source: tests

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(edit) @4538c0   6 weeks frederik.heber Recreated guicheck from regression tests. Candidate_v1.7.1 stable
(edit) @47ebb2   6 weeks frederik.heber TESTFIX: Fragmentation tests lacked load bondtable. Candidate_v1.7.1 stable
(edit) @dce5a3   6 weeks frederik.heber Adds AddSelectedAtomsAsFragmentAction. - this action allows … Candidate_v1.7.1 stable
(edit) @d2be22   7 weeks frederik.heber Actions relying on BondGraph fail if not bond table is loaded. - this … Candidate_v1.7.1 stable
(edit) @91c409   3 months frederik.heber TESTFIX: Fixes integration jobs. - also changes to due new k8s setup … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @15678e   5 months frederik.heber TESTFIX: mpqc-jobs fixed with new k8s working mode. - we forgot to … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @26cfa51   5 months frederik.heber FIX: Adds missing default options to options.dat. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @a4b917   5 months frederik.heber Adds add and remove potential actions. - DOC: Adds missing actions to … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @d56114   5 months frederik.heber TESTFIX: very tiny changes in VerletIntegration. - Changes in the … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @454d7a   5 months frederik.heber TESTFIX: adapts regression test on changed temperature units. - This … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @a93896   5 months frederik.heber Ignores pyMoleCuilder import in python script. - TEST: LoadSession … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @dfe653   5 months frederik.heber TESTFIX: Finalizes evaluate stability regression test. - recomputed … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @d25515   6 months frederik.heber TESTFIX: Finalizes pair correlation agains element regression test … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @f5e28b   6 months frederik.heber TESTFIX: Fixes graph6 string printing regression test case. - This … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @400ee4   6 months frederik.heber TESTFIX: finalizes regression test cases for atom neighbor selection. … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @9175c8   6 months frederik.heber TESTFIX: select random number of atoms test cases finalized. - the … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @1e6591   6 months frederik.heber FIX: Saturating nitrogen produces very slight changed coordinates. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @780bfa   6 months frederik.heber FIX: FormatParserStorage did not add parser instance on SetOutput. - … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @bcc29ca   6 months frederik.heber Splits off Undo mark actions. - Undo action has again no parameters … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @9782e20   23 months frederik.heber BondifyAction: added undo/redo. - DOC: fixed small typo in Action's … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @02f14d   2 years frederik.heber Adapting python regression tests to python3. - AT_TESTED cannot … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @d083cc   2 years frederik.heber Python3: Test/Python changed. - print -> print() Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @82e5fb   5 years frederik.heber Added option error-file to fit potential actions. - DOCU: Added … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @889067e   5 years frederik.heber Added force-overwrite to OutputAsAction. - DOCU: Also added … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @9b0dcd   5 years frederik.heber Added potential-list argument to GeneratePotentialsAction. - DOCU: … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @c98620   5 years frederik.heber FIX: StreamFactory did not set BindingModel. - we streamed into a … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @b3bd7d   5 years frederik.heber TEST: Added regression tests for fitting compound potential. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @55c494   5 years frederik.heber Added GeneratePotentialsAction. - this generates all potential … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @15fc6a   5 years frederik.heber TEST: Added tersoff fit-potential test. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @1e490ec   5 years frederik.heber tempcommit: Removed sys.exit() in pymolecuilder test. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @8c9cce   5 years frederik.heber Numpy exporters are fully operational. - TESTS: added test on working … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @999eaf   5 years frederik.heber Added EvaluateStabilityAction to estimate a molecule's stability. - … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @0ec9f5   5 years frederik.heber Added UndoMarkAction. NOTE: This action is necessary as not all … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @5061d9   5 years frederik.heber Added action to print selected atoms as graph6 string. - added … Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @1be100   5 years frederik.heber FIX: Several small errors in Graph6Reader. - off-by-one error with … 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) @4de4f6   5 years frederik.heber Added AtomBondNeighbors selection action. - DOCU: Added to userguide. … 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) @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) @b0060a   5 years frederik.heber Making test code python2&3 compatible. 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) @5d2403   6 years frederik.heber FIX: DiffFragmentResultContainer lacked lib-specific boost ldflags. Candidate_v1.7.0 Candidate_v1.7.1 stable
(edit) @209f4c   8 years frederik.heber TESTS: Fixed FillSurface and FillVolumne, recreated GuiChecks. - … 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) @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) @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) @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) @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) @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) @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) @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) @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) @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) @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) @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) @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) @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) @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) @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) @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) @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) @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) @1e58bb   8 years frederik.heber FIX: Integration tests now abort safely when one of the programs dies. … 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 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) @9b32071   8 years frederik.heber TESTS: Added CodeCheck on uniqueness of ports in 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) @53a85a   8 years frederik.heber Added integration test on Potential Fitting for water. - we fit … 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) @167523   8 years frederik.heber Added integration tests on Structure Optimization. - we use the same … 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) @37fe17   8 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 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) @0aae02   8 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 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) @775f3f   8 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 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) @6491d3   8 years frederik.heber Moved fragment jobs integration test into subfolder. 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) @9a1e099   9 years frederik.heber Added regression test on DiffFragmentResultContainer. 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) @b10593   9 years frederik.heber Recreated all GuiChecks. - GuiChecks lacked … 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) @ecacf0   9 years frederik.heber FIX: regression test Makefile.am lacked difffragmentresultcontainer … Action_Thermostats Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 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) @a9db89   9 years frederik.heber FIX: regression test Geometry common still used position instead of … Action_Thermostats Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 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) @92d0e6   9 years frederik.heber ManyWaysToTranslateAtom: Added stretch-bond test. Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 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) @3b74fa   9 years frederik.heber Rewrite of StretchBondAction to take bondgraph into account. - i.e. … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 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) @f56e14   9 years frederik.heber Added Examples testcase for the many ways to translate an atom blog entry. Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision stable
(edit) @33af20   9 years frederik.heber TremoloParser::save() now supports multiple time steps. - TESTS: … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps stable
(edit) @220d2c   9 years frederik.heber TremoloParser::load() can deal with multiple time steps. - TESTS: … Action_Thermostats Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps stable
(edit) @3f6aac   9 years frederik.heber Added (Un)selectAtomByName. - Descriptor for AtomByName was already … Action_Thermostats Add_SelectAtomByNameAction Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_StructOpt_integration_tests AutomationFragmentation_failures Candidate_v1.6.1 Candidate_v1.7.0 Candidate_v1.7.1 ChemicalSpaceEvaluator EmpiricalPotential_contain_HomologyGraph_documentation Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph Fix_Verbose_Codepatterns ForceAnnealing_oldresults ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion Gui_displays_atomic_force_velocity IndependentFragmentGrids_IntegrationTest JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool PythonUI_with_named_parameters Recreated_GuiChecks StoppableMakroAction TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps stable
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