UIElements/TextWindow.cpp (modified) * molecuilder/src/UIElements/TextWindow.hpp (modified) * molecuilder/src/UIElements/UIFactory.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/menu.cpp (modified) * molecuilder/src/menu.hpp (modified) Seperated building of mainWindow and contained Menus - Moved code ... Thu, 07 Jan 2010 14:46:34 GMT Tillmann Crueger [3e8325] * molecuilder/src/Actions/Action.cpp (modified) * molecuilder/src/Actions/Action.hpp (modified) * molecuilder/src/Actions/ActionRegistry.cpp (added) * molecuilder/src/Actions/ActionRegistry.hpp (added) * molecuilder/src/Actions/ErrorAction.cpp (modified) * molecuilder/src/Actions/ErrorAction.hpp (modified) * molecuilder/src/Actions/MakroAction.cpp (modified) * molecuilder/src/Actions/MakroAction.hpp (modified) * molecuilder/src/Actions/MethodAction.cpp (modified) * molecuilder/src/Actions/MethodAction.hpp (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/UIElements/TextUIFactory.cpp (modified) * molecuilder/src/UIElements/TextUIFactory.hpp (modified) * molecuilder/src/UIElements/TextWindow.cpp (modified) * molecuilder/src/UIElements/UIFactory.cpp (modified) * molecuilder/src/UIElements/UIFactory.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/menu.cpp (modified) * molecuilder/src/unittests/ActionSequenceTest.cpp (modified) Added a central registry that allows access to actions by name. Tue, 05 Jan 2010 09:23:25 GMT Tillmann Crueger [538744] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/menu.cpp (modified) * molecuilder/src/menu.hpp (modified) Moved saveConfig method from oldmenu to a method inside config class Sat, 19 Dec 2009 19:31:34 GMT Frederik Heber [f78203] * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) Smaller fixes. - analysis_correlation.cpp: Info objects created at ... 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 [d20ed5] * molecuilder/src/Actions/Action.cpp (added) * molecuilder/src/Actions/Action.hpp (added) * molecuilder/src/Actions/MethodAction.cpp (added) * molecuilder/src/Actions/MethodAction.hpp (added) * molecuilder/src/Makefile.am (modified) * molecuilder/src/Menu/ActionMenuItem.cpp (added) * molecuilder/src/Menu/ActionMenuItem.hpp (added) * molecuilder/src/Menu/Menu.cpp (added) * molecuilder/src/Menu/Menu.hpp (added) * molecuilder/src/Menu/MenuItem.cpp (added) * molecuilder/src/Menu/MenuItem.hpp (added) * molecuilder/src/Menu/SeperatorItem.cpp (added) * molecuilder/src/Menu/SeperatorItem.hpp (added) * molecuilder/src/Menu/SubMenuItem.cpp (added) * molecuilder/src/Menu/SubMenuItem.hpp (added) * molecuilder/src/Menu/TextMenu.cpp (added) * molecuilder/src/Menu/TextMenu.hpp (added) * molecuilder/src/builder.cpp (modified) * molecuilder/src/menu.cpp (modified) * molecuilder/src/menu.hpp (modified) Added basic menu and action framework - Added action base class - ... Wed, 16 Dec 2009 12:30:16 GMT Frederik Heber [7df43b] * molecuilder/doc/Doxyfile (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/menu.cpp (added) * molecuilder/src/menu.hpp (added) Started refactoring of the menu. - Created new menu class - moved all ... Wed, 16 Dec 2009 11:47:47 GMT Frederik Heber [ef87ee] * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (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) Added versioning to each executable. - credits to Ralf Wildenhues ... Thu, 26 Nov 2009 11:40:01 GMT Frederik Heber [a68d44] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/tests/Tesselations/defs.in (added) removing automatic dissection on loading, Tesselations test now ... Wed, 25 Nov 2009 15:29:18 GMT Frederik Heber [be2997] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) Multi-Candidate-Add included and incorporated class Info into ... 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 ... Tue, 10 Nov 2009 20:58:31 GMT Frederik Heber [2fbbc96] * molecuilder/src/builder.cpp (modified) Only biggest molecule is tesselated for now in ... 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 ... Thu, 05 Nov 2009 18:14:08 GMT Frederik Heber [4ef101] * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) LEAKFIX: ReturnFullMatrixForSymmetric() and InverseMatrix() have ... 