# # ChangeLog for src # # Generated by Trac 1.4.4 # Jan 14, 2025, 12:57:38 PM Fri, 19 Mar 2010 15:42:58 GMT Frederik Heber [f18185] * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/builder.cpp (modified) Implemented counting of bonds over all atoms. - new functions in ... Thu, 18 Mar 2010 15:38:56 GMT Frederik Heber [1cbf47] * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/builder.cpp (modified) Introduced CountHydrogenBridgeBonds() function. - ... Thu, 18 Mar 2010 11:39:57 GMT Frederik Heber [c7b1e7] * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) Merge branch 'FixGeneralizeStoreAdjacencyToFile' into ... Thu, 18 Mar 2010 11:39:21 GMT Frederik Heber [b48ba6] * src/bondgraph.hpp (modified) * src/defs.hpp (modified) Shifted BONDTHRESHOLD from defs.hpp over to bondgraph.hpp and lowered ... Thu, 18 Mar 2010 11:37:26 GMT Frederik Heber [8ab0407] * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) molecule::StoreAdjacencyToFile() and molecule::StoreBondsToFile() now ... Thu, 18 Mar 2010 11:33:54 GMT Frederik Heber [58ed4a] * src/analysis_bonds.cpp (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/helpers.hpp (modified) * src/linkedcell.cpp (modified) * src/log.cpp (modified) * src/log.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/triangleintersectionlist.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/vector.cpp (modified) Log() and eLog() are prepended by a DoLog()/DoeLog() construct. - ... Thu, 18 Mar 2010 10:21:13 GMT Frederik Heber [7ee87f] * src/World.cpp (modified) BUGFIX: DefaultName of molecule was too small an array. - We saw ... Thu, 04 Mar 2010 14:57:48 GMT Frederik Heber [6e6e10] * src/config.cpp (modified) BUGFIX: config::SaveTREMOLO() - TREMOLO does not like particle Id 0 ... Wed, 03 Mar 2010 19:17:58 GMT Frederik Heber [70429af] * src/moleculelist.cpp (modified) Merge branch 'FixDissectIntoSubgraphs_ConstructBondGraphcheck' into ... Wed, 03 Mar 2010 19:17:49 GMT Frederik Heber [f42e95] * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) Merge branch 'FixBinDataStartEnd' into Analysis_PairCorrelation Wed, 03 Mar 2010 19:17:19 GMT Frederik Heber [6e8dc2] * src/linkedcell.cpp (modified) Merge branch 'FixLinkedCellConstructor_Setempytcheck' into ... Wed, 03 Mar 2010 19:14:31 GMT Frederik Heber [85da4e] * src/analysis_correlation.hpp (modified) BUGFIX: in BinData() binmap should be initialized from start to end ... Wed, 03 Mar 2010 19:13:43 GMT Frederik Heber [271e17] * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) Merge branch 'FixGetBin_tointeger' into FixBinDataStartEnd Wed, 03 Mar 2010 19:10:36 GMT Frederik Heber [bd61b41] * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) BUGFIX: rounding imprecision let values appear twice in BinMap. - ... Wed, 03 Mar 2010 18:43:55 GMT Frederik Heber [b72091] * src/moleculelist.cpp (modified) BUGFIX: MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs() - ... Wed, 03 Mar 2010 18:37:28 GMT Frederik Heber [caf4ba] * src/linkedcell.cpp (modified) BUGFIX: LinkedCell::LinkedCell() - before set->empty() check whether ... Wed, 03 Mar 2010 14:53:07 GMT Frederik Heber [046783] * src/World.cpp (modified) * src/World.hpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) Default molecule name can be set via command line, BUGFIX: ... Wed, 03 Mar 2010 14:45:28 GMT Frederik Heber [a837d0] * src/boundary.cpp (modified) BUGFIX: FillBoxWithMolecule() - bonds were added after adding of each ... Wed, 03 Mar 2010 10:13:19 GMT Frederik Heber [b34306] * src/Makefile.am (modified) * src/World.cpp (added) * src/World.hpp (added) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/vector.cpp (modified) singleton class World introduced, contains only cell_size from class ... Wed, 03 Mar 2010 09:31:24 GMT Frederik Heber [c5805a] * src/boundary.cpp (modified) * src/config.cpp (modified) FIX: allowing empty config files, and filling can deal with no ... Tue, 02 Mar 2010 16:12:19 GMT Frederik Heber [cb85c2e] * src/builder.cpp (modified) ManipulateAtoms() can turn atoms around bonds again, in ... Mon, 01 Mar 2010 22:10:13 GMT Frederik Heber [8db598] * src/Makefile.am (modified) * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/triangleintersectionlist.cpp (added) * src/triangleintersectionlist.hpp (added) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp (modified) New class TriangleIntersection List and (hopefully) final fix of ... Mon, 01 Mar 2010 20:46:40 GMT Frederik Heber [30d9e7] * src/boundary.cpp (modified) Bigger change to FillBoxWithMolecule(). - BUG: Position check was ... Mon, 01 Mar 2010 20:41:21 GMT Frederik Heber [b74f7d] * src/builder.cpp (modified) FIX: ParseCommandLineOptions - case 'C' used wrong LC width, case 'F' ... Mon, 01 Mar 2010 20:28:32 GMT Frederik Heber [821907] * src/vector.cpp (modified) * src/vector.hpp (modified) Added Vector Copy constructors, Vector::GetDistanceVectorToPlane() ... Mon, 01 Mar 2010 20:28:00 GMT Frederik Heber [b11d3b] * src/gslvector.cpp (modified) * src/gslvector.hpp (modified) * src/unittests/gslvectorunittest.cpp (modified) * src/unittests/gslvectorunittest.hpp (modified) Added operators and state checkers to GSLVector. - added operators ... Sun, 21 Feb 2010 13:34:41 GMT Frederik Heber [775d133] * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) Filling has a MaxDistance, somes changes to the Correlation Analysis. ... Mon, 08 Feb 2010 15:29:35 GMT Frederik Heber [164a33] * src/builder.cpp (modified) changed case 'C' of ParseCommandLineOptions to allow selecting ... Tue, 02 Feb 2010 09:43:52 GMT Frederik Heber [1f1b23] * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/builder.cpp (modified) * src/molecule.hpp (modified) * src/molecule_graph.cpp (modified) Possibility to store all bonds to file added. So far we only could ... Sat, 30 Jan 2010 19:00:47 GMT Frederik Heber [790807] * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) Output....Correlation() don't prepend header line with '#', BinData() ... Sat, 30 Jan 2010 18:04:05 GMT Frederik Heber [d6eb80] * src/boundary.cpp (modified) FIX: FillBoxWithMolecule() - seed of random number generator was not ... Sat, 30 Jan 2010 17:35:48 GMT Frederik Heber [481601] * src/builder.cpp (modified) Added output of surfacemap in ParseCommandLineOptions(), case 'C' again. Tue, 26 Jan 2010 12:52:31 GMT Frederik Heber [244a84] * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/bondgraph.cpp (modified) * src/builder.cpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) GetDistanceToSurface() separated, filling now with water instead of ... Tue, 26 Jan 2010 12:41:04 GMT Frederik Heber [315164] * src/version.h (added) Merge branch 'FixVersioning3' into Analysis_PairCorrelation Tue, 26 Jan 2010 12:32:00 GMT Frederik Heber [f34def] * src/version.h (added) Fixed versioning. - FIX: version.h was falsely excluded in ... Thu, 14 Jan 2010 18:06:40 GMT Frederik Heber [498ea0] * src/tesselation.cpp (modified) BUGFIX: Tesselation::IsInnerPoint() returned wrong result. - We ... Thu, 14 Jan 2010 17:46:24 GMT Frederik Heber [124e14] * src/helpers.hpp (modified) Merge