# # ChangeLog for molecuilder/src/boundary.cpp # # Generated by Trac 1.6 # Sep 20, 2025, 9:10:30 PM Sat, 30 Jan 2010 18:04:05 GMT Frederik Heber [14c0f0] * molecuilder/src/boundary.cpp (modified) FIX: FillBoxWithMolecule() - seed of random number generator was not ... 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 14:00:14 GMT Frederik Heber [8a34e69] * molecuilder/src/boundary.cpp (modified) Boolean return value of Tesselation::IsInnerPoint in ... 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 ... Sat, 19 Dec 2009 19:32:24 GMT Frederik Heber [ff4611] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_pointcloud.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) Attempt to fix the embedding. Basically it would be working, but ... Wed, 16 Dec 2009 11:53:06 GMT Frederik Heber [65f1dba] * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Fix attempts of the Tesselation. One problem still remains: - ... Sat, 28 Nov 2009 15:45:59 GMT Frederik Heber [ea3627] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) Correction of degenerated polygons is working. - Correction of ... 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 ... Wed, 25 Nov 2009 12:18:18 GMT Frederik Heber [4af89b] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Now the best (in terms of ShortestAngle) baseline is picked among all ... 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 20:59:00 GMT Frederik Heber [09d3b8] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) Attempt to fix tesselation for case 1_2-dimethylbenzene. - The ... Sat, 07 Nov 2009 09:44:11 GMT Frederik Heber [fc420f] * molecuilder/src/boundary.cpp (modified) LEAKFIX: FillBoxWithMolecule() had mismatch delete/delete[] - ... 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 ... Tue, 03 Nov 2009 16:34:31 GMT Frederik Heber [c1b4a4] * molecuilder/src/bondgraph.cpp (modified) * molecuilder/src/bondgraph.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/molecule_fragmentation.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) "not working parsed molecule into subgraph splitting"-BUG fixed, ... Mon, 02 Nov 2009 12:50:57 GMT Frederik Heber [df0520] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) Small changes. - VolumeOfConvexEnvelope() - setprecision corrected ... Tue, 27 Oct 2009 16:11:22 GMT Frederik Heber [a9b2a0a] * molecuilder/configure.ac (modified) * molecuilder/src/analysis_correlation.cpp (modified) * molecuilder/src/analysis_correlation.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/leastsquaremin.cpp (modified) * molecuilder/src/leastsquaremin.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) * molecuilder/src/molecule_graph.cpp (modified) * molecuilder/src/molecule_pointcloud.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) * molecuilder/src/unittests/ActOnAllUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToPointUnitTest.cpp (modified) * molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Huge refactoring to make const what is const (ticket #38), continued. ... Tue, 27 Oct 2009 11:51:52 GMT Frederik Heber [55a71b] * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecule.hpp (modified) analyzer.cpp and boundary.cpp refactored. - ticket #39 is done with ... 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 13:11:28 GMT Frederik Heber [567b7f] * molecuilder/src/atom.cpp (modified) * molecuilder/src/atom.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/molecule.cpp (modified) * molecuilder/src/molecule.hpp (modified) * molecuilder/src/molecule_dynamics.cpp (modified) * molecuilder/src/molecule_geometry.cpp (modified) In molecule::OutputTrajectories() ActOnAllAtoms() with new function ... 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: ... Fri, 02 Oct 2009 15:19:51 GMT Frederik Heber [daf956] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) Fixes to the (Non)ConvexTesselation, working with ... Mon, 28 Sep 2009 20:00:33 GMT Frederik Heber [60cbe5] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/tesselationhelpers.hpp (modified) Various fixes and attempt to get convex hull working. - ... Mon, 21 Sep 2009 11:48:42 GMT Saskia Metzler [390a2b] * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/memoryallocator.hpp (added) * molecuilder/src/memoryallocatorunittest.cpp (added) * molecuilder/src/memoryallocatorunittest.hpp (added) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/vector.cpp (modified) Ticket 11: use templates and/or traits to fix Malloc/ReAlloc-Free ... 