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(edit) @a844d8   6 years frederik.heber FIX: PKG_CHECK_MODULES used empty fail action. Candidate_v1.6.1
(edit) @425516   6 years frederik.heber Set version to 1.6.1. - MoleCuilder library is now 18:0:1. - Codename … Candidate_v1.6.1 v1.6.1
(edit) @209f4c   6 years frederik.heber TESTS: Fixed FillSurface and FillVolumne, recreated GuiChecks. - … Candidate_v1.6.1
(edit) @9ac3d3   6 years frederik.heber FIX: Constrained locking in CodePattern's Notification and Observable. … Candidate_v1.6.1
(edit) @ca2880   6 years frederik.heber DISTFIX: numpy_check.py was missing in EXTRA_DIST. Candidate_v1.6.1
(edit) @c4cba2   6 years frederik.heber DISTFIX: python test ForceAnnealing folder was missing in EXTRA_DIST. Candidate_v1.6.1
(edit) @108c88   6 years frederik.heber TESTFIX: ChemicalSpaceEvaluator regression test was working on wrong file. Candidate_v1.6.1
(edit) @43552e   6 years frederik.heber DISTFIX: Atom regression test RandomPerturbation did mark the input … Candidate_v1.6.1
(edit) @1e06ed   6 years frederik.heber DISTFIX: tests/regression folder Geometry was missing in EXTRA_DIST. Candidate_v1.6.1
(edit) @0bc2c6   6 years frederik.heber Added gcc 5.4.0 to boost.m4. Candidate_v1.6.1
(edit) @883599   6 years frederik.heber DISTFIX: EXTRA_DIST in tests/integration did not contain new test folders. Candidate_v1.6.1
(edit) @c52abd   7 years frederik.heber Added unit test for Graph6Reader. Candidate_v1.6.1 ChemicalSpaceEvaluator
(edit) @d661b2   7 years frederik.heber Added regression test for simplest of graphs with two carbon elements. Candidate_v1.6.1 ChemicalSpaceEvaluator
(edit) @99c705   7 years frederik.heber ChemicalSpaceEvaluator working for graph with 2 nodes. Candidate_v1.6.1 ChemicalSpaceEvaluator
(edit) @f5ea10   7 years frederik.heber Added Graph6Reader, extended BoostGraphCreator, added … Candidate_v1.6.1 ChemicalSpaceEvaluator
(edit) @8d56a6   7 years frederik.heber Merge branch 'TremoloParser_IncreasedPrecision' into Candidate_v1.6.1 … Candidate_v1.6.1 ChemicalSpaceEvaluator
(edit) @3e334e   7 years frederik.heber Merge branch 'AutomationFragmentation_failures' into Candidate_v1.6.1 Candidate_v1.6.1 ChemicalSpaceEvaluator
(edit) @2ee2cc   7 years frederik.heber TESTS: Reactivated again all tests related to bond graph optimization. Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph
(edit) @3183f5   7 years frederik.heber DOCU: Added explanation of bond graph optimization to userguide. Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph
(edit) @0682c2   7 years frederik.heber Excluded hydrogens due to their small mass from spreading updates. - … Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph
(edit) @bd19c1   7 years frederik.heber Capping BB update step at 0.2 and general BB stepwidth at maximum of … Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion
(edit) @06536b   7 years frederik.heber annealWithBondGraph_BarzilaiBorwein() is using getBBStepWidth(), too. Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion
(edit) @8c0ac9   7 years frederik.heber TESTFIX: Made integration tests for structure optimization of water … Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion
(edit) @e72d94   7 years frederik.heber TESTFIX: threshold check in integration tests on structure … Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion
(edit) @31baf0   7 years frederik.heber TESTFIX: Readded missing Structure Optimization integration tests. - … Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion
(edit) @b3aaf4   7 years frederik.heber Preventing cancelling updates for optimization with bond graph. - we … Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion
(edit) @883d98   7 years frederik.heber FIX: Removed deltat reduction from anneal_BarzilaiBorwein() as it … Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion
(edit) @a6c11a   7 years frederik.heber All failures in FragmentationAutomation are explained by log statements. AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator
(edit) @70caa3   7 years frederik.heber FIX: FormatParserStorage would open new streams per SaveAll(). - we … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction
(edit) @4b2adf   7 years frederik.heber ForceAnnealiing now returns bool to indicate stop condition for … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction
(edit) @e3ce0e   7 years frederik.heber MakroAction allows getting the internal ActionSequence's current step. AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction
(edit) @559293   7 years frederik.heber ActionQueue has predicates to check if current Action is Process or … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction
(edit) @646f73   7 years frederik.heber annealWithBondGraph_..() prints the largest update on default … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction
(edit) @83956e   7 years frederik.heber Rewrote annealWithBondGraph_BarzilaiBorwein() to simply distinguish … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction
(edit) @6a5921   7 years frederik.heber TESTS: Deactivated temporarily all tests related to bond graph … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion StoppableMakroAction