branch 'FixTemplatedMinMax' into FixFillingWithMolecule Thu, 14 Jan 2010 17:45:22 GMT Frederik Heber [76102e] * src/helpers.hpp (modified) Rather use parameter passing by value instead of reference. - We ... Thu, 14 Jan 2010 17:43:34 GMT Frederik Heber [e9c677] * src/unittests/Makefile.am (modified) * src/unittests/tesselation_boundarytriangleunittest.cpp (added) * src/unittests/tesselation_boundarytriangleunittest.hpp (added) Unit test for BoundaryTriangleSet member functions added. - for now ... Thu, 14 Jan 2010 17:36:09 GMT Frederik Heber [9473f6] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) FillBoxWithMolecule now allows boundary between filler molecules and ... Thu, 14 Jan 2010 17:32:47 GMT Frederik Heber [7b36fe] * src/vector.cpp (modified) Changed verbosity for Vector::GetIntersectionWithPlane(). - when ... Wed, 13 Jan 2010 14:01:55 GMT Frederik Heber [48b47a] * src/tesselation.cpp (modified) FillWithMolecule() is now working correctly. - FillWithMolecule() ... Wed, 13 Jan 2010 14:01:30 GMT Frederik Heber [9dbea5] * src/helpers.hpp (modified) Templated Min and Max functions added. Signed-off-by: Frederik ... Wed, 13 Jan 2010 14:00:14 GMT Frederik Heber [8468cb] * src/boundary.cpp (modified) Boolean return value of Tesselation::IsInnerPoint in ... Wed, 13 Jan 2010 13:37:01 GMT Frederik Heber [fc9992] * src/tesselationhelpers.cpp (modified) * tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/2/post/NonConvexEnvelope.r3d (modified) Small fixes to make checks working again. - Tesselations tests 13 ... Mon, 11 Jan 2010 09:35:52 GMT Frederik Heber [241485] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) Removed unnecessary epsilon parameter. - epsilon before was used as ... Mon, 11 Jan 2010 09:16:36 GMT Frederik Heber [fee69b] * src/tesselation.cpp (modified) * src/vector.cpp (modified) Fixed Tesselation::IsInnerPoint() - Both unit tests ... Mon, 11 Jan 2010 03:06:30 GMT Frederik Heber [fcad4b] * src/tesselation.cpp (modified) * src/vector.cpp (modified) InsideOutside unit test of tesselation is working correctly. - FIX: ... Mon, 11 Jan 2010 03:04:59 GMT Frederik Heber [68a53b] * src/unittests/tesselation_insideoutsideunittest.cpp (modified) BUGFIX - Test was wrong in upper bounds of inside area. - upper ... Sun, 10 Jan 2010 19:25:50 GMT Frederik Heber [865272f] * src/gslmatrix.cpp (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (modified) Added Determinant() function to class GSLMatrix. - new function ... Sun, 10 Jan 2010 19:24:58 GMT Frederik Heber [2793ef] * src/gslvector.cpp (modified) FIX - GSLVector::Set() return value was double instead of void. ... Sun, 10 Jan 2010 19:24:02 GMT Frederik Heber [9d6308] * src/vector.cpp (modified) Vector::GetIntersectionOfTwoLinesOnPlane() rewritten. Use routine ... Sun, 10 Jan 2010 19:15:01 GMT Frederik Heber [31a6af] * src/unittests/Makefile.am (modified) libgslwrapper.a added to LDADD of most tests. Since Vector class ... Sun, 10 Jan 2010 19:12:40 GMT Frederik Heber [a5a630] * src/tesselationhelpers.cpp (modified) BUGFIX - GetCenterOfSphere(): condition were not put correctly in ... Sun, 10 Jan 2010 19:10:52 GMT Frederik Heber [ebe4d6] * src/molecule_dynamics.cpp (modified) BUGFIX - molecule::MinimiseConstrainedPotential() OldPotential was ... Sun, 10 Jan 2010 19:09:56 GMT Frederik Heber [1f61b6] * src/gslmatrix.hpp (modified) * src/gslvector.hpp (modified) * src/linearsystemofequations.hpp (modified) Inclusion of config.h was missing. This caused a bug with GSL's ... Sun, 10 Jan 2010 19:09:14 GMT Frederik Heber [3e50ff] * src/memoryallocator.hpp (modified) * src/memoryusageobserver.cpp (modified) cstdlib header was missing, necessary for free, malloc and calloc ... Sun, 10 Jan 2010 19:05:34 GMT Frederik Heber [49e1ae] * src/analyzer.