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 18:15:10 GMT Frederik Heber [5f1d021] * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/vector.cpp (modified) Periodic variants of AnalysisPair...() implemented. - BUGFIX: ... Wed, 04 Nov 2009 14:54:31 GMT Frederik Heber [e1900f] * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) Closed ticket #48 (AnalysisCorrelation...() take MoleculeListClass ... Wed, 04 Nov 2009 12:57:24 GMT Frederik Heber [a3ffb44] * molecuilder/src/builder.cpp (modified) Closing ticket #47, case 'C' uses biggest molecule as surface for ... 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 ... Fri, 30 Oct 2009 16:09:29 GMT Frederik Heber [245826] * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) BondGraph is initialized within config::Load(), as it has to happen ... Fri, 30 Oct 2009 15:49:38 GMT Frederik Heber [b84ab4] * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (modified) BondGraph is parsed if command line switch '-g' is given. - ... Fri, 30 Oct 2009 09:05:30 GMT Frederik Heber [5f697c] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom_bondedparticle.cpp (modified) * molecuilder/src/atom_bondedparticle.hpp (modified) * molecuilder/src/bondgraph.cpp (added) * molecuilder/src/bondgraph.hpp (added) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/unittests/Makefile.am (modified) * molecuilder/src/unittests/bondgraphunittest.cpp (added) * molecuilder/src/unittests/bondgraphunittest.hpp (added) New class BondGraph. - BondGraph parses a file containing bond ... 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 ... Sat, 17 Oct 2009 17:06:42 GMT Frederik Heber [bee48d] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) Renamed and rewritten CreateAdjacencyList2(). - rename ... Sat, 17 Oct 2009 16:54:46 GMT Frederik Heber [d70bf6] * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/builder.cpp (modified) Added case 'C' to ParseCommandLineOptions with ... Thu, 15 Oct 2009 08:10:10 GMT Frederik Heber [746bb4] * molecuilder/src/builder.cpp (modified) * molecuilder/src/periodentafel.cpp (modified) Fixed two memory leaks. - FIX: if the element database could not be ... Fri, 09 Oct 2009 12:30:54 GMT Frederik Heber [e71890] * molecuilder/Makefile.am (modified) * molecuilder/configure.ac (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/memoryusageobserver.hpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (moved) * molecuilder/src/unittests/ActOnAllUnitTest.hpp (moved) * molecuilder/src/unittests/ActOnAlltest.hpp (moved) * molecuilder/src/unittests/Makefile.am (added) * molecuilder/src/unittests/memoryallocatorunittest.cpp (moved) * molecuilder/src/unittests/memoryallocatorunittest.hpp (moved) * molecuilder/src/unittests/memoryusageobserverunittest.cpp (moved) * molecuilder/src/unittests/memoryusageobserverunittest.hpp (moved) * molecuilder/src/unittests/tesselationunittest.cpp (moved) * molecuilder/src/unittests/tesselationunittest.hpp (moved) * molecuilder/src/unittests/vectorunittest.cpp (moved) * molecuilder/src/unittests/vectorunittest.hpp (moved) Merge branch 'new-delete-conversion' into CodeRefactoring ... 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. - ... Wed, 07 Oct 2009 15:04:23 GMT Saskia Metzler [53f32e] * molecuilder/configure.ac (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/unittests/Makefile.am (added) * molecuilder/src/unittests/memoryallocatorunittest.cpp (moved) * molecuilder/src/unittests/memoryallocatorunittest.hpp (moved) * molecuilder/src/unittests/memoryusageobserverunittest.cpp (moved) * molecuilder/src/unittests/memoryusageobserverunittest.hpp (moved) * molecuilder/src/unittests/tesselationunittest.cpp (moved) * molecuilder/src/unittests/tesselationunittest.hpp (moved) * molecuilder/src/unittests/vectorunittest.cpp (moved) * molecuilder/src/unittests/vectorunittest.hpp (moved) temp commit Tue, 06 Oct 2009 17:56:15 GMT Frederik Heber [a4644b] * molecuilder/src/builder.cpp (modified) * molecuilder/tests/Makefile.am (modified) * molecuilder/tests/regression/Fragmentation/1/pre/test.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment0.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment0.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment1.