# # ChangeLog for src/Actions # # Generated by Trac 1.6 # Dec 26, 2025, 1:36:15 PM Sat, 13 Sep 2025 14:44:01 GMT Frederik Heber [5d18f3] * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Potentials/PotentialTrainer.cpp (modified) FIX: PotentialTrainer did not heed take-best correctly. - we used ... Sat, 13 Sep 2025 14:43:45 GMT Frederik Heber [a4b917] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/AddPotentialAction.cpp (added) * src/Actions/PotentialAction/AddPotentialAction.def (added) * src/Actions/PotentialAction/AddPotentialAction.hpp (added) * src/Actions/PotentialAction/RemovePotentialAction.cpp (added) * src/Actions/PotentialAction/RemovePotentialAction.def (added) * src/Actions/PotentialAction/RemovePotentialAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Potential/AddPotential/pre/harmonic.potentials (added) * tests/regression/Potential/AddPotential/testsuite-potential-add-potential-various_cases.at (added) * tests/regression/Potential/AddPotential/testsuite-potential-add-potential.at (added) * tests/regression/Potential/RemovePotential/pre/harmonic.potentials (added) * tests/regression/Potential/RemovePotential/testsuite-potential-remove-potential-various_cases.at (added) * tests/regression/Potential/RemovePotential/testsuite-potential-remove-potential.at (added) * tests/regression/Potential/testsuite-potential.at (modified) Adds add and remove potential actions. - DOC: Adds missing actions ... Wed, 13 Aug 2025 21:46:30 GMT Frederik Heber [463bfb] * src/Actions/AtomAction/SaturateAction.def (modified) FIX: SaturateAction had typo in default. - this originated in ... Wed, 13 Aug 2025 21:46:30 GMT Frederik Heber [780bfa] * src/Actions/ActionHistory.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * tests/regression/Options/UndoMark/testsuite-options-undo-mark.at (modified) FIX: FormatParserStorage did not add parser instance on SetOutput. ... Wed, 13 Aug 2025 08:24:42 GMT Frederik Heber [bcc29ca] * doc/userguide/userguide.xml (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/CommandAction/RedoAction.cpp (moved) * src/Actions/CommandAction/RedoAction.def (moved) * src/Actions/CommandAction/RedoAction.hpp (moved) * src/Actions/CommandAction/SetUndoMarkAction.cpp (moved) * src/Actions/CommandAction/SetUndoMarkAction.def (moved) * src/Actions/CommandAction/SetUndoMarkAction.hpp (moved) * src/Actions/CommandAction/UndoAction.cpp (moved) * src/Actions/CommandAction/UndoAction.def (moved) * src/Actions/CommandAction/UndoAction.hpp (moved) * src/Actions/CommandAction/UndoTillMarkAction.cpp (added) * src/Actions/CommandAction/UndoTillMarkAction.def (added) * src/Actions/CommandAction/UndoTillMarkAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Options/UndoMark/testsuite-options-undo-mark.at (modified) Splits off Undo mark actions. - Undo action has again no parameters ... Mon, 11 Aug 2025 17:43:56 GMT Frederik Heber [6294b6] * ThirdParty/mpqc_open/src/bin/mpqc/mpqc.cc (modified) * ThirdParty/mpqc_open/src/bin/mpqc/mpqc.h (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/MPQCJob_Work.cpp (modified) * src/Jobs/MPQCJob_binding.hpp (modified) MPQCJob mutes output on verbosity level 0 and unmutes else. - we ... Mon, 11 Aug 2025 17:43:53 GMT Frederik Heber [c099dc] * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) SetParserParameters prints old and new params. Sat, 16 Mar 2024 10:22:34 GMT Frederik Heber [9782e20] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/BondifyAction.cpp (modified) * src/Actions/AtomAction/BondifyAction.def (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/BondInfo.hpp (modified) * tests/regression/Atoms/Bondify/post/bondify-test.data (added) * tests/regression/Atoms/Bondify/pre/bondify-test.data (added) * tests/regression/Atoms/Bondify/testsuite-atoms-bondify.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) BondifyAction: added undo/redo. - DOC: fixed small typo in Action's ... Sun, 03 Mar 2024 10:10:53 GMT Frederik Heber [399c69] * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/AddAction.def (modified) Rewrote AddAction to use UndoRedoHelpers. Tue, 27 Feb 2024 22:18:17 GMT Frederik Heber [0427d1] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) FIX: ActionQueue no locked on CurrentAction access. - ... Tue, 27 Dec 2022 23:36:18 GMT Frederik Heber [d91a8f] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/ClearHomologiesAction.cpp (added) * src/Actions/PotentialAction/ClearHomologiesAction.def (added) * src/Actions/PotentialAction/ClearHomologiesAction.hpp (added) Added ClearHomologiesAction. - this is necessary during sampling ... Tue, 01 Nov 2022 22:35:20 GMT Frederik Heber [80bf6e] * src/Actions/PotentialAction/GeneratePotentialsAction.cpp (modified) FIX: GeneratePotentialsAction generates all combination. Merge with ... Tue, 25 May 2021 23:04:50 GMT Frederik Heber [82e5fb] * doc/userguide/userguide.xml (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/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/PotentialTrainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitCompoundPotential/testsuite-potential-fit-compound-potential.at (modified) Added option error-file to fit potential actions. - DOCU: Added ... Tue, 25 May 2021 21:55:52 GMT Frederik Heber [889067e] * doc/userguide/userguide.xml (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.def (modified) * tests/Python/AllActions/options.dat (modified) Added force-overwrite to OutputAsAction. - DOCU: Also added ... Wed, 19 May 2021 19:06:29 GMT Frederik Heber [9b0dcd] * doc/userguide/userguide.xml (modified) * src/Actions/PotentialAction/GeneratePotentialsAction.cpp (modified) * src/Actions/PotentialAction/GeneratePotentialsAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/GeneratePotentials/post/water_restricted.potentials (added) * tests/regression/Potential/GeneratePotentials/testsuite-potential-generate-potentials.at (modified) Added potential-list argument to GeneratePotentialsAction. - DOCU: ... Wed, 19 May 2021 19:06:29 GMT Frederik Heber [55c494] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/GeneratePotentialsAction.cpp (added) * src/Actions/PotentialAction/GeneratePotentialsAction.def (added) * src/Actions/PotentialAction/GeneratePotentialsAction.hpp (added) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/GeneratePotentials/post/water.potentials (added) * tests/regression/Potential/GeneratePotentials/pre/water.pdb (added) * tests/regression/Potential/GeneratePotentials/pre/water_homologies.dat (added) * tests/regression/Potential/GeneratePotentials/testsuite-potential-generate-potentials.at (added) * tests/regression/Potential/testsuite-potential.at (modified) Added GeneratePotentialsAction. - this generates all potential ... Wed, 28 Apr 2021 22:02:49 GMT Frederik Heber [999eaf] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/EvaluateStabilityAction.cpp (added) * src/Actions/FragmentationAction/EvaluateStabilityAction.def (added) * src/Actions/FragmentationAction/EvaluateStabilityAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Fragmentation/Evaluation/StabilityEvaluator.cpp (added) * src/Fragmentation/Evaluation/StabilityEvaluator.hpp (added) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeysetStub.cpp (modified) * src/Fragmentation/Makefile.am (modified) * tests/regression/Fragmentation/EvaluateStability/pre/C3H8.data (added) * tests/regression/Fragmentation/EvaluateStability/pre/homology-6-31G.dat (added) * tests/regression/Fragmentation/EvaluateStability/testsuite-fragmentation-evaluate-stability.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added EvaluateStabilityAction to estimate a molecule's stability. - ... Wed, 28 Apr 2021 22:02:49 GMT Frederik Heber [564f17] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) Extended HomologyContainer::value_t by fragment energy. - renamed ... Wed, 28 Apr 2021 22:02:49 GMT Frederik Heber [2390e6] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Actions/AtomAction/SaturateAction.def (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.hpp (modified) * src/Fragmentation/Exporters/unittests/SphericalPointDistributionUnitTest.cpp (modified) SaturateAction may use outer shell information. - when considering ... Fri, 23 Apr 2021 21:02:12 GMT Frederik Heber [87c1cc] * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.def (modified) FIX: NotAtomByElementAction used atom ptr instead of ids for undo state. Fri, 23 Apr 2021 21:02:12 GMT Frederik Heber [d54e37] * src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/PopAtomsAction.def (modified) FIX: PopAtomAction must not store atom ptr but atom ids for undoing. Fri, 23 Apr 2021 21:02:12 GMT Frederik Heber [7d2ee1] * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) ActionHistory's marked states is now a stack. - i.e. multiple marks ... Fri, 23 Apr 2021 21:02:12 GMT Frederik Heber [0fbea3] * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) FIX: set all analysis actions hasUndo to false. - none of these ... Fri, 23 Apr 2021 21:02:12 GMT Frederik Heber [0ec9f5] * doc/userguide/userguide.xml (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/CommandAction/UndoMarkAction.cpp (added) * src/Actions/CommandAction/UndoMarkAction.def (added) * src/Actions/CommandAction/UndoMarkAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/UndoAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/UndoMark/testsuite-options-undo-mark.at (added) * tests/regression/Options/testsuite-options.at (modified) Added UndoMarkAction. NOTE: This action is necessary as not all ... Fri, 23 Apr 2021 21:01:20 GMT Frederik Heber [5061d9] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/PrintSelectedAtomsAsGraphStringAction.cpp (added) * src/Actions/GraphAction/PrintSelectedAtomsAsGraphStringAction.def (added) * src/Actions/GraphAction/PrintSelectedAtomsAsGraphStringAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Graph/Graph6Writer.cpp (added) * src/Graph/Graph6Writer.hpp (added) * src/Graph/Makefile.am (modified) * src/Python/Makefile.am (modified) * src/Python/PythonScripting_impl.hpp (modified) * src/Python/getGraph6String.cpp (added) * src/Python/modules.hpp (modified) * tests/regression/Graph/ChemicalSpaceEvaluator/testsuite-graph-chemical-space-evaluator.at (moved) * tests/regression/Graph/PrintSelectedAtomsAsGraphString/pre/test.data (added) * tests/regression/Graph/PrintSelectedAtomsAsGraphString/testsuite-graph-print-selected-atoms-as-graphstring.at (added) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Makefile.am (modified) Added action to print selected atoms as graph6 string. - added ... Fri, 23 Apr 2021 20:55:32 GMT Frederik Heber [cd79d0] * src/Actions/ActionHistory.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) Undo and Redo state debug info about involved action. Fri, 23 Apr 2021 20:55:19 GMT Frederik Heber [ff2c52] * doc/userguide/userguide.xml (modified) * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp (modified) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) ParseHomologies action lists values and their energy range per key. ... Fri, 23 Apr 2021 20:53:22 GMT Frederik Heber [9171d8] * doc/userguide/userguide.xml (modified) * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp (modified) Using lowest contribution found in homology container. - also ... Fri, 23 Apr 2021 20:51:43 GMT Frederik Heber [1be100] * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp (modified) * src/Graph/Graph6Reader.cpp (modified) * src/Graph/Graph6Reader.hpp (modified) * tests/regression/Graph/ChemicalSpaceEvaluator/testsuite-chemical-space-evaluator.at (modified) FIX: Several small errors in Graph6Reader. - off-by-one error with ... Fri, 23 Apr 2021 20:51:43 GMT Frederik Heber [d951a5] * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) FIX: Small changes to ChemicalSpaceEvaluatorAction. - discarding ... Fri, 23 Apr 2021 20:51:43 GMT Frederik Heber [c30959] * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondAddAction.def (modified) BondAddAction also adds to molecule. - NOTE: This basically does ... Fri, 23 Apr 2021 20:51:24 GMT Frederik Heber [5fa1e86] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/BondifyAction.cpp (added) * src/Actions/AtomAction/BondifyAction.def (added) * src/Actions/AtomAction/BondifyAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Bond/Bondify/post/test.data (added) * tests/regression/Bond/Bondify/pre/test.data (added) * tests/regression/Bond/Bondify/testsuite-bond-bondify.at (added) * tests/regression/Bond/testsuite-bond.at (modified) * tests/regression/Makefile.am (modified) Added BondifyAction. - this allows to add non-hydrogen bonds and is ... Fri, 23 Apr 2021 20:43:27 GMT Frederik Heber [38bcbe] * doc/userguide/userguide.xml (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Bond/StretchBond.cpp (modified) * src/Graph/BondGraph.hpp (modified) StretchBondAction will used tabled distances when given distance is ... Fri, 23 Apr 2021 20:42:57 GMT Frederik Heber [4de4f6] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AtomBondNeighborsAction.cpp (added) * src/Actions/SelectionAction/Atoms/AtomBondNeighborsAction.def (added) * src/Actions/SelectionAction/Atoms/AtomBondNeighborsAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomsNeighbors/post/H_missing.xyz (added) * tests/regression/Selection/Atoms/AtomsNeighbors/post/empty.xyz (added) * tests/regression/Selection/Atoms/AtomsNeighbors/pre/test.xyz (added) * tests/regression/Selection/Atoms/AtomsNeighbors/testsuite-selection-select-atoms-neighbors.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added AtomBondNeighbors selection action. - DOCU: Added to ... Fri, 23 Apr 2021 20:34:22 GMT Frederik Heber [9f55b9] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Bond/StretchBond.cpp (added) * src/Bond/StretchBond.hpp (added) * src/Graph/BoostGraphHelpers.hpp (modified) * src/Makefile.am (modified) Extracted functor StretchBondUtil from StretchBondAction. Fri, 23 Apr 2021 20:34:11 GMT Frederik Heber [d9e1d1] * doc/userguide/userguide.xml (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (modified) * tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified) Extending PairCorrelation to correlate element and set of atoms. - ... Fri, 23 Apr 2021 20:31:23 GMT Frederik Heber [addb51] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/ClearFragmentationStateAction.cpp (added) * src/Actions/FragmentationAction/ClearFragmentationStateAction.def (added) * src/Actions/FragmentationAction/ClearFragmentationStateAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) Add action to clear fragmentation state. Fri, 23 Apr 2021 20:31:23 GMT Frederik Heber [0ad4781] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AtomByRandomAction.cpp (added) * src/Actions/SelectionAction/Atoms/AtomByRandomAction.def (added) * src/Actions/SelectionAction/Atoms/AtomByRandomAction.hpp (added) * src/RandomNumbers/RandomNumberDistributionFactory.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomByRandom/post/empty.xyz (added) * tests/regression/Selection/Atoms/AtomByRandom/post/test-undo.xyz (added) * tests/regression/Selection/Atoms/AtomByRandom/pre/test.xyz (added) * tests/regression/Selection/Atoms/AtomByRandom/testsuite-selection-select-atom-by-random.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added action to randomly select a set of atoms. - needed to make ... Fri, 23 Apr 2021 20:31:23 GMT Frederik Heber [61cc0f] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/MoleculeAction/SaveEnergiesAction.cpp (modified) Enhanced verbosity of FragmentationAutomation. Fri, 23 Apr 2021 20:31:23 GMT Frederik Heber [d40189] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/SaveEnergiesAction.cpp (moved) * src/Actions/MoleculeAction/SaveEnergiesAction.def (moved) * src/Actions/MoleculeAction/SaveEnergiesAction.hpp (moved) * src/Atom/AtomSet.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Dynamics/OutputEnergies.hpp (moved) * src/Makefile.am (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Molecules/SaveEnergies/testsuite-molecules-save-energies.at (moved) * tests/GuiChecks/Molecules/testsuite-molecules.at (modified) * tests/Python/AllActions/missing.dat (modified) * tests/Python/AllActions/options.dat (modified) * tests/integration/MolecularDynamics/post/ethane.ekin (modified) * tests/integration/MolecularDynamics/post/methane.ekin (modified) * tests/integration/MolecularDynamics/post/water-system.ekin (modified) * tests/integration/MolecularDynamics/post/water.ekin (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-ethane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-methane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water-system.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/SaveEnergies/post/test.ekin (added) * tests/regression/Molecules/SaveEnergies/pre/test.conf (moved) * tests/regression/Molecules/SaveEnergies/testsuite-molecules-save-energies.at (moved) * tests/regression/Molecules/SaveTemperature/post/test.ekin (deleted) * tests/regression/Molecules/testsuite-molecules.at (modified) OutputTemperature -> OutputEnergies, SaveTemperature -> SaveEnergies. ... Fri, 23 Apr 2021 20:31:23 GMT Frederik Heber [cbbb6a] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) FIX: AnalyseFragmentationResultsAction ignored prefix mostly. Fri, 23 Apr 2021 20:31:23 GMT Frederik Heber [26062f] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def (modified) StoreSaturatedFragmentAction may now export to FragmentQueue as well. ... Fri, 22 Jun 2018 07:26:30 GMT Frederik Heber [99c705] * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp (modified) * src/Graph/BoostGraphCreator.cpp (modified) * src/Graph/Graph6Reader.cpp (modified) * src/Graph/Graph6Reader.hpp (modified) ChemicalSpaceEvaluator working for graph with 2 nodes. Fri, 22 Jun 2018 07:26:09 GMT Frederik Heber [f5ea10] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp (added) * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.def (added) * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.hpp (added) * src/Actions/Makefile.am (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Graph/BoostGraphCreator.cpp (modified) * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/Graph6Reader.cpp (added) * src/Graph/Graph6Reader.hpp (added) * src/Graph/Makefile.am (modified) * tests/Python/AllActions/moltest_check.py (modified) * tests/Python/AllActions/options.dat (modified) Added Graph6Reader, extended BoostGraphCreator, added ... Thu, 21 Jun 2018 08:31:25 GMT Frederik Heber [8d56a6] * doc/userguide/userguide.xml (modified) * src/Actions/Action.