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(edit) @1e4f0a   8 years frederik.heber ForceAnnealing returns whether to stop and ForceAnnealingAction stops …
(edit) @15acdb   8 years frederik.heber MakroAction allows getting the internal ActionSequence's current step.
(edit) @17fceea   8 years frederik.heber ActionQueue has predicates to check if current Action is Process or …
(edit) @ab3827   8 years frederik.heber Rewrote annealWithBondGraph_BarzilaiBorwein() to simply distinguish …
(edit) @0cc08c   8 years frederik.heber FIX: GLWorldView no longer caught changes after deactivating DreiBein. … ForceAnnealing_with_BondGraph_continued
(edit) @35364f0   8 years frederik.heber QtTimeLine has an additional QSpinBox. ForceAnnealing_with_BondGraph_continued
(edit) @ff1696   8 years frederik.heber FIX: QTimeLine now exactly controls world time. ForceAnnealing_with_BondGraph_continued
(edit) @78830b   8 years frederik.heber FIX: atominfo now provides correct TrajectoryUpdate notifications. ForceAnnealing_with_BondGraph_continued
(edit) @9e4e21   8 years frederik.heber Arrows display velocity and force of each atom. ForceAnnealing_with_BondGraph_continued
(edit) @5bbaca   8 years frederik.heber tempcommit: Gradient is printed with magnitude. ForceAnnealing_with_BondGraph_continued
(edit) @ff60380   8 years frederik.heber FIX: maxComponents was not chosen by absolute magnitude. ForceAnnealing_with_BondGraph_continued
(edit) @d74bb5   8 years frederik.heber tempcommit: Removed step-world-time from StructuralOptimizationAction. ForceAnnealing_with_BondGraph_continued
(edit) @c0baa8   8 years frederik.heber tempcommit: data files for regression test AnalyseFragmentResults OBC … ForceAnnealing_with_BondGraph_continued
(edit) @cee565   8 years frederik.heber tempcommit: FIX: ForceAnnealingAction's Undo is again working. ForceAnnealing_with_BondGraph_continued
(edit) @4919f0   8 years frederik.heber atom::removeStep() extended to removing interval of steps. - … ForceAnnealing_with_BondGraph_continued
(edit) @fcc860   8 years frederik.heber ForceAnnealing functions now have better readable time step variables. … ForceAnnealing_with_BondGraph_continued
(edit) @93fd2a6   8 years frederik.heber tempcommit: Fixes to Python tests due to changed anneal() and modified … ForceAnnealing_with_BondGraph_continued
(edit) @bef5b3   8 years frederik.heber tempcommit: TESTFIX: Modifying regression tests ForceAnnealing to … ForceAnnealing_with_BondGraph_continued
(edit) @5f18f1   8 years frederik.heber tempcommit: Further fixing to how steps are treated. - last but two … ForceAnnealing_with_BondGraph_continued
(edit) @f10066   8 years frederik.heber tempcommit: In ForceAnnealing currentStep was used in some places, … ForceAnnealing_with_BondGraph_continued
(edit) @26de2a   8 years frederik.heber tempcommit: ForceAnnealing first parses forces, then copies step and … ForceAnnealing_with_BondGraph_continued
(edit) @7ef5d32   8 years frederik.heber tempcommit: With DoOutput() removed, i.e. always true, we need to look … ForceAnnealing_with_BondGraph_continued
(edit) @504492   8 years frederik.heber tempcommit: anneal() returns maxComponents, does not neet _offset. ForceAnnealing_with_BondGraph_continued
(edit) @152599   8 years frederik.heber tempcommit: Removed note about stupid DoOutput copying. ForceAnnealing_with_BondGraph_continued
(edit) @208b60   8 years frederik.heber Removed DoOutput param from ForceAnnealing. ForceAnnealing_with_BondGraph_continued
(edit) @a78360   8 years frederik.heber TESTFIX: bondgraph annealing is working better than expected. ForceAnnealing_with_BondGraph_continued
(edit) @8bfb58   8 years frederik.heber tempcommit: Center of weight translation removed from GatheredUpdates. ForceAnnealing_with_BondGraph_continued
(edit) @ac79b2   8 years frederik.heber tempcommit: Merge with 698308e2 ForceAnnealing_with_BondGraph_continued
(edit) @ef59aa   8 years frederik.heber tempcommit: CurrentStep was wrongly calculated. ForceAnnealing_with_BondGraph_continued
(edit) @c4a725   8 years frederik.heber tempcommit: No more default anneal() without bondgrapg, and can't … ForceAnnealing_with_BondGraph_continued
(edit) @ccbdf4   8 years frederik.heber tempcommit: BondVectors::getRemnant...() now requires atom's gradient. ForceAnnealing_with_BondGraph_continued
(edit) @90e540   8 years frederik.heber We now obtain weights via levmar minimization. - this should yield … ForceAnnealing_with_BondGraph_continued
(edit) @6d7c73   8 years frederik.heber FIX: unnecessary output iterator present in … ForceAnnealing_with_BondGraph_continued
(edit) @c9f4a0   8 years frederik.heber tempcommit: Added failing weights test case to BondVectors. ForceAnnealing_with_BondGraph_continued
(edit) @d3d964   8 years frederik.heber Added unit tests for BondVectors. - Added tests on up-to-date … ForceAnnealing_with_BondGraph_continued
(edit) @cb80d4   8 years frederik.heber Extracted calculation of weights per atom into BondVectors. ForceAnnealing_with_BondGraph_continued
(edit) @461a7f   8 years frederik.heber BondVectors now return subset of BondVectors for a given atom. - … ForceAnnealing_with_BondGraph_continued
(edit) @12d20c   8 years frederik.heber Fixed and extended Python tests on ForceAnnealing with and without … ForceAnnealing_with_BondGraph_continued
(edit) @698308   8 years frederik.heber Fixing annealWithBondgraph(). ForceAnnealing_with_BondGraph_continued
