# # ChangeLog for / # # Generated by Trac 1.6 # May 24, 2025, 3:21:35 PM Wed, 02 Jun 2010 16:17:17 GMT Frederik Heber [e30ce8] * src/Actions/MapOfActions.cpp (modified) * src/Actions/MapOfActions.hpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (added) * src/Descriptors/MoleculePtrDescriptor.hpp (added) * src/Descriptors/MoleculePtrDescriptor_impl.hpp (added) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/builder.cpp (modified) Case 'd' is now handled by CommandLineUI (RepeatBoxAction). - ... Wed, 02 Jun 2010 14:40:30 GMT Frederik Heber [584a2a] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case '-O' is now handled by CommandLineUI (CenterOnEdgeAction). ... Wed, 02 Jun 2010 14:38:07 GMT Frederik Heber [116f37] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/builder.cpp (modified) Case '-c' is now handled by CommandLineUI. - BUGFIX: ... Wed, 02 Jun 2010 14:30:31 GMT Frederik Heber [accebe] * src/boundary.cpp (modified) * src/tesselation.cpp (modified) Fix of PrepareClustersInWater (at least it does not stumble over ... Wed, 02 Jun 2010 12:22:47 GMT Frederik Heber [7fd416] * src/analysis_correlation.cpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/moleculelist.cpp (modified) FIX: CorrelationToSurface() was broken. - DOCU: ... Wed, 02 Jun 2010 12:21:38 GMT Frederik Heber [6ef0a4] * src/molecule_pointcloud.cpp (modified) Removed Info objects from the small pointcloud implementation ... Wed, 02 Jun 2010 08:37:17 GMT Frederik Heber [98a8b4] * tests/regression/Analysis/1/post/bin_output.csv (modified) * tests/regression/Analysis/2/post/bin_output-10.csv (modified) * tests/regression/Analysis/2/post/bin_output-20.csv (modified) * tests/regression/Analysis/2/post/bin_output-5.csv (modified) * tests/regression/testsuite-analysis.at (modified) TESTFIX: Analysis/... no more diff of output.csv (nameing dependent) ... Tue, 01 Jun 2010 21:36:36 GMT Frederik Heber [009607e] * src/analysis_correlation.cpp (modified) * src/builder.cpp (modified) Small changes to ...Correlation...(). - Calling doCountAtoms on all ... Tue, 01 Jun 2010 21:36:22 GMT Frederik Heber [d51975] * src/boundary.cpp (modified) Small changes to FindConvexBorder(). Signed-off-by: Frederik Heber ... Tue, 01 Jun 2010 21:04:17 GMT Frederik Heber [e0aee2b] * src/boundary.cpp (modified) * tests/regression/Filling/1/post/test.conf (modified) Bugfix of FillBoxWithMolecule() and Testfix of Filling/1 - BUGFIX: ... Tue, 01 Jun 2010 20:25:36 GMT Frederik Heber [15b670] * src/molecule_geometry.cpp (modified) * src/tesselationhelpers.cpp (modified) * tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) Testfixes for Tesselations/1-3 and bugfixes for ... Tue, 01 Jun 2010 19:59:25 GMT Frederik Heber [0de7e8] * src/helpers.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * tests/regression/testsuite-fragmentation.at (modified) FIX: Test Fragmentation is at MaxOrder was broken. - BUGFIX: ... Tue, 01 Jun 2010 08:02:48 GMT Frederik Heber [acf800] * src/molecule_graph.cpp (modified) * tests/regression/Molecules/2/post/test.adj (modified) * tests/regression/Molecules/2/post/test.dbond (modified) * tests/regression/Molecules/2/pre/test.conf (modified) TESTFIX: Wrong (old) ordering of conf files (IonTyp2 before IonType1) ... Tue, 01 Jun 2010 07:28:15 GMT Frederik Heber [bd6bfa] * src/bondgraph.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * tests/regression/Molecules/6/post/test.conf (modified) * tests/regression/Molecules/7/post/test.conf (modified) Fixes after first,last removal. - BUGFIX: ... Mon, 31 May 2010 19:46:59 GMT Frederik Heber [1b9321] * tests/regression/Domain/6/post/test.conf.xyz (added) Added missing test.conf.xyz for Domain/6. Signed-off-by: Frederik ... Mon, 31 May 2010 18:41:12 GMT Frederik Heber [e08c46] * src/Legacy/oldmenu.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) Removed molecule::first, molecule::last. - molecule does not have a ... Mon, 31 May 2010 17:32:27 GMT Frederik Heber [1024cb] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Helpers/Assert.cpp (modified) * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedIterator.hpp (added) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/Plane.cpp (modified) * src/Plane.