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Action_impl_python.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.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/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.hpp (modified) * tests/Python/AllActions/moltest.py (modified) * tests/Python/AllActions/moltest_check.py (modified) * tests/Python/AllActions/options.dat (modified) * tests/Python/AllActions/testsuite-python-allactions.at (modified) * tests/Python/AllActions/testsuite-python-options_dat.at (modified) * tests/Python/BoxMaker/testsuite-python-boxmaker.at (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_no-bondgraph.data (modified) * tests/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (modified) * tests/integration/MolecularDynamics/post/ethane.ekin (modified) * tests/integration/MolecularDynamics/post/ethane_initial_steps.data (modified) * tests/integration/MolecularDynamics/post/methane.ekin (modified) * tests/integration/MolecularDynamics/post/methane_initial_steps.data (modified) * tests/integration/MolecularDynamics/post/water-system.ekin (modified) * tests/integration/MolecularDynamics/post/water-system_initial_steps.data (modified) * tests/integration/MolecularDynamics/post/water.ekin (modified) * tests/integration/MolecularDynamics/post/water_initial_steps.data (modified) * tests/regression/Domain/RepeatBox/post/ec.data (modified) * tests/regression/Filling/FillSurface/post/tensid-undo.data (modified) * tests/regression/Filling/FillSurface/post/tensid.data (modified) * tests/regression/Filling/RegularGrid/post/solved_single_sles.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data (modified) * tests/regression/Molecules/Copy/post/tensid.data (modified) * tests/regression/Options/DryRun/post/session.py (modified) * tests/regression/Options/Session/post/complextest.py (modified) * tests/regression/Options/Session/post/test.py (modified) * tests/regression/Parser/Tremolo-Potentials/post/argon.data (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/output.data (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/undo.data (modified) * tests/regression/Parser/Tremolo/post/argon.data (modified) Merge branch 'TremoloParser_IncreasedPrecision' into Candidate_v1.6.1 ... Wed, 20 Jun 2018 08:21:03 GMT Frederik Heber [a6c11a] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) All failures in FragmentationAutomation are explained by log statements. Wed, 20 Jun 2018 08:20:43 GMT Frederik Heber [4b2adf] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) ForceAnnealiing now returns bool to indicate stop condition for ... Wed, 20 Jun 2018 08:20:43 GMT Frederik Heber [e3ce0e] * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionSequence.hpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/MakroAction.hpp (modified) MakroAction allows getting the internal ActionSequence's current step. Wed, 20 Jun 2018 08:20:43 GMT Frederik Heber [559293] * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) ActionQueue has predicates to check if current Action is Process or ... Wed, 11 Apr 2018 06:30:10 GMT Frederik Heber [e7ad08] * doc/userguide/userguide.xml (modified) * src/Actions/Action.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Action_impl_python.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * tests/Python/AllActions/testsuite-python-options_dat.at (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) Python interface now converts dashes in tokens to underscores, store- ... Tue, 10 Apr 2018 06:43:31 GMT Frederik Heber [8450da] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) ForceAnnealing functions now have better readable time step ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [c87d6e] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo.conf (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo2.conf (added) * tests/regression/Molecules/ForceAnnealing/pre/test2.conf (added) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) ForceAnnealingAction's Undo removes trajectory item if it was added. ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [6145577] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/AtomicInfo.hpp (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo.conf (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) FIX: ForceAnnealingAction's Undo is again working. - ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [8c6b68] * 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_bondedparticleinfo.cpp (modified) * src/Atom/atom_bondedparticleinfo.hpp (modified) atom::removeStep() extended to removing interval of steps. - ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [efd020] * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) Readded step-world-time to StructuralOptimization. - adapted ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [12f16c] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) ForceAnnealing first parses forces, then copies step and finally ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [2bb3be] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * tests/regression/Molecules/ForceAnnealing/post/test.conf (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) Removed DoOutput param from ForceAnnealing. - TESTFIX: Modifying ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [866dec] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data (modified) ForceAnnealing no longer resets forces, AnalyseFragmentResults now ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [216840] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) ForceAnnealing accepts option deltat. Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [b2acca] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) ForceAnnealing can now be used either atom- or bond-centered. - new ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [ecfcf6] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) FIX: ForceAnnealing would not reset force components prior to loading ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [8ddd07] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Dynamics/AtomicForceManipulator.hpp (modified) Sorting given selected atoms by ids in ForceAnnealing. Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [56b4c6] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added damping-factor as another option to ForceAnnealing for proper ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [985d1f] * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) FIX: Removed step-world-tme from StructuralOptimizationAction. - ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [cdfb6f] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/AllActions/options.dat (modified) ForceAnnealing now shifts atoms in the bond graph to anneal forces, ... Wed, 04 Apr 2018 16:59:48 GMT Frederik Heber [322d58] * doc/userguide/userguide.xml (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/GuiChecks/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) * tests/integration/testsuite-integration.at (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) ForceAnnealing now uses step width according to Barzilai-Borwein ... Wed, 04 Apr 2018 16:59:24 GMT Frederik Heber [f4b6bc9] * src/Actions/FragmentationAction/FragmentationAction.def (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.def (modified) * src/Actions/ParserAction/SetParserParametersAction.def (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/CommandLineQuery.hpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/EmptyCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FilesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/KeyValuePairCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/KeyValuePairsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RealSpaceMatrixCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Dialog_impl_pre.hpp (modified) * src/UIElements/Qt4/QtDialog.cpp (modified) * src/UIElements/Qt4/Query/AtomQtQuery.cpp (modified) * src/UIElements/Qt4/Query/AtomsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/BooleanQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoubleQtQuery.cpp (modified) * src/UIElements/Qt4/Query/DoublesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementQtQuery.cpp (modified) * src/UIElements/Qt4/Query/ElementsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/EmptyQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Qt4/Query/FilesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/IntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/KeyValuePairQtQuery.cpp (modified) * src/UIElements/Qt4/Query/KeyValuePairsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculeQtQuery.cpp (modified) * src/UIElements/Qt4/Query/MoleculesQtQuery.cpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/RealSpaceMatrixQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringQtQuery.cpp (modified) * src/UIElements/Qt4/Query/StringsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntQtQuery.cpp (modified) * src/UIElements/Qt4/Query/UnsignedIntsQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FilesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/KeyValuePairTextQuery.cpp (modified) * src/UIElements/TextUI/Query/KeyValuePairsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RealSpaceMatrixTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/TextQuery.hpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) Query::handle() no longer returns bool but has internal result flag. ... Wed, 12 Jul 2017 19:12:47 GMT Frederik Heber [d86d97] * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.hpp (modified) * tests/regression/DiffFragmentResultContainer.cpp (modified) FIX: FragmentResultsContainer is no longer purged during run. - so ... Wed, 12 Jul 2017 19:12:43 GMT Frederik Heber [4c6f0d] * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * tests/GuiChecks/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (modified) * tests/regression/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (modified) FIX: server-port was invalid. - now, we use empty string as param ... Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [d1134d] * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (modified) * tests/regression/Molecules/RotateAroundBond/post/benzene_90degree.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/benzene.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (modified) FIX: rotate-around-bond now rotates only one side of mol's bond ... Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [bccbe9] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.def (modified) * src/Graph/BoostGraphCreator.cpp (modified) * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/BoostGraphHelpers.hpp (added) * src/Graph/BreadthFirstSearchGatherer.cpp (added) * src/Graph/BreadthFirstSearchGatherer.hpp (added) * src/Graph/Makefile.am (modified) Extracted extraction (subset of) nodes from BoostGraph into ... Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [d24ef58] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Graph/BoostGraphCreator.cpp (added) * src/Graph/BoostGraphCreator.hpp (added) * src/Graph/Makefile.am (modified) Extracted conversion to boost::graph into distinct struct. - ... Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [3b74fa] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.def (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/StretchBond/post/benzene.pdb (added) * tests/regression/Molecules/StretchBond/pre/benzene.pdb (added) * tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond-cyclic_bond.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Rewrite of StretchBondAction to take bondgraph into account. - i.e. ... Wed, 12 Jul 2017 19:10:22 GMT Frederik Heber [0716eac] * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.def (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.def (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.def (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.def (modified) SelectMoleculeByOrder and SelectionAtomByOrder now allows multiple ... Mon, 03 Jul 2017 15:06:31 GMT Frederik Heber [3f6aac] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AtomByNameAction.cpp (added) * src/Actions/SelectionAction/Atoms/AtomByNameAction.def (added) * src/Actions/SelectionAction/Atoms/AtomByNameAction.hpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.cpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.def (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomByName/post/ethane-H5_missing.pdb (added) * tests/regression/Selection/Atoms/AtomByName/pre/ethane.pdb (added) * tests/regression/Selection/Atoms/AtomByName/testsuite-selection-select-atoms-by-name.at (added) * tests/regression/Selection/Atoms/AtomByName/testsuite-selection-unselect-atoms-by-name.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added (Un)selectAtomByName. - Descriptor for AtomByName was already ... Mon, 03 Jul 2017 15:01:38 GMT Frederik Heber [9a4772] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) AnalyseFragmentResults now always prints energy table, verbosity 1. Thu, 22 Jun 2017 22:28:16 GMT Frederik Heber [310445] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/RandomPerturbationAction.cpp (added) * src/Actions/AtomAction/RandomPerturbationAction.def (added) * src/Actions/AtomAction/RandomPerturbationAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Atoms/RandomPerturbation/post/water.xyz (added) * tests/regression/Atoms/RandomPerturbation/pre/water.xyz (added) * tests/regression/Atoms/RandomPerturbation/testsuite-atoms-random-perturbation.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) Added RandomPerturbationAction. - this should be when doing ... Wed, 21 Jun 2017 22:02:50 GMT Frederik Heber [78ea3c] * doc/userguide/userguide.xml (modified) * src/Actions/Action.hpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (added) * src/Actions/MoleculeAction/RotateAroundBondAction.def (added) * src/Actions/MoleculeAction/RotateAroundBondAction.hpp (added) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.def (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.hpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/World.cpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/RotateAroundBond/post/test-195-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-90-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-95-false.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/test.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/test_cycle.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (added) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/regression/Molecules/testsuite-molecules.at (modified) * tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (modified) Merge branch 'Docu_Python_wait' into Candidate_v1.6.1 Conflicts: ... Tue, 20 Jun 2017 20:02:18 GMT Frederik Heber [137845] * src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (modified) StepWorldTime now has a single argument. - this was not possible ... Tue, 20 Jun 2017 20:01:46 GMT Frederik Heber [da7ef9] * src/Actions/Action.hpp (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) FIX: STATUS msg only pushed to GUI, now also always in log. Tue, 20 Jun 2017 20:01:31 GMT Frederik Heber [536b13] * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def (modified) * tests/regression/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) RotateToPrincipalAxisSystemAction now has Undo/Redo working. - ... Tue, 20 Jun 2017 19:58:37 GMT Frederik Heber [5e17bf] * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (modified) * tests/regression/Molecules/RotateAroundBond/pre/test_cycle.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (modified) Added test in RotateAroundBondAction whether given bond is cyclic. ... Tue, 20 Jun 2017 19:58:36 GMT Frederik Heber [788dce] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (added) * src/Actions/MoleculeAction/RotateAroundBondAction.def (added) * src/Actions/MoleculeAction/RotateAroundBondAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/RotateAroundBond/post/test-195-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-90-true.pdb (added) * tests/regression/Molecules/RotateAroundBond/post/test-95-false.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/test.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Added RotateAroundBondAction. - TESTS: added regression test. - ... Mon, 19 Jun 2017 08:24:17 GMT Frederik Heber [836972] * doc/userguide/userguide.xml (modified) * src/Actions/GeometryAction/GeometryRemoveAction.cpp (added) * src/Actions/GeometryAction/GeometryRemoveAction.def (added) * src/Actions/GeometryAction/GeometryRemoveAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Geometry/Remove/post/test.xyz (added) * tests/regression/Geometry/Remove/pre/test.xyz (added) * tests/regression/Geometry/Remove/testsuite-geometry-remove.at (added) * tests/regression/Geometry/testsuite-geometry.at (modified) * tests/regression/Makefile.am (modified) Added GeometryRemoveAction. - TESTS: Also added regression test. Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [1ba51c] * doc/userguide/userguide.xml (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) Updated userguide with lots of notes on using geometry object. Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [f79d65] * src/Actions/Values.cpp (modified) * src/Actions/Values.hpp (modified) * src/Parameters/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Dialog.cpp (modified) * src/UIElements/Dialog.hpp (modified) * src/UIElements/Qt4/Query/QtQuery.hpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * tests/regression/Geometry/DistanceToVector/testsuite-geometry-distance-to-vector.at (modified) * tests/regression/Geometry/InputToVector/testsuite-geometry-input-to-vector.at (modified) * tests/regression/Geometry/PlaneToVector/testsuite-geometry-plane-to-vector.at (modified) * tests/regression/Geometry/PositionToVector/post/test.xyz (modified) * tests/regression/Geometry/PositionToVector/testsuite-geometry-position-to-vector.at (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) Vector(s) are now stored as strings in Querys intermediately. - ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [6d78b6f] * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Parameters/Parameter.hpp (modified) * src/Parameters/Parameter_impl.hpp (modified) * src/Parameters/Value.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) Action::outputAsPython() access Parameters via ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [db1048] * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Parameters/Value_impl.hpp (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) * tests/regression/Options/Session/post/complextest.py (modified) * tests/regression/Options/Session/pre/complextest.py (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) Moved toPythonString() from Action::outputAsPython() to ... Mon, 19 Jun 2017 08:24:16 GMT Frederik Heber [987145] * doc/userguide/userguide.xml (modified) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.def (added) * src/Actions/GeometryAction/GeometryDistanceToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.def (added) * src/Actions/GeometryAction/GeometryInputToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.def (added) * src/Actions/GeometryAction/GeometryPlaneToVectorAction.hpp (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.cpp (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.def (added) * src/Actions/GeometryAction/GeometryPositionToVectorAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.hpp (modified) * src/UIElements/Menu/MenuDescription.cpp (modified) * tests/Python/AllActions/options.dat (modified) Added four GeometryActions to convert atom positions into vectors. ... Mon, 08 May 2017 13:51:00 GMT Frederik Heber [557b39] * configure.ac (modified) * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (modified) * tests/regression/DiffFragmentResultContainer.cpp (added) * tests/regression/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/difffragmentresultcontainer.in (added) boost::serialization changed text output format. - needed to write ... Fri, 05 May 2017 14:08:59 GMT Frederik Heber [9eb71b3] * ThirdParty/CodePatterns/src/Helpers/Assert.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Chronos.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Info.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Log.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/Verbose.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/errorlogger.cpp (modified) * ThirdParty/CodePatterns/src/Helpers/logger.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Channels.cpp (modified) * ThirdParty/CodePatterns/src/Observer/GlobalObservableInfo.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Graveyard.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Notification.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Observable.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Observer.cpp (modified) * ThirdParty/CodePatterns/src/Observer/ObserverLog.cpp (modified) * ThirdParty/CodePatterns/src/Observer/Relay.cpp (modified) * ThirdParty/CodePatterns/src/Patterns/unittests/stubs/Cacheable_threeNumbers.cpp (modified) * ThirdParty/CodePatterns/src/Patterns/unittests/stubs/ObservedValue_threeNumbers.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/ControllerCommandRegistry.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/ControllerOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/ControllerOptions_SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/FragmentController.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/FragmentController_JobIdProxy.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller_AddOn_SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller_SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Controller/controller_main.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/DefaultOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentQueue.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler_ControllerListener.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/FragmentScheduler_WorkerListener.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/GlobalJobId.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/JobId.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Jobs/FragmentJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Jobs/NoOpJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Jobs/SystemCommandJob.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Listener.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/AsyncOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/CheckResultsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/GetNextJobIdOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/ReceiveResultsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/RemoveAllJobsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/RemoveAllResultsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/RemoveAllWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/SendJobsOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Controllers/ShutdownOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/OperationQueue.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/OperationRegistry.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Servers/CheckAliveWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Servers/SendJobToWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Servers/ShutdownWorkerOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/SyncOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/EnrollInPoolOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/ObtainJobOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/RemoveFromPoolOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Operations/Workers/SubmitResultOperation.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Pool/PoolGuard.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Pool/PoolWorker.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Pool/WorkerPool.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/Results/FragmentResult.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/ServerOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/SignalHandler.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/SignalOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/WorkerAddress.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/WorkerOptions.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/atexit.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/poolworker.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/poolworker_main.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/server.cpp (modified) * ThirdParty/JobMarket/src/JobMarket/server_main.cpp (modified) * ThirdParty/JobMarket/src/unittests/stubs/FragmentJobStub.cpp (modified) * ThirdParty/JobMarket/src/unittests/stubs/FragmentResultStub.cpp (modified) * ThirdParty/JobMarket/src/unittests/stubs/ObserverStub.cpp (modified) * ThirdParty/JobMarket/tests/CodeChecks/testsuite-memdebug.at (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Line.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinePoint.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Plane.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Space.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Vector.