# # ChangeLog for tests # # Generated by Trac 1.6 # Feb 4, 2026, 1:01:28 PM Fri, 26 Dec 2025 21:40:14 GMT Frederik Heber [4538c0] * tests/GuiChecks/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/testsuite-analysis-dipole-angular-correlation-periodic-boundaries.at (modified) * tests/GuiChecks/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) * tests/GuiChecks/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/GuiChecks/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified) * tests/GuiChecks/Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at (modified) * tests/GuiChecks/Atoms/Bondify/testsuite-atoms-bondify.at (added) * tests/GuiChecks/Atoms/testsuite-atoms.at (modified) * tests/GuiChecks/Bond/Bondify/testsuite-bond-bondify.at (added) * tests/GuiChecks/Bond/testsuite-bond.at (modified) * tests/GuiChecks/Filling/SuspendInWater/testsuite-suspend-in-water.at (modified) * tests/GuiChecks/Fragmentation/AddSelectedAtomsAsFragment/testsuite-fragmentation-add-selected-atoms-as-fragment.at (added) * tests/GuiChecks/Fragmentation/EvaluateStability/testsuite-fragmentation-evaluate-stability.at (added) * tests/GuiChecks/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) * tests/GuiChecks/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) * tests/GuiChecks/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (modified) * tests/GuiChecks/Fragmentation/testsuite-fragmentation.at (modified) * tests/GuiChecks/Graph/ChemicalSpaceEvaluator/testsuite-graph-chemical-space-evaluator.at (added) * tests/GuiChecks/Graph/CreateAdjacency/testsuite-graph-create-adjacency.at (modified) * tests/GuiChecks/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified) * tests/GuiChecks/Graph/PrintSelectedAtomsAsGraphString/testsuite-graph-print-selected-atoms-as-graphstring.at (added) * tests/GuiChecks/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at (modified) * tests/GuiChecks/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified) * tests/GuiChecks/Graph/testsuite-graph.at (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) * tests/GuiChecks/Molecules/Remove/testsuite-molecules-remove.at (modified) * tests/GuiChecks/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) * tests/GuiChecks/Molecules/SaveBonds/testsuite-molecules-save-bonds.at (modified) * tests/GuiChecks/Molecules/SaveEnergies/testsuite-molecules-save-energies.at (modified) * tests/GuiChecks/Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at (modified) * tests/GuiChecks/Molecules/StretchBond/testsuite-molecules-stretch-bond-cyclic_bond.at (modified) * tests/GuiChecks/Molecules/StretchBond/testsuite-molecules-stretch-bond.at (modified) * tests/GuiChecks/Options/UndoMark/testsuite-options-undo-mark.at (added) * tests/GuiChecks/Options/testsuite-options.at (modified) * tests/GuiChecks/Potential/AddPotential/testsuite-potential-add-potential-various_cases.at (added) * tests/GuiChecks/Potential/AddPotential/testsuite-potential-add-potential.at (added) * tests/GuiChecks/Potential/FitCompoundPotential/testsuite-potential-fit-compound-potential.at (added) * tests/GuiChecks/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) * tests/GuiChecks/Potential/GeneratePotentials/testsuite-potential-generate-potentials.at (added) * tests/GuiChecks/Potential/RemovePotential/testsuite-potential-remove-potential-various_cases.at (added) * tests/GuiChecks/Potential/RemovePotential/testsuite-potential-remove-potential.at (added) * tests/GuiChecks/Potential/testsuite-potential.at (modified) * tests/GuiChecks/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-select-all-atoms-of-molecule.at (modified) * tests/GuiChecks/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-unselect-all-atoms-of-molecule.at (modified) * tests/GuiChecks/Selection/Atoms/AtomByRandom/testsuite-selection-select-atom-by-random.at (added) * tests/GuiChecks/Selection/Atoms/AtomsNeighbors/testsuite-selection-select-atoms-neighbors.at (added) * tests/GuiChecks/Selection/Atoms/testsuite-selection-atoms.at (modified) * tests/GuiChecks/Selection/Molecules/AllMolecules/testsuite-selection-select-all-molecules.at (modified) * tests/GuiChecks/Selection/Molecules/AllMolecules/testsuite-selection-unselect-all-molecules.at (modified) * tests/GuiChecks/Selection/Molecules/ClearMolecules/testsuite-selection-clear-molecules.at (modified) * tests/GuiChecks/Selection/Molecules/InvertMolecules/testsuite-selection-invert-molecules.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeByFormula/testsuite-selection-select-molecules-by-formula.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeByFormula/testsuite-selection-unselect-molecules-by-formula.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeByName/testsuite-selection-select-molecules-by-name.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeByName/testsuite-selection-unselect-molecules-by-name.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-backward.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-forward.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-backward.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-forward.