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/joiner.cpp (modified) * src/molecule.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/listofbondsunittest.cpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) cstring header was missing in files, supplying definition of strlen, ... Fri, 08 Jan 2010 17:48:35 GMT Frederik Heber [f60610] * src/Makefile.am (modified) * src/linearsystemofequations.cpp (added) * src/linearsystemofequations.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/linearsystemofequationsunittest.cpp (added) * src/unittests/linearsystemofequationsunittest.hpp (added) Wrapper class for gsl_linalg along with working Unit test. - new ... Fri, 08 Jan 2010 17:46:51 GMT Frederik Heber [fc3b67] * src/Makefile.am (modified) * src/gslmatrix.cpp (added) * src/gslmatrix.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/gslmatrixsymmetricunittest.cpp (added) * src/unittests/gslmatrixsymmetricunittest.hpp (added) * src/unittests/gslmatrixunittest.cpp (added) * src/unittests/gslmatrixunittest.hpp (added) Wrapper class for gsl_matrix along with working Unit test. - new ... Fri, 08 Jan 2010 17:44:51 GMT Frederik Heber [9fb860] * src/Makefile.am (modified) * src/gslvector.cpp (added) * src/gslvector.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/gslvectorunittest.cpp (added) * src/unittests/gslvectorunittest.hpp (added) Wrapper class for gsl_vector along with working Unit test. - new ... Fri, 08 Jan 2010 14:04:22 GMT Frederik Heber [97498a] * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (modified) * src/vector.cpp (modified) Attempt to fix the tesselation::IsInnerPoint(). We try the ... Tue, 29 Dec 2009 14:48:49 GMT Frederik Heber [c15ca2] * src/analysis_correlation.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/tesselation_insideoutsideunittest.cpp (added) * src/unittests/tesselation_insideoutsideunittest.hpp (added) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/tesselationunittest.hpp (modified) Changes to FindClosest...ToVector() and use of ..Map,..Set,..List ... Sat, 19 Dec 2009 19:32:24 GMT Frederik Heber [71b20e] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/molecule.hpp (modified) * src/molecule_pointcloud.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) Attempt to fix the embedding. Basically it would be working, but ... Sat, 19 Dec 2009 19:31:34 GMT Frederik Heber [3930eb] * src/analysis_correlation.cpp (modified) * src/builder.cpp (modified) * src/molecule_geometry.cpp (modified) Smaller fixes. - analysis_correlation.cpp: Info objects created at ... Thu, 17 Dec 2009 17:45:35 GMT Frederik Heber [125b3c] * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) Non-convex tesselation seems to be working. Seems like it has been ... Wed, 16 Dec 2009 16:18:46 GMT Frederik Heber [0b2dd2] * src/builder.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (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) * tests/testsuite.at (modified) Merge branch 'FixTestSuite' into FixDegeneratedTesselation Wed, 16 Dec 2009 16:18:41 GMT Frederik Heber [009e37b] * src/Makefile.am (modified) Merge branch 'FixVersioning2' into FixDegeneratedTesselation Wed, 16 Dec 2009 16:17:50 GMT Frederik Heber [482373] * src/builder.