(edit) @4fc0ea   7 years frederik.heber TESTFIX: Changes to various regression and Python tests because of … Candidate_v1.6.1 ChemicalSpaceEvaluator TremoloParser_IncreasedPrecision
(edit) @fba720   7 years frederik.heber Increased output precision in tremolo's data files to 10 digits. - … Candidate_v1.6.1 ChemicalSpaceEvaluator TremoloParser_IncreasedPrecision
(edit) @cd91bd   7 years frederik.heber TESTFIX: Changes to test scripts because now keyword arguments are … Candidate_v1.6.1 ChemicalSpaceEvaluator PythonUI_with_named_parameters TremoloParser_IncreasedPrecision
(edit) @e7ad08   7 years frederik.heber Python interface now converts dashes in tokens to underscores, … Candidate_v1.6.1 ChemicalSpaceEvaluator PythonUI_with_named_parameters TremoloParser_IncreasedPrecision
(edit) @8819d2   7 years frederik.heber FIX: GLWorldView no longer caught changes after deactivating DreiBein. … Candidate_v1.6.1 ChemicalSpaceEvaluator Gui_displays_atomic_force_velocity PythonUI_with_named_parameters TremoloParser_IncreasedPrecision
(edit) @2c97ad   7 years frederik.heber QtTimeLine has an additional QSpinBox. Candidate_v1.6.1 ChemicalSpaceEvaluator Gui_displays_atomic_force_velocity PythonUI_with_named_parameters TremoloParser_IncreasedPrecision
(edit) @8c5e2a   7 years frederik.heber FIX: QTimeLine now exactly controls world time. Candidate_v1.6.1 ChemicalSpaceEvaluator Gui_displays_atomic_force_velocity PythonUI_with_named_parameters TremoloParser_IncreasedPrecision
(edit) @8ac6d0e   7 years frederik.heber FIX: atominfo now provides correct TrajectoryUpdate notifications. Candidate_v1.6.1 ChemicalSpaceEvaluator Gui_displays_atomic_force_velocity PythonUI_with_named_parameters TremoloParser_IncreasedPrecision
(edit) @897a01   7 years frederik.heber Arrows display velocity and force of each atom. Candidate_v1.6.1 ChemicalSpaceEvaluator Gui_displays_atomic_force_velocity PythonUI_with_named_parameters TremoloParser_IncreasedPrecision
(edit) @8450da   7 years frederik.heber ForceAnnealing functions now have better readable time step variables. … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @90ece9   7 years frederik.heber TESTFIX: Fixes to Python tests due to changed anneal() and modified … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @0c4f24   7 years frederik.heber anneal() returns maxComponents, does not neet _offset. AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @441d40   7 years frederik.heber TESTFIX: bondgraph annealing is working better than expected. AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @90050b   7 years frederik.heber Center of weight translation removed from GatheredUpdates. AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @07d4b1   7 years frederik.heber BondVectors::getRemnant...() now requires atom's gradient. - No more … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @f433ec   7 years frederik.heber We now obtain weights via levmar minimization. - this should yield … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @7b4e67   7 years frederik.heber Added failing weights test case to BondVectors. - TESTFIX: Marked … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @c1c6cb   7 years frederik.heber Added unit tests for BondVectors. - Added tests on up-to-date … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @825d33   7 years frederik.heber Extracted calculation of weights per atom into BondVectors. AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @9861d0   7 years frederik.heber BondVectors now return subset of BondVectors for a given atom. - … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @2f3905   7 years frederik.heber Fixing annealWithBondgraph(). AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @038ccd   7 years frederik.heber TESTFIX: Needed to change ForceAnnealing Python and regression test … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @be729b   7 years frederik.heber ForceAnnealing::anneal() now only once reduces deltat. - TESTFIX: … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @6458e7   7 years frederik.heber ForceAnnealing can now be used either atom- or bond-centered. - atom … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @77d0cd   7 years frederik.heber ForceAnnealing now uses BondVectors to optimize the structure from the … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @d51e62   7 years frederik.heber Added helper class BondVectors. AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @355915   7 years frederik.heber ForceAnnealing now calculates force on either side of bond in … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @e77580   7 years frederik.heber ForceAnnealing converts atomic forces to bond forces and optimize … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @d3e1d5   7 years frederik.heber FIX: unnecessary output iterator present in … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @e21d55   7 years frederik.heber FIX: annealWithBondgraph() did not check for zero GradientDifference. … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @075357   7 years frederik.heber TEST: Adding Python test on ForceAnnealing using an Ising model with … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @41de6e   7 years frederik.heber TESTFIX: ForceAnnealing regression test used zero force. - all atoms … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @9bb8c8   7 