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment1.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment2.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment2.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment3.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment3.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment4.conf (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragment4.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragmentAdjacency.dat (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragmentForces-Factors.dat (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragmentKeySets.dat (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragmentOrderAtSite.dat (added) * molecuilder/tests/regression/Fragmentation/2/post/BondFragmentTE-Factors.dat (added) * molecuilder/tests/regression/Fragmentation/2/post/test.conf (added) * molecuilder/tests/regression/Fragmentation/2/pre/test.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment0.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment0.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment1.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment1.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment2.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment2.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment3.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment3.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment4.conf (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragment4.conf.xyz (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragmentAdjacency.dat (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragmentForces-Factors.dat (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragmentKeySets.dat (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragmentOrderAtSite.dat (added) * molecuilder/tests/regression/Fragmentation/3/pre/BondFragmentTE-Factors.dat (added) * molecuilder/tests/regression/Fragmentation/3/pre/test.conf (added) * molecuilder/tests/regression/Graph/1/post/test.conf (added) * molecuilder/tests/regression/Graph/1/pre/test.conf (added) * molecuilder/tests/regression/Simple_configuration/1/post/test.xyz (added) * molecuilder/tests/regression/Simple_configuration/2/post/test.conf (added) * molecuilder/tests/regression/Simple_configuration/2/post/test.conf.xyz (added) * molecuilder/tests/regression/Simple_configuration/2/pre/test.xyz (added) * molecuilder/tests/regression/Simple_configuration/3/post/test.conf (added) * molecuilder/tests/regression/Simple_configuration/3/post/test.conf.xyz (added) * molecuilder/tests/regression/Simple_configuration/4/post/test.conf (added) * molecuilder/tests/regression/Simple_configuration/4/post/test.conf.xyz (added) * molecuilder/tests/regression/Simple_configuration/4/pre/test.conf (added) * molecuilder/tests/regression/Simple_configuration/5/post/test.conf (added) * molecuilder/tests/regression/Simple_configuration/5/post/test.conf.xyz (added) * molecuilder/tests/regression/Simple_configuration/5/pre/test.conf (added) * molecuilder/tests/regression/Simple_configuration/6/pre/empty.conf (added) * molecuilder/tests/regression/Simple_configuration/7/pre/test.conf (added) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (added) * molecuilder/tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (added) * molecuilder/tests/regression/Tesselation/1/post/test.conf (added) * molecuilder/tests/regression/Tesselation/1/pre/test.conf (added) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.dat (added) * molecuilder/tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (added) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (added) * molecuilder/tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (added) * molecuilder/tests/regression/Tesselation/2/post/test.conf (added) * molecuilder/tests/regression/Tesselation/2/pre/test.conf (added) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (added) * molecuilder/tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (added) * molecuilder/tests/regression/Tesselation/3/post/tecplot.phy (added) * molecuilder/tests/regression/Tesselation/3/post/test.conf (added) * molecuilder/tests/regression/Tesselation/3/pre/test.conf (added) * molecuilder/tests/regression/Tesselation/4/post/NonConvexEnvelope.dat (added) * molecuilder/tests/regression/Tesselation/4/post/NonConvexEnvelope.r3d (added) * molecuilder/tests/regression/Tesselation/4/post/test.conf (added) * molecuilder/tests/regression/Tesselation/4/pre/test.conf (added) * molecuilder/tests/testsuite.at (modified) Extended the testsuite to encompass the vital areas of molecuilder. ... 