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (modified) * ThirdParty/LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (modified) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (modified) * src/Actions/Action.cpp (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionRegistry.cpp (modified) * src/Actions/ActionSequence.cpp (modified) * src/Actions/ActionStatusList.cpp (modified) * src/Actions/ActionTrait.cpp (modified) * src/Actions/AnalysisAction/AverageMoleculeForceAction.cpp (modified) * src/Actions/AnalysisAction/DipoleAngularCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/DipoleCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/MolecularVolumeAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PointCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp (modified) * src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp (modified) * src/Actions/AtomAction/AddAction.cpp (modified) * src/Actions/AtomAction/ChangeElementAction.cpp (modified) * src/Actions/AtomAction/MirrorAction.cpp (modified) * src/Actions/AtomAction/RemoveAction.cpp (modified) * src/Actions/AtomAction/RotateAroundOriginByAngleAction.cpp (modified) * src/Actions/AtomAction/SaturateAction.cpp (modified) * src/Actions/AtomAction/SaveSelectedAtomsAction.cpp (modified) * src/Actions/AtomAction/TranslateAction.cpp (modified) * src/Actions/AtomAction/TranslateToOriginAction.cpp (modified) * src/Actions/BondAction/BondAddAction.cpp (modified) * src/Actions/BondAction/BondRemoveAction.cpp (modified) * src/Actions/BondAction/BondSetDegreeAction.cpp (modified) * src/Actions/CommandAction/BondLengthTableAction.cpp (modified) * src/Actions/CommandAction/DryRunAction.cpp (modified) * src/Actions/CommandAction/ElementDbAction.cpp (modified) * src/Actions/CommandAction/FastParsingAction.cpp (modified) * src/Actions/CommandAction/HelpAction.cpp (modified) * src/Actions/CommandAction/HelpRedistributeAction.cpp (modified) * src/Actions/CommandAction/LoadSessionAction.cpp (modified) * src/Actions/CommandAction/NoDryRunAction.cpp (modified) * src/Actions/CommandAction/StoreSessionAction.cpp (modified) * src/Actions/CommandAction/VerboseAction.cpp (modified) * src/Actions/CommandAction/VersionAction.cpp (modified) * src/Actions/CommandAction/WarrantyAction.cpp (modified) * src/Actions/ErrorAction.cpp (modified) * src/Actions/FillAction/FillRegularGridAction.cpp (modified) * src/Actions/FillAction/FillSurfaceAction.cpp (modified) * src/Actions/FillAction/FillVolumeAction.cpp (modified) * src/Actions/FillAction/SuspendInMoleculeAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/ClearFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (modified) * src/Actions/FragmentationAction/SaveFragmentResultsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/GraphAction/CorrectBondDegreeAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DepthFirstSearchAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/ManipulateAtomsProcess.cpp (modified) * src/Actions/MethodAction.cpp (modified) * src/Actions/MoleculeAction/BondFileAction.cpp (modified) * src/Actions/MoleculeAction/ChangeBondAngleAction.cpp (modified) * src/Actions/MoleculeAction/ChangeNameAction.cpp (modified) * src/Actions/MoleculeAction/CopyAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp (modified) * src/Actions/MoleculeAction/LoadAction.cpp (modified) * src/Actions/MoleculeAction/RemoveAction.cpp (modified) * src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.cpp (modified) * src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp (modified) * src/Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) * src/Actions/MoleculeAction/SaveBondsAction.cpp (modified) * src/Actions/MoleculeAction/SaveSelectedMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/SaveTemperatureAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/TranslateAction.cpp (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/OptionRegistry.cpp (modified) * src/Actions/OptionTrait.cpp (modified) * src/Actions/ParserAction/SaveSelectedAtomsAsExtTypesAction.cpp (modified) * src/Actions/ParserAction/SetOutputFormatsAction.cpp (modified) * src/Actions/ParserAction/SetParserParametersAction.cpp (modified) * src/Actions/ParserAction/SetTremoloAtomdataAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/ParseAtomFragmentsAction.cpp (modified) * src/Actions/PotentialAction/ParseHomologiesAction.cpp (modified) * src/Actions/PotentialAction/ParseParticleParametersAction.cpp (modified) * src/Actions/PotentialAction/ParsePotentialsAction.cpp (modified) * src/Actions/PotentialAction/SaveAtomFragmentsAction.cpp (modified) * src/Actions/PotentialAction/SaveHomologiesAction.cpp (modified) * src/Actions/PotentialAction/SaveParticleParametersAction.cpp (modified) * src/Actions/PotentialAction/SavePotentialsAction.cpp (modified) * src/Actions/Process.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp (modified) * src/Actions/RandomNumbersAction/SetRandomNumbersEngineAction.cpp (modified) * src/Actions/RedoAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/InvertAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsInsideVolumeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAllAtomsOfMoleculeAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp (modified) * src/Actions/SelectionAction/Atoms/PopAtomsAction.cpp (modified) * src/Actions/SelectionAction/Atoms/PushAtomsAction.cpp (modified) * src/Actions/SelectionAction/Molecules/AllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/ClearAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/InvertMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/MoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotAllMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByIdAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeByOrderAction.cpp (modified) * src/Actions/SelectionAction/Molecules/NotMoleculeOfAtomAction.cpp (modified) * src/Actions/SelectionAction/Molecules/PopMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Molecules/PushMoleculesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/AllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotAllShapesAction.cpp (modified) * src/Actions/SelectionAction/Shapes/NotShapeByNameAction.cpp (modified) * src/Actions/SelectionAction/Shapes/ShapeByNameAction.cpp (modified) * src/Actions/ShapeAction/CombineShapesAction.cpp (modified) * src/Actions/ShapeAction/CreateShapeAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/RotateShapeAction.cpp (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (modified) * src/Actions/ShapeAction/TranslateShapeAction.cpp (modified) * src/Actions/TesselationAction/ConvexEnvelopeAction.cpp (modified) * src/Actions/TesselationAction/NonConvexEnvelopeAction.cpp (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/Values.cpp (modified) * src/Actions/WorldAction/AddEmptyBoundaryAction.cpp (modified) * src/Actions/WorldAction/BoundInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterInBoxAction.cpp (modified) * src/Actions/WorldAction/CenterOnEdgeAction.cpp (modified) * src/Actions/WorldAction/ChangeBoxAction.cpp (modified) * src/Actions/WorldAction/InputAction.cpp (modified) * src/Actions/WorldAction/OutputAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/WorldAction/ScaleBoxAction.cpp (modified) * src/Actions/WorldAction/SetBoundaryConditionsAction.cpp (modified) * src/Actions/WorldAction/SetDefaultNameAction.cpp (modified) * src/Actions/WorldAction/SetWorldTimeAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) * src/Actions/toCLIString.cpp (modified) * src/Actions/toPythonString.cpp (modified) * src/Analysis/analysis_bonds.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_SaturateDanglingBonds.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/TesselPoint.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_bondedparticleinfo.cpp (modified) * src/Atom/atom_graphnode.cpp (modified) * src/Atom/atom_graphnodeinfo.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/atom_particleinfo.cpp (modified) * src/AtomIdSet.cpp (modified) * src/Bond/AdjacencyMatcher/AdjacencyMatcher.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/GraphEdge.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/Box_BoundaryConditions.cpp (modified) * src/ControllerOptions_MPQCCommandJob.cpp (modified) * src/Descriptors/AtomDescriptor.cpp (modified) * src/Descriptors/AtomIdDescriptor.cpp (modified) * src/Descriptors/AtomNameDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeDescriptor.cpp (modified) * src/Descriptors/AtomOfMoleculeSelectionDescriptor.cpp (modified) * src/Descriptors/AtomOrderDescriptor.cpp (modified) * src/Descriptors/AtomSelectionDescriptor.cpp (modified) * src/Descriptors/AtomShapeDescriptor.cpp (modified) * src/Descriptors/AtomTypeDescriptor.cpp (modified) * src/Descriptors/AtomsWithinDistanceOfDescriptor.cpp (modified) * src/Descriptors/MoleculeDescriptor.cpp (modified) * src/Descriptors/MoleculeFormulaDescriptor.cpp (modified) * src/Descriptors/MoleculeIdDescriptor.cpp (modified) * src/Descriptors/MoleculeNameDescriptor.cpp (modified) * src/Descriptors/MoleculeOfAtomSelectionDescriptor.cpp (modified) * src/Descriptors/MoleculeOrderDescriptor.cpp (modified) * src/Descriptors/MoleculePtrDescriptor.cpp (modified) * src/Descriptors/MoleculeSelectionDescriptor.cpp (modified) * src/Dynamics/MinimiseConstrainedPotential.cpp (modified) * src/Element/element.cpp (modified) * src/Element/elements_db.cpp (modified) * src/Element/ion.cpp (modified) * src/Element/periodentafel.cpp (modified) * src/Filling/Cluster.cpp (modified) * src/Filling/ClusterInterface.cpp (modified) * src/Filling/Filler.cpp (modified) * src/Filling/Generators/NodeGenerator.cpp (modified) * src/Filling/Inserter/Inserter.cpp (modified) * src/Filling/Inserter/RandomInserter.cpp (modified) * src/Filling/Inserter/SimpleInserter.cpp (modified) * src/Filling/Inserter/SurfaceInserter.cpp (modified) * src/Filling/Inserter/SurfaceRandomInserter.cpp (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Filling/Mesh/Mesh.cpp (modified) * src/Filling/Predicates/AnyFillPredicate.cpp (modified) * src/Filling/Predicates/FillPredicate.cpp (modified) * src/Filling/Predicates/IsCloseEnoughToSurface_FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsInsideSurface_FillPredicate.cpp (modified) * src/Filling/Predicates/IsValidInDomain_FillPredicate.cpp (modified) * src/Filling/Predicates/IsVoidNode_FillPredicate.cpp (modified) * src/Filling/Predicates/Ops_FillPredicate.cpp (modified) * src/Filling/Preparators/BaseFillerPreparator.cpp (modified) * src/Filling/Preparators/BoxFillerPreparator.cpp (modified) * src/Filling/Preparators/ShapeSurfaceFillerPreparator.cpp (modified) * src/Filling/Preparators/ShapeVolumeFillerPreparator.cpp (modified) * src/Formula.