years frederik.heber FIX: maxComponents was not chosen by absolute magnitude. AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @c87d6e   7 years frederik.heber ForceAnnealingAction's Undo removes trajectory item if it was added. … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @6145577   7 years frederik.heber FIX: ForceAnnealingAction's Undo is again working. - … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @8c6b68   7 years frederik.heber atom::removeStep() extended to removing interval of steps. - … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @efd020   7 years frederik.heber Readded step-world-time to StructuralOptimization. - adapted … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @12f16c   7 years frederik.heber ForceAnnealing first parses forces, then copies step and finally optimizes. AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @2bb3be   7 years frederik.heber Removed DoOutput param from ForceAnnealing. - TESTFIX: Modifying … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @866dec   7 years frederik.heber ForceAnnealing no longer resets forces, AnalyseFragmentResults now … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @216840   7 years frederik.heber ForceAnnealing accepts option deltat. AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @b2acca   7 years frederik.heber ForceAnnealing can now be used either atom- or bond-centered. - new … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @ecfcf6   7 years frederik.heber FIX: ForceAnnealing would not reset force components prior to loading … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @8ddd07   7 years frederik.heber Sorting given selected atoms by ids in ForceAnnealing. AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @0477b0   7 years frederik.heber Added sortByIds() to AtomSetMixin. AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @56b4c6   7 years frederik.heber Added damping-factor as another option to ForceAnnealing for proper … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @985d1f   7 years frederik.heber FIX: Removed step-world-tme from StructuralOptimizationAction. - this … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @cdfb6f   7 years frederik.heber ForceAnnealing now shifts atoms in the bond graph to anneal forces, … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @a5c293   7 years frederik.heber FIX: SyncOperation now checks error codes from connect and close. - … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @1e58bb   7 years frederik.heber FIX: Integration tests now abort safely when one of the programs dies. … AutomationFragmentation_failures Candidate_v1.6.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization_continued Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults PythonUI_with_named_parameters StoppableMakroAction TremoloParser_IncreasedPrecision
(edit) @456f19   7 years frederik.heber SpecificFragmentController checks whether there are still workers left … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @0542e2   7 years frederik.heber Added GetNumberWorkersOperation, Controller returns number of workers. … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @1181a3   7 years frederik.heber ControllerListener now also gets const ref to WorkerPool. - this is … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @354a5f   7 years frederik.heber FIX: PoolGuard did not decrease WaitingOp counter when checkalive op … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @bca6b6   7 years frederik.heber OperationQueue states when queue is empty (instead of all are running). AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @322d58   7 years frederik.heber ForceAnnealing now uses step width according to Barzilai-Borwein … AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @1e49e6   7 years frederik.heber Added reset() function to ForceAnnealing. AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @9b32071   7 years frederik.heber TESTS: Added CodeCheck on uniqueness of ports in integration tests. Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @53a85a   7 years frederik.heber Added integration test on Potential Fitting for water. - we fit … Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @167523   7 years frederik.heber Added integration tests on Structure Optimization. - we use the same … Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @37fe17   7 years frederik.heber TESTS: Added MD tests on methane, ethane, and water-filled system. Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @7e4d0a6   7 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 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
(edit) @0aae02   7 years frederik.heber Added integration test molecular dynamics of a water molecule. - we … Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 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
(edit) @f4b6bc9   7 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 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
(edit) @775f3f   7 years frederik.heber TESTFIX: Convex Tesselation did not specify nonconvex-file which they … Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 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
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