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 17:21:58 GMT Frederik Heber [58808e] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (modified) * molecuilder/src/memoryusageobserver.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationunittest.cpp (modified) * molecuilder/tests/testsuite.at (modified) Fixed testsuite, removed some minor bugs. - ... 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, 05 Oct 2009 14:50:43 GMT metzler [39d983] * molecuilder/src/Makefile.am (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/memoryallocator.hpp (modified) * molecuilder/src/memoryusageobserver.cpp (added) * molecuilder/src/memoryusageobserver.hpp (added) * molecuilder/src/memoryusageobserverunittest.cpp (added) * molecuilder/src/memoryusageobserverunittest.hpp (added) #19 Observe memory usage Mon, 28 Sep 2009 18:41:52 GMT Frederik Heber [606dfb] * molecuilder/src/builder.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Implemenation of embedding merge, untested. LinearInterpolation now ... Fri, 21 Aug 2009 12:17:52 GMT Frederik Heber [8b7e0a] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) New function RemoveAllBoundaryPoints() for sequentially removing all ... Thu, 20 Aug 2009 07:48:07 GMT Frederik Heber [84b811] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) Merge branch 'ConcaveHull' of ... Wed, 19 Aug 2009 12:22:08 GMT Frederik Heber [66ce7a] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) Replaced Vector::Projection() by Vector::ScalarProduct() - ... Mon, 17 Aug 2009 13:20:16 GMT Saskia Metzler [48cd93] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) Ticket 14: Rename .._.. functions in boundary.cpp Mon, 17 Aug 2009 10:29:03 GMT Frederik Heber [844cf5] * molecuilder/src/builder.cpp (modified) Sorted the menu list in ParseCommandLineParamaters() and print volume ... Mon, 10 Aug 2009 16:11:47 GMT Frederik Heber [70c4567] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) New function ConvexizeNonconvexEnvelope() to calculate the volume of ... Sat, 08 Aug 2009 19:22:28 GMT Frederik Heber [51abbe] * molecuilder/src/builder.cpp (modified) ParseCommandLineOptions(), NonConvex tesselation is now clocked. Fri, 07 Aug 2009 09:13:21 GMT Frederik Heber [0fc0b5] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) Test case of filling a simulation domain with water included. Tue, 04 Aug 2009 13:55:11 GMT Frederik Heber [d93bb24] * molecuilder/src/builder.cpp (modified) FillWithMolecule() for testing built into ParseCommandLine() Mon, 03 Aug 2009 14:48:42 GMT Frederik Heber [834ff3] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (added) * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (added) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (added) * molecuilder/src/tesselation.hpp (added) * molecuilder/src/tesselationhelpers.cpp (added) * molecuilder/src/tesselationhelpers.hpp (added) * molecuilder/src/vector.hpp (modified) Huge refactoring of Tesselation routines, but not finished yet. - ... Mon, 03 Aug 2009 08:10:09 GMT Frederik Heber [4e4940] * molecuilder/src/Makefile.am (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) We are one step further in fixing the convex hull: There are two ... Tue, 28 Jul 2009 10:33:53 GMT Frederik Heber [78b45a] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) ConvexTesselation working again. - File was not written, as NULL ... Mon, 27 Jul 2009 14:08:27 GMT Frederik Heber [a0fb02] * molecuilder/src/builder.cpp (modified) BUGFIX: ManipulateAtoms() had mol = NULL - in ManipulateAtoms() the ... Mon, 27 Jul 2009 08:16:03 GMT Frederik Heber [53d153] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) Split VolumeOfConvexEnvelope() into find_convex_border() and ... Fri, 24 Jul 2009 10:38:32 GMT Frederik