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * tests/regression/Tesselation/1/post/NonConvexEnvelope.dat (modified) * tests/regression/Tesselation/1/post/NonConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.dat (modified) * tests/regression/Tesselation/2/post/ConvexEnvelope.r3d (modified) * tests/regression/Tesselation/2/post/NonConvexEnvelope.dat (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) * tests/testsuite.at (modified) Fixing the testsuite. - Putting performCriticalExit() everywhere ... Wed, 16 Dec 2009 16:01:11 GMT Frederik Heber [c135eb7] * src/Makefile.am (modified) Removed --tags as we have signed the "initial_commit" tag. - git ... Wed, 16 Dec 2009 11:53:06 GMT Frederik Heber [b998c3] * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) Fix attempts of the Tesselation. One problem still remains: - ... Wed, 16 Dec 2009 11:51:17 GMT Frederik Heber [5e8f82] * src/parser.cpp (modified) FIX: MatrixContainer::ParseMatrix() should not call ... Wed, 16 Dec 2009 11:49:40 GMT Frederik Heber [cd7b0f] * src/config.cpp (modified) BUGFIX: delete(mol) belongs to the commented-out ... Wed, 16 Dec 2009 11:47:47 GMT Frederik Heber [a8eb4a] * src/Makefile.am (modified) * src/builder.cpp (modified) Added versioning to each executable. - credits to Ralf Wildenhues ... Sat, 28 Nov 2009 18:01:00 GMT Frederik Heber [fad93c] * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) The finding of the degenerated polygons' endpoints was not yet ... Sat, 28 Nov 2009 15:45:59 GMT Frederik Heber [856098] * src/boundary.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) Correction of degenerated polygons is working. - Correction of ... Fri, 27 Nov 2009 14:39:06 GMT Frederik Heber [262bae] * src/boundary.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) First compiling version of CorrectDegeneratedPolygons. - several ... Fri, 27 Nov 2009 14:38:33 GMT Frederik Heber [523917] * src/config.cpp (modified) Rename of internal variable due to upcoming name-conflict with ... Thu, 26 Nov 2009 11:40:01 GMT Frederik Heber [4fc93f] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * tests/Tesselations/defs.in (added) removing automatic dissection on loading, Tesselations test now ... Thu, 26 Nov 2009 11:36:44 GMT Frederik Heber [27bd2f] * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) BUGFIX: testcase heptan was not correctly tesselated, as edges of a ... Wed, 25 Nov 2009 15:52:27 GMT Frederik Heber [7273fc] * src/tesselation.cpp (modified) Tesselation::FindStartingTriangle() now also uses ... Wed, 25 Nov 2009 15:29:18 GMT Frederik Heber [f67b6e] * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) Multi-Candidate-Add included and incorporated class Info into ... Wed, 25 Nov 2009 15:28:39 GMT Frederik Heber [8725ed] * src/Makefile.am (modified) * src/info.cpp (added) * src/info.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/infounittest.cpp (added) * src/unittests/infounittest.hpp (added) * src/verbose.cpp (modified) New Info class that contains a global verbosity level, increased per ... Wed, 25 Nov 2009 12:18:18 GMT Frederik Heber [1e168b] * src/boundary.