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeOfAtom/testsuite-selection-select-atoms-molecules.at (modified) * tests/GuiChecks/Selection/Molecules/MoleculeOfAtom/testsuite-selection-unselect-atoms-molecules.at (modified) * tests/GuiChecks/Selection/Molecules/PopMoleculeSelection/testsuite-selection-pop-molecule-selection.at (modified) * tests/GuiChecks/Selection/Molecules/PushMoleculeSelection/testsuite-selection-push-molecule-selection.at (modified) Recreated guicheck from regression tests. Fri, 26 Dec 2025 21:40:14 GMT Frederik Heber [47ebb2] * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethoxyethane/testsuite-fragmenting-1_2-dimethoxyethane-order4.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order1.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order2.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order3.at (modified) * tests/Fragmentations/Fragmenting/1_2-dimethylbenzene/testsuite-fragmenting-1_2-dimethylbenzene-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order1.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order2.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order5.at (modified) * tests/Fragmentations/Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order6.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order1.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order2.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order3.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order4.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at (modified) * tests/Fragmentations/Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order3.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order4.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order5.at (modified) * tests/Fragmentations/Fragmenting/benzene/testsuite-fragmenting-benzene-order6.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order1.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order2.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order5.at (modified) * tests/Fragmentations/Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order6.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order3.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order4.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order5.at (modified) * tests/Fragmentations/Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order6.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order1.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order2.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order3.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order4.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order5.at (modified) * tests/Fragmentations/Fragmenting/dimethyl_bromomalonate/testsuite-fragmenting-dimethyl_bromomalonate-order6.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order1.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order2.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order3.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order4.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order5.at (modified) * tests/Fragmentations/Fragmenting/glucose/testsuite-fragmenting-glucose-order6.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order1.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order2.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order3.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order4.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order5.at (modified) * tests/Fragmentations/Fragmenting/heptan/testsuite-fragmenting-heptan-order6.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order1.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order2.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order3.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order4.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at (modified) * tests/Fragmentations/Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order3.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order4.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order5.at (modified) * tests/Fragmentations/Fragmenting/neohexane/testsuite-fragmenting-neohexane-order6.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order1.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order2.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order3.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order4.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order5.at (modified) * tests/Fragmentations/Fragmenting/proline/testsuite-fragmenting-proline-order6.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order1.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order2.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order3.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order4.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order5.at (modified) * tests/Fragmentations/Fragmenting/putrescine/testsuite-fragmenting-putrescine-order6.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order1.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order2.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order3.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order4.