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/lists.cpp (deleted) * src/lists.hpp (modified) * src/memoryallocator.cpp (added) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/listofbondsunittest.hpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * tests/regression/Domain/5/post/test.conf (modified) * tests/regression/Domain/5/pre/test.conf (modified) * tests/regression/Domain/6/post/test-x.conf (deleted) * tests/regression/Domain/6/post/test-x.conf.xyz (added) * tests/regression/Domain/6/post/test-y.conf (deleted) * tests/regression/Domain/6/post/test-y.conf.xyz (added) * tests/regression/Domain/6/post/test-z.conf (deleted) * tests/regression/Domain/6/post/test-z.conf.xyz (added) * tests/regression/Domain/6/post/test.conf (deleted) * tests/regression/Domain/6/pre/test.conf (modified) * tests/regression/Simple_configuration/8/post/test.conf (deleted) * tests/regression/Simple_configuration/8/post/test.conf.xyz (added) * tests/regression/testsuite-domain.at (modified) * tests/regression/testsuite-simple_configuration.at (modified) Merge commit 'jupiter/MoleculeStartEndSwitch' into ... Mon, 31 May 2010 14:33:11 GMT Frederik Heber [42af9e] * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/periodentafel.cpp (modified) * tests/regression/testsuite-simple_configuration.at (modified) MEMFIXES: no more default saving/loading of element's db, ... Mon, 31 May 2010 13:09:58 GMT Frederik Heber [920c70] * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) * src/Makefile.am (modified) * src/analysis_correlation.cpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom_graphnodeinfo.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/stackclass.hpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) Removed all Malloc/Calloc/ReAlloc (&Free) and replaced by new and ... Mon, 31 May 2010 08:34:52 GMT Frederik Heber [87b597] * tests/regression/testsuite-analysis.at (modified) TESTFIX: Removed diff of output.csv for surface correlation as this ... Mon, 31 May 2010 08:34:09 GMT Frederik Heber [5ddb8a] * tests/regression/Makefile.am (modified) * tests/regression/testsuite (deleted) Added out-sourced testsuite files to Makefile.am such that they are ... Sun, 30 May 2010 23:40:04 GMT Frederik Heber [158c594] * src/Actions/MapOfActions.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/builder.cpp (modified) Case '-b' now handled by CommandLineUI and fixes. - ... Sun, 30 May 2010 23:18:48 GMT Frederik Heber [2a92ff] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) Case '-s' now handled by CommandLineUI. - FIX: Type Vector has to ... Sun, 30 May 2010 23:03:49 GMT Frederik Heber [6ca1f7] * src/Actions/MapOfActions.cpp (modified) * src/builder.cpp (modified) case '-B' now handled by CommandLineUI. Sun, 30 May 2010 22:49:13 GMT Frederik Heber [26f75a] * src/Actions/MapOfActions.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/Dialog.cpp (modified) FIX: Box was not parsed correctly. - ListOf... types have to be ... Sun, 30 May 2010 20:55:12 GMT Frederik Heber [8c574b] * tests/regression/testsuite (added) * tests/regression/testsuite-analysis.at (added) * tests/regression/testsuite-domain.at (added) * tests/regression/testsuite-filling.at (added) * tests/regression/testsuite-fragmentation.at (added) * tests/regression/testsuite-graph.at (added) * tests/regression/testsuite-molecules.at (added) * tests/regression/testsuite-simple_configuration.at (added) * tests/regression/testsuite-specifics.at (added) * tests/regression/testsuite-standard_options.at (added) * tests/regression/testsuite-tesselation.at (added) * tests/regression/testsuite.at (modified) Split up testsuite into several at-scripts. - the testsuite has ... Sun, 30 May 2010 19:40:32 GMT Frederik Heber [afd01c] * tests/regression/Domain/6/post/test-x.conf (added) * tests/regression/Domain/6/post/test-y.conf (added) * tests/regression/Domain/6/post/test-z.conf (added) * tests/regression/Domain/6/post/test.conf (added) * tests/regression/Domain/6/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-d' (duplicate box) to testsuite. Sun, 30 May 2010 19:05:43 GMT Frederik Heber [746c57] * tests/regression/Filling/2/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-u' (suspend in water) to testsuite. - this is broken ... Sun, 30 May 2010 18:28:14 GMT Frederik Heber [d6d6c1] * tests/regression/Analysis/5/pre/test.conf (added) * tests/regression/Molecules/8/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-m' (principal axis system) to testsuite. Sun, 30 May 2010 17:31:15 GMT Frederik Heber [8048a4] * tests/regression/Domain/5/post/test.conf (added) * tests/regression/Domain/5/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-s' (scaling box) to testsuite. Sun, 30 May 2010 17:29:38 GMT Frederik Heber [eddea2] * src/molecule.hpp (modified) * src/molecule_geometry.cpp (modified) * src/vector.cpp (modified) * tests/regression/Molecules/7/post/test.conf (added) * tests/regression/Molecules/7/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-T' (periodic translation) to testsuite. - BUGFIX: ... Sun, 30 May 2010 16:55:04 GMT Frederik Heber [5d12d2] * tests/regression/Molecules/6/post/test.conf (added) * tests/regression/Molecules/6/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-t' (translation) to testsuite. Sun, 30 May 2010 16:51:45 GMT Frederik Heber [9b7db1] * src/builder.cpp (modified) * tests/regression/Simple_configuration/8/post/test.conf (added) * tests/regression/Simple_configuration/8/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-R' (removing atoms outside of sphere) to testsuite. - ... Sun, 30 May 2010 16:09:06 GMT Frederik Heber [c7a473] * src/atom_trajectoryparticle.cpp (modified) * src/molecule_dynamics.cpp (modified) * tests/regression/Molecules/5/pre/test.conf (added) * tests/regression/Molecules/5/pre/test.forces (added) * tests/regression/testsuite.at (modified) Added cased '-P' (force integration) to testsuite. - this is ... Sun, 30 May 2010 15:38:38 GMT Frederik Heber [f8f14d] * src/builder.cpp (modified) * tests/regression/Molecules/4/post/test.conf (added) * tests/regression/Molecules/4/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-L' (linear interpolation) to testsuite. - this just ... Sun, 30 May 2010 15:30:32 GMT Frederik Heber [13bfeb] * tests/regression/Molecules/3/post/test.ekin (added) * tests/regression/Molecules/3/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-S' (storing temperature) to testsuite. - made three ... Sun, 30 May 2010 15:24:29 GMT Frederik Heber [72e36f] * tests/regression/Molecules/2/post/test.adj (added) * tests/regression/Molecules/2/post/test.dbond (added) * tests/regression/Molecules/2/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added cases '-j' (storing bonds) and '-J' (storing adjacency) to ... Sun, 30 May 2010 15:18:50 GMT Frederik Heber [c68c90] * src/builder.cpp (modified) * src/molecule_graph.cpp (modified) * tests/regression/Molecules/1/pre/test.conf (added) * tests/regression/Molecules/1/pre/test.dbond (added) * tests/regression/testsuite.at (modified) Added case '-A' (parsing bonds) to testsuite. - ... Sun, 30 May 2010 14:46:39 GMT Frederik Heber [1325ba] * tests/regression/Filling/1/post/test.conf (added) * tests/regression/Filling/1/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-F' (filling with molecule) to testsuite. Sun, 30 May 2010 14:45:50 GMT Frederik Heber [5e11e4] * src/builder.cpp (modified) In-code created water molecule has been removed in ... Sun, 30 May 2010 13:58:31 GMT Frederik Heber [ef2b39] * tests/regression/Analysis/4/post/bin_output.csv (added) * tests/regression/Analysis/4/post/output.csv (added) * tests/regression/Analysis/4/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-C S' (correlation to surface) to testsuite. - created ... Sun, 30 May 2010 13:42:26 GMT Frederik Heber [08f6ff] * src/builder.cpp (modified) * tests/regression/Analysis/3/post/bin_output.csv (added) * tests/regression/Analysis/3/post/output.csv (added) * tests/regression/Analysis/3/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-C P' (correlation to point) to testsuite. - DOCUFIX: ... Sun, 30 May 2010 13:41:37 GMT Frederik Heber [06f8ee] * src/builder.cpp (modified) * tests/regression/Analysis/1/post/bin_output.csv (added) * tests/regression/Analysis/1/post/output.csv (added) * tests/regression/Analysis/1/pre/test.conf (added) * tests/regression/Analysis/2/post/bin_output-10.csv (added) * tests/regression/Analysis/2/post/bin_output-20.csv (added) * tests/regression/Analysis/2/post/bin_output-5.csv (added) * tests/regression/Analysis/2/post/output-10.csv (added) * tests/regression/Analysis/2/post/output-20.csv (added) * tests/regression/Analysis/2/post/output-5.csv (added) * tests/regression/Analysis/2/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-C E' (pair correlation analysis) to testsuite. - ... Sun, 30 May 2010 11:51:28 GMT Frederik Heber [046a1e] * tests/regression/Graph/2/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-I' (subgraph dissection) to testsuite. - constructed ... Sun, 30 May 2010 11:32:05 GMT Frederik Heber [5188f5] * src/builder.cpp (modified) * tests/regression/testsuite.at (modified) Added case '-M' (MPQC basis) to testsuite. - ... Sun, 30 May 2010 11:05:54 GMT Frederik Heber [93d732b] * src/World.cpp (modified) * src/builder.cpp (modified) * tests/regression/testsuite.at (modified) Added case '-X' (default mol name) to testsuite and bugfix. - ... Sun, 30 May 2010 10:57:14 GMT Frederik Heber [e8e48ab] * tests/regression/testsuite.at (modified) Added case '-n' (fast parsing) to testsuite. Sun, 30 May 2010 10:57:01 GMT Frederik Heber [403637] * tests/regression/testsuite.at (modified) Added case '-g' (load bond table) to testsuite. Sun, 30 May 2010 10:53:16 GMT Frederik Heber [ff73a2] * src/periodentafel.cpp (modified) * tests/regression/testsuite.at (modified) Refined check for case '-e' of testsuite and some found bugfixes of ... Sun, 30 May 2010 10:00:41 GMT Frederik Heber [2f0c42] * tests/regression/testsuite.at (modified) Added test for parsing specified element database to testsuite. Sun, 30 May 2010 09:54:26 GMT Frederik Heber [a97f55] * tests/regression/testsuite.at (modified) Extended standard options part of testsuite to include further tests. Sun, 30 May 2010 09:49:37 GMT Frederik Heber [745874] * tests/regression/Domain/4/post/test.conf (added) * tests/regression/Domain/4/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-O' to testsuite. Sun, 30 May 2010 09:46:13 GMT Frederik Heber [8df4e3] * Makefile.am (modified) Removed src/Actions from subdirs as this is handled in ... Sun, 30 May 2010 09:45:41 GMT Frederik Heber [0335a2] * tests/regression/Domain/3/post/test.conf (added) * tests/regression/Domain/3/pre/test.conf (added) * tests/regression/testsuite.at (modified) Added case '-c' to testsuite. Sun, 30 May 2010 09:21:01 GMT Frederik Heber [318cea] * tests/Tesselations/defs.in (modified) FIX: Tesselations test failed on first. - defs.in would go into ... Sun, 30 May 2010 09:18:14 GMT Frederik Heber [b2b47f] * configure.ac (modified) * tests/Makefile.am (modified) * tests/regression/Makefile.am (added) * tests/regression/atlocal.in (moved) * tests/regression/molecuilder.in (moved) * tests/regression/testsuite.at (moved) Shifted regression testsuite into folder regression. This is to ... Sat, 29 May 2010 18:57:36 GMT Frederik Heber [e3989a] * tests/regression/Domain/2/post/test.conf (added) * tests/regression/Domain/2/pre/test.conf (added) * tests/testsuite.at (modified) Added case '-b' to testsuite. Sat, 29 May 2010 18:29:33 GMT Frederik Heber [c82720] * tests/regression/Domain/1/post/test.conf (added) * tests/testsuite.at (modified) Added case '-B' to testsuite. - added new set of tests 'Domain' Sat, 29 May 2010 15:13:36 GMT Frederik Heber [d8c0ed] * tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) Merge branch 'FixTestsuiteDetermineCenterOfAllBug' into ... Sat, 29 May 2010 15:12:43 GMT Frederik Heber [f37746] * tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/3/post/NonConvexEnvelope.r3d (modified) FIX: As molecule::DetermineCenterOfAll() was broken, centers used in ... Sat, 29 May 2010 14:18:41 GMT Frederik Heber [62680e] * src/builder.cpp (modified) Merge branch 'FixReintroduceExitFlagtoParseCommandLineCall' into ... Sat, 29 May 2010 14:15:27 GMT Frederik Heber [99fcaf] * src/builder.cpp (modified) FIX: Flag returned by ParseCommandLineOptions() needs to be