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) Now the best (in terms of ShortestAngle) baseline is picked among all ... Tue, 24 Nov 2009 15:48:36 GMT Frederik Heber [791138] * src/atom_bondedparticle.cpp (modified) BUGFIX atom::CorrectBonDegree() wrongly increased bond degrees. - ... Tue, 24 Nov 2009 15:34:49 GMT Frederik Heber [6a7f78c] * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/molecule.hpp (modified) * src/molecule_pointcloud.cpp (modified) * src/moleculelist.cpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * tests/Tesselations/1_2-dimethoxyethane/NonConvexEnvelope-1_2-dimethoxyethane.dat (modified) * tests/Tesselations/1_2-dimethylbenzene/NonConvexEnvelope-1_2-dimethylbenzene.dat (modified) * tests/Tesselations/2-methylcyclohexanone/NonConvexEnvelope-2-methylcyclohexanone.dat (modified) * tests/Tesselations/C16_0-Torus/NonConvexEnvelope-C16_0-Torus.dat (modified) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/N_N-dimethylacetamide/NonConvexEnvelope-N_N-dimethylacetamide.dat (modified) * tests/Tesselations/benzene.test (added) * tests/Tesselations/benzene/NonConvexEnvelope-benzene.dat (added) * tests/Tesselations/benzene/benzene.xyz (added) * tests/Tesselations/cholesterol/NonConvexEnvelope-cholesterol.dat (modified) * tests/Tesselations/cluster/NonConvexEnvelope-cluster.dat (modified) * tests/Tesselations/cycloheptane/NonConvexEnvelope-cycloheptane.dat (modified) * tests/Tesselations/dimethyl_bromomalonate/NonConvexEnvelope-dimethyl_bromomalonate.dat (modified) * tests/Tesselations/glucose/NonConvexEnvelope-glucose.dat (modified) * tests/Tesselations/heptan/NonConvexEnvelope-heptan.dat (modified) * tests/Tesselations/isoleucine/NonConvexEnvelope-isoleucine.dat (modified) * tests/Tesselations/neohexane/NonConvexEnvelope-neohexane.dat (modified) * tests/Tesselations/proline/NonConvexEnvelope-proline.dat (modified) * tests/Tesselations/putrescine/NonConvexEnvelope-putrescine.dat (modified) * tests/Tesselations/round_cluster/NonConvexEnvelope-round_cluster.dat (modified) * 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 19:09:42 GMT Frederik Heber [c5f836] * src/config.cpp (modified) * src/errorlogger.cpp (modified) * src/tesselationhelpers.cpp (modified) bugfix to errorLogger and some error verbosity changes. - BUGFIX: ... Mon, 23 Nov 2009 18:51:50 GMT Frederik Heber [e359a8] * src/analysis_correlation.hpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/helpers.hpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/molecule_graph.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/tesselation.cpp (modified) * 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 [717e0c] * src/analyzer.cpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/ellipsoid.cpp (modified) * src/linkedcell.cpp (modified) * src/memoryusageobserver.cpp (modified) * src/molecule.cpp (modified) * src/molecule_dynamics.cpp (modified) * src/molecule_fragmentation.cpp (modified) * src/moleculelist.cpp (modified) * src/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselationhelpers.cpp (modified) * src/vector.cpp (modified) Verbosity corrected for ERROR and WARNING - present ERROR and ... Tue, 10 Nov 2009 20:59:00 GMT Frederik Heber [f1ef60a] * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) Attempt to fix tesselation for case 1_2-dimethylbenzene. - The ... Tue, 10 Nov 2009 20:58:31 GMT Frederik Heber [9a0dc8] * src/builder.cpp (modified) Only biggest molecule is tesselated for now in ... Tue, 10 Nov 2009 20:53:33 GMT Frederik Heber [89f768] * src/errorlogger.cpp (modified) * src/logger.cpp (modified) * src/verbose.hpp (modified) BUGFIX: Output is again indented, errorLogger prefixes according to ... Sat, 07 Nov 2009 12:27:15 GMT Frederik Heber [9a7186] * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/bondgraphunittest.hpp (modified) BUGFIX: unnecessary include in header, file not closed in definition ... Sat, 07 Nov 2009 12:25:32 GMT Frederik Heber [220cf37] * src/analysis_bonds.cpp (modified) * src/analysis_bonds.hpp (modified) * src/unittests/analysisbondsunittest.cpp (modified) * src/unittests/analysisbondsunittest.hpp (modified) Two new bond analysis functions. - GetMaxMinMeanBondCount() - ... Sat, 07 Nov 2009 12:17:55 GMT Frederik Heber [b9947d] * src/bond.cpp (modified) * src/bond.hpp (modified) New function bond::GetDistance...