# # ChangeLog for / # # Generated by Trac 1.6 # May 25, 2025, 8:59:57 PM Wed, 28 Jan 2015 19:07:03 GMT Frederik Heber [2050b2] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) Commented-out all debugging messages in QtMoleculeList rewrite. Wed, 28 Jan 2015 19:07:03 GMT Frederik Heber [2696b1] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) Visibility checkstate is working for molecule and group item. - ... Wed, 28 Jan 2015 19:07:03 GMT Frederik Heber [d2dbb5d] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.hpp (modified) Moved rowsSelected() over to QtMoleculeListView. Wed, 28 Jan 2015 19:07:03 GMT Frederik Heber [53c1ff] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) Modified QtMoleculeList to use QtMoleculeItemFactory. - ... Wed, 28 Jan 2015 19:07:01 GMT Frederik Heber [6d1e0a] * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (added) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (added) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (added) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp (added) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (added) Added a slew of specific QtMoleculeItem for each of the COLUMNs. - ... Wed, 28 Jan 2015 19:06:04 GMT Frederik Heber [bed759] * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (added) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (added) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (added) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.hpp (added) Added basic QtMoleculeItem and ...Factory. Tue, 27 Jan 2015 17:18:30 GMT Frederik Heber [f62e60] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (moved) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (moved) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (added) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.hpp (added) Moved QtMoleculeList files into own subfolder. - added ... Tue, 27 Jan 2015 17:18:30 GMT Frederik Heber [1c3390] * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.hpp (modified) Header row is correct again in QtMoleculeList. - had to overwrite ... Tue, 27 Jan 2015 17:18:30 GMT Frederik Heber [8ccf3b] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.hpp (modified) First change to convert QtMoleculeList into QStandardItemModel. - ... Tue, 27 Jan 2015 17:18:30 GMT Frederik Heber [6770fa] * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.hpp (modified) Extracted add/removeItem in QtMoleculeList, no more complete ... Tue, 27 Jan 2015 17:18:29 GMT Frederik Heber [0a5beb] * src/molecule.cpp (modified) MEMFIX: removeAtomsinMolecule() worked directly with ... Tue, 27 Jan 2015 17:18:29 GMT Frederik Heber [24edfe] * src/molecule.cpp (modified) * src/molecule.hpp (modified) Added AboutToBeRemoved channel to molecule. - this allows UI ... Tue, 27 Jan 2015 17:18:28 GMT Frederik Heber [d05088] * src/Atom/AtomicInfo.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_observable.hpp (modified) FIX: Atom is notified when its father dies and resets father to ... Tue, 27 Jan 2015 16:46:25 GMT Frederik Heber [910a5d] * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/molecule.cpp (modified) * src/moleculelist.cpp (modified) atom::father is now accessible through getter and setter only. - ... Mon, 26 Jan 2015 19:32:28 GMT Frederik Heber [cf5b40] * src/builder.cpp (modified) FIX: On defined LOG_OBSERVER we also enableLogging() in main(). - I ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [4f2895] * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/World.cpp (modified) FIX: World::SetTime() erased molecules twice. - once in SetTime() ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [066442] * doc/userguide/userguide.xml (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/AtomAction/TranslateAction.def (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (added) * src/Actions/MoleculeAction/TranslateAction.def (added) * src/Actions/MoleculeAction/TranslateAction.hpp (added) * tests/regression/Atoms/Translation/testsuite-atoms-translation.at (modified) * tests/regression/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified) * tests/regression/Molecules/Translation/testsuite-molecules-translation.at (modified) * tests/regression/Options/InvalidCommands/testsuite-options-invalid-commands.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load-multiply.at (modified) * tests/regression/Parser/Pcp/testsuite-parser-pcp-load-multiply.at (modified) * tests/regression/Parser/Pdb/testsuite-parser-pdb-load-multiply.at (modified) * tests/regression/Parser/Psi3/testsuite-parser-psi3-load-multiply.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiply.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-load-multiply.at (modified) Added TranslateMolecule action. - added translate-molecule to ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [a84e8d] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.cpp (added) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.def (added) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.hpp (added) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.cpp (added) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.def (added) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/box.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/empty.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/id2_4_missing.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/post/water_id2_4.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/pre/box.xyz (added) * tests/regression/Selection/Molecules/PopMoleculeSelection/testsuite-selection-pop-molecule-selection.at (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/box.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/empty.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/id2_4_missing.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/post/water_id2_4.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/pre/box.xyz (added) * tests/regression/Selection/Molecules/PushMoleculeSelection/testsuite-selection-push-molecule-selection.at (added) * tests/regression/Selection/Molecules/testsuite-selection-molecules.at (modified) Added Push/PopMolecules selection action. - added push-molecule to ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [3213f2] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp (added) * src/Actions/SelectionAction/Atoms/PopAtomsAction.def (added) * src/Actions/SelectionAction/Atoms/PopAtomsAction.hpp (added) * src/Actions/SelectionAction/Atoms/PushAtomsAction.cpp (added) * src/Actions/SelectionAction/Atoms/PushAtomsAction.def (added) * src/Actions/SelectionAction/Atoms/PushAtomsAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/PopAtomSelection/post/empty.