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order5.at (modified) * tests/Fragmentations/Fragmenting/tartaric_acid/testsuite-fragmenting-tartaric_acid-order6.at (modified) TESTFIX: Fragmentation tests lacked load bondtable. Sun, 21 Dec 2025 21:50:22 GMT Frederik Heber [dce5a3] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/AddSelectedAtomsAsFragmentAction.cpp (added) * src/Actions/FragmentationAction/AddSelectedAtomsAsFragmentAction.def (added) * src/Actions/FragmentationAction/AddSelectedAtomsAsFragmentAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Fragmentation/AddSelectedAtomsAsFragment/pre/benzene.pdb (added) * tests/regression/Fragmentation/AddSelectedAtomsAsFragment/pre/test.conf (added) * tests/regression/Fragmentation/AddSelectedAtomsAsFragment/testsuite-fragmentation-add-selected-atoms-as-fragment.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Adds AddSelectedAtomsAsFragmentAction. - this action allows ... Fri, 19 Dec 2025 23:29:38 GMT Frederik Heber [d2be22] * src/Actions/AtomAction/BondifyAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Graph/BondGraph.hpp (modified) * tests/regression/Analysis/DipoleAngularCorrelation-PeriodicBoundaries/testsuite-analysis-dipole-angular-correlation-periodic-boundaries.at (modified) * tests/regression/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at (modified) * tests/regression/Analysis/DipoleCorrelation-DiscreteAngles/testsuite-analysis-dipole-correlation-discrete-angles.at (modified) * tests/regression/Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at (modified) * tests/regression/Atoms/Bondify/testsuite-atoms-bondify.at (modified) * tests/regression/Filling/SuspendInWater/testsuite-suspend-in-water.at (modified) * tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) * tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) * tests/regression/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (modified) * tests/regression/Graph/CreateAdjacency/testsuite-graph-create-adjacency.at (modified) * tests/regression/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at (modified) * tests/regression/Graph/SubgraphDissection-BoundaryConditions/testsuite-graph-subgraph-dissection_boundary-conditions.at (modified) * tests/regression/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) * tests/regression/Molecules/Remove/testsuite-molecules-remove.at (modified) * tests/regression/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at (modified) * tests/regression/Molecules/SaveBonds/testsuite-molecules-save-bonds.at (modified) * tests/regression/Molecules/SaveSelectedMolecules/testsuite-molecules-save-selected-molecules.at (modified) * tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond-cyclic_bond.at (modified) * tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond.at (modified) * tests/regression/Options/Session/post/complextest.py (modified) * tests/regression/Options/Session/post/complextest.sh (modified) * tests/regression/Options/Session/pre/complextest.py (modified) * tests/regression/Options/Session/pre/complexwait.py (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-cli.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-select-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-unselect-all-atoms-of-molecule.at (modified) * tests/regression/Selection/Atoms/AtomsNeighbors/testsuite-selection-select-atoms-neighbors.at (modified) * tests/regression/Selection/Molecules/AllMolecules/testsuite-selection-select-all-molecules.at (modified) * tests/regression/Selection/Molecules/AllMolecules/testsuite-selection-unselect-all-molecules.at (modified) * tests/regression/Selection/Molecules/ClearMolecules/testsuite-selection-clear-molecules.at (modified) * tests/regression/Selection/Molecules/InvertMolecules/testsuite-selection-invert-molecules.at (modified) * tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-select-molecules-by-formula.at (modified) * tests/regression/Selection/Molecules/MoleculeByFormula/testsuite-selection-unselect-molecules-by-formula.at (modified) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-select-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeById/testsuite-selection-unselect-molecule-by-id.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-select-molecules-by-name.at (modified) * tests/regression/Selection/Molecules/MoleculeByName/testsuite-selection-unselect-molecules-by-name.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-backward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-select-molecule-by-order-forward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-backward.at (modified) * tests/regression/Selection/Molecules/MoleculeByOrder/testsuite-selection-unselect-molecule-by-order-forward.at (modified) * tests/regression/Selection/Molecules/MoleculeOfAtom/testsuite-selection-select-atoms-molecules.at (modified) * tests/regression/Selection/Molecules/MoleculeOfAtom/testsuite-selection-unselect-atoms-molecules.at (modified) * tests/regression/Selection/Molecules/PopMoleculeSelection/testsuite-selection-pop-molecule-selection.at (modified) * tests/regression/Selection/Molecules/PushMoleculeSelection/testsuite-selection-push-molecule-selection.at (modified) Actions relying on BondGraph fail if not bond table is loaded. - ... Wed, 22 Oct 2025 17:08:33 GMT Frederik Heber [91c409] * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs-mpqc-jobs.at (modified) * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs-vmg-jobs.at (modified) * tests/integration/MolecularDynamics/post/ethane.ekin (modified) * tests/integration/MolecularDynamics/post/methane.ekin (modified) * tests/integration/MolecularDynamics/post/water-system.ekin (modified) * tests/integration/MolecularDynamics/post/water.ekin (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-ethane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-methane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water-system.