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/MPQCCommandFragmentController.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/SpecificFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/EnergyMatrix.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToAtomFragments.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/SaturatedBond.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/SaturationDistanceMaximizer.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution_getConnections.cpp (modified) * src/Fragmentation/Exporters/SphericalPointDistribution_getPoints.cpp (modified) * src/Fragmentation/Exporters/unittests/stubs/SaturatedBondStub.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Graph.cpp (modified) * src/Fragmentation/HessianMatrix.cpp (modified) * src/Fragmentation/Homology/AtomFragmentsMap.cpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (modified) * src/Fragmentation/Homology/FragmentNode.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeysetStub.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Interfragmenter.cpp (modified) * src/Fragmentation/KeySet.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/MatrixContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/SortIndex.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/GridDownsampler.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (modified) * src/Fragmentation/Summation/IndexSet.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/FragmentForces.cpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/UniqueFragments.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/helpers.cpp (modified) * src/Fragmentation/parseKeySetFile.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionArgument.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Graph/AdjacencyList.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/ConnectedSubgraph.cpp (modified) * src/Graph/CyclicStructureAnalysis.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Helpers/defs.cpp (modified) * src/Jobs/ChargeSmearer.cpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/JobMarket/FragmentJob.cpp (modified) * src/Jobs/JobMarket/FragmentResult.cpp (modified) * src/Jobs/JobMarket/JobId.cpp (modified) * src/Jobs/JobMarket/SystemCommandJob.cpp (modified) * src/Jobs/MPQCCommandJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGDebugGridJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LinkedCell/LinkedCell.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/LinkedCell_Model.cpp (modified) * src/LinkedCell/LinkedCell_Model_LinkedCellArrayCache.cpp (modified) * src/LinkedCell/LinkedCell_Model_Update.cpp (modified) * src/LinkedCell/LinkedCell_Model_changeModel.cpp (modified) * src/LinkedCell/LinkedCell_View.cpp (modified) * src/LinkedCell/linkedcell.cpp (modified) * src/LinkedCell/tripleIndex.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/TesselPointStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/MoleculeLeafClass.cpp (modified) * src/MoleculeObserver.cpp (modified) * src/Parameters/Specifics/Value_atom.cpp (modified) * src/Parameters/Specifics/Value_element.cpp (modified) * src/Parameters/Specifics/Value_elements.cpp (modified) * src/Parameters/Specifics/Value_molecule.cpp (modified) * src/Parameters/Specifics/Value_string.cpp (modified) * src/Parameters/Validators/Specific/ActionNameValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomDataValidator.cpp (modified) * src/Parameters/Validators/Specific/AtomIdValidator.cpp (modified) * src/Parameters/Validators/Specific/BoundaryConditionValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxLengthValidator.cpp (modified) * src/Parameters/Validators/Specific/BoxVectorValidator.cpp (modified) * src/Parameters/Validators/Specific/FileSuffixValidator.cpp (modified) * src/Parameters/Validators/Specific/FormulaValidator.cpp (modified) * src/Parameters/Validators/Specific/KeyValueValidator.cpp (modified) * src/Parameters/Validators/Specific/MoleculeIdValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserFileValidator.cpp (modified) * src/Parameters/Validators/Specific/ParserTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/PotentialTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/RandomNumberValidators.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixInvertibleValidator.cpp (modified) * src/Parameters/Validators/Specific/RealSpaceMatrixSymmetricValidator.cpp (modified) * src/Parameters/Validators/Specific/SessionTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/ShapeNameValidator.cpp (modified) * src/Parameters/Validators/Specific/ShapeOpValidator.cpp (modified) * src/Parameters/Validators/Specific/ShapeTypeValidator.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorNotZeroValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorPositiveComponentsValidator.cpp (modified) * src/Parameters/Validators/Specific/VectorZeroOneComponentsValidator.cpp (modified) * src/Parameters/unittests/stubs/ActionNameValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxLengthValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/BoxVectorValidatorStub.cpp (modified) * src/Parameters/unittests/stubs/TimeStepPresentValidatorStub.cpp (modified) * src/Parser/ChangeTracker.cpp (modified) * src/Parser/ConfigFileBuffer.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * src/Parser/FormatParser_Parameters.cpp (modified) * src/Parser/FormatParser_common.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/MpqcParser_Parameters.cpp (modified) * src/Parser/MpqcParser_Parameters_initBasis.cpp (modified) * src/Parser/Parameters/ParameterStorage.cpp (modified) * src/Parser/ParserTypes.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbAtomInfoContainer.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/Psi3Parser_Parameters.cpp (modified) * src/Parser/TremoloAtomInfoContainer.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Potentials/BindingModel.cpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/InternalCoordinates/CoordinatorFactory.cpp (modified) * src/Potentials/InternalCoordinates/FourBody_ImproperAngle.cpp (modified) * src/Potentials/InternalCoordinates/FourBody_TorsionAngle.cpp (modified) * src/Potentials/InternalCoordinates/OneBody_Constant.cpp (modified) * src/Potentials/InternalCoordinates/ThreeBody_Angle.cpp (modified) * src/Potentials/InternalCoordinates/TwoBody_Length.cpp (modified) * src/Potentials/PartialNucleiChargeFitter.cpp (modified) * src/Potentials/ParticleTypeCheckers.cpp (modified) * src/Potentials/Particles/Particle.cpp (modified) * src/Potentials/Particles/ParticleFactory.cpp (modified) * src/Potentials/Particles/ParticleRegistry.cpp (modified) * src/Potentials/Particles/StreamFactory_Particle.cpp (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialRegistry.cpp (modified) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/RegistryDeserializer_impl.hpp (modified) * src/Potentials/RegistrySerializer_Particle.cpp (modified) * src/Potentials/RegistrySerializer_impl.hpp (modified) * src/Potentials/SerializablePotential.cpp (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/PotentialTypes.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/StreamFactory_EmpiricalPotential.cpp (modified) * src/Potentials/TremoloPotentialFileParser.cpp (modified) * src/Potentials/TremoloPotentialTypes.cpp (modified) * src/Potentials/unittests/stubs/SerializablePotentialMock.cpp (modified) * src/Python/PythonScripting.cpp (modified) * src/Python/exit.cpp (modified) * src/Python/getBoundingBox.cpp (modified) * src/Python/getDomainVolume.cpp (modified) * src/Python/getSelectedMolarMass.cpp (modified) * src/Python/reinit.cpp (modified) * src/Python/wait.cpp (modified) * src/RandomNumbers/RandomNumberDistributionFactory.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberDistribution_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberEngineFactory.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Encapsulation.cpp (modified) * src/RandomNumbers/RandomNumberEngine_Parameters.cpp (modified) * src/RandomNumbers/RandomNumberGenerator.cpp (modified) * src/RandomNumbers/RandomNumberGeneratorFactory.cpp (modified) * src/Server.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/Shape.cpp (modified) * src/Shapes/ShapeFactory.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeAreaStub.cpp (modified) * src/Shapes/unittests/stubs/ApproximateShapeVolumeStub.cpp (modified) * src/Shapes/unittests/stubs/WorldSelectedMoleculesStub.cpp (modified) * src/Shapes/unittests/stubs/moleculeStub.cpp (modified) * src/Tesselation/ApproximateShapeArea.cpp (modified) * src/Tesselation/ApproximateShapeVolume.cpp (modified) * src/Tesselation/BoundaryLineSet.cpp (modified) * src/Tesselation/BoundaryPointSet.cpp (modified) * src/Tesselation/BoundaryPolygonSet.cpp (modified) * src/Tesselation/BoundaryTriangleSet.