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id01_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id01_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id0_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id0_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id1_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id1_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id2_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id2_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id3_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id3_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id4_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id4_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id5_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id5_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id6_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id6_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id7_missing.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/id7_present.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/post/test-undo.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/pre/test.xyz (added) * tests/regression/Selection/Atoms/PopAtomSelection/testsuite-selection-pop-atom-selection.at (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/empty.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id01_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id01_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id0_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id0_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id1_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id1_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id2_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id2_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id3_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id3_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id4_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id4_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id5_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id5_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id6_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id6_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id7_missing.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/id7_present.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/post/test-undo.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/pre/test.xyz (added) * tests/regression/Selection/Atoms/PushAtomSelection/testsuite-selection-push-atom-selection.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added Push/PopAtom selection actions. - added push-atom to ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [cad383] * src/World.cpp (modified) * src/World.hpp (modified) Added push/pop[Atoms|Molecules]Selection to World. - this is mostly ... Wed, 14 Jan 2015 21:03:24 GMT Frederik Heber [2440ce] * src/Actions/FillAction/SuspendInMoleculeAction.cpp (modified) * src/Actions/FillAction/SuspendInMoleculeAction.def (modified) * tests/regression/Filling/SuspendInWater/pre/single_molecule.conf (added) * tests/regression/Filling/SuspendInWater/pre/test.conf (modified) * tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at (modified) FIX: Changed SuspendInMoleculeAction to catch segfault when rho=1 was ... Mon, 12 Jan 2015 22:10:30 GMT Frederik Heber [601ef8] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) FIX: ActionQueue is no longer cleared when Action fails. - we only ... Mon, 12 Jan 2015 22:10:30 GMT Frederik Heber [33c97e] * src/Actions/Action.cpp (modified) * src/Actions/ActionQueue.cpp (modified) FIX: Failing Actions do not clear ActionQueue/History anymore. Mon, 12 Jan 2015 22:10:30 GMT Frederik Heber [52cd7b] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) FIX: Bonds from new molecules are instantiated, too. - when filling ... Mon, 12 Jan 2015 22:10:30 GMT Frederik Heber [c01fec] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/UIElements/Views/Qt4/QtToolBar.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.hpp (modified) * src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp (modified) Undo/Redobuttons are grayed out when respective Action not possible. Mon, 12 Jan 2015 22:10:30 GMT Frederik Heber [867473] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/RemoveAction.cpp (added) * src/Actions/MoleculeAction/RemoveAction.def (added) * src/Actions/MoleculeAction/RemoveAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/Remove/post/id0_2_missing.pdb (added) * tests/regression/Molecules/Remove/post/water_box.pdb (added) * tests/regression/Molecules/Remove/pre/water_box.pdb (added) * tests/regression/Molecules/Remove/testsuite-molecules-remove.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added new RemoveAction for molecules. - also add regression test. ... Mon, 12 Jan 2015 22:10:30 GMT Frederik Heber [596cfa] * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) Extended UndoRedoHelpers by AddingMultipleMoleculesfromAtomicInfo. Sun, 11 Jan 2015 16:42:43 GMT Frederik Heber [d7cad1] * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.def (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * tests/regression/Selection/Molecules/MoleculeById/post/id2_4_missing.xyz (moved) * tests/regression/Selection/Molecules/MoleculeById/post/water_id2_4.xyz (moved) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at (modified) Extended selection action for Molecule ids to multiple ids. Sun, 11 Jan 2015 16:42:43 GMT Frederik Heber [b6d92e] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) GLWorldView's view may be changed via keyboard (especially zoom). - ... Sun, 11 Jan 2015 16:42:43 GMT Frederik Heber [f115cc] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) For GLMoleculeObject_atom element and position are only reset..() on ... Sun, 11 Jan 2015 16:41:14 GMT Frederik Heber [a7aebd] * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/World.