heeded, ... Sat, 29 May 2010 14:00:12 GMT Frederik Heber [9757d9] * tests/testsuite.at (modified) Merge branch 'FixTestsuiteCode134onElementsDB' into ... Sat, 29 May 2010 14:00:08 GMT Frederik Heber [b13ea4] * src/Actions/MapOfActions.cpp (modified) * tests/testsuite.at (modified) Merge branch 'FixtestsuiteforVerboseChanges' into ... Sat, 29 May 2010 13:52:51 GMT Frederik Heber [6670a97] * src/Actions/MapOfActions.cpp (modified) * tests/testsuite.at (modified) Change to testsuite as verbosity is now defined as (-v 3) not as ... Sat, 29 May 2010 13:24:29 GMT Frederik Heber [60f50a] * tests/testsuite.at (modified) TESTFIX: Testuite expected return code 134 instead of 255 for wrong ... Sat, 29 May 2010 13:11:22 GMT Frederik Heber [0fb9f6] * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/builder.cpp (modified) * src/helpers.cpp (modified) Fixes to prevent seg'faults. - ... Thu, 27 May 2010 10:46:54 GMT Tillmann Crueger [a7b761b] * src/Helpers/Assert.cpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Patterns/Cacheable.hpp (modified) * src/Patterns/ObservedIterator.hpp (added) * src/Patterns/Observer.cpp (modified) * src/Patterns/Observer.hpp (modified) * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/atom.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.hpp (modified) * src/lists.cpp (deleted) * src/lists.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/molecule_pointcloud.cpp (modified) * src/molecule_template.hpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/ObserverTest.cpp (modified) * src/unittests/ObserverTest.hpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/listofbondsunittest.hpp (modified) Merge branch 'MoleculeStartEndSwitch' into StructureRefactoring ... Fri, 21 May 2010 10:08:40 GMT Tillmann Crueger [8f215d] * src/boundary.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) Simplified tesselation.cpp by allowing direct access to derived ... Thu, 20 May 2010 16:12:03 GMT Tillmann Crueger [f2f4ae] * src/Helpers/MemDebug.cpp (modified) * src/unittests/Makefile.am (modified) Made the memory debugger thread safe Thu, 20 May 2010 15:57:02 GMT Tillmann Crueger [93dfc7b] * src/Helpers/MemDebug.cpp (modified) Made the delete handle deletion of NULL pointers more gracefully Thu, 20 May 2010 15:51:14 GMT Tillmann Crueger [d4c9ae] * src/Plane.cpp (modified) * src/Plane.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Removed the DistanceToPlane method in the Vector class in favor of a ... Thu, 20 May 2010 13:45:01 GMT Tillmann Crueger [5702280] * src/Helpers/MemDebug.cpp (modified) * src/Helpers/MemDebug.hpp (modified) Made it possible to disable the MemoryTracker using Compileflags Wed, 19 May 2010 18:46:52 GMT Frederik Heber [8de375] * src/Helpers/MemDebug.cpp (modified) * src/analysis_bonds.cpp (modified) * src/atom.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_particleinfo.cpp (modified) * src/atom_particleinfo.hpp (modified) * src/bond.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) Merge branch 'StructureRefactoring' into CommandLineActionMapping ... Wed, 19 May 2010 18:41:05 GMT Frederik Heber [eff648] * src/builder.cpp (modified) BUGFIX: In ParseCommandLineOptions() -v and -V were mixed. - ... Wed, 19 May 2010 14:03:42 GMT Tillmann Crueger [bab12a] * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) FIX: Fix of bug introduced during Vector Refactoring Testsuite now ... Tue, 18 May 2010 15:58:58 GMT Frederik Heber [673c7f] * src/molecule_geometry.cpp (modified) * tests/regression/Simple_configuration/2/post/test.conf.in (added) * tests/regression/Simple_configuration/3/post/test.conf.in (added) BUGFIX: molecule::DetermineCenterOfAll() was broken for single atom. ... Tue, 18 May 2010 15:20:52 GMT Frederik Heber [4eb4fe] * src/analysis_bonds.cpp (modified) * src/analysis_bonds.hpp (modified) * src/builder.cpp (modified) * src/elements.db (modified) * src/elements_db.cpp (added) * src/elements_db.hpp (added) * src/periodentafel.cpp (modified) * src/periodentafel.hpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.hpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.hpp (modified) * src/unittests/CountBondsUnitTest.cpp (modified) * src/unittests/CountBondsUnitTest.hpp (modified) * src/unittests/LinkedCellUnitTest.cpp (modified) * src/unittests/LinkedCellUnitTest.