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/TriangleMatcher/TriangleMatcher.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/ellipsoid.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/Tesselation/triangleintersectionlist.cpp (modified) * src/Thermostats/Berendsen.cpp (modified) * src/Thermostats/GaussianThermostat.cpp (modified) * src/Thermostats/Langevin.cpp (modified) * src/Thermostats/NoThermostat.cpp (modified) * src/Thermostats/NoseHoover.cpp (modified) * src/Thermostats/ThermoStatContainer.cpp (modified) * src/Thermostats/Thermostat.cpp (modified) * src/Thermostats/Woodcock.cpp (modified) * src/UIElements/CommandLineUI/CommandLineDialog.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) * src/UIElements/CommandLineUI/CommandLineParser_validate.cpp (modified) * src/UIElements/CommandLineUI/CommandLineStatusIndicator.cpp (modified) * src/UIElements/CommandLineUI/CommandLineUIFactory.cpp (modified) * src/UIElements/CommandLineUI/CommandLineWindow.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * 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src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Qt4/Query/VectorsQtQuery.cpp (modified) * src/UIElements/Query/EmptyQuery.cpp (modified) * src/UIElements/Query/Query.cpp (modified) * src/UIElements/TextUI/Query/AtomTextQuery.cpp (modified) * src/UIElements/TextUI/Query/AtomsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/BooleanTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoubleTextQuery.cpp (modified) * src/UIElements/TextUI/Query/DoublesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementTextQuery.cpp (modified) * src/UIElements/TextUI/Query/ElementsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/EmptyTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FileTextQuery.cpp (modified) * src/UIElements/TextUI/Query/FilesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/IntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/KeyValuePairTextQuery.cpp (modified) * src/UIElements/TextUI/Query/KeyValuePairsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculeTextQuery.cpp (modified) * src/UIElements/TextUI/Query/MoleculesTextQuery.cpp (modified) * src/UIElements/TextUI/Query/RealSpaceMatrixTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringTextQuery.cpp (modified) * src/UIElements/TextUI/Query/StringsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntTextQuery.cpp (modified) * src/UIElements/TextUI/Query/UnsignedIntsTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorTextQuery.cpp (modified) * src/UIElements/TextUI/Query/VectorsTextQuery.cpp (modified) * src/UIElements/TextUI/TextDialog.cpp (modified) * src/UIElements/TextUI/TextStatusIndicator.cpp (modified) * src/UIElements/TextUI/TextUIFactory.cpp (modified) * src/UIElements/TextUI/TextWindow.cpp (modified) * src/UIElements/UIFactory.cpp (modified) * src/UIElements/Views/MethodStringView.cpp (modified) * src/UIElements/Views/Qt4/ElementList/QtElementList.cpp (modified) * src/UIElements/Views/Qt4/ElementList/QtObservedAtomObserver.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItem.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeItemFactory.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeList.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtMoleculeListView.cpp (modified) * src/UIElements/Views/Qt4/MoleculeList/QtObservedMoleculeObserver.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QListWidgetCurveItem.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QScrollZoomer/ScrollBar.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QScrollZoomer/ScrollZoomer.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisCurveRegistry.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisData.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPageRegistry.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlot.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotCurve.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser.cpp (modified) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser_plotcurve.cpp (modified) * src/UIElements/Views/Qt4/Plotting/XMLParser/QSeisXMLParser_plottype.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtLogBox.cpp (modified) * src/UIElements/Views/Qt4/QtNumericalItem.cpp (modified) * src/UIElements/Views/Qt4/QtShapeController.cpp (modified) * src/UIElements/Views/Qt4/QtShapeList.cpp (modified) * src/UIElements/Views/Qt4/QtStatusBar.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar.cpp (modified) * src/UIElements/Views/Qt4/QtToolBar_QtFavoriteActions.cpp (modified) * src/UIElements/Views/StreamStringView.cpp (modified) * src/UIElements/Views/StringView.cpp (modified) * src/UIElements/Views/View.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/builder_init.cpp (modified) * src/cleanUp.cpp (modified) * src/config.cpp (modified) * src/controller.cpp (modified) * src/controller_AddOn_MPQCCommandJob.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/molecule.cpp (modified) * src/molecule_geometry.cpp (modified) * src/molecule_graph.cpp (modified) * src/poolworker.cpp (modified) * src/unittests/stubs/AtomStub.cpp (modified) * src/unittests/stubs/ObserverStub.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-memdebug.at (modified) * tests/JobMarket/mpqc.cpp (modified) Commented out MemDebug include and Memory::ignore. - MemDebug ... Wed, 15 Mar 2017 18:16:47 GMT Frederik Heber [cb20c0] * src/Actions/WorldAction/StepWorldTimeAction.cpp (modified) MEMFIX: StepWorldTimeAction leaked mem on failure. Thu, 02 Mar 2017 14:01:50 GMT Frederik Heber [cb98f1] * src/Actions/unittests/Makefile.am (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/MPQCJob_Work.cpp (added) * src/Jobs/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: One Definition Rule violation by mpqc. - mpqc.cc implements ... Thu, 02 Mar 2017 07:17:26 GMT Frederik Heber [53ef0d4] * src/Actions/unittests/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) FIX: Missing CodePatterns_LDFLAGS or AM_LDFLAGS or missing boost ... Fri, 11 Nov 2016 14:25:36 GMT Frederik Heber [f5dbea] * src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) VERBOSE: Verbosity fix to ... Fri, 04 Nov 2016 09:37:52 GMT Frederik Heber [814b8c] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) AnalyseFragmentResults stores edge per fragment in value_t of ... Fri, 04 Nov 2016 09:37:51 GMT Frederik Heber [ea63cb] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) * tests/regression/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (modified) Edges per Fragment passed on to FragmentationShortRangeResults. - ... Fri, 04 Nov 2016 09:37:49 GMT Frederik Heber [95304c] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) REFACTOR: Extracted registerPotentialIfNotPresent out of ... Fri, 04 Nov 2016 09:37:48 GMT Frederik Heber [2d1280] * doc/userguide/userguide.xml (modified) * src/Actions/BondAction/BondSetDegreeAction.cpp (added) * src/Actions/BondAction/BondSetDegreeAction.def (added) * src/Actions/BondAction/BondSetDegreeAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Bond/SetDegree/post/test.pdb (added) * tests/regression/Bond/SetDegree/post/test_degree1.pdb (added) * tests/regression/Bond/SetDegree/post/test_degree2.pdb (added) * tests/regression/Bond/SetDegree/post/test_multiple.pdb (added) * tests/regression/Bond/SetDegree/post/test_multiple_degree1.pdb (added) * tests/regression/Bond/SetDegree/post/test_multiple_degree2.pdb (added) * tests/regression/Bond/SetDegree/pre/.pdb (added) * tests/regression/Bond/SetDegree/pre/test.pdb (added) * tests/regression/Bond/SetDegree/pre/test_multiple.pdb (added) * tests/regression/Bond/SetDegree/pre/test_multiple_fail.pdb (added) * tests/regression/Bond/SetDegree/testsuite-bond-set-degree.at (added) * tests/regression/Bond/SetDegree/testsuite-bond-set-degree_multiple.at (added) * tests/regression/Bond/testsuite-bond.at (modified) * tests/regression/Makefile.am (modified) Added BondSetDegreeAction for manipulating bond degrees. Thu, 20 Oct 2016 20:54:48 GMT Frederik Heber [72e40d0] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/MolecularDynamicsAction.cpp (modified) * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) * src/Actions/WorldAction/StepWorldTimeAction.cpp (added) * src/Actions/WorldAction/StepWorldTimeAction.def (added) * src/Actions/WorldAction/StepWorldTimeAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/testsuite-options.at (modified) * tests/regression/WorldTime/SetWorldTime/testsuite-worldtime-set-world-time.at (moved) * tests/regression/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (added) * tests/regression/WorldTime/testsuite-worldtime.at (added) * tests/regression/testsuite.at (modified) Added single action to step backward and forward through time. - ...