# # ChangeLog for / # # Generated by Trac 1.4.4 # Mar 22, 2025, 2:23:42 PM Sun, 11 Oct 2015 07:11:38 GMT Frederik Heber [e3c4c5] * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * tests/regression/Atoms/Add/post/test.in (modified) * tests/regression/Atoms/Remove/post/test.in (modified) * tests/regression/Parser/Mpqc/post/doublewater.in (modified) * tests/regression/Parser/Mpqc/post/empty.in (modified) * tests/regression/Parser/Mpqc/post/test.in (modified) * tests/regression/Parser/Mpqc/post/testCLHF.in (modified) * tests/regression/Parser/Mpqc/post/testCLKS.in (modified) * tests/regression/Parser/Mpqc/post/testMBPT2.in (modified) * tests/regression/Parser/Mpqc/post/testMBPT2_R12.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF_n.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF_n_ascend_ids.in (modified) * tests/regression/Parser/Mpqc/pre/testCLHF_n_mixed_ids.in (modified) * tests/regression/Parser/Mpqc/pre/testCLKS.in (modified) * tests/regression/Parser/Mpqc/pre/testMBPT2.in (modified) * tests/regression/Parser/Mpqc/pre/testMBPT2_R12.in (modified) * tests/regression/Parser/Mpqc/pre/water.in (modified) * tests/regression/Parser/SetParameters/Mpqc/post/testCLHF.in (modified) * tests/regression/Parser/SetParameters/Mpqc/pre/testCLHF.in (modified) MpqcParser additionally allows to save optimization jobs. - this is ... Sun, 11 Oct 2015 07:11:38 GMT Frederik Heber [6c30ab] * src/Fragmentation/Exporters/SaturatedBond.cpp (modified) Assertion in SaturateBond now states element. Sun, 11 Oct 2015 07:11:38 GMT Frederik Heber [d79ca1] * src/Actions/AtomAction/SaturateAction.cpp (modified) * tests/regression/Atoms/Saturate/post/saturated_carbon.xyz (modified) * tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz (modified) FIX: SaturateAction would use double instead of single hydrogen bond ... Sun, 11 Oct 2015 07:11:38 GMT Frederik Heber [2a7dbe] * src/Actions/WorldAction/SetBoundaryConditionsAction.def (modified) FIX: Help on SetBoundaryConditionsAction did not have capitalized ... Sun, 11 Oct 2015 07:09:51 GMT Frederik Heber [08d9df7] * debian/control (modified) * makeDebianPackage.sh (modified) FIX: Rename codepatterns -> libcodepatterns. - updated ... Sun, 11 Oct 2015 07:09:42 GMT Frederik Heber [ba3539] * LinearAlgebra-debug.pc.in (modified) * MoleCuilder.pc.in (modified) * m4/ax_codepatterns.m4 (modified) Package CodePatterns is now called libcodepatterns. - updated m4 ... Thu, 13 Aug 2015 21:53:14 GMT Frederik Heber [bff5e2] * configure.ac (modified) Set version to 1.5.0. - MoleCuilder library is now 15:0:0. - ... Thu, 13 Aug 2015 21:52:27 GMT Frederik Heber [5284ff] * src/UIElements/Qt4/QtUIFactory.cpp (modified) FIX: This prevent crash of molecuildergui in debian package. - ... Thu, 13 Aug 2015 21:52:27 GMT Frederik Heber [57c253] * tests/CodeChecks/testsuite-config_h.at (modified) * tests/CodeChecks/testsuite-memdebug.at (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) TESTFIX: for source builds we need to exclude all moc'ed files from ... Thu, 13 Aug 2015 21:52:27 GMT Frederik Heber [196702] * configure.ac (modified) FIX: Qt can now be found even without --with-Qtbin... Thu, 13 Aug 2015 21:52:27 GMT Frederik Heber [65ca73] * tests/Fragmentations/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) * tests/Python/Makefile.am (modified) * tests/Tesselations/Makefile.am (modified) * tests/regression/Makefile.am (modified) DISTFIX: EXTRA_DIST in tests/../Makefile.ams depended on not yet set ... Thu, 13 Aug 2015 21:52:27 GMT Frederik Heber [66b092] * Makefile.am (modified) * debian/control (modified) * debian/molecuilder-dev.install (added) * debian/molecuilder.install (added) * debian/rules (modified) Added debugging package molecuilder-dbg and source package ... Thu, 13 Aug 2015 21:52:27 GMT Frederik Heber [8fbd7b] * debian/rules (modified) Enabled GUI compilation for debian package. Thu, 13 Aug 2015 21:52:26 GMT Frederik Heber [b8b2e6] * makeDebianPackage.sh (added) Added script for creating debian package. Thu, 13 Aug 2015 21:52:26 GMT Frederik Heber [d68514] * Makefile.am (modified) * debian/changelog (added) * debian/compat (added) * debian/control (added) * debian/copyright (added) * debian/rules (added) * debian/source/format (added) Added debian/.. files for debian packaging. - added all ... Fri, 07 Aug 2015 22:38:46 GMT Frederik Heber [b8f0a8d] * utils/Bash/Makefile.am (modified) * utils/Python/Makefile.am (modified) FIX: bash_completion was accidentally removed by clean target. - ... Fri, 07 Aug 2015 22:38:46 GMT Frederik Heber [3995711] * src/documentation/install.dox (modified) DOCU: Described workaround for missing pyconfig.h. Fri, 07 Aug 2015 22:38:46 GMT Frederik Heber [d07a38] * tests/CodeChecks/testsuite-config_h.at (modified) FIX: AllPotentialHealder.hpp not excluded from CodeCheck