# # ChangeLog for / # # Generated by Trac 1.6 # Jun 23, 2025, 11:14:10 PM Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [5cf341] * src/World.cpp (modified) * src/World.hpp (modified) Added recreateAtom() and recreateMolecule() to World. - in order to ... Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [840d02] * src/molecule.cpp (modified) FIX: not using const ref in binding updateBoundingBox() for molecule. Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [7eec64] * src/World.cpp (modified) FIX: World needs to first destroy the molecule, then release its ids. ... Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [4965d9f] * src/World.cpp (modified) FIX: World::destroy..() did not emit SelectionChanged signal. Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [50c45f] * src/UIElements/Qt4/QtMainWindow.cpp (modified) FIX: Fitting domain to window on QtMainWindow's init. Sun, 07 Feb 2016 05:57:03 GMT Frederik Heber [e2c2b1] * configure.ac (modified) * src/World.cpp (modified) * src/World.hpp (modified) World's ObservedContainer no longer observe. - This requires ... Sat, 06 Feb 2016 22:39:30 GMT Frederik Heber [69a420] * configure.ac (modified) * debian/changelog (modified) * debian/copyright (modified) Set version to 1.5.1. - MoleCuilder library is now 15:1:0. - ... Sat, 06 Feb 2016 22:39:30 GMT Frederik Heber [9ae11c] * debian/control (modified) DEBIANFIX: requiring libcodepatterns instead of ..-dev variant. Tue, 02 Feb 2016 17:50:29 GMT Frederik Heber [3690e4] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/ResultContainer_impl.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Interfragmenter.hpp (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/FragmentForces.cpp (added) * src/Fragmentation/Summation/SetValues/FragmentForces.hpp (added) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/Jobs/ChargeSmearer.cpp (added) * src/Jobs/ChargeSmearer.hpp (added) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/Jobs/WindowGrid_converter.hpp (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Plotting/Makefile.am (modified) * src/controller_MPQCCommandJob.cpp (modified) * tests/Python/AllActions/options.dat (modified) Merge branch 'Enhancing_Interdistance' into Candidate_v1.5.1 Tue, 02 Feb 2016 17:50:22 GMT Frederik Heber [d1831e] * configure.ac (modified) * debian/changelog (modified) * debian/control (modified) * m4/qwt.m4 (modified) Merge branch 'Fix_debianpackage' into Candidate_v1.5.1 Sun, 31 Jan 2016 12:47:23 GMT Frederik Heber [e38750] * tests/GuiChecks/atlocal.in (modified) Merge branch 'Fix_molecuilderguitest_with_valgrind' into Candidate_v1.5.1 Sun, 31 Jan 2016 12:47:12 GMT Frederik Heber [d26fb7] * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.def (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) * src/Fragmentation/Exporters/SaturatedBond.cpp (modified) * src/Parameters/Specifics/Value_element.cpp (modified) * src/Parameters/Specifics/Value_elements.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters.hpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * tests/regression/Atoms/Add/post/test.in (modified) * tests/regression/Atoms/Remove/post/test.in (modified) * tests/regression/Atoms/Saturate/post/saturated_carbon.xyz (modified) * tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz (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) Merge branch 'Better_HBondDistances' into Candidate_v1.5.1 Sun, 31 Jan 2016 12:47:04 GMT Frederik Heber [6a922b] * src/Graph/BondGraph.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/World.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) Merge branch 'Molecule_Enhanced_BoundingBox' into Candidate_v1.5.1 Sun, 31 Jan 2016 12:46:56 GMT Frederik Heber [9a8a6b] * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (modified) * src/Atom/atom.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * tests/regression/Atoms/Add/post/test.pdb (modified) Merge branch 'AtomAlwaysHasMolecule' into Candidate_v1.5.1 Sun, 31 Jan 2016 12:43:17 GMT Frederik Heber [e39e7a] * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) Implemented more efficient per-molecule bounding box information. - ... Sun, 31 Jan 2016 12:43:17 GMT Frederik Heber [e3e52a] * src/Graph/BondGraph.hpp (modified) FIX: BondGraph::Createdjacency compare atoms on position in memory. ... Tue, 13 Oct 2015 20:14:33 GMT Frederik Heber [62d092] * src/Jobs/ChargeSmearer.cpp (modified) * src/Jobs/ChargeSmearer.hpp (modified) Rewrote ChargeSmearer to use visitor pattern. - this is used for ... Tue, 13 Oct 2015 20:14:33 GMT Frederik Heber [17e4fd] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/Jobs/WindowGrid_converter.