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) World removes empty molecules. - on destroyAtom() of molecule's ... Sat, 10 Jan 2015 17:14:32 GMT Frederik Heber [7b93f9] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp (modified) Added MeshFreeType to GLMoleculeObject. Sat, 10 Jan 2015 17:14:32 GMT Frederik Heber [3eb91c] * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.hpp (modified) Molecule's Visibility can be changed "group-wise". - FIX: Removed ... Sat, 10 Jan 2015 17:14:32 GMT Frederik Heber [9a7ef9] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) Molecules can be (un)selected by clicking on the tesselation hull. Sat, 10 Jan 2015 17:14:32 GMT Frederik Heber [2b596f] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.hpp (modified) Hovering over molecules is working including update of QtInfoBox. - ... Sat, 10 Jan 2015 17:14:32 GMT Frederik Heber [7b5984] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) GLMoleculeObject_molecule listens to AtomMoved signal to update hull ... Sat, 10 Jan 2015 17:14:32 GMT Frederik Heber [c32d21] * src/Atom/atom.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) Molecule relays atom's PositionChanged as AtomMoved signal. - this ... Sat, 10 Jan 2015 17:14:32 GMT Frederik Heber [34e7fdb] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) GLMoleculeObject_molecule display tesselated surface in m_visible ... Sat, 10 Jan 2015 17:14:32 GMT Frederik Heber [739ee9] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/QtMoleculeList.hpp (modified) GLMoleculeObject have m_visible, settable in QtMoleculeList. - is ... Sat, 10 Jan 2015 17:14:21 GMT Frederik Heber [8c001a] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) GLMoleculeObject_atoms and .._bonds are now children of .._molecule. ... Wed, 22 Oct 2014 22:19:36 GMT Frederik Heber [7b38d3] * configure.ac (modified) Set version to 1.4.9. - MoleCuilder library is now 14:2:0. - ... Wed, 22 Oct 2014 19:16:17 GMT Frederik Heber [423449] * src/Potentials/Makefile.am (modified) DISTFIX: POTENTIALSOURCES was overwritten, not added to. Wed, 22 Oct 2014 19:15:59 GMT Frederik Heber [e63edb] * src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) * src/Potentials/PotentialTrainer.cpp (modified) MEMFIX: PotentialTrainer::getFirstGraphwithSpecifiedElements() used ... Sun, 19 Oct 2014 17:13:32 GMT Frederik Heber [0516fd] * LinearAlgebra/src/LinearAlgebra/Line.cpp (modified) * configure.ac (modified) * doc/userguide/userguide.xml (modified) * m4/boost.m4 (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/boundary.hpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/documentation/constructs/tesselation.dox (modified) * tests/Python/AllActions/options.dat (modified) * tests/Tesselations/Convex/1_2-dimethoxyethane/pre/1_2-dimethoxyethane.xyz (moved) * tests/Tesselations/Convex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (added) * tests/Tesselations/Convex/1_2-dimethylbenzene/pre/1_2-dimethylbenzene.xyz (moved) * tests/Tesselations/Convex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (added) * tests/Tesselations/Convex/2-methylcyclohexanone/pre/2-methylcyclohexanone.xyz (moved) * tests/Tesselations/Convex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (added) * tests/Tesselations/Convex/N_N-dimethylacetamide/pre/N_N-dimethylacetamide.xyz (moved) * tests/Tesselations/Convex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (added) * tests/Tesselations/Convex/amylose/pre/amylose.pdb (added) * tests/Tesselations/Convex/amylose/testsuite-amylose.at (added) * tests/Tesselations/Convex/benzene/pre/benzene.xyz (moved) * tests/Tesselations/Convex/benzene/testsuite-benzene.at (added) * tests/Tesselations/Convex/cholesterol/pre/cholesterol.xyz (moved) * tests/Tesselations/Convex/cholesterol/testsuite-cholesterol.at (added) * tests/Tesselations/Convex/cycloheptane/pre/cycloheptane.xyz (moved) * tests/Tesselations/Convex/cycloheptane/testsuite-cycloheptane.at (added) * tests/Tesselations/Convex/dimethyl_bromomalonate/pre/dimethyl_bromomalonate.xyz (moved) * tests/Tesselations/Convex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (added) * tests/Tesselations/Convex/glucose/pre/glucose.xyz (moved) * tests/Tesselations/Convex/glucose/testsuite-glucose.at (added) * tests/Tesselations/Convex/heptan/pre/heptan.xyz (moved) * tests/Tesselations/Convex/heptan/testsuite-heptan.at (added) * tests/Tesselations/Convex/isoleucine/pre/isoleucine.xyz (moved) * tests/Tesselations/Convex/isoleucine/testsuite-isoleucine.at (added) * tests/Tesselations/Convex/neohexane/pre/neohexane.xyz (moved) * tests/Tesselations/Convex/neohexane/testsuite-neohexane.at (added) * tests/Tesselations/Convex/proline/pre/proline.xyz (moved) * tests/Tesselations/Convex/proline/testsuite-proline.at (added) * tests/Tesselations/Convex/putrescine/pre/putrescine.xyz (moved) * tests/Tesselations/Convex/putrescine/testsuite-putrescine.at (added) * tests/Tesselations/Convex/tartaric_acid/pre/tartaric_acid.xyz (moved) * tests/Tesselations/Convex/tartaric_acid/testsuite-tartaric_acid.at (added) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-1.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-2.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-2.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-25.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-3.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-3.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-4.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/pre/1_2-dimethoxyethane.xyz (added) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-1.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-2.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-2.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-25.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-3.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-3.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-4.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/pre/1_2-dimethylbenzene.xyz (added) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-1.5.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-2.5.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-2.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-25.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-3.5.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-3.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-4.