config_h. ... Wed, 05 Aug 2015 17:32:13 GMT Frederik Heber [6fe4f7] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) FIX: updateBoundingBox() must not call molecule::getBoundingBox() on ... Wed, 05 Aug 2015 17:32:13 GMT Frederik Heber [ec8471] * src/UIElements/Makefile.am (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/QDebugStream.hpp (modified) * src/UIElements/Views/Qt4/QtLogBox.cpp (modified) * src/UIElements/Views/Qt4/QtLogBox.hpp (modified) FIX: QtLogBox is again included and working thread-safe. - ... Wed, 05 Aug 2015 17:32:13 GMT Frederik Heber [b9e47e] * tests/GuiChecks/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at (modified) * tests/GuiChecks/Molecules/Translation/testsuite-molecules-translation.at (modified) * utils/developer/createGuiChecks.sh (modified) TESTFIX: Marked molecule translation guicheck tests as XFAIL. - so ... Wed, 05 Aug 2015 17:32:13 GMT Frederik Heber [7e2adc] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) FIX: GLMoleculeObject_bond had both flipped ids and the side. - in ... Wed, 05 Aug 2015 17:32:12 GMT Frederik Heber [a9161d] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtShapeList.cpp (modified) FIX: GLWorldView and QtShapeList do not assert single source in ... Wed, 05 Aug 2015 17:32:12 GMT Frederik Heber [07136a] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.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) FIX: Fixing display of shapes in GLWorldView. - we propagate shape ... Wed, 05 Aug 2015 17:32:12 GMT Frederik Heber [369cb1] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) GLWorldScene lacked assert of Walker in atomClicked(). Wed, 05 Aug 2015 17:32:12 GMT Frederik Heber [92ee41] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) Asserted that GLMoleculeObject_molecule::update() is never called. Wed, 05 Aug 2015 17:32:12 GMT Frederik Heber [ca4b63b] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) AddAtomBonds() now uses just id not ptr as param. Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [68989c] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) Avoided use of getId() on molecules and atoms in Qt code where ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [25a81d] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) GLMoleculeObject_molecule does not use getAtomCount() anymore. - ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [5b61e5] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) GLMoleculeObject_molecule also has ObservedValue for name. - this ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [07b800] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) FIX: Setting molecule's name via QtMoleculeList item is again ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [a39d72] * 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/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) Fixed formula usage in Qt part of code. - formula of a molecule is ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [015f8c] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * 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) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.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) QtMainWindow uses QtSelectionChangedAgent. - QtMoleculeListView and ... Wed, 05 Aug 2015 17:32:11 GMT Frederik Heber [e5a477] * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/QtSelectionChangedAgent.cpp (added) * src/UIElements/Views/Qt4/QtSelectionChangedAgent.hpp (added) Added QtSelectionChangedAgent to transform O/O to S/S system. - ... Wed, 05 Aug 2015 17:32:10 GMT Frederik Heber [cc2976] * 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) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) QtMoleculeItem_.. now shout when they receive subjectKilled(). - ... Wed, 05 Aug 2015 17:32:10 GMT Frederik Heber [b9680b] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (modified) FIX: Fixing "pure virtual function called" in QtMoleculeItem. - as ... Wed, 05 Aug 2015 17:32:10 GMT Frederik Heber [f02b53] * src/World.cpp (modified) World now first releases id and then destroys the atom/molecule. - ... Wed, 05 Aug 2015 17:32:10 GMT Frederik Heber [5be798] * src/molecule.cpp (modified) * src/molecule.hpp (modified) Removed molecule::lastChanged(). - we have lastChangedAtomId() and ... Wed, 05 Aug 2015 17:32:10 GMT Frederik Heber [54bdaa] * src/Parser/FormatParser_common.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) Qt4 instance use new lastChanged..Id() in place of lastChanged(). - ... Wed, 05 Aug 2015 17:32:09 GMT Frederik Heber [fb95a5] * src/World.cpp (modified) * src/World.