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(edit) @f01bb3   5 years frederik.heber CppUnit detected by pkg-config as fallback. - ubunntu 18.04 no longer … Candidate_v1.7.0 Candidate_v1.7.1 stable
(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) @7a434f   6 years frederik.heber FIX: vmg's test/interfaces lacked boost cppflags. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @5d2403   6 years frederik.heber FIX: DiffFragmentResultContainer lacked lib-specific boost ldflags. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @ffeb81   6 years frederik.heber FIX: mpqc included boost bind and function unnecessarily. 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) @033dbc   6 years frederik.heber DISTFIX: mpqc_open did not distribute listlibs.pl. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @a844d8   7 years frederik.heber FIX: PKG_CHECK_MODULES used empty fail action. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @425516   7 years frederik.heber Set version to 1.6.1. - MoleCuilder library is now 18:0:1. - Codename … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 stable v1.6.1
(edit) @209f4c   7 years frederik.heber TESTS: Fixed FillSurface and FillVolumne, recreated GuiChecks. - … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @9ac3d3   7 years frederik.heber FIX: Constrained locking in CodePattern's Notification and Observable. … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @ca2880   8 years frederik.heber DISTFIX: numpy_check.py was missing in EXTRA_DIST. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @c4cba2   8 years frederik.heber DISTFIX: python test ForceAnnealing folder was missing in EXTRA_DIST. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @108c88   8 years frederik.heber TESTFIX: ChemicalSpaceEvaluator regression test was working on wrong file. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @43552e   8 years frederik.heber DISTFIX: Atom regression test RandomPerturbation did mark the input … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @1e06ed   8 years frederik.heber DISTFIX: tests/regression folder Geometry was missing in EXTRA_DIST. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @0bc2c6   8 years frederik.heber Added gcc 5.4.0 to boost.m4. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @883599   8 years frederik.heber DISTFIX: EXTRA_DIST in tests/integration did not contain new test folders. Candidate_v1.6.1 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) @d661b2   8 years frederik.heber Added regression test for simplest of graphs with two carbon elements. 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) @2ee2cc   8 years frederik.heber TESTS: Reactivated again all tests related to bond graph optimization. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph stable
(edit) @3183f5   8 years frederik.heber DOCU: Added explanation of bond graph optimization to userguide. Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph 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) @8c0ac9   8 years frederik.heber TESTFIX: Made integration tests for structure optimization of water … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion stable
(edit) @e72d94   8 years frederik.heber TESTFIX: threshold check in integration tests on structure … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Exclude_Hydrogens_annealWithBondGraph ForceAnnealing_with_BondGraph_contraction-expansion stable
(edit) @31baf0   8 years frederik.heber TESTFIX: Readded missing Structure Optimization integration tests. - … 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) @6a5921   8 years frederik.heber TESTS: Deactivated temporarily all tests related to bond graph … 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) @4fc0ea   8 years frederik.heber TESTFIX: Changes to various regression and Python tests because of … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator TremoloParser_IncreasedPrecision 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) @cd91bd   8 years frederik.heber TESTFIX: Changes to test scripts because now keyword arguments are … Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator PythonUI_with_named_parameters 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) @90ece9   8 years frederik.heber TESTFIX: Fixes to Python tests due to changed anneal() and modified … 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) @441d40   8 years frederik.heber TESTFIX: bondgraph annealing is working better than expected. 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) @038ccd   8 years frederik.heber TESTFIX: Needed to change ForceAnnealing Python and regression test … 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) @075357   8 years frederik.heber TEST: Adding Python test on ForceAnnealing using an Ising model with … 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) @41de6e   8 years frederik.heber TESTFIX: ForceAnnealing regression test used zero force. - all atoms … 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
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