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/pre/2-methylcyclohexanone.xyz (added) * tests/Tesselations/NonConvex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-1.5.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-2.5.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-2.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-25.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-3.5.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-3.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-4.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/pre/N_N-dimethylacetamide.xyz (added) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-1.5.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-2.5.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-2.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-25.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-3.5.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-3.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-4.dat (moved) * tests/Tesselations/NonConvex/benzene/pre/benzene.xyz (added) * tests/Tesselations/NonConvex/benzene/testsuite-benzene.at (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-1.5.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-2.5.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-2.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-25.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-3.5.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-3.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-4.dat (moved) * tests/Tesselations/NonConvex/cholesterol/pre/cholesterol.xyz (added) * tests/Tesselations/NonConvex/cholesterol/testsuite-cholesterol.at (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-1.5.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-2.5.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-2.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-25.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-3.5.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-3.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-4.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/pre/cycloheptane.xyz (added) * tests/Tesselations/NonConvex/cycloheptane/testsuite-cycloheptane.at (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-1.5.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-2.5.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-2.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-25.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-3.5.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-3.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-4.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/pre/dimethyl_bromomalonate.xyz (added) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-1.5.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-2.5.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-2.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-25.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-3.5.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-3.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-4.dat (moved) * tests/Tesselations/NonConvex/glucose/pre/glucose.xyz (added) * tests/Tesselations/NonConvex/glucose/testsuite-glucose.at (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-1.5.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-2.5.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-2.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-25.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-3.5.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-3.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-4.dat (moved) * tests/Tesselations/NonConvex/heptan/pre/heptan.xyz (added) * tests/Tesselations/NonConvex/heptan/testsuite-heptan.at (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-1.5.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-2.5.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-2.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-25.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-3.5.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-3.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-4.dat (moved) * tests/Tesselations/NonConvex/isoleucine/pre/isoleucine.xyz (added) * tests/Tesselations/NonConvex/isoleucine/testsuite-isoleucine.at (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-1.5.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-2.5.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-2.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-25.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-3.5.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-3.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-4.dat (moved) * tests/Tesselations/NonConvex/neohexane/pre/neohexane.xyz (added) * tests/Tesselations/NonConvex/neohexane/testsuite-neohexane.at (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-1.5.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-2.5.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-2.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-25.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-3.5.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-3.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-4.dat (moved) * tests/Tesselations/NonConvex/proline/pre/proline.xyz (added) * tests/Tesselations/NonConvex/proline/testsuite-proline.at (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-1.5.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-2.5.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-2.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-25.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-3.5.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-3.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-4.dat (moved) * tests/Tesselations/NonConvex/putrescine/pre/putrescine.xyz (added) * tests/Tesselations/NonConvex/putrescine/testsuite-putrescine.at (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-1.5.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-2.5.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-2.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-25.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-3.5.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-3.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-4.