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/ParserUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/analysisbondsunittest.hpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/listofbondsunittest.hpp (modified) * src/unittests/periodentafelTest.cpp (added) * src/unittests/periodentafelTest.hpp (added) * tests/testsuite.at (modified) "-e " not necessary anymore. Removed necessity of ... Tue, 18 May 2010 15:18:24 GMT Frederik Heber [5079a0] * Makefile.am (modified) * configure.ac (modified) * src/Actions/Makefile.am (added) * src/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (moved) * src/UIElements/CommandLineUI/CommandLineDialog.hpp (moved) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (moved) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.hpp (moved) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (moved) * src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (moved) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (moved) * src/UIElements/CommandLineUI/CommandLineWindow.hpp (moved) * src/UIElements/Dialog.cpp (modified) * src/UIElements/MainWindow.cpp (modified) * src/UIElements/Makefile.am (added) * src/UIElements/Menu/ActionMenuItem.cpp (moved) * src/UIElements/Menu/ActionMenuItem.hpp (moved) * src/UIElements/Menu/DisplayMenuItem.cpp (moved) * src/UIElements/Menu/DisplayMenuItem.hpp (moved) * src/UIElements/Menu/Menu.cpp (moved) * src/UIElements/Menu/Menu.hpp (moved) * src/UIElements/Menu/MenuItem.cpp (moved) * src/UIElements/Menu/MenuItem.hpp (moved) * src/UIElements/Menu/SeperatorItem.cpp (moved) * src/UIElements/Menu/SeperatorItem.hpp (moved) * src/UIElements/Menu/SubMenuItem.cpp (moved) * src/UIElements/Menu/SubMenuItem.hpp (moved) * src/UIElements/Menu/TextMenu.cpp (moved) * src/UIElements/Menu/TextMenu.hpp (moved) * src/UIElements/TextUI/TextDialog.cpp (moved) * src/UIElements/TextUI/TextDialog.hpp (moved) * src/UIElements/TextUI/TextStatusIndicator.cpp (moved) * src/UIElements/TextUI/TextStatusIndicator.hpp (moved) * src/UIElements/TextUI/TextUIFactory.cpp (moved) * src/UIElements/TextUI/TextUIFactory.hpp (moved) * src/UIElements/TextUI/TextWindow.cpp (moved) * src/UIElements/TextUI/TextWindow.hpp (moved) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (moved) * src/UIElements/Views/MethodStringView.hpp (moved) * src/UIElements/Views/StreamStringView.cpp (moved) * src/UIElements/Views/StreamStringView.hpp (moved) * src/UIElements/Views/StringView.cpp (moved) * src/UIElements/Views/StringView.hpp (moved) * src/UIElements/Views/View.cpp (moved) * src/UIElements/Views/View.hpp (moved) Actions put into libMolecuilderActions, UIElements into ... Mon, 17 May 2010 17:32:33 GMT Frederik Heber [2a5eb7] * tests/testsuite.at (modified) TESTFIX: Changed return code on wrong arguments from 255 to 134. - ... Mon, 17 May 2010 17:31:35 GMT Frederik Heber [f65e1f] * src/builder.cpp (modified) FIX: list of arguments passed to ParseCommandLineOptions() should be ... Mon, 17 May 2010 17:31:00 GMT Frederik Heber [a77976] * src/Actions/MapOfActions.cpp (modified) TESTFIX: testsuite looks for a very specific help message. - ... Sun, 16 May 2010 12:06:42 GMT Frederik Heber [daa714] Merge remote branch 'bespin/CommandLineActionMapping' into ... Sat, 15 May 2010 22:14:44 GMT Frederik Heber [f941b1] * tests/Tesselations/defs.in (modified) Merge branch 'FixTesselationTestDiff' into CommandLineActionMapping Sat, 15 May 2010 22:11:50 GMT Frederik Heber [12872d] * tests/Tesselations/defs.in (modified) FIX: Don't compare tesselation files directly but rather sorted list ... Sat, 15 May 2010 17:56:57 GMT Frederik Heber [97ebf8] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (added) * src/Actions/AnalysisAction/MolecularVolumeAction.hpp (added) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (added) * src/Actions/AnalysisAction/PairCorrelationAction.hpp (added) * src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp (added) * src/Actions/AnalysisAction/PairCorrelationToPointAction.hpp (added) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp (added) * src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (added) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.hpp (added) * src/Actions/AtomAction/AddAction.cpp (added) * src/Actions/AtomAction/AddAction.hpp (added) * src/Actions/AtomAction/ChangeElementAction.cpp (added) * src/Actions/AtomAction/ChangeElementAction.hpp (added) * src/Actions/AtomAction/RemoveAction.cpp (added) * src/Actions/AtomAction/RemoveAction.hpp (added) * src/Actions/CmdAction/BondLengthTableAction.cpp (added) * src/Actions/CmdAction/BondLengthTableAction.hpp (added) * src/Actions/CmdAction/ElementDbAction.cpp (added) * src/Actions/CmdAction/ElementDbAction.hpp (added) * src/Actions/CmdAction/FastParsingAction.cpp (added) * src/Actions/CmdAction/FastParsingAction.hpp (added) * src/Actions/CmdAction/HelpAction.cpp (modified) * src/Actions/CmdAction/VerboseAction.cpp (added) * src/Actions/CmdAction/VerboseAction.hpp (added) * src/Actions/CmdAction/VersionAction.cpp (modified) * src/Actions/FragmentationAction/DepthFirstSearchAction.cpp (added) * src/Actions/FragmentationAction/DepthFirstSearchAction.hpp (added) * src/Actions/FragmentationAction/FragmentationAction.cpp (added) * src/Actions/FragmentationAction/FragmentationAction.hpp (added) * src/Actions/FragmentationAction/SubgraphDissectionAction.cpp (added) * src/Actions/FragmentationAction/SubgraphDissectionAction.hpp (added) * src/Actions/MapOfActions.cpp (added) * src/Actions/MapOfActions.hpp (added) * src/Actions/MoleculeAction/BondFileAction.cpp (added) * src/Actions/MoleculeAction/BondFileAction.hpp (added) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.hpp (modified) * src/Actions/MoleculeAction/FillWithMoleculeAction.cpp (added) * src/Actions/MoleculeAction/FillWithMoleculeAction.hpp (added) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (added) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp (added) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (added) * src/Actions/MoleculeAction/SaveAdjacencyAction.hpp (added) * src/Actions/MoleculeAction/SaveBondsAction.cpp (added) * src/Actions/MoleculeAction/SaveBondsAction.hpp (added) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (added) * src/Actions/MoleculeAction/SaveTemperatureAction.hpp (added) * src/Actions/MoleculeAction/SuspendInWaterAction.cpp (added) * src/Actions/MoleculeAction/SuspendInWaterAction.hpp (added) * src/Actions/MoleculeAction/TranslateAction.cpp (added) * src/Actions/MoleculeAction/TranslateAction.hpp (added) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (added) * src/Actions/MoleculeAction/VerletIntegrationAction.hpp (added) * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (added) * src/Actions/TesselationAction/ConvexEnvelopeAction.hpp (added) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (added) * src/Actions/TesselationAction/NonConvexEnvelopeAction.hpp (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (added) * src/Actions/WorldAction/AddEmptyBoundaryAction.hpp (added) * src/Actions/WorldAction/BoundInBoxAction.cpp (added) * src/Actions/WorldAction/BoundInBoxAction.hpp (added) * src/Actions/WorldAction/CenterInBoxAction.cpp (added) * src/Actions/WorldAction/CenterInBoxAction.hpp (added) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (added) * src/Actions/WorldAction/CenterOnEdgeAction.hpp (added) * src/Actions/WorldAction/ChangeBoxAction.cpp (added) * src/Actions/WorldAction/ChangeBoxAction.hpp (added) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.cpp (added) * src/Actions/WorldAction/RemoveSphereOfAtomsAction.hpp (added) * src/Actions/WorldAction/RepeatBoxAction.cpp (added) * src/Actions/WorldAction/RepeatBoxAction.hpp (added) * src/Actions/WorldAction/ScaleBoxAction.cpp (added) * src/Actions/WorldAction/ScaleBoxAction.hpp (added) * src/Actions/WorldAction/SetDefaultNameAction.cpp (added) * src/Actions/WorldAction/SetDefaultNameAction.hpp (added) * src/Actions/WorldAction/SetGaussianBasisAction.cpp (added) * src/Actions/WorldAction/SetGaussianBasisAction.hpp (added) * src/CommandLineParser.cpp (modified) * src/CommandLineParser.hpp (modified) * src/Legacy/oldmenu.cpp (modified) * src/Makefile.am (modified) * src/Parser/XyzParser.cpp (modified) * src/UIElements/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineWindow.hpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextDialog.cpp (modified) * src/UIElements/TextDialog.hpp (modified) * src/UIElements/TextWindow.cpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/bondgraph.hpp (modified) * src/builder.cpp (modified) * src/molecule.hpp (modified) * src/unittests/MapofActionsTest.cpp (added) * src/unittests/MapofActionsTest.hpp (added) Added all commands defined in ParseCommandLineOptions() as Actions. ... Fri, 14 May 2010 19:57:06 GMT Frederik Heber [498c519] * src/unittests/TestRunnerMain.cpp (modified) Merge remote branch 'bespin/FixTestRunnerClient' into ... Fri, 14 May 2010 19:55:36 GMT Frederik Heber [4917cc4] * src/unittests/TestRunnerMain.cpp (modified) Merge branch 'FixTestRunnerClient' into CommandLineActionMapping Fri, 14 May 2010 19:53:36 GMT Frederik Heber [cee0a17] * src/unittests/TestRunnerMain.cpp (modified) FIX: TestRunner is broken when TestRunnerClient.[h|cpp] can not be ... Sun, 09 May 2010 12:00:08 GMT Frederik Heber [50dfda] * src/Actions/CmdAction/VersionAction.cpp (added) * src/Actions/CmdAction/VersionAction.hpp (added) * src/Makefile.am (modified) * src/UIElements/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineWindow.hpp (modified) * src/builder.cpp (modified) Added VersionAction. - new CmdAction/VersionAction that prints the ... Sun, 09 May 2010 11:59:35 GMT Frederik Heber [86466e] * src/Actions/CmdAction/HelpAction.cpp (modified) * src/UIElements/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineDialog.hpp (modified) * src/UIElements/CommandLineUIFactory.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/TextDialog.cpp (modified) * src/UIElements/TextDialog.hpp (modified) new query class EmptyQuery for showing text messages. - new class ... Sat, 08 May 2010 22:59:14 GMT Frederik Heber [148d8f0] * src/builder.cpp (modified) FIX: cleanup() still deleted configuration although is part of the ... Sat, 08 May 2010 22:57:18 GMT Frederik Heber [bcd072] * src/CommandLineParser.cpp (modified) * src/CommandLineParser.hpp (modified) FIX: wrong use of Singleton pattern for CommandLineParser. - we set ... Sat, 08 May 2010 22:57:04 GMT Frederik Heber [d90762] * src/UIElements/CommandLineDialog.cpp (modified) Rewrote all CommandLineDialog's Query... to use the ... Sat, 08 May 2010 22:51:22 GMT Frederik Heber [4380af] * src/UIElements/CommandLineWindow.cpp (modified) CommandLineWindow::display() goes through all Actions in ... Sat, 08 May 2010 22:00:57 GMT Frederik Heber [e3ecc1a] * src/Actions/CmdAction/HelpAction.cpp (added) * src/Actions/CmdAction/HelpAction.hpp (added) * src/CommandLineParser.hpp (modified) * src/Makefile.am (modified) * src/UIElements/CommandLineWindow.cpp (modified) New HelpAction that will print the help from boost::program_options. ... Sat, 08 May 2010 22:00:16 GMT Frederik Heber [fa56f0] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) ActionRegistry now is iterable due to new functons getBeginIter() and ... Sat, 08 May 2010 22:00:03 GMT Frederik Heber [808fd3] * src/Actions/ParserAction/LoadXyzAction.cpp (modified) * src/Actions/ParserAction/SaveXyzAction.cpp (modified) performUndo/Redo were missing for ParserLoadXyzAction and ... Sat, 08 May 2010 21:59:27 GMT Frederik Heber [d893f79] * src/UIElements/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUIFactory.hpp (modified) * src/UIElements/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineWindow.hpp (modified) * src/UIElements/MainWindow.hpp (modified) * src/UIElements/TextUIFactory.cpp (modified) * src/UIElements/TextUIFactory.hpp (modified) * src/UIElements/TextWindow.cpp (modified) * src/UIElements/TextWindow.hpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/builder.cpp (modified) removed menuPopulaters from MainWindow. - menuPopulaters is too ... Sat, 08 May 2010 20:34:05 GMT Frederik Heber [8e1f7af] * src/UIElements/TextWindow.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) * src/builder.cpp (modified) class config added to World. - World now has the global ...