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 14:31:29 GMT Frederik Heber [78dac6] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) Smaller fixes, but convex tesselation not working yet - ... Wed, 19 Aug 2009 12:30:21 GMT Frederik Heber [daf5d6] * molecuilder/configure.ac (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/leastsquaremin.cpp (added) * molecuilder/src/leastsquaremin.hpp (added) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselationhelpers.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/vectorunittest.cpp (added) * molecuilder/src/vectorunittest.hpp (added) Merge branch 'VectorUnitTest' into ConcaveHull 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() - ... Tue, 18 Aug 2009 13:59:11 GMT Saskia Metzler [d6b011] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Ticket 15: new function RemoveDegeneratedTriangles() Added functions ... Tue, 18 Aug 2009 08:42:39 GMT Frederik Heber [27459a] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) Further bugfixes to three-step-procedure in convex envelope, not yet ... 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 10:48:03 GMT Frederik Heber [3de1d2] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) Rewrite of ConvexizeNonconvexEnvelope() with three steps: Remove ... 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 19:25:28 GMT Frederik Heber [0cf171] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/tesselation.cpp (modified) * molecuilder/src/tesselation.hpp (modified) BUGFIXes to Find_convex_... and Find_non_convex_... algorithms - ... Fri, 07 Aug 2009 12:48:06 GMT Frederik Heber [609e48] * molecuilder/src/boundary.cpp (modified) output of terminating special property comment in .r3d file had no ... 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 13:53:55 GMT Frederik Heber [7aa922] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) find_(non)_convex_border TesselStruct is not free'd anymore, ... Mon, 03 Aug 2009 20:21:05 GMT Frederik Heber [f4a346] * 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/config.hpp (added) * molecuilder/src/element.cpp (modified) * molecuilder/src/element.hpp (added) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) * molecuilder/src/helpers.hpp (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.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.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.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.hpp (added) Merge branch 'TesselationRefactoring' into ConcaveHull Conflicts: ... Mon, 03 Aug 2009 18:58:46 GMT Frederik Heber [0e2190] * molecuilder/src/atom.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * util/depcomp (modified) * util/install-sh (modified) Merge branch 'ConcaveHull' of ... Mon, 03 Aug 2009 16:48:46 GMT Saskia Metzler [e8de2e] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) Adding functions IsInnerAtom() and IsInnerPoint() which can check ... Mon, 03 Aug 2009 15:26:32 GMT Frederik Heber [eb167d] * molecuilder/src/bond.cpp (modified) * molecuilder/src/bond.hpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/config.hpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) Some minor fixes with regards to what needs to be included where and ... 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 13:02:51 GMT Frederik Heber [3dc682] * molecuilder/src/boundary.cpp (modified) Convex tesselation is now working also for heptan. But the convex ... 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 14:53:57 GMT Frederik Heber [dd69cc] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/molecules.cpp (modified) FIX: DetermineCenterOfAll() did point in wrong direction, convex ... 