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/pre/tartaric_acid.xyz (added) * tests/Tesselations/NonConvex/tartaric_acid/testsuite-tartaric_acid.at (moved) * tests/Tesselations/testsuite.at (modified) * tests/regression/Tesselation/BigConvex/post/ConvexEnvelope.dat (added) * tests/regression/Tesselation/BigConvex/post/ConvexEnvelope.r3d (added) * tests/regression/Tesselation/BigConvex/post/NonConvexEnvelope.dat (deleted) * tests/regression/Tesselation/BigConvex/post/NonConvexEnvelope.r3d (deleted) * tests/regression/Tesselation/BigConvex/post/test.conf (deleted) * tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * utils/developer/raster3d/header.r3d (added) * utils/developer/tcl/analyseconvexizing.tcl (added) * utils/developer/tcl/convexizing.tcl (added) Merge branch 'Fix_ConvexizeNonconvexEnvelope' into Candidate_v1.4.9 Sun, 19 Oct 2014 17:13:12 GMT Frederik Heber [33ee99] * tests/Tesselations/Convex/1_2-dimethoxyethane/pre/1_2-dimethoxyethane.xyz (moved) * tests/Tesselations/Convex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (added) * tests/Tesselations/Convex/1_2-dimethylbenzene/pre/1_2-dimethylbenzene.xyz (moved) * tests/Tesselations/Convex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (added) * tests/Tesselations/Convex/2-methylcyclohexanone/pre/2-methylcyclohexanone.xyz (moved) * tests/Tesselations/Convex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (added) * tests/Tesselations/Convex/N_N-dimethylacetamide/pre/N_N-dimethylacetamide.xyz (moved) * tests/Tesselations/Convex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (added) * tests/Tesselations/Convex/amylose/pre/amylose.pdb (added) * tests/Tesselations/Convex/amylose/testsuite-amylose.at (added) * tests/Tesselations/Convex/benzene/pre/benzene.xyz (moved) * tests/Tesselations/Convex/benzene/testsuite-benzene.at (added) * tests/Tesselations/Convex/cholesterol/pre/cholesterol.xyz (moved) * tests/Tesselations/Convex/cholesterol/testsuite-cholesterol.at (added) * tests/Tesselations/Convex/cycloheptane/pre/cycloheptane.xyz (moved) * tests/Tesselations/Convex/cycloheptane/testsuite-cycloheptane.at (added) * tests/Tesselations/Convex/dimethyl_bromomalonate/pre/dimethyl_bromomalonate.xyz (moved) * tests/Tesselations/Convex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (added) * tests/Tesselations/Convex/glucose/pre/glucose.xyz (moved) * tests/Tesselations/Convex/glucose/testsuite-glucose.at (added) * tests/Tesselations/Convex/heptan/pre/heptan.xyz (moved) * tests/Tesselations/Convex/heptan/testsuite-heptan.at (added) * tests/Tesselations/Convex/isoleucine/pre/isoleucine.xyz (moved) * tests/Tesselations/Convex/isoleucine/testsuite-isoleucine.at (added) * tests/Tesselations/Convex/neohexane/pre/neohexane.xyz (moved) * tests/Tesselations/Convex/neohexane/testsuite-neohexane.at (added) * tests/Tesselations/Convex/proline/pre/proline.xyz (moved) * tests/Tesselations/Convex/proline/testsuite-proline.at (added) * tests/Tesselations/Convex/putrescine/pre/putrescine.xyz (moved) * tests/Tesselations/Convex/putrescine/testsuite-putrescine.at (added) * tests/Tesselations/Convex/tartaric_acid/pre/tartaric_acid.xyz (moved) * tests/Tesselations/Convex/tartaric_acid/testsuite-tartaric_acid.at (added) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-1.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-2.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-2.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-25.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-3.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-3.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/post/NonConvexEnvelope-1_2-dimethoxyethane-4.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/pre/1_2-dimethoxyethane.xyz (added) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-1.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-2.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-2.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-25.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-3.5.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-3.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/post/NonConvexEnvelope-1_2-dimethylbenzene-4.dat (moved) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/pre/1_2-dimethylbenzene.xyz (added) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-1.5.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-2.5.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-2.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-25.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-3.5.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-3.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/post/NonConvexEnvelope-2-methylcyclohexanone-4.dat (moved) * tests/Tesselations/NonConvex/2-methylcyclohexanone/pre/2-methylcyclohexanone.xyz (added) * tests/Tesselations/NonConvex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-1.5.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-2.5.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-2.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-25.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-3.5.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-3.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/post/NonConvexEnvelope-N_N-dimethylacetamide-4.dat (moved) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/pre/N_N-dimethylacetamide.xyz (added) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-1.5.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-2.5.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-2.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-25.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-3.5.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-3.dat (moved) * tests/Tesselations/NonConvex/benzene/post/NonConvexEnvelope-benzene-4.dat (moved) * tests/Tesselations/NonConvex/benzene/pre/benzene.xyz (added) * tests/Tesselations/NonConvex/benzene/testsuite-benzene.at (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-1.5.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-2.5.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-2.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-25.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-3.5.