(edit) @b7fe6e   8 years frederik.heber ForceAnnealing::anneal() now only once reduces deltat. ForceAnnealing_with_BondGraph_continued
(edit) @3a5de5   8 years frederik.heber ForceAnnealing no longer resets forces, AnalyseFragmentResults now … ForceAnnealing_with_BondGraph_continued
(edit) @6dfa37   8 years frederik.heber ForceAnnealing accepts option deltat. ForceAnnealing_with_BondGraph_continued
(edit) @8270be   8 years frederik.heber FIX: ForceAnnealing would not reset force components prior to loading … ForceAnnealing_with_BondGraph_continued
(edit) @1050ac   8 years frederik.heber Sorting given selected atoms by ids in ForceAnnealing. ForceAnnealing_with_BondGraph_continued
(edit) @44441a   8 years frederik.heber TESTFIX: ForceAnnealing regression test used zero force. - all atoms … ForceAnnealing_with_BondGraph_continued
(edit) @70d034   8 years frederik.heber Added sortByIds() to AtomSetMixin. ForceAnnealing_with_BondGraph_continued
(edit) @9d3846   8 years frederik.heber TEST: Adding Python test on ForceAnnealing using an Ising model. ForceAnnealing_with_BondGraph_continued
(edit) @6d360a   8 years frederik.heber ForceAnnealing can now be used either atom- or bond-centered. - new … ForceAnnealing_with_BondGraph_continued
(edit) @4cd46b   8 years frederik.heber ForceAnnealing now uses BondVectors to optimize the structure from the … ForceAnnealing_with_BondGraph_continued
(edit) @cc3964   8 years frederik.heber Added helper class BondVectors. ForceAnnealing_with_BondGraph_continued
(edit) @57092a   8 years frederik.heber ForceAnnealing now calculates force on either side of bond in … ForceAnnealing_with_BondGraph_continued
(edit) @ab7bfa6   8 years frederik.heber ForceAnnealing converts atomic forces to bond forces and optimize … ForceAnnealing_with_BondGraph_continued
(edit) @539845   8 years frederik.heber Added damping-factor as another option to ForceAnnealing for proper … ForceAnnealing_with_BondGraph_continued
(edit) @58787b   8 years frederik.heber ForceAnnealing now shifts atoms in the bond graph to anneal forces, too. ForceAnnealing_with_BondGraph_continued
(edit) @7d2364   8 years frederik.heber ForceAnnealing now uses step width according to Barzilai-Borwein … ForceAnnealing_with_BondGraph_continued
(edit) @f49361   8 years frederik.heber Added reset() function to ForceAnnealing. ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults
(edit) @c3703b   8 years frederik.heber TESTS: Added CodeCheck on uniqueness of ports in integration tests. ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults
(edit) @60fb30   8 years frederik.heber Added integration test on Potential Fitting for water. - we fit … ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults
(edit) @e43a6d   8 years frederik.heber Added integration tests on Structure Optimization. - we use the same … ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults
(edit) @c837db7   8 years frederik.heber TESTS: Added MD tests on methane, ethane, and water-filled system. Action_Thermostats ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults
(edit) @b93bc5   8 years frederik.heber FIX: Fragmentation does no longer use getTrueFather(). - in a very … Action_Thermostats ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults
(edit) @3bd4a66   8 years frederik.heber Added integration test molecular dynamics of a water molecule. - we … Action_Thermostats ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults
(edit) @bf87c2   8 years frederik.heber Query::handle() no longer returns bool but has internal result flag. … Action_Thermostats ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults
(edit) @9346af   8 years frederik.heber TESTFIX: Convex Tesselation did not specify nonconvex-file which they … Action_Thermostats ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults
(edit) @780f25   8 years frederik.heber Moved fragment jobs integration test into subfolder. Action_Thermostats ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults
(edit) @d86d97   8 years frederik.heber FIX: FragmentResultsContainer is no longer purged during run. - so … Action_Thermostats Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @9a1e099   8 years frederik.heber Added regression test on DiffFragmentResultContainer. Action_Thermostats Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @3c9ac3   8 years frederik.heber Qt..Lists now take note of subjectKilled propery. Action_Thermostats Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @4c6f0d   8 years frederik.heber FIX: server-port was invalid. - now, we use empty string as param … Action_Thermostats Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @7516f6   8 years frederik.heber FIX: several Qt...Lists required mutex to control refill triggered by … Action_Thermostats Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @b10593   8 years frederik.heber Recreated all GuiChecks. - GuiChecks lacked … Action_Thermostats Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @ecacf0   8 years frederik.heber FIX: regression test Makefile.am lacked difffragmentresultcontainer … Action_Thermostats Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @a9db89   8 years frederik.heber FIX: regression test Geometry common still used position instead of … Action_Thermostats Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @92d0e6   8 years frederik.heber ManyWaysToTranslateAtom: Added stretch-bond test. Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @d1134d   8 years frederik.heber FIX: rotate-around-bond now rotates only one side of mol's bond graph. … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @4a6ef3   8 years frederik.heber Moved AlwaysTruePredicate from BoostGraphCreatorUnitTest into … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @e0b960   8 years frederik.heber Edges may be added and removed in BoostGraphCreator. - TESTS: added … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @966ce7   8 years frederik.heber BreadthFirstSearchGatherer::getDistances() added. Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @e3ec8a8   8 years frederik.heber Extended BreadthFirstSearchGatherer to allow BFS with limited … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @0dc8bf2   8 years frederik.heber Added unit test for BoostGraphCreator. Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @1356af   8 years frederik.heber Moved BoostGraphCreator::createFromRange into extra impl module. Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @6e5b8d   8 years frederik.heber Added BreadthFirstSearchGathererUnitTest. Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @bccbe9   8 years frederik.heber Extracted extraction (subset of) nodes from BoostGraph into … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @d24ef58   8 years frederik.heber Extracted conversion to boost::graph into distinct struct. - … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @3b74fa   8 years frederik.heber Rewrite of StretchBondAction to take bondgraph into account. - i.e. … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @0716eac   8 years frederik.heber SelectMoleculeByOrder and SelectionAtomByOrder now allows multiple … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @f56e14   8 years frederik.heber Added Examples testcase for the many ways to translate an atom blog entry. Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @70f2a1   8 years frederik.heber DOCU: Added restrictions of file formats to userguide. Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @33af20   8 years frederik.heber TremoloParser::save() now supports multiple time steps. - TESTS: … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @0e894a   8 years frederik.heber Extracted getMinMaxTrajectories() into FormatParser_common. Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @220d2c   8 years frederik.heber TremoloParser::load() can deal with multiple time steps. - TESTS: … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @95b64f   8 years frederik.heber Implemented missing AtomInfo::setAtStep(). Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_oldresults ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @3cfb31   8 years frederik.heber DOCU: Updated potentials.dox. Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator EmpiricalPotential_contain_HomologyGraph_documentation Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_oldresults ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @b52710e   8 years frederik.heber DOCU: Enhanced documentation of fit-potential to explain new … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator EmpiricalPotential_contain_HomologyGraph_documentation Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_oldresults ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @8f2f4e   8 years frederik.heber FIX: GLWorldScene::removeShape() invalidated iter before delete. Action_Thermostats Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator EmpiricalPotential_contain_HomologyGraph_documentation Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_oldresults ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @3f6aac   8 years frederik.heber Added (Un)selectAtomByName. - Descriptor for AtomByName was already … Action_Thermostats Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator EmpiricalPotential_contain_HomologyGraph_documentation Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_oldresults ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @9a4772   8 years frederik.heber AnalyseFragmentResults now always prints energy table, verbosity 1. Action_Thermostats Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator EmpiricalPotential_contain_HomologyGraph_documentation Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_oldresults ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @f1cacb   8 years frederik.heber Fixed several small issues with the userguide. - additional … Action_Thermostats Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator EmpiricalPotential_contain_HomologyGraph_documentation Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_oldresults ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @4dfe724   8 years frederik.heber FIX: QtGui again reacts to WorldTime changes. - QtObservedAtom now … Action_Thermostats Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator EmpiricalPotential_contain_HomologyGraph_documentation Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_oldresults ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
(edit) @70fee0   8 years frederik.heber ObservedValue has forceUpdate() public function to externally force an … Action_Thermostats Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator EmpiricalPotential_contain_HomologyGraph_documentation Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_oldresults ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps
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