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at (modified) * tests/integration/PotentialFitting/testsuite-integration-potentialfitting-water.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-ethane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-methane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-water.at (modified) TESTFIX: Fixes integration jobs. - also changes to due new k8s ... Sat, 13 Sep 2025 18:56:06 GMT Frederik Heber [15678e] * tests/JobMarket/testsuite-jobmarket-mpqc-jobs.at (modified) TESTFIX: mpqc-jobs fixed with new k8s working mode. - we forgot to ... Sat, 13 Sep 2025 15:00:26 GMT Frederik Heber [26cfa51] * tests/Python/AllActions/options.dat (modified) FIX: Adds missing default options to options.dat. Sat, 13 Sep 2025 14:43:45 GMT Frederik Heber [a4b917] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/AddPotentialAction.cpp (added) * src/Actions/PotentialAction/AddPotentialAction.def (added) * src/Actions/PotentialAction/AddPotentialAction.hpp (added) * src/Actions/PotentialAction/RemovePotentialAction.cpp (added) * src/Actions/PotentialAction/RemovePotentialAction.def (added) * src/Actions/PotentialAction/RemovePotentialAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Potential/AddPotential/pre/harmonic.potentials (added) * tests/regression/Potential/AddPotential/testsuite-potential-add-potential-various_cases.at (added) * tests/regression/Potential/AddPotential/testsuite-potential-add-potential.at (added) * tests/regression/Potential/RemovePotential/pre/harmonic.potentials (added) * tests/regression/Potential/RemovePotential/testsuite-potential-remove-potential-various_cases.at (added) * tests/regression/Potential/RemovePotential/testsuite-potential-remove-potential.at (added) * tests/regression/Potential/testsuite-potential.at (modified) Adds add and remove potential actions. - DOC: Adds missing actions ... Sat, 30 Aug 2025 14:41:40 GMT Frederik Heber [d56114] * tests/regression/Molecules/VerletIntegration/post/test.conf (modified) TESTFIX: very tiny changes in VerletIntegration. - Changes in the ... Sat, 30 Aug 2025 14:41:40 GMT Frederik Heber [454d7a] * tests/regression/Molecules/SaveEnergies/post/test.ekin (modified) TESTFIX: adapts regression test on changed temperature units. - ... Sat, 30 Aug 2025 14:41:40 GMT Frederik Heber [a93896] * src/Python/PythonScripting.cpp (modified) * src/Python/PythonScripting.hpp (modified) * tests/regression/Options/Session/pre/complexwait.py (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) Ignores pyMoleCuilder import in python script. - TEST: LoadSession ... Sat, 30 Aug 2025 14:41:31 GMT Frederik Heber [dfe653] * doc/userguide/userguide.xml (modified) * tests/regression/Fragmentation/EvaluateStability/post/BondFragment_Stability.csv (added) * tests/regression/Fragmentation/EvaluateStability/pre/H2.data (added) * tests/regression/Fragmentation/EvaluateStability/pre/homology-6-31G.dat (modified) * tests/regression/Fragmentation/EvaluateStability/pre/homology-H2.dat (added) * tests/regression/Fragmentation/EvaluateStability/testsuite-fragmentation-evaluate-stability.at (modified) TESTFIX: Finalizes evaluate stability regression test. - recomputed ... Wed, 13 Aug 2025 22:04:51 GMT Frederik Heber [d25515] * tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified) TESTFIX: Finalizes pair correlation agains element regression test ... Wed, 13 Aug 2025 21:55:21 GMT Frederik Heber [f5e28b] * tests/regression/Graph/PrintSelectedAtomsAsGraphString/testsuite-graph-print-selected-atoms-as-graphstring.at (modified) TESTFIX: Fixes graph6 string printing regression test case. - This ... Wed, 13 Aug 2025 21:50:48 GMT Frederik Heber [400ee4] * tests/regression/Selection/Atoms/AtomsNeighbors/testsuite-selection-select-atoms-neighbors.at (modified) TESTFIX: finalizes regression test cases for atom neighbor selection. ... Wed, 13 Aug 2025 21:46:30 GMT Frederik Heber [9175c8] * tests/regression/Selection/Atoms/AtomByRandom/testsuite-selection-select-atom-by-random.at (modified) TESTFIX: select random number of atoms test cases finalized. - the ... Wed, 13 Aug 2025 21:46:30 GMT Frederik Heber [1e6591] * tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz (modified) FIX: Saturating nitrogen produces very slight changed coordinates. Wed, 13 Aug 2025 21:46:30 GMT Frederik Heber [780bfa] * src/Actions/ActionHistory.cpp (modified) * src/Parser/FormatParserStorage.cpp (modified) * tests/regression/Options/UndoMark/testsuite-options-undo-mark.at (modified) FIX: FormatParserStorage did not add parser instance on SetOutput. ... Wed, 13 Aug 2025 08:24:42 GMT Frederik Heber [bcc29ca] * doc/userguide/userguide.xml (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/CommandAction/RedoAction.cpp (moved) * src/Actions/CommandAction/RedoAction.def (moved) * src/Actions/CommandAction/RedoAction.hpp (moved) * src/Actions/CommandAction/SetUndoMarkAction.cpp (moved) * src/Actions/CommandAction/SetUndoMarkAction.def (moved) * src/Actions/CommandAction/SetUndoMarkAction.hpp (moved) * src/Actions/CommandAction/UndoAction.cpp (moved) * src/Actions/CommandAction/UndoAction.def (moved) * src/Actions/CommandAction/UndoAction.hpp (moved) * src/Actions/CommandAction/UndoTillMarkAction.cpp (added) * src/Actions/CommandAction/UndoTillMarkAction.def (added) * src/Actions/CommandAction/UndoTillMarkAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Options/UndoMark/testsuite-options-undo-mark.at (modified) Splits off Undo mark actions. - Undo action has again no parameters ... Sat, 16 Mar 2024 10:22:34 GMT Frederik Heber [9782e20] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/BondifyAction.cpp (modified) * src/Actions/AtomAction/BondifyAction.def (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/BondInfo.hpp (modified) * tests/regression/Atoms/Bondify/post/bondify-test.data (added) * tests/regression/Atoms/Bondify/pre/bondify-test.data (added) * tests/regression/Atoms/Bondify/testsuite-atoms-bondify.at (added) * tests/regression/Atoms/testsuite-atoms.at (modified) * tests/regression/Makefile.am (modified) BondifyAction: added undo/redo. - DOC: fixed small typo in Action's ... Sun, 03 Mar 2024 10:13:48 GMT Frederik Heber [02f14d] * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) Adapting python regression tests to python3. - AT_TESTED cannot ... Wed, 24 Jan 2024 00:09:57 GMT Frederik Heber [d083cc] * tests/Python/AllActions/moltest.py (modified) * tests/Python/AllActions/moltest_check.py (modified) * tests/Python/AllActions/testsuite-python-allactions.at (modified) * tests/Python/ForceAnnealing/pre/ising_model_chain.py (modified) Python3: Test/Python changed. - print -> print() Tue, 25 May 2021 23:04:50 GMT Frederik Heber [82e5fb] * doc/userguide/userguide.xml (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/PotentialTrainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/FitCompoundPotential/testsuite-potential-fit-compound-potential.at (modified) Added option error-file to fit potential actions. - DOCU: Added ... Tue, 25 May 2021 21:55:52 GMT Frederik Heber [889067e] * doc/userguide/userguide.xml (modified) * src/Actions/WorldAction/OutputAsAction.cpp (modified) * src/Actions/WorldAction/OutputAsAction.def (modified) * tests/Python/AllActions/options.dat (modified) Added force-overwrite to OutputAsAction. - DOCU: Also added ... Wed, 19 May 2021 19:06:29 GMT Frederik Heber [9b0dcd] * doc/userguide/userguide.xml (modified) * src/Actions/PotentialAction/GeneratePotentialsAction.cpp (modified) * src/Actions/PotentialAction/GeneratePotentialsAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Potential/GeneratePotentials/post/water_restricted.potentials (added) * tests/regression/Potential/GeneratePotentials/testsuite-potential-generate-potentials.at (modified) Added potential-list argument to GeneratePotentialsAction. - DOCU: ... Wed, 19 May 2021 19:06:29 GMT Frederik Heber [c98620] * src/Potentials/BindingModel.cpp (modified) * src/Potentials/BindingModel.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/StreamFactory_EmpiricalPotential.cpp (modified) * src/Potentials/StreamFactory_EmpiricalPotential.hpp (modified) * tests/regression/Potential/FitCompoundPotential/pre/water.potentials (modified) * tests/regression/Potential/FitCompoundPotential/testsuite-potential-fit-compound-potential.at (modified) FIX: StreamFactory did not set BindingModel. - we streamed into a ... Wed, 19 May 2021 19:06:29 GMT Frederik Heber [b3bd7d] * tests/regression/Makefile.am (modified) * tests/regression/Potential/FitCompoundPotential/pre/water.pdb (added) * tests/regression/Potential/FitCompoundPotential/pre/water.potentials (added) * tests/regression/Potential/FitCompoundPotential/pre/water_homology.dat (added) * tests/regression/Potential/FitCompoundPotential/testsuite-potential-fit-compound-potential.at (added) * tests/regression/Potential/testsuite-potential.at (modified) TEST: Added regression tests for fitting compound potential. Wed, 19 May 2021 19:06:29 GMT Frederik Heber [55c494] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/PotentialAction/GeneratePotentialsAction.cpp (added) * src/Actions/PotentialAction/GeneratePotentialsAction.def (added) * src/Actions/PotentialAction/GeneratePotentialsAction.hpp (added) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Potential/GeneratePotentials/post/water.potentials (added) * tests/regression/Potential/GeneratePotentials/pre/water.pdb (added) * tests/regression/Potential/GeneratePotentials/pre/water_homologies.dat (added) * tests/regression/Potential/GeneratePotentials/testsuite-potential-generate-potentials.at (added) * tests/regression/Potential/testsuite-potential.at (modified) Added GeneratePotentialsAction. - this generates all potential ... Wed, 19 May 2021 19:06:29 GMT Frederik Heber [15fc6a] * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) TEST: Added tersoff fit-potential test. Wed, 19 May 2021 19:06:29 GMT Frederik Heber [1e490ec] * tests/Python/pyMoleCuilder/testsuite-python-pymolecuilder.at (modified) tempcommit: Removed sys.exit() in pymolecuilder test. Wed, 19 May 2021 19:06:29 GMT Frederik Heber [8c9cce] * src/Python/export_numpy.cpp (modified) * tests/Python/Makefile.am (modified) * tests/Python/pyMoleCuilder/testsuite-python-pymolecuilder.at (added) * tests/Python/testsuite.at (modified) Numpy exporters are fully operational. - TESTS: added test on ... Wed, 28 Apr 2021 22:02:49 GMT Frederik Heber [999eaf] * doc/userguide/userguide.xml (modified) * src/Actions/FragmentationAction/EvaluateStabilityAction.cpp (added) * src/Actions/FragmentationAction/EvaluateStabilityAction.def (added) * src/Actions/FragmentationAction/EvaluateStabilityAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Fragmentation/Evaluation/StabilityEvaluator.cpp (added) * src/Fragmentation/Evaluation/StabilityEvaluator.hpp (added) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.hpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp (modified) * src/Fragmentation/Homology/HomologyGraph_getFromKeysetStub.cpp (modified) * src/Fragmentation/Makefile.am (modified) * tests/regression/Fragmentation/EvaluateStability/pre/C3H8.data (added) * tests/regression/Fragmentation/EvaluateStability/pre/homology-6-31G.dat (added) * tests/regression/Fragmentation/EvaluateStability/testsuite-fragmentation-evaluate-stability.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added EvaluateStabilityAction to estimate a molecule's stability. - ... Fri, 23 Apr 2021 21:02:12 GMT Frederik Heber [0ec9f5] * doc/userguide/userguide.xml (modified) * src/Actions/ActionHistory.cpp (modified) * src/Actions/ActionHistory.hpp (modified) * src/Actions/ActionQueue.cpp (modified) * src/Actions/ActionQueue.hpp (modified) * src/Actions/CommandAction/UndoMarkAction.cpp (added) * src/Actions/CommandAction/UndoMarkAction.def (added) * src/Actions/CommandAction/UndoMarkAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/UndoAction.cpp (modified) * src/Actions/UndoAction.def (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Options/UndoMark/testsuite-options-undo-mark.at (added) * tests/regression/Options/testsuite-options.at (modified) Added UndoMarkAction. NOTE: This action is necessary as not all ... Fri, 23 Apr 2021 21:01:20 GMT Frederik Heber [5061d9] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/PrintSelectedAtomsAsGraphStringAction.cpp (added) * src/Actions/GraphAction/PrintSelectedAtomsAsGraphStringAction.def (added) * src/Actions/GraphAction/PrintSelectedAtomsAsGraphStringAction.hpp (added) * src/Actions/Makefile.am (modified) * src/Graph/Graph6Writer.cpp (added) * src/Graph/Graph6Writer.hpp (added) * src/Graph/Makefile.am (modified) * src/Python/Makefile.am (modified) * src/Python/PythonScripting_impl.hpp (modified) * src/Python/getGraph6String.cpp (added) * src/Python/modules.hpp (modified) * tests/regression/Graph/ChemicalSpaceEvaluator/testsuite-graph-chemical-space-evaluator.at (moved) * tests/regression/Graph/PrintSelectedAtomsAsGraphString/pre/test.data (added) * tests/regression/Graph/PrintSelectedAtomsAsGraphString/testsuite-graph-print-selected-atoms-as-graphstring.at (added) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Makefile.am (modified) Added action to print selected atoms as graph6 string. - added ... Fri, 23 Apr 2021 20:51:43 GMT Frederik Heber [1be100] * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp (modified) * src/Graph/Graph6Reader.cpp (modified) * src/Graph/Graph6Reader.hpp (modified) * tests/regression/Graph/ChemicalSpaceEvaluator/testsuite-chemical-space-evaluator.at (modified) FIX: Several small errors in Graph6Reader. - off-by-one error with ... Fri, 23 Apr 2021 20:51:24 GMT Frederik Heber [5fa1e86] * doc/userguide/userguide.xml (modified) * src/Actions/AtomAction/BondifyAction.cpp (added) * src/Actions/AtomAction/BondifyAction.def (added) * src/Actions/AtomAction/BondifyAction.hpp (added) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * tests/regression/Bond/Bondify/post/test.data (added) * tests/regression/Bond/Bondify/pre/test.data (added) * tests/regression/Bond/Bondify/testsuite-bond-bondify.at (added) * tests/regression/Bond/testsuite-bond.at (modified) * tests/regression/Makefile.am (modified) Added BondifyAction. - this allows to add non-hydrogen bonds and is ... Fri, 23 Apr 2021 20:42:57 GMT Frederik Heber [4de4f6] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AtomBondNeighborsAction.cpp (added) * src/Actions/SelectionAction/Atoms/AtomBondNeighborsAction.def (added) * src/Actions/SelectionAction/Atoms/AtomBondNeighborsAction.hpp (added) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomsNeighbors/post/H_missing.xyz (added) * tests/regression/Selection/Atoms/AtomsNeighbors/post/empty.xyz (added) * tests/regression/Selection/Atoms/AtomsNeighbors/pre/test.xyz (added) * tests/regression/Selection/Atoms/AtomsNeighbors/testsuite-selection-select-atoms-neighbors.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added AtomBondNeighbors selection action. - DOCU: Added to ... Fri, 23 Apr 2021 20:34:11 GMT Frederik Heber [d9e1d1] * doc/userguide/userguide.xml (modified) * src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) * src/Actions/AnalysisAction/PairCorrelationAction.def (modified) * tests/regression/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at (modified) Extending PairCorrelation to correlate element and set of atoms. - ... Fri, 23 Apr 2021 20:31:23 GMT Frederik Heber [0ad4781] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AtomByRandomAction.cpp (added) * src/Actions/SelectionAction/Atoms/AtomByRandomAction.def (added) * src/Actions/SelectionAction/Atoms/AtomByRandomAction.hpp (added) * src/RandomNumbers/RandomNumberDistributionFactory.