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(edit) @c30959   5 years frederik.heber BondAddAction also adds to molecule. - NOTE: This basically does … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @e70818   5 years frederik.heber Added getSelectedAtomPositions() python function. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @5fa1e86   5 years frederik.heber Added BondifyAction. - this allows to add non-hydrogen bonds and is … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @51d384a   5 years frederik.heber Added BondedParticle::IsBondedTo that uses current worldtime. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @ea30e6   5 years frederik.heber Added python getters for selected atom ids and elements. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @38bcbe   5 years frederik.heber StretchBondAction will used tabled distances when given distance is … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @4de4f6   5 years frederik.heber Added AtomBondNeighbors selection action. - DOCU: Added to userguide. … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @9f55b9   5 years frederik.heber Extracted functor StretchBondUtil from StretchBondAction. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @f3eb6a   5 years frederik.heber FIX: LinkedCell_model executes deletes right away. - we use the … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @ef0f8f   5 years frederik.heber LinkCell model has name on update for debugging. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @d9e1d1   5 years frederik.heber Extending PairCorrelation to correlate element and set of atoms. - … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @addb51   5 years frederik.heber Add action to clear fragmentation state. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @0ad4781   5 years frederik.heber Added action to randomly select a set of atoms. - needed to make new … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @3f5b0a   5 years frederik.heber Added mutex on changes_present in GLWorldView. - this should prevent … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @b0060a   5 years frederik.heber Making test code python2&3 compatible. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @ba49d8   5 years frederik.heber Removing Ambient and Specular color from Qt4 atoms. - this way the … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @da30ddf   5 years frederik.heber FIX: tooltip in Qt4 menu caused sigsev. - I don't know why it … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @61cc0f   5 years frederik.heber Enhanced verbosity of FragmentationAutomation. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @d40189   5 years frederik.heber OutputTemperature -> OutputEnergies, SaveTemperature -> SaveEnergies. … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @cbbb6a   5 years frederik.heber FIX: AnalyseFragmentationResultsAction ignored prefix mostly. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @26062f   5 years frederik.heber StoreSaturatedFragmentAction may now export to FragmentQueue as well. … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @b56827   5 years frederik.heber Program_options 1.63 behavior breaks. - in program_options with 1.63 … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @1ca493a   6 years frederik.heber Allowing python3 usage. - Init function name changes on python2/3. - … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @912a6f   6 years frederik.heber Adapted to boost 1.64. - need array_wrapper.hpp when using … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @4045d4   6 years frederik.heber FIX: libMolecuilderJobs had hard-coded boost_serialization dep. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @c52abd   8 years frederik.heber Added unit test for Graph6Reader. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator stable
(edit) @99c705   8 years frederik.heber ChemicalSpaceEvaluator working for graph with 2 nodes. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator stable
(edit) @f5ea10   8 years frederik.heber Added Graph6Reader, extended BoostGraphCreator, added … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator stable
(edit) @8d56a6   8 years frederik.heber Merge branch 'TremoloParser_IncreasedPrecision' into Candidate_v1.6.1 … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator stable
(edit) @3e334e   8 years frederik.heber Merge branch 'AutomationFragmentation_failures' into Candidate_v1.6.1 Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator stable
(edit) @0682c2   8 years frederik.heber Excluded hydrogens due to their small mass from spreading updates. - … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph stable
(edit) @bd19c1   8 years frederik.heber Capping BB update step at 0.2 and general BB stepwidth at maximum of … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion stable
(edit) @06536b   8 years frederik.heber annealWithBondGraph_BarzilaiBorwein() is using getBBStepWidth(), too. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion stable
(edit) @b3aaf4   8 years frederik.heber Preventing cancelling updates for optimization with bond graph. - we … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion stable
(edit) @883d98   8 years frederik.heber FIX: Removed deltat reduction from anneal_BarzilaiBorwein() as it … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion stable
(edit) @a6c11a   8 years frederik.heber All failures in FragmentationAutomation are explained by log statements. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator stable
(edit) @70caa3   8 years frederik.heber FIX: FormatParserStorage would open new streams per SaveAll(). - we … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction stable
(edit) @4b2adf   8 years frederik.heber ForceAnnealiing now returns bool to indicate stop condition for … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction stable
(edit) @e3ce0e   8 years frederik.heber MakroAction allows getting the internal ActionSequence's current step. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction stable
(edit) @559293   8 years frederik.heber ActionQueue has predicates to check if current Action is Process or … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction stable
(edit) @646f73   8 years frederik.heber annealWithBondGraph_..() prints the largest update on default … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction stable
(edit) @83956e   8 years frederik.heber Rewrote annealWithBondGraph_BarzilaiBorwein() to simply distinguish … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction stable
(edit) @fba720   8 years frederik.heber Increased output precision in tremolo's data files to 10 digits. - … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator TremoloParser_IncreasedPrecision stable
(edit) @e7ad08   8 years frederik.heber Python interface now converts dashes in tokens to underscores, … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator PythonUI_with_named_parameters TremoloParser_IncreasedPrecision stable
(edit) @8819d2   8 years frederik.heber FIX: GLWorldView no longer caught changes after deactivating DreiBein. … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Gui_displays_atomic_force_velocity PythonUI_with_named_parameters TremoloParser_IncreasedPrecision stable
(edit) @2c97ad   8 years frederik.heber QtTimeLine has an additional QSpinBox. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Gui_displays_atomic_force_velocity PythonUI_with_named_parameters TremoloParser_IncreasedPrecision stable