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-3.dat (moved) * tests/Tesselations/NonConvex/cholesterol/post/NonConvexEnvelope-cholesterol-4.dat (moved) * tests/Tesselations/NonConvex/cholesterol/pre/cholesterol.xyz (added) * tests/Tesselations/NonConvex/cholesterol/testsuite-cholesterol.at (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-1.5.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-2.5.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-2.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-25.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-3.5.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-3.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/post/NonConvexEnvelope-cycloheptane-4.dat (moved) * tests/Tesselations/NonConvex/cycloheptane/pre/cycloheptane.xyz (added) * tests/Tesselations/NonConvex/cycloheptane/testsuite-cycloheptane.at (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-1.5.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-2.5.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-2.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-25.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-3.5.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-3.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/post/NonConvexEnvelope-dimethyl_bromomalonate-4.dat (moved) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/pre/dimethyl_bromomalonate.xyz (added) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-1.5.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-2.5.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-2.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-25.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-3.5.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-3.dat (moved) * tests/Tesselations/NonConvex/glucose/post/NonConvexEnvelope-glucose-4.dat (moved) * tests/Tesselations/NonConvex/glucose/pre/glucose.xyz (added) * tests/Tesselations/NonConvex/glucose/testsuite-glucose.at (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-1.5.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-2.5.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-2.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-25.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-3.5.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-3.dat (moved) * tests/Tesselations/NonConvex/heptan/post/NonConvexEnvelope-heptan-4.dat (moved) * tests/Tesselations/NonConvex/heptan/pre/heptan.xyz (added) * tests/Tesselations/NonConvex/heptan/testsuite-heptan.at (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-1.5.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-2.5.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-2.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-25.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-3.5.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-3.dat (moved) * tests/Tesselations/NonConvex/isoleucine/post/NonConvexEnvelope-isoleucine-4.dat (moved) * tests/Tesselations/NonConvex/isoleucine/pre/isoleucine.xyz (added) * tests/Tesselations/NonConvex/isoleucine/testsuite-isoleucine.at (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-1.5.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-2.5.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-2.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-25.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-3.5.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-3.dat (moved) * tests/Tesselations/NonConvex/neohexane/post/NonConvexEnvelope-neohexane-4.dat (moved) * tests/Tesselations/NonConvex/neohexane/pre/neohexane.xyz (added) * tests/Tesselations/NonConvex/neohexane/testsuite-neohexane.at (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-1.5.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-2.5.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-2.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-25.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-3.5.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-3.dat (moved) * tests/Tesselations/NonConvex/proline/post/NonConvexEnvelope-proline-4.dat (moved) * tests/Tesselations/NonConvex/proline/pre/proline.xyz (added) * tests/Tesselations/NonConvex/proline/testsuite-proline.at (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-1.5.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-2.5.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-2.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-25.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-3.5.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-3.dat (moved) * tests/Tesselations/NonConvex/putrescine/post/NonConvexEnvelope-putrescine-4.dat (moved) * tests/Tesselations/NonConvex/putrescine/pre/putrescine.xyz (added) * tests/Tesselations/NonConvex/putrescine/testsuite-putrescine.at (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-1.5.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-2.5.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-2.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-25.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-3.5.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-3.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/post/NonConvexEnvelope-tartaric_acid-4.dat (moved) * tests/Tesselations/NonConvex/tartaric_acid/pre/tartaric_acid.xyz (added) * tests/Tesselations/NonConvex/tartaric_acid/testsuite-tartaric_acid.at (moved) * tests/Tesselations/testsuite.at (modified) TESTS: Extended Tesselations tests to convex case. - moved all ... Sun, 19 Oct 2014 17:13:12 GMT Frederik Heber [565695] * tests/regression/Tesselation/BigConvex/post/ConvexEnvelope.dat (added) * tests/regression/Tesselation/BigConvex/post/ConvexEnvelope.r3d (added) * tests/regression/Tesselation/BigConvex/post/NonConvexEnvelope.dat (deleted) * tests/regression/Tesselation/BigConvex/post/NonConvexEnvelope.r3d (deleted) * tests/regression/Tesselation/BigConvex/post/test.conf (deleted) * tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) TESTFIX: Regression test Tesselation/BigConvex is now working. Sun, 19 Oct 2014 17:13:12 GMT Frederik Heber [5f7b95] * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/boundary.hpp (modified) * tests/Python/AllActions/options.dat (modified) Convex-envelope has debug parameter DoOutputEveryStep. - this ... Sun, 19 Oct 2014 17:13:12 GMT Frederik Heber [bcb831] * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) Added SphereRadius parameter to ConvexEnvelopeAction. Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [991c35] * utils/developer/tcl/analyseconvexizing.tcl (added) * utils/developer/tcl/convexizing.tcl (added) Added tcl scripts for viewing and debugging convexized surfaces. Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [8544b32] * doc/userguide/userguide.xml (modified) * src/documentation/constructs/tesselation.dox (modified) DOCU: Added extensive explanation how convexization works. - ... Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [e2396e] * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) Added check whether all points remain inside surface and whether it ... Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [aac19f] * src/Tesselation/boundary.cpp (modified) ConvexizeNonconvexEnvelope() uses now ... Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [2ef2cc] * src/Tesselation/boundary.cpp (modified) FIX: ConvexizeNonconvexEnvelope() needs to purge degenerate triangles ... Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [81ffd8] * src/Tesselation/boundary.cpp (modified) FIX: GainMap is used to store the concavity angle, we flip now always ... Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [d289c6] * src/Tesselation/boundary.cpp (modified) Rewrote ConvexizeNonconvexEnvelope(). - now works for some sphere ... Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [6da9e9] * src/Tesselation/tesselation.cpp (modified) FIX: Tesselation::RemoveDegeneratedTriangles() ended up in endless ... Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [30ce7d] * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) Extracted RemovePointSurroundedByPolygon() out of ... Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [77eec5] * src/Tesselation/tesselation.cpp (modified) FIX: Removed flipping for maximal gain in ... Sun, 19 Oct 2014 17:13:11 GMT Frederik Heber [e26c35] * src/Tesselation/tesselation.cpp (modified) FIX: Tesselation::RemovePointFromTesselatedSurface() uses wrong ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [d45a5b] * src/Tesselation/tesselation.cpp (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) FIX: Tesselation::getVolumeOfConvexEnvelope() calculated volume ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [32d7e4] * src/Tesselation/tesselation.cpp (modified) FIX: Tesselation::FlipBaseline() caclculated NormalVectors wrong. - ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [d33bb8] * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) Added Tesselation::IsPointBelowSurroundingPolygon(). - ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [f1ae15] * src/Tesselation/tesselation.cpp (modified) FIX: Filling of non-convex polygon with only minimal angles did not ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [c2c786] * src/Tesselation/tesselation.cpp (modified) FIX: RemovePointFromTesselatedSurface() used Start,Middle,EndNode ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [6d5280] * LinearAlgebra/src/LinearAlgebra/Line.cpp (modified) FIX: Reduced verbosity noise from Line::getIntersection(). - ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [b8d215] * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) Changed some verbosities in Tesselation code. - modifications in ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [dfe054] * src/Tesselation/tesselationhelpers.cpp (modified) DOCUFIX: Corrected formula for general tetrahedron in docu. - also ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [75d42a] * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselation.hpp (modified) FIX: RemovePointFromTesselatedSurface() needs to pick smallest angle ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [c2f306] * src/Tesselation/tesselation.cpp (modified) FIX: RemoveTesselationLine() needs to erase line from OpenLines if ... Sun, 19 Oct 2014 17:13:10 GMT Frederik Heber [bb86bd] * src/Tesselation/tesselation.cpp (modified) FIX: AddTesselationLine() would only work in initial tesselation ... Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [613790] * src/Tesselation/tesselation.cpp (modified) FIX: Changed all performCriticalExit() into ASSERT() in tesselation. Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [cead3f] * doc/userguide/userguide.xml (modified) * utils/developer/raster3d/header.r3d (added) FIX: Raster3D needs header.r3d, which had been missing so far. Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [cfb9c5] * src/Actions/ActionQueue.cpp (modified) FIX: Setting ActionQueue::_lastchangedaction without heeding whether ... Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [1b6cec] * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) FIX: QSeisPlotPage's dstor calls deinitializeLayout() only when ... Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [7d320c] * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) MEMFIX: Static coordinator instances of specificv potentials need to ... Sun, 19 Oct 2014 17:13:09 GMT Frederik Heber [4da4de] * configure.ac (modified) * m4/boost.m4 (modified) FIX: Added Boost::MultiIndexContainer check for MemDebug. - this ... Sun, 19 Oct 2014 17:12:37 GMT Frederik Heber [3b1798] * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.hpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FIX: QtHomologyList's plot widget was too high (and fixed). - also ... Sun, 19 Oct 2014 17:12:11 GMT Frederik Heber [5c8807] * doc/userguide/userguide.xml (modified) * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.def (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.hpp (added) * src/Actions/AtomAction/TranslateToOriginAction.cpp (added) * src/Actions/AtomAction/TranslateToOriginAction.def (added) * src/Actions/AtomAction/TranslateToOriginAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted-weighted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/pre/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'Experiment_Amylose_Water' into Candidate_v1.4.9 ... Sun, 19 Oct 2014 17:10:16 GMT Frederik Heber [b119a0] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/TesselPoint.