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 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 13:33:39 GMT Frederik Heber [a8c8ba] * molecuilder/src/boundary.cpp (modified) FIX: Now tries each of the axis direction to find a starting triangle ... Thu, 09 Jul 2009 12:02:46 GMT Frederik Heber [8bbe43] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) Lots of changes to the number of output messages. As the finding of ... Thu, 09 Jul 2009 11:40:14 GMT Frederik Heber [438506] * molecuilder/src/boundary.cpp (modified) Fixed all of the remaining memory leaks due to ... Thu, 09 Jul 2009 10:38:34 GMT Frederik Heber [669a7e] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/ellipsoid.cpp (modified) * molecuilder/src/ellipsoid.hpp (modified) fixed compiler warning by changing int to size_t because C++ STL ... Thu, 09 Jul 2009 10:22:05 GMT Frederik Heber [12cf763] * molecuilder/src/boundary.cpp (modified) Removed unnecessary code - Choose_preferable_third_point() - ... Thu, 09 Jul 2009 09:45:00 GMT Frederik Heber [49c774] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) BUGFIX: Memory leak due to special triangles and similar lines in ... Tue, 07 Jul 2009 14:48:21 GMT Frederik Heber [30212a8] * molecuilder/src/boundary.cpp (modified) FIX: CheckLineCriteriaforDegeneratedTriangle contains criteria when ... Tue, 07 Jul 2009 09:12:54 GMT Frederik Heber [a811a0] * molecuilder/src/boundary.cpp (modified) BUGFIX: Initial edge for starting triangle may be up to TWICE the ... 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 ... Tue, 07 Jul 2009 06:49:32 GMT Frederik Heber [d2639f] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecules.hpp (modified) All of Saskia Metzler's changes so far to remove bugs from ... 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 ... Thu, 02 Apr 2009 16:42:53 GMT Frederik Heber [899029f] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.hpp (modified) Framework for embedding one molecule into another, now the embedding ... Mon, 09 Feb 2009 17:24:10 GMT Frederik Heber [e08f45] * .gitignore (modified) * ChangeLog (modified) * Makefile.am (modified) * configure.ac (modified) * m4/ac_doxygen.m4 (modified) * m4/acx_compilerflags.m4 (modified) * molecuilder/ChangeLog (modified) * molecuilder/Makefile.am (modified) * molecuilder/configure.ac (modified) * molecuilder/doc/Doxyfile (modified) * molecuilder/doc/Makefile.am (modified) * molecuilder/m4/ac_doxygen.m4 (modified) * molecuilder/m4/acx_compilerflags.m4 (modified) * molecuilder/src/.#border.cpp (deleted) * molecuilder/src/.#molecules.hpp (deleted) * molecuilder/src/Hbondangle.db (modified) * molecuilder/src/Hbonddistance.db (modified) * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/atom.cpp (modified) * molecuilder/src/bond.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/config.cpp (modified) * molecuilder/src/datacreator.cpp (modified) * molecuilder/src/datacreator.hpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/elements.db (modified) * molecuilder/src/ellipsoid.cpp (added) * molecuilder/src/ellipsoid.hpp (added) * molecuilder/src/graph.cpp (modified) * molecuilder/src/helpers.cpp (modified) * molecuilder/src/helpers.hpp (modified) * molecuilder/src/joiner.cpp (modified) * molecuilder/src/linkedcell.cpp (modified) * molecuilder/src/linkedcell.hpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/orbitals.db (modified) * molecuilder/src/parser.cpp (modified) * molecuilder/src/parser.hpp (modified) * molecuilder/src/periodentafel.cpp (modified) * molecuilder/src/periodentafel.hpp (modified) * molecuilder/src/stackclass.hpp (modified) * molecuilder/src/valence.db (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * molecuilder/src/verbose.cpp (modified) * molecuilder/tests/Makefile.am (modified) * molecuilder/tests/atlocal.in (modified) * molecuilder/tests/molecuilder.in (modified) * molecuilder/tests/testsuite.at (modified) * pcp/ChangeLog (modified) * pcp/Makefile.am (modified) * pcp/configure.ac (modified) * pcp/doc/Doxyfile (modified) * pcp/doc/Makefile.am (modified) * pcp/m4/ac_doxygen.m4 (modified) * pcp/m4/acx_compilerflags.m4 (modified) * pcp/m4/acx_mpi.m4 (modified) * pcp/pseudopot/pseudo.01 (modified) * pcp/pseudopot/pseudo.02 (modified) * pcp/pseudopot/pseudo.03 (modified) * pcp/pseudopot/pseudo.04 (modified) * pcp/pseudopot/pseudo.05 (modified) * pcp/pseudopot/pseudo.06 (modified) * pcp/pseudopot/pseudo.07 (modified) * pcp/pseudopot/pseudo.08 (modified) * pcp/pseudopot/pseudo.09 (modified) * pcp/pseudopot/pseudo.10 (modified) * pcp/pseudopot/pseudo.11 (modified) * pcp/pseudopot/pseudo.12 (modified) * pcp/pseudopot/pseudo.13 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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 ... Fri, 06 Feb 2009 09:48:09 GMT Frederik Heber [d3d15c] * molecuilder/src/boundary.cpp (modified) Find_non_convex_border(): calls CreateAdjacencyList() to fill bond list 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 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pcp/src/defs.h (modified) * pcp/src/density.c (modified) * pcp/src/density.h (modified) * pcp/src/energy.c (modified) * pcp/src/energy.h (modified) * pcp/src/errors.c (modified) * pcp/src/errors.h (modified) * pcp/src/excor.c (modified) * pcp/src/excor.h (modified) * pcp/src/grad.c (modified) * pcp/src/grad.h (modified) * pcp/src/gramsch.c (modified) * pcp/src/gramsch.h (modified) * pcp/src/helpers.c (modified) * pcp/src/helpers.h (modified) * pcp/src/init.c (modified) * pcp/src/init.h (modified) * pcp/src/ions.c (modified) * pcp/src/ions.h (modified) * pcp/src/mergesort2.c (modified) * pcp/src/mergesort2.h (modified) * pcp/src/myfft.c (modified) * pcp/src/myfft.h (modified) * pcp/src/mymath.c (modified) * pcp/src/mymath.h (modified) * pcp/src/opt.c (modified) * pcp/src/opt.h (modified) * pcp/src/output.c (modified) * pcp/src/output.h (modified) * pcp/src/parsetest.c (modified) * pcp/src/pcp.c (modified) * pcp/src/pcp.h (modified) * pcp/src/pdbformat.c (modified) * pcp/src/pdbformat.h (modified) * pcp/src/perturbed.c (modified) * pcp/src/perturbed.h (modified) * pcp/src/pseudo.c (modified) * pcp/src/pseudo.h (modified) * pcp/src/riemann.c (modified) * pcp/src/riemann.h (modified) * pcp/src/run.c (modified) * pcp/src/run.h (modified) * pcp/src/test.c (modified) * pcp/src/wannier.c (modified) * pcp/src/wannier.h (modified) * pcp/tests/Makefile.am (modified) * pcp/tests/atlocal.in (modified) * pcp/tests/pcp.in (modified) * pcp/tests/testsuite.at (modified) * util/ChangeLog (modified) * util/Makefile.am (modified) * util/configure.ac (modified) * util/doc/Doxyfile (modified) * util/doc/Makefile.am (modified) * util/m4/ac_doxygen.m4 (modified) * util/m4/acx_compilerflags.m4 (modified) * util/specvisual.cfg (modified) * util/specvisual.net (modified) * util/specvisualOnly.net (modified) * util/src/CreateGaAs.c (modified) * util/src/CreateH2.c (modified) * util/src/GetPdb.c (modified) * util/src/Makefile.am (modified) * util/src/NanoCreator.c (modified) * util/src/NanoCreator.h (modified) * util/src/ReadSrcIon.c (modified) * util/src/VibrAlyzer.c (modified) * util/src/average.cpp (modified) * util/src/diagonalize.c (modified) * util/src/mergesort.c (modified) * util/src/mergesort.h (modified) * util/src/stochastik.cpp (modified) * util/suffix (modified) * util/tests/Makefile.am (modified) * util/tests/NanoCreator.in (modified) * util/tests/atlocal.in (modified) * util/tests/testsuite.at (modified) * util/visual.cfg (modified) * util/visual.net (modified) * util/visualOnly.net (modified) Just a temporary commit Mon, 29 Dec 2008 12:29:21 GMT Frederik Heber [3d9045] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Merge branch 'ConcaveHull' of ... Mon, 29 Dec 2008 12:25:04 GMT Frederik Heber [eec6c8] * molecuilder/src/#border.cpp# (deleted) * molecuilder/src/#makefile# (deleted) * molecuilder/src/#molecules.hpp# (deleted) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) Now we also produce Raster3D output files additionally to TecPlot ... Tue, 23 Dec 2008 13:28:05 GMT Christian Neuen [2ac928] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) fancy commit Tue, 23 Dec 2008 13:06:36 GMT Frederik Heber [fe3c9a] * molecuilder/src/boundary.cpp (modified) Merge branch 'ConcaveHull' of ... Tue, 23 Dec 2008 11:22:57 GMT Frederik Heber [07c050] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Cleaned up all debugging output Tue, 23 Dec 2008 11:21:29 GMT Christian Neuen [56a489] * molecuilder/src/boundary.cpp (modified) BallAngel enhanced, added new alternative direction for issues with ... Fri, 19 Dec 2008 16:21:11 GMT Christian Neuen [edf4a0] * molecuilder/src/boundary.cpp (modified) Switched choice process to Ball angle completely. Problem remains. ... Thu, 18 Dec 2008 17:21:34 GMT Christian Neuen [2b7a1a] * molecuilder/src/boundary.cpp (modified) First change to Ball angle as criteria, however, change sucks. Wed, 17 Dec 2008 15:56:07 GMT Christian Neuen [87c8e7] * molecuilder/src/boundary.cpp (modified) Solved possible problem with Second quadrant overhaul Tue, 16 Dec 2008 18:39:28 GMT Christian Neuen [313dff] * molecuilder/configure.ac (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) * pcp/configure.ac (modified) * util/configure.ac (modified) Tesselation starts to look good, minor discrepancies are still there ... Thu, 11 Dec 2008 15:23:01 GMT Christian Neuen [5a447f] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecules.cpp (modified) Atom indices are now correctly processed. Mon, 08 Dec 2008 14:16:34 GMT Christian Neuen [735468] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/molecules.cpp (modified) Another update w.r.t. the Tesselation. Some signs switched, but atom ... Thu, 04 Dec 2008 15:15:00 GMT Christian Neuen [db177a] * molecuilder/src/border.cpp (deleted) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) several changes, now output is created, quality unknown Wed, 03 Dec 2008 14:12:05 GMT Christian Neuen [e0c5b1] * molecuilder/src/#border.cpp# (added) * molecuilder/src/#makefile# (added) * molecuilder/src/#molecules.hpp# (added) * molecuilder/src/.#border.cpp (added) * molecuilder/src/.#molecules.hpp (added) * molecuilder/src/TAGS (added) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) Multiple changes to boundary, currently not fully operational. ... Thu, 27 Nov 2008 09:55:08 GMT Christian Neuen [6b3826] * molecuilder/src/border.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) In vector a function for calculation of the vector-(cross-)product ... 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 ... Tue, 14 Oct 2008 19:14:10 GMT Frederik Heber [7a3724] * molecuilder/src/boundary.cpp (modified) new version of Tesselation::GuessStartingTriangle() seems to fix ... Tue, 14 Oct 2008 13:26:02 GMT Frederik Heber [51d33c] * molecuilder/src/boundary.cpp (modified) BUGFIX: Tesselation::AddPoint() always increased ... Fri, 05 Sep 2008 17:02:18 GMT Frederik Heber [dfc1c7] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/molecules.hpp (modified) moved all definitions from boundary.hpp to molecules.hpp, and renamed ... Wed, 06 Aug 2008 09:02:01 GMT Frederik Heber [8f8621] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/moleculelist.cpp (modified) * molecuilder/src/molecules.cpp (modified) * molecuilder/src/molecules.hpp (modified) * molecuilder/src/vector.cpp (modified) * molecuilder/src/vector.hpp (modified) Rename of class vector to Vector to avoid conflict with vector from STL. Fri, 27 Jun 2008 21:14:58 GMT Frederik Heber [375dcf] * molecuilder/src/Makefile.am (modified) * molecuilder/src/analyzer.cpp (modified) * molecuilder/src/boundary.cpp (modified) * molecuilder/src/builder.cpp (modified) * molecuilder/src/defs.hpp (modified) * molecuilder/src/element.cpp (modified) * molecuilder/src/joiner.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 (added) * pcp/src/perturbed.c (modified) introduced shieldings to analyzer and joiner both now handle ... Fri, 13 Jun 2008 14:26:50 GMT Frederik Heber [0779a9] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) * util/src/CalculateDensity.sh (modified) * util/src/CalculateMass.sh (modified) some mor changes to fine-tune the cluster generation. Sadly, ... Fri, 13 Jun 2008 09:18:57 GMT Frederik Heber [3f0c46] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) Final touches for Create Clusters in water repetition in ... Thu, 12 Jun 2008 19:34:36 GMT Frederik Heber [7fcea6] * molecuilder/src/boundary.cpp (modified) * molecuilder/src/boundary.hpp (modified) * molecuilder/src/builder.cpp (modified) Smaller fixes CreateClustersinWater is now PrepareClustersinWater ... Thu, 12 Jun 2008 19:13:43 GMT Frederik Heber [dcf51d] * molecuilder/src/boundary.cpp (added) * molecuilder/src/boundary.hpp (added) * molecuilder/src/periodentafel.cpp (modified) StorePeriodentafel(): BUGFIX - there still was elements.db instead of ...