() - bond::GetDistance() and ... Sat, 07 Nov 2009 12:16:57 GMT Frederik Heber [568be7] * src/builder.cpp (modified) * src/config.cpp (modified) * src/config.hpp (modified) * src/molecule.hpp (modified) * src/moleculelist.cpp (modified) Added config::SavePDB() and config::SaveMPQC(). - note: for CODICE ... Sat, 07 Nov 2009 09:46:08 GMT Frederik Heber [96c961] * src/Makefile.am (modified) * src/analysis_bonds.cpp (added) * src/analysis_bonds.hpp (added) * src/unittests/Makefile.am (modified) * src/unittests/analysisbondsunittest.cpp (added) * src/unittests/analysisbondsunittest.hpp (added) Added initial analysis_bonds.cpp and unit test for Analysis of bonds. ... Sat, 07 Nov 2009 09:44:11 GMT Frederik Heber [7f4bee] * src/boundary.cpp (modified) LEAKFIX: FillBoxWithMolecule() had mismatch delete/delete[] - ... Thu, 05 Nov 2009 18:14:08 GMT Frederik Heber [1614174] * src/analysis_correlation.cpp (modified) * src/boundary.cpp (modified) * src/builder.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) LEAKFIX: ReturnFullMatrixForSymmetric() and InverseMatrix() have ... Wed, 04 Nov 2009 19:56:04 GMT Frederik Heber [e138de] * src/Makefile.am (modified) * src/analysis_correlation.cpp (modified) * src/analysis_correlation.hpp (modified) * src/analyzer.cpp (modified) * src/atom.cpp (modified) * src/atom.hpp (modified) * src/atom_bondedparticle.cpp (modified) * src/atom_bondedparticle.hpp (modified) * src/atom_graphnode.cpp (modified) * src/atom_graphnode.hpp (modified) * src/atom_trajectoryparticle.cpp (modified) * src/bond.cpp (modified) * src/bondgraph.cpp (modified) * src/bondgraph.hpp (modified) * src/boundary.cpp (modified) * src/boundary.hpp (modified) * src/builder.cpp (modified) * src/config.cpp (modified) * src/datacreator.cpp (modified) * src/element.cpp (modified) * src/element.hpp (modified) * src/ellipsoid.cpp (modified) * src/ellipsoid.hpp (modified) * src/errorlogger.cpp (moved) * src/errorlogger.hpp (moved) * src/graph.cpp (modified) * src/graph.hpp (modified) * src/helpers.cpp (modified) * src/helpers.hpp (modified) * src/joiner.cpp (modified) * src/linkedcell.cpp (modified) * src/log.cpp (modified) * src/log.hpp (modified) * src/logger.cpp (modified) * src/memoryallocator.hpp (modified) * src/memoryusageobserver.cpp (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/parser.cpp (modified) * src/periodentafel.cpp (modified) * src/stackclass.hpp (modified) * src/tesselation.cpp (modified) * src/tesselation.hpp (modified) * src/tesselationhelpers.cpp (modified) * src/tesselationhelpers.hpp (modified) * src/test/ActOnAlltest.hpp (modified) * src/unittests/ActOnAllUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * src/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/unittests/Makefile.am (modified) * src/unittests/bondgraphunittest.cpp (modified) * src/unittests/logunittest.cpp (modified) * src/unittests/memoryallocatorunittest.cpp (modified) * src/unittests/stackclassunittest.cpp (modified) * src/unittests/tesselationunittest.cpp (modified) * src/unittests/vectorunittest.cpp (modified) * src/vector.cpp (modified) * src/vector.hpp (modified) * src/verbose.cpp (modified) Huge change from ofstream * (const) out --> Log(). - first shift ...