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/World.cpp (modified) * src/molecule_geometry.cpp (modified) Merge branch 'DynamicMolecules' into Candidate_v1.4.9 Sun, 19 Oct 2014 17:09:30 GMT Frederik Heber [9e1bfb] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.hpp (added) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (added) * src/Actions/PotentialAction/ParsePotentialsAction.def (added) * src/Actions/PotentialAction/ParsePotentialsAction.hpp (added) * src/Actions/PotentialAction/SavePotentialsAction.cpp (added) * src/Actions/PotentialAction/SavePotentialsAction.def (added) * src/Actions/PotentialAction/SavePotentialsAction.hpp (added) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialTrainer.cpp (added) * src/Potentials/PotentialTrainer.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Merge branch 'Refactoring_PotentialActions' into Candidate_v1.4.9 Sun, 19 Oct 2014 17:08:51 GMT Frederik Heber [0ea063] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Actions/PotentialAction/SavePotentialsAction.cpp (added) * src/Actions/PotentialAction/SavePotentialsAction.def (added) * src/Actions/PotentialAction/SavePotentialsAction.hpp (added) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/PotentialTrainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Extracted SavePotentialsAction. - PotentialTrainer::StorePotentials ... Sun, 19 Oct 2014 17:08:50 GMT Frederik Heber [f1eabd] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (added) * src/Actions/PotentialAction/ParsePotentialsAction.def (added) * src/Actions/PotentialAction/ParsePotentialsAction.hpp (added) * tests/Python/AllActions/options.dat (modified) Extracted ParsePotentialsAction from FitCompoundPotentialAction. Sun, 19 Oct 2014 17:08:36 GMT Frederik Heber [98d166] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (added) * src/Actions/PotentialAction/FitCompoundPotentialAction.hpp (added) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialTrainer.cpp (added) * src/Potentials/PotentialTrainer.hpp (added) Split FitPotentialAction into two actions. - FitPotentialAction ... Fri, 19 Sep 2014 07:10:04 GMT Frederik Heber [2ed3bf] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/MirrorAction.cpp (added) * src/Actions/AtomAction/MirrorAction.def (added) * src/Actions/AtomAction/MirrorAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Atoms/Mirror/post/test-mirrored.xyz (added) * tests/regression/Atoms/Mirror/post/test.xyz (added) * tests/regression/Atoms/Mirror/pre/test.xyz (added) * tests/regression/Atoms/Mirror/testsuite-atoms-mirror.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Merge branch 'MirrorAtoms' into Candidate_v1.4.9 Fri, 19 Sep 2014 07:09:53 GMT Frederik Heber [7acbfc] * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) Merge branch 'ActionFixes' into Candidate_v1.4.9 Thu, 18 Sep 2014 23:32:23 GMT Frederik Heber [bbf6dc] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/MirrorAction.cpp (added) * src/Actions/AtomAction/MirrorAction.def (added) * src/Actions/AtomAction/MirrorAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Atoms/Mirror/post/test-mirrored.xyz (added) * tests/regression/Atoms/Mirror/post/test.xyz (added) * tests/regression/Atoms/Mirror/pre/test.xyz (added) * tests/regression/Atoms/Mirror/testsuite-atoms-mirror.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added AtomMirrorAction. - also added regression tests. Thu, 18 Sep 2014 18:24:53 GMT Frederik Heber [46ce1c] * src/World.cpp (modified) FIX: World::setTime() now first copies Bondgraph and then sets the ... Thu, 18 Sep 2014 18:24:51 GMT Frederik Heber [8cc22f] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/TesselPoint.hpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/molecule_geometry.cpp (modified) Changed how trajectories are stored, not as vecor but as map. - ... Thu, 18 Sep 2014 17:23:14 GMT Frederik Heber [c7fe90] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/TranslateToOriginAction.cpp (added) * src/Actions/AtomAction/TranslateToOriginAction.def (added) * src/Actions/AtomAction/TranslateToOriginAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted-weighted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test-shifted.xyz (added) * tests/regression/Atoms/TranslationToOrigin/post/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/pre/test.xyz (added) * tests/regression/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added TranslateToOriginAction. - also added regression test. Thu, 18 Sep 2014 17:19:38 GMT Frederik Heber [f4b626a] * doc/userguide/userguide.xml (modified) * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.def (added) * src/Actions/AnalysisAction/AverageMoleculeForceAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) Added AverageMoleculeForceAction for measuring average force acting ... Wed, 17 Sep 2014 22:30:50 GMT Frederik Heber [7a7b34] * src/Atom/atom.cpp (modified) FIX: atom's copy cstor does not need to copy positions, ... again. Wed, 17 Sep 2014 22:30:29 GMT Frederik Heber [054d47] * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) FIX: (Not)AtomByIdAction would fail with assert if not atoms are ... Wed, 17 Sep 2014 21:30:38 GMT Frederik Heber [9bce96] * doc/userguide/userguide.xml (modified) DOCU: Fixed all missing links in userguide. - each section now has ... Wed, 17 Sep 2014 21:29:44 GMT Frederik Heber [f73e06] * doc/userguide/userguide.xml (modified) * tests/CodeChecks/testsuite-action_present_in_userguide.at (modified) DOCU: Added all missing Actions to userguide. - removed XFAIL from ... Wed, 17 Sep 2014 19:44:31 GMT Frederik Heber [c62e27] * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-action_present_in_userguide.at (added) * tests/CodeChecks/testsuite.at (modified) Added CodeChecks test that every action appears in the userguide. - ... Wed, 17 Sep 2014 19:44:31 GMT Frederik Heber [2a6d8c] * src/Fragmentation/Exporters/SaturationDistanceMaximizer.hpp (modified) DOCUFIX: Doyxygen formula was broken in SaturationDistanceMaximizer. Wed, 17 Sep 2014 19:44:31 GMT Frederik Heber [ced7f0] * src/Actions/CommandAction/VersionAction.cpp (modified) VersionAction also prints to log, not only to status. Wed, 17 Sep 2014 17:03:30 GMT Frederik Heber [7f6a2f] * configure.ac (modified) Set version to 1.4.8. - MoleCuilder library is now 14:1:0. - ... Tue, 16 Sep 2014 06:21:20 GMT Frederik Heber [06b5df] * src/Actions/ActionQueue.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) FIX: CommandLineParser causes idling thread when parsing goes wrong. ... Mon, 15 Sep 2014 21:46:01 GMT Frederik Heber [7e1a88] * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) MEMFIX: Thrown ParserException causes mem leak in LoadAction - also ...