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) Added lastChanged..Id() to both World and molecule. Wed, 05 Aug 2015 17:32:09 GMT Frederik Heber [f714763] * 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) GLWorldView no longer listens to WorldTime::TimeChanged. - ... Wed, 05 Aug 2015 17:32:09 GMT Frederik Heber [3d5b5b] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) GLWorldView does not emit changed() on each general update() from the ... Wed, 05 Aug 2015 17:32:09 GMT Frederik Heber [52c5d4] * src/documentation/constructs/qt-gui.dox (modified) DOCU: Updated documentation on Qt Gui construct. Wed, 05 Aug 2015 17:32:09 GMT Frederik Heber [fcdf05] * 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) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_occurrence.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (modified) * src/UIElements/Views/Qt4/QtElementList.hpp (modified) Fixing QtMoleculeList with list containing only formulas and ids. - ... Wed, 05 Aug 2015 17:32:08 GMT Frederik Heber [95f49f] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) QtMoleculeList::informDirtyState() does not need to lock refill_mutex ... Wed, 05 Aug 2015 17:32:08 GMT Frederik Heber [88846b] * src/UIElements/Views/Qt4/QtElementList.cpp (modified) Fixing QtElementList::updateElement(). Wed, 05 Aug 2015 17:32:08 GMT Frederik Heber [20f9b5] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) GLWorldScene propagates changed mol id to GLMoleculeObject_molecule. ... Wed, 05 Aug 2015 17:32:08 GMT Frederik Heber [6c16a0] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) GLMoleculeObject_molecule uses ObservedValue for internally ... Wed, 05 Aug 2015 17:32:08 GMT Frederik Heber [3e52834] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_atomcount.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_formula.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_name.hpp (modified) * src/UIElements/Views/Qt4/MoleculeList/SpecificItems/QtMoleculeItem_visibility.hpp (modified) QtMoleculeItem_... use ObservedValue for internally representing ... Wed, 05 Aug 2015 17:32:07 GMT Frederik Heber [009e2e2] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) GLMoleculeObject_bond uses ObservedValue for internally representing ... Wed, 05 Aug 2015 17:32:07 GMT Frederik Heber [534374] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) GLMoleculeObject_atom uses ObservedValue for internally representing ... Wed, 05 Aug 2015 17:32:07 GMT Frederik Heber [b3a33d] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) Removed init() and signal WorldSelectionChanged() from GLWorldScene. Wed, 05 Aug 2015 17:32:07 GMT Frederik Heber [574d377] * configure.ac (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionStatusList.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Shapes/unittests/stubs/WorldSelectedMoleculesStub.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/cleanUp.cpp (modified) * src/molecule.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) Using static Observable::..NotificationsChannel() functions. - ... Wed, 05 Aug 2015 07:12:24 GMT Frederik Heber [0ea4dd] * configure.ac (modified) Set version to v1.4.12. Wed, 05 Aug 2015 07:12:24 GMT Frederik Heber [c307ba] * src/documentation/tests/tests.dox (modified) DOCU: Enhanced description of test policy on version update. Wed, 05 Aug 2015 07:12:24 GMT Frederik Heber [10aee4] * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionRegistry.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/documentation/constructs/actions.dox (modified) Cleaned up ActionQueue's interface: Actions are always cloned. - ... Wed, 05 Aug 2015 07:12:09 GMT Frederik Heber [94232b] * src/Actions/Action.cpp (modified) * src/Actions/Action.hpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/ActionMenuItem.hpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.cpp (modified) * src/UIElements/Menu/TextMenu/MenuItem.hpp (modified) Action::isActive() is now const member function. - also changed ... Mon, 03 Aug 2015 15:03:34 GMT Frederik Heber [725a1d] * src/Bond/AdjacencyMatcher/Adjacency.hpp (modified) FIX: Adjacency's operator<<() printed fixed number (3) of entries. ... Mon, 03 Aug 2015 15:03:34 GMT Frederik Heber [3532b7] * src/Bond/AdjacencyMatcher/Makefile.am (modified) * src/Tesselation/TriangleMatcher/Makefile.am (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/adjacencymatcher.in (modified) * tests/GuiChecks/trianglematcher.in (modified) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/trianglematcher.in (modified) * tests/regression/Makefile.am (modified) * tests/regression/adjacencymatcher.in (modified) * tests/regression/trianglematcher.in (modified) DISTFIX: adjacencymatcher and trianglematcher are check_PROGRAMS, not ... Fri, 31 Jul 2015 09:27:06 GMT Frederik Heber [8e790eb] * src/Bond/AdjacencyMatcher/Makefile.am (modified) DISTFIX: Additional types.hpp in AdjacencyMatcher/Makefile.am. Wed, 29 Jul 2015 18:15:49 GMT Frederik Heber [c66ae6] * Makefile.am (modified) * configure.ac (modified) * src/Bond/AdjacencyMatcher/Adjacency.hpp (added) * src/Bond/AdjacencyMatcher/AdjacencyMatcher.cpp (added) * src/Bond/AdjacencyMatcher/Makefile.am (added) * src/Tesselation/TriangleMatcher/TriangleMatcher.cpp (modified) * tests/GuiChecks/Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at (added) * tests/GuiChecks/Bond/testsuite-bond.at (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) * tests/GuiChecks/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at (modified) * tests/GuiChecks/adjacencymatcher.in (added) * tests/regression/Bond/AdjacencyMatcher/pre/notequal.adj (added) * tests/regression/Bond/AdjacencyMatcher/pre/notequal2.adj (added) * tests/regression/Bond/AdjacencyMatcher/pre/test.adj (added) * tests/regression/Bond/AdjacencyMatcher/pre/test2.adj (added) * tests/regression/Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at (added) * tests/regression/Bond/testsuite-bond.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) * tests/regression/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at (modified) * tests/regression/adjacencymatcher.in (added) TESTFIX: Added AdjacencyMatcher to correctly compare .adj files in ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [f7054c] * tests/GuiChecks/Selection/Molecules/MoleculeByName/testsuite-selection-select-molecules-by-name.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeByName/testsuite-selection-unselect-molecules-by-name.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-select-molecules-by-name.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-unselect-molecules-by-name.at (modified) TESTFIX: selection molecule by name had escaped ticks. - also ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [80f678] * src/Parameters/Makefile.am (modified) * src/Parameters/Specifics/Value_elements.cpp (added) * src/Parameters/Specifics/Value_elements.hpp (added) FIX: Added Parameters Value_Elements to correctly set vector of ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [c56922] * tests/GuiChecks/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified) * tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified) TESTFIX: regression test DepthFirstSearch had extra linebreak. Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [024c65] * tests/GuiChecks/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) * tests/GuiChecks/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) * tests/GuiChecks/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) * tests/GuiChecks/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/GuiChecks/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (modified) * tests/GuiChecks/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) * tests/GuiChecks/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid-with-defaults.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-select-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-unselect-atoms-inside-cuboid.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-select-atoms-inside-tiny-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-sphere.at (modified) * tests/regression/Selection/Atoms/AtomsInsideSphere/testsuite-selection-unselect-atoms-inside-tiny-sphere.at (modified) TESTFIX: atom selection regression tests with shapes were very noisy ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [7a0456] * tests/GuiChecks/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified) * tests/regression/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified) TESTFIX: regression test SubgraphDissection Redo was broken. - also ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [42b40a] * configure.ac (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at (added) * tests/GuiChecks/trianglematcher.in (added) Added TriangleMatcher to safely compare tesselation .dat files. - ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [a82f61] * src/Actions/Action.hpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/Action_impl_header.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Calculation.hpp (modified) * src/Actions/Calculation_impl.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/ManipulateAtomsProcess.hpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MethodAction.hpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.cpp (modified) * src/UIElements/Menu/TextMenu/TxMenuLeaveAction.hpp (modified) Added Action::setOptionValue() which allows setting the option via a ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [143263] * src/Helpers/helpers.hpp (modified) * src/World.cpp (modified) * src/World.hpp (modified) Added getSelected..Ids() for both atoms and molecules. - added ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [fe0ddf] * src/Atom/atom_atominfo.cpp (modified) FIX: atom_atominfo lacked some notifies or had them wrong. - ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [f54524] * src/molecule.cpp (modified) * src/molecule.hpp (modified) FIX: Molecule has new signal IndexChanged. - this has been ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [c6719d] * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticle.hpp (modified) FIX: atom_bondedparticle signatures changed to more const versions. ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [df3f2f] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) Group item with atom count of 0 is confusing in QtMoleculeList, ... Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [a963cf] * src/Python/PythonScripting.cpp (modified) executePythonScriptFile() calls executePythonScript() now. Tue, 28 Jul 2015 14:03:59 GMT Frederik Heber [883ea0] * src/UIElements/Qt4/QtUIFactory.cpp (modified) FIX: QTUIFactory's test-single was not working right. Tue, 28 Jul 2015 13:42:52 GMT Frederik Heber [561b94] * tests/GuiChecks/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (modified) * tests/regression/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (modified) FIX: tests/regression FragmentationAutomation had a white space after ... Tue, 28 Jul 2015 13:42:51 GMT Frederik Heber [f27c2c] * tests/GuiChecks/Makefile.am (modified) FIX: Added molecuilderguitest to testsuite dependencies. Tue, 28 Jul 2015 13:42:43 GMT Frederik Heber [7d146a] * Makefile.am (modified) * configure.ac (modified) * src/Tesselation/TriangleMatcher/Makefile.am (added) * src/Tesselation/TriangleMatcher/Triangle.hpp (added) * src/Tesselation/TriangleMatcher/TriangleMatcher.cpp (added) * src/Tesselation/TriangleMatcher/types.hpp (added) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) * tests/GuiChecks/Tesselation/testsuite-tesselation.at (modified) * tests/Tesselations/Convex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (modified) * tests/Tesselations/Convex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (modified) * tests/Tesselations/Convex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (modified) * tests/Tesselations/Convex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (modified) * tests/Tesselations/Convex/amylose/testsuite-amylose.at (modified) * tests/Tesselations/Convex/benzene/testsuite-benzene.at (modified) * tests/Tesselations/Convex/cholesterol/testsuite-cholesterol.at (modified) * tests/Tesselations/Convex/cycloheptane/testsuite-cycloheptane.at (modified) * tests/Tesselations/Convex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (modified) * tests/Tesselations/Convex/glucose/testsuite-glucose.at (modified) * tests/Tesselations/Convex/heptan/testsuite-heptan.at (modified) * tests/Tesselations/Convex/isoleucine/testsuite-isoleucine.at (modified) * tests/Tesselations/Convex/neohexane/testsuite-neohexane.at (modified) * tests/Tesselations/Convex/proline/testsuite-proline.at (modified) * tests/Tesselations/Convex/putrescine/testsuite-putrescine.at (modified) * tests/Tesselations/Convex/tartaric_acid/testsuite-tartaric_acid.at (modified) * tests/Tesselations/Makefile.am (modified) * tests/Tesselations/NonConvex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (modified) * tests/Tesselations/NonConvex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (modified) * tests/Tesselations/NonConvex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (modified) * tests/Tesselations/NonConvex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (modified) * tests/Tesselations/NonConvex/benzene/testsuite-benzene.at (modified) * tests/Tesselations/NonConvex/cholesterol/testsuite-cholesterol.at (modified) * tests/Tesselations/NonConvex/cycloheptane/testsuite-cycloheptane.at (modified) * tests/Tesselations/NonConvex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (modified) * tests/Tesselations/NonConvex/glucose/testsuite-glucose.at (modified) * tests/Tesselations/NonConvex/heptan/testsuite-heptan.at (modified) * tests/Tesselations/NonConvex/isoleucine/testsuite-isoleucine.at (modified) * tests/Tesselations/NonConvex/neohexane/testsuite-neohexane.at (modified) * tests/Tesselations/NonConvex/proline/testsuite-proline.at (modified) * tests/Tesselations/NonConvex/putrescine/testsuite-putrescine.at (modified) * tests/Tesselations/NonConvex/tartaric_acid/testsuite-tartaric_acid.at (modified) * tests/Tesselations/trianglematcher.in (added) * tests/regression/Makefile.am (modified) * tests/regression/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at (modified) * tests/regression/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at (modified) * tests/regression/Tesselation/Convex/testsuite-tesselation-convex-envelope.at (modified) * tests/regression/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at (modified) * tests/regression/Tesselation/TriangleMatcher/pre/convex.dat (added) * tests/regression/Tesselation/TriangleMatcher/pre/convex_none.dat (added) * tests/regression/Tesselation/TriangleMatcher/pre/convex_other.dat (added) * tests/regression/Tesselation/TriangleMatcher/testsuite-tesselation-trianglematcher.at (added) * tests/regression/Tesselation/testsuite-tesselation.at (modified) * tests/regression/trianglematcher.in (added) Added TriangleMatcher to safely compare tesselation .dat files. - ... Sat, 25 Jul 2015 13:02:12 GMT Frederik Heber [d4c869] * src/Actions/MakroAction_impl_pre.hpp (modified) FIX: MakroAction's outputAsPython() uses outputAsPython() not ... Sat, 25 Jul 2015 13:02:12 GMT Frederik Heber [9a4880] * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) FIX: QtMoleculeListView caused Command to be executed when selection ... Sat, 25 Jul 2015 13:02:12 GMT Frederik Heber [a87d1e2] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) FIX: ActionQueue::isIdle() states whether actions are executed or ... Sat, 25 Jul 2015 13:02:12 GMT Frederik Heber [9ec4b8] * src/Shapes/BaseShapes.cpp (modified) FIX: Cuboid_impl::getNormal() did not take numerical imprecision into ... Sat, 25 Jul 2015 13:02:12 GMT Frederik Heber [bcf056] * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.hpp (modified) FIX: QtTimeLine would cause another WorldSetTime action. - we did ... Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [9fb213] * src/UIElements/Views/Qt4/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.hpp (modified) FIX: QtElementList now uses new updateElement(). - old refill() ... Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [92df04] * src/UIElements/Qt4/QtMainWindow.cpp (modified) TEMP: Removed QtLogBox for the moment. - ever and again causes ... Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [ea73ce] * src/UIElements/Views/Qt4/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/QtElementList.hpp (modified) Added QMutex to QtElementList for refill(). Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [7d0ddb] * 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/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.hpp (modified) FIX: QtMoleculeItem would not correctly signOff prior to molecule ... Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [9d4f964] * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.hpp (modified) FIX: QtHomologyList::refill() is now called via signal/slot. Sat, 25 Jul 2015 13:02:11 GMT Frederik Heber [7d0a4e] * configure.ac (modified) * src/Makefile.am (modified) * src/ThreadGuard.hpp (added) * src/builder_init.cpp (modified) * src/builder_init.hpp (modified) Storing the id of the main thread in static global variable. - this ... Sat, 25 Jul 2015 13:01:45 GMT Frederik Heber [9ad4d6] * src/UIElements/Qt4/QtUIFactory.cpp (modified) FIX: QtUIFactory copied to wrong argv. Sat, 25 Jul 2015 13:01:45 GMT Frederik Heber [2a4b05] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) FIX: GLWorldView was signed in to atomInserted and atomRemoved ... Sat, 25 Jul 2015 13:01:45 GMT Frederik Heber [9b56f0a] * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) FIX: GLWorldScene did not initialize SelectionMode properly. Sat, 25 Jul 2015 13:01:44 GMT Frederik Heber [73b13c] * 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) Extracted signing on to molecule into activateObserver. - is called ... Sat, 25 Jul 2015 13:01:21 GMT Frederik Heber [9737db] * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Views/Qt4/QDebugStream.hpp (modified) * src/UIElements/Views/Qt4/QtLogBox.cpp (modified) FIX: QDebugStream is now thread-safe. - also Fix to QTextCursor not ... Sat, 25 Jul 2015 13:01:21 GMT Frederik Heber [4965922] * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.hpp (modified) QtInfoBox updates information on update signal. Sat, 25 Jul 2015 13:01:21 GMT Frederik Heber [2f76d2] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) FIX: Fixing atomicNumber_t atomicId_t in atomRemoved and atomInserted. Sat, 25 Jul 2015 13:01:21 GMT Frederik Heber [f759e5] * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) FIX: GLWorldView must not listen to moleculeRemoved but to its ... Sat, 25 Jul 2015 13:01:20 GMT Frederik Heber [9c259e] * 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) FIX: GLWorldScene/View capture all missed signals for each ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [8923ad8] * 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) Removed GLMoleculeObject_molecule's init() and reinit(). - also ... Fri, 24 Jul 2015 16:44:35 GMT Frederik Heber [28864c] * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/Qt4/QtUIFactory.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/UIFactory.hpp (modified) * src/builder_init.cpp (modified) UIs are now initialized before any action takes place. - ...