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added new option DoSmearElectronicCharges to ... Tue, 13 Oct 2015 20:14:32 GMT Frederik Heber [445ce6] * src/Jobs/WindowGrid_converter.cpp (modified) Modified WindowGrid_converter::addWindowOntoGrid(): first reset, then ... Tue, 13 Oct 2015 20:14:32 GMT Frederik Heber [cceb8c] * src/Jobs/ChargeSmearer.cpp (added) * src/Jobs/ChargeSmearer.hpp (added) * src/Jobs/Makefile.am (modified) Added ChargeSmearer that is only compiled for CONDVMG. - we store ... Tue, 13 Oct 2015 20:14:32 GMT Frederik Heber [92232f] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) Adding warning when inter-distance is given less then minimum ... Tue, 13 Oct 2015 20:14:32 GMT Frederik Heber [cee9e8] * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Interfragmenter.hpp (modified) Added Interfragmenter::findLargestCutoff() to find largest Rcut not ... Tue, 13 Oct 2015 20:14:32 GMT Frederik Heber [b1c5f46] * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Interfragmenter.hpp (modified) Interfragmenter now combines two fragments up to (in sum) till ... Tue, 13 Oct 2015 20:14:32 GMT Frederik Heber [0d9053] * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/Interfragmenter.hpp (modified) Exracted several functions out of Interfragmenter::operator(). - ... Tue, 13 Oct 2015 20:14:16 GMT Frederik Heber [7537d1] * src/Fragmentation/Automation/ResultContainer_impl.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) Removing setting net force to zero and setting hasForce to true. Tue, 13 Oct 2015 20:13:12 GMT Frederik Heber [00d815] * src/Jobs/InterfaceVMGJob.cpp (modified) FIX: Need to divide by global number of particles, when summing ... Tue, 13 Oct 2015 20:12:54 GMT Frederik Heber [6e73f5] * src/Jobs/InterfaceVMGJob.cpp (modified) Added debugging changes to InterfaceVMGJob on force summation. Tue, 13 Oct 2015 20:12:54 GMT Frederik Heber [ff347f] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) Added gathering of full and longrange forces into extra file. - ... Tue, 13 Oct 2015 20:12:54 GMT Frederik Heber [20bb3b] * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) MPQCData now also uses FragmentForces (instead of typedef ... Tue, 13 Oct 2015 20:12:54 GMT Frederik Heber [94db13] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) Again changes to obtain correct longrange forces, also forces are ... Tue, 13 Oct 2015 16:42:06 GMT Frederik Heber [a063787] * src/molecule.cpp (modified) FIX: Removed double coding in molecule::erase(). Tue, 13 Oct 2015 16:42:06 GMT Frederik Heber [59e7996] * src/World.cpp (modified) FIX: World needs to first destroy the atom, then release its ids. Mon, 12 Oct 2015 18:08:52 GMT Frederik Heber [ceaab1] * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (modified) * src/Atom/atom.cpp (modified) * src/molecule.cpp (modified) * src/molecule.hpp (modified) * tests/regression/Atoms/Add/post/test.pdb (modified) AddAtom now adds a molecule (atom always associated with a molecule). ... Sun, 11 Oct 2015 07:13:04 GMT Frederik Heber [b61bd5] * configure.ac (modified) * m4/qwt.m4 (modified) Fixed levmar m4 to use pkgconfig and locate. - we don't need to ... Sun, 11 Oct 2015 07:13:04 GMT Frederik Heber [622720] * debian/control (modified) Added all required libboost.. to Build-depends. Sun, 11 Oct 2015 07:13:04 GMT Frederik Heber [3c6b40] * debian/changelog (modified) Changed debian files to heber@molecuilder.com and changed boost dep. ... Sun, 11 Oct 2015 07:11:38 GMT Frederik Heber [2f429e] * src/Parameters/Specifics/Value_element.cpp (modified) * src/Parameters/Specifics/Value_elements.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) Elements are now parsed as string (and tried for being int). - this ... Sun, 11 Oct 2015 07:11:38 GMT Frederik Heber [3b1c36] * src/Element/elements_db.cpp (modified) * tests/regression/Atoms/Saturate/post/saturated_carbon.xyz (modified) * tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz (modified) Entered HBondDistance results from VSpeShape into elements_db. - we ... Sun, 11 Oct 2015 07:11:38 GMT Frederik Heber [c85c2e] * src/Element/element.cpp (modified) * src/Element/unittests/ElementUnitTest.cpp (modified) FIX: Element's HBondDistance and HBondAngle were not initialized as ... Sun, 11 Oct 2015 07:11:38 GMT Frederik Heber [4f8079] * src/Element/elements_db.cpp (modified) Added Hbonddistance and -angle for sodium (Na). 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 07:11:15 GMT Frederik Heber [83a425] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Converter/DataConverter.hpp (modified) Split off sampled_potential im VMGDataMap_t into separate fusion ... Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [ce9874] * src/Jobs/InterfaceVMGJob.cpp (modified) Added extraction of long-range forces from VMGData's array f. Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [d200ae] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) * src/Fragmentation/Summation/SetValues/FragmentForces.cpp (added) * src/Fragmentation/Summation/SetValues/FragmentForces.hpp (added) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) Added new SetValues FragmentForces. - struct is particle_forces ... Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [057c8a] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) FIX: When there's just a single fragment, don't remove the ... Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [9593d1] * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) FIX: Picking maximum axis length in ExportGraph_ToJobs for MPQCJob. ... Sun, 11 Oct 2015 07:11:15 GMT Frederik Heber [c20839] * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Views/Qt4/Plotting/Makefile.am (modified) FIX: Shared libraries's Makefile.am rules are now consistent. - ... Sun, 11 Oct 2015 07:10:48 GMT Frederik Heber [dace6c] * tests/GuiChecks/atlocal.in (modified) FIX: tests/GuiChecks/atlocal lacked valgrind variable. - note that ... 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. - ...