Heber [c3a303] * .gitignore (modified) * Makefile.am (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/graph.cpp (modified) * molecuilder/src/graph.hpp (added) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * pcp/Makefile.am (modified) * util/src/CalculateDensity.sh.in (modified) * util/src/CalculateMass.sh.in (modified) * util/src/average.cpp (modified) * util/src/dynamicANOVA.sh.in (modified) Merge branch 'master' into ConcaveHull Conflicts: ... Thu, 23 Jul 2009 14:21:57 GMT Frederik Heber [a048fa] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) fixed indentation from tabs to two spaces. Thu, 23 Jul 2009 14:04:47 GMT Frederik Heber [47548d] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * util/src/CalculateDensity.sh.in (modified) * util/src/CalculateMass.sh.in (modified) Merge branch 'AtomRemoval' Conflicts: ... Thu, 23 Jul 2009 13:53:01 GMT Frederik Heber [1f6efb] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) fixed indentation from tabs to two spaces. Thu, 23 Jul 2009 13:45:24 GMT Frederik Heber [f39735] * .gitignore (modified) * molecuilder/src/#border.cpp# (deleted) * molecuilder/src/#makefile# (deleted) * molecuilder/src/#molecules.hpp# (deleted) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/ellipsoid.cpp (added) * molecuilder/src/ellipsoid.hpp (added) * molecuilder/src/graph.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (added) * molecuilder/src/linkedcell.hpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * util/src/NanoCreator.c (modified) * util/src/NanoCreator.h (modified) Merge branch 'MultipleMolecules' Conflicts: ... Thu, 23 Jul 2009 12:32:48 GMT Frederik Heber [560995] * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/verbose.cpp (modified) Fix indentation from tabs to two spaces to prepare merging with ... Thu, 23 Jul 2009 12:14:13 GMT Frederik Heber [1b2aa1] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) Fix indentation from tab to two spaces. The trouble was caused at ... Thu, 23 Jul 2009 11:23:59 GMT Frederik Heber [3b470f] * .gitignore (modified) * Makefile.am (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * pcp/Makefile.am (modified) * util/src/average.cpp (modified) Merge branch 'Thermostat' Conflicts: .gitignore ... Fri, 10 Jul 2009 12:48:05 GMT Frederik Heber [6fb785] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) molecule::CenterInBox puts atoms now periodically into the given box, ... Thu, 09 Jul 2009 11:38:33 GMT Frederik Heber [ab7b5e7] * molecuilder/src/builder.cpp (modified) Memory leak fix: ParseCommandLineOptions() and main() free'd mol ... Thu, 09 Jul 2009 11:01:08 GMT Frederik Heber [bd86e8] * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) Changed the unsatisfactory PathToDatabases construct, removing ... Thu, 09 Jul 2009 10:31:05 GMT Frederik Heber [61e92a] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) Removed unneeded variables Tue, 07 Jul 2009 08:17:53 GMT Frederik Heber [d98327] * molecuilder/src/builder.cpp (modified) BUGFIX: LinkedCell list had to created with 2.*RADIUS of sphere ... Tue, 07 Jul 2009 08:11:47 GMT Frederik Heber [eeae5b] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) Cosmetical changes in Find_third_point_for_tesselation() and ... Fri, 03 Jul 2009 14:25:17 GMT Frederik Heber [ea9696] * molecuilder/src/builder.cpp (modified) Removing of atoms via command line possible -R switchs allows for ... Wed, 03 Jun 2009 16:16:37 GMT Frederik Heber [378e87] * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) BUGFIX: RemoveAtom() would remove the iterator, ... 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 ... 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 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 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(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) * 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) Just a temporary commit 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 ... 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 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 13:20:42 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, 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 ...