(edit) @8c5e2a   8 years frederik.heber FIX: QTimeLine now exactly controls world time. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Gui_displays_atomic_force_velocity PythonUI_with_named_parameters TremoloParser_IncreasedPrecision stable
(edit) @8ac6d0e   8 years frederik.heber FIX: atominfo now provides correct TrajectoryUpdate notifications. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Gui_displays_atomic_force_velocity PythonUI_with_named_parameters TremoloParser_IncreasedPrecision stable
(edit) @897a01   8 years frederik.heber Arrows display velocity and force of each atom. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Gui_displays_atomic_force_velocity PythonUI_with_named_parameters TremoloParser_IncreasedPrecision stable
(edit) @8450da   8 years frederik.heber ForceAnnealing functions now have better readable time step variables. … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @0c4f24   8 years frederik.heber anneal() returns maxComponents, does not neet _offset. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @90050b   8 years frederik.heber Center of weight translation removed from GatheredUpdates. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @07d4b1   8 years frederik.heber BondVectors::getRemnant...() now requires atom's gradient. - No more … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @f433ec   8 years frederik.heber We now obtain weights via levmar minimization. - this should yield … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @7b4e67   8 years frederik.heber Added failing weights test case to BondVectors. - TESTFIX: Marked … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @c1c6cb   8 years frederik.heber Added unit tests for BondVectors. - Added tests on up-to-date … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @825d33   8 years frederik.heber Extracted calculation of weights per atom into BondVectors. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @9861d0   8 years frederik.heber BondVectors now return subset of BondVectors for a given atom. - … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @2f3905   8 years frederik.heber Fixing annealWithBondgraph(). AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @be729b   8 years frederik.heber ForceAnnealing::anneal() now only once reduces deltat. - TESTFIX: … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @6458e7   8 years frederik.heber ForceAnnealing can now be used either atom- or bond-centered. - atom … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @77d0cd   8 years frederik.heber ForceAnnealing now uses BondVectors to optimize the structure from the … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @d51e62   8 years frederik.heber Added helper class BondVectors. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @355915   8 years frederik.heber ForceAnnealing now calculates force on either side of bond in … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @e77580   8 years frederik.heber ForceAnnealing converts atomic forces to bond forces and optimize … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @d3e1d5   8 years frederik.heber FIX: unnecessary output iterator present in … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @e21d55   8 years frederik.heber FIX: annealWithBondgraph() did not check for zero GradientDifference. … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @9bb8c8   8 years frederik.heber FIX: maxComponents was not chosen by absolute magnitude. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @c87d6e   8 years frederik.heber ForceAnnealingAction's Undo removes trajectory item if it was added. … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @6145577   8 years frederik.heber FIX: ForceAnnealingAction's Undo is again working. - … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @8c6b68   8 years frederik.heber atom::removeStep() extended to removing interval of steps. - … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @efd020   8 years frederik.heber Readded step-world-time to StructuralOptimization. - adapted … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @12f16c   8 years frederik.heber ForceAnnealing first parses forces, then copies step and finally optimizes. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @2bb3be   8 years frederik.heber Removed DoOutput param from ForceAnnealing. - TESTFIX: Modifying … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @866dec   8 years frederik.heber ForceAnnealing no longer resets forces, AnalyseFragmentResults now … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @216840   8 years frederik.heber ForceAnnealing accepts option deltat. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @b2acca   8 years frederik.heber ForceAnnealing can now be used either atom- or bond-centered. - new … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @ecfcf6   8 years frederik.heber FIX: ForceAnnealing would not reset force components prior to loading … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @8ddd07   8 years frederik.heber Sorting given selected atoms by ids in ForceAnnealing. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @0477b0   8 years frederik.heber Added sortByIds() to AtomSetMixin. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @56b4c6   8 years frederik.heber Added damping-factor as another option to ForceAnnealing for proper … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @985d1f   8 years frederik.heber FIX: Removed step-world-tme from StructuralOptimizationAction. - this … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @cdfb6f   8 years frederik.heber ForceAnnealing now shifts atoms in the bond graph to anneal forces, … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @456f19   8 years frederik.heber SpecificFragmentController checks whether there are still workers left … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @322d58   8 years frederik.heber ForceAnnealing now uses step width according to Barzilai-Borwein … AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @1e49e66   8 years frederik.heber Added reset() function to ForceAnnealing. AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @7e4d0a6   8 years frederik.heber FIX: Fragmentation does no longer use getTrueFather(). - in a very … Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @f4b6bc9   8 years frederik.heber Query::handle() no longer returns bool but has internal result flag. … Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @d86d97   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
(edit) @3c9ac3   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
(edit) @4c6f0d   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
(edit) @7516f6   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
(edit) @d1134d   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
(edit) @4a6ef3   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
(edit) @e0b960   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
(edit) @966ce7   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
(edit) @e3ec8a8   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
(edit) @0dc8bf2   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
(edit) @1356af   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
(edit) @6e5b8d   9 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 Candidate_v1.7.0 Candidate_v1.7.1 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 stable
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