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomByRandom/post/empty.xyz (added) * tests/regression/Selection/Atoms/AtomByRandom/post/test-undo.xyz (added) * tests/regression/Selection/Atoms/AtomByRandom/pre/test.xyz (added) * tests/regression/Selection/Atoms/AtomByRandom/testsuite-selection-select-atom-by-random.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added action to randomly select a set of atoms. - needed to make ... Fri, 23 Apr 2021 20:31:24 GMT Frederik Heber [b0060a] * src/Python/PythonScripting.cpp (modified) * tests/regression/Options/Session/pre/complexwait.py (modified) Making test code python2&3 compatible. Fri, 23 Apr 2021 20:31:23 GMT Frederik Heber [d40189] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/MoleculeAction/SaveEnergiesAction.cpp (moved) * src/Actions/MoleculeAction/SaveEnergiesAction.def (moved) * src/Actions/MoleculeAction/SaveEnergiesAction.hpp (moved) * src/Atom/AtomSet.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Atom/atom_atominfo.hpp (modified) * src/Dynamics/OutputEnergies.hpp (moved) * src/Makefile.am (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Molecules/SaveEnergies/testsuite-molecules-save-energies.at (moved) * tests/GuiChecks/Molecules/testsuite-molecules.at (modified) * tests/Python/AllActions/missing.dat (modified) * tests/Python/AllActions/options.dat (modified) * tests/integration/MolecularDynamics/post/ethane.ekin (modified) * tests/integration/MolecularDynamics/post/methane.ekin (modified) * tests/integration/MolecularDynamics/post/water-system.ekin (modified) * tests/integration/MolecularDynamics/post/water.ekin (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-ethane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-methane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water-system.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/SaveEnergies/post/test.ekin (added) * tests/regression/Molecules/SaveEnergies/pre/test.conf (moved) * tests/regression/Molecules/SaveEnergies/testsuite-molecules-save-energies.at (moved) * tests/regression/Molecules/SaveTemperature/post/test.ekin (deleted) * tests/regression/Molecules/testsuite-molecules.at (modified) OutputTemperature -> OutputEnergies, SaveTemperature -> SaveEnergies. ... Tue, 23 Jun 2020 21:44:14 GMT Frederik Heber [5d2403] * tests/regression/Makefile.am (modified) FIX: DiffFragmentResultContainer lacked lib-specific boost ldflags. Fri, 20 Jul 2018 05:37:39 GMT Frederik Heber [209f4c] * tests/GuiChecks/Atoms/RandomPerturbation/testsuite-atoms-random-perturbation.at (modified) * tests/GuiChecks/Filling/FillSurface/testsuite-fill-surface-cube.at (modified) * tests/GuiChecks/Filling/FillSurface/testsuite-fill-surface-cylinder.at (modified) * tests/GuiChecks/Filling/FillSurface/testsuite-fill-surface-everywhere.at (modified) * tests/GuiChecks/Filling/FillSurface/testsuite-fill-surface-micelle.at (modified) * tests/GuiChecks/Filling/FillSurface/testsuite-fill-surface-nowhere.at (modified) * tests/GuiChecks/Filling/FillSurface/testsuite-fill-surface-sphere.at (modified) * tests/GuiChecks/Filling/FillVolume/testsuite-fill-volume-cube.at (modified) * tests/GuiChecks/Filling/FillVolume/testsuite-fill-volume-cylinder.at (modified) * tests/GuiChecks/Filling/FillVolume/testsuite-fill-volume-everywhere.at (modified) * tests/GuiChecks/Filling/FillVolume/testsuite-fill-volume-nowhere.at (modified) * tests/GuiChecks/Filling/FillVolume/testsuite-fill-volume-sphere.at (modified) * tests/GuiChecks/Fragmentation/DiffFragmentResultContainer/testsuite-fragmentation-difffragmenresultcontainer.at (added) * tests/GuiChecks/Fragmentation/testsuite-fragmentation.at (modified) * tests/GuiChecks/Graph/ChemicalSpaceEvaluator/testsuite-chemical-space-evaluator.at (added) * tests/GuiChecks/Graph/testsuite-graph.at (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) * tests/regression/Filling/FillSurface/testsuite-fill-surface-cube.at (modified) * tests/regression/Filling/FillSurface/testsuite-fill-surface-cylinder.at (modified) * tests/regression/Filling/FillSurface/testsuite-fill-surface-everywhere.at (modified) * tests/regression/Filling/FillSurface/testsuite-fill-surface-micelle.at (modified) * tests/regression/Filling/FillSurface/testsuite-fill-surface-nowhere.at (modified) * tests/regression/Filling/FillSurface/testsuite-fill-surface-sphere.at (modified) * tests/regression/Filling/FillVolume/testsuite-fill-volume-cube.at (modified) * tests/regression/Filling/FillVolume/testsuite-fill-volume-cylinder.at (modified) * tests/regression/Filling/FillVolume/testsuite-fill-volume-everywhere.at (modified) * tests/regression/Filling/FillVolume/testsuite-fill-volume-nowhere.at (modified) * tests/regression/Filling/FillVolume/testsuite-fill-volume-sphere.at (modified) TESTS: Fixed FillSurface and FillVolumne, recreated GuiChecks. - ... Fri, 06 Jul 2018 11:15:18 GMT Frederik Heber [ca2880] * tests/Python/Makefile.am (modified) DISTFIX: numpy_check.py was missing in EXTRA_DIST. Tue, 03 Jul 2018 12:51:15 GMT Frederik Heber [c4cba2] * tests/Python/Makefile.am (modified) DISTFIX: python test ForceAnnealing folder was missing in EXTRA_DIST. Tue, 03 Jul 2018 12:06:36 GMT Frederik Heber [108c88] * tests/regression/Graph/ChemicalSpaceEvaluator/testsuite-chemical-space-evaluator.at (modified) TESTFIX: ChemicalSpaceEvaluator regression test was working on wrong ... Tue, 03 Jul 2018 10:51:02 GMT Frederik Heber [43552e] * tests/regression/Atoms/RandomPerturbation/testsuite-atoms-random-perturbation.at (modified) DISTFIX: Atom regression test RandomPerturbation did mark the input ... Tue, 03 Jul 2018 10:50:40 GMT Frederik Heber [1e06ed] * tests/regression/Makefile.am (modified) DISTFIX: tests/regression folder Geometry was missing in EXTRA_DIST. Mon, 25 Jun 2018 11:58:47 GMT Frederik Heber [883599] * tests/integration/Makefile.am (modified) DISTFIX: EXTRA_DIST in tests/integration did not contain new test ... Fri, 22 Jun 2018 07:26:30 GMT Frederik Heber [d661b2] * tests/regression/Graph/ChemicalSpaceEvaluator/pre/homologies_CC.dat (added) * tests/regression/Graph/ChemicalSpaceEvaluator/testsuite-chemical-space-evaluator.at (added) * tests/regression/Graph/CreateAdjacency/pre/homologies.dat (added) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Makefile.am (modified) Added regression test for simplest of graphs with two carbon elements. Fri, 22 Jun 2018 07:26:09 GMT Frederik Heber [f5ea10] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.cpp (added) * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.def (added) * src/Actions/GraphAction/ChemicalSpaceEvaluatorAction.hpp (added) * src/Actions/Makefile.am (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Graph/BoostGraphCreator.cpp (modified) * src/Graph/BoostGraphCreator.hpp (modified) * src/Graph/Graph6Reader.cpp (added) * src/Graph/Graph6Reader.hpp (added) * src/Graph/Makefile.am (modified) * tests/Python/AllActions/moltest_check.py (modified) * tests/Python/AllActions/options.dat (modified) Added Graph6Reader, extended BoostGraphCreator, added ... Thu, 21 Jun 2018 08:31:25 GMT Frederik Heber [8d56a6] * doc/userguide/userguide.xml (modified) * src/Actions/Action.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Action_impl_python.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * src/Atom/atom_atominfo.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.cpp (modified) * src/UIElements/Qt4/InstanceBoard/QtObservedAtom.hpp (modified) * src/UIElements/Qt4/QtMainWindow.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/UIElements/Views/Qt4/QtInfoBox.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.hpp (modified) * tests/Python/AllActions/moltest.py (modified) * tests/Python/AllActions/moltest_check.py (modified) * tests/Python/AllActions/options.dat (modified) * tests/Python/AllActions/testsuite-python-allactions.at (modified) * tests/Python/AllActions/testsuite-python-options_dat.at (modified) * tests/Python/BoxMaker/testsuite-python-boxmaker.at (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_no-bondgraph.data (modified) * tests/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (modified) * tests/integration/MolecularDynamics/post/ethane.ekin (modified) * tests/integration/MolecularDynamics/post/ethane_initial_steps.data (modified) * tests/integration/MolecularDynamics/post/methane.ekin (modified) * tests/integration/MolecularDynamics/post/methane_initial_steps.data (modified) * tests/integration/MolecularDynamics/post/water-system.ekin (modified) * tests/integration/MolecularDynamics/post/water-system_initial_steps.data (modified) * tests/integration/MolecularDynamics/post/water.ekin (modified) * tests/integration/MolecularDynamics/post/water_initial_steps.data (modified) * tests/regression/Domain/RepeatBox/post/ec.data (modified) * tests/regression/Filling/FillSurface/post/tensid-undo.data (modified) * tests/regression/Filling/FillSurface/post/tensid.data (modified) * tests/regression/Filling/RegularGrid/post/solved_single_sles.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data (modified) * tests/regression/Molecules/Copy/post/tensid.data (modified) * tests/regression/Options/DryRun/post/session.py (modified) * tests/regression/Options/Session/post/complextest.py (modified) * tests/regression/Options/Session/post/test.py (modified) * tests/regression/Parser/Tremolo-Potentials/post/argon.data (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/output.data (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/undo.data (modified) * tests/regression/Parser/Tremolo/post/argon.data (modified) Merge branch 'TremoloParser_IncreasedPrecision' into Candidate_v1.6.1 ... Wed, 20 Jun 2018 08:21:49 GMT Frederik Heber [2ee2cc] * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-ethane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-methane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-water.at (modified) TESTS: Reactivated again all tests related to bond graph optimization. Wed, 20 Jun 2018 08:21:14 GMT Frederik Heber [bd19c1] * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) Capping BB update step at 0.2 and general BB stepwidth at maximum of ... Wed, 20 Jun 2018 08:21:14 GMT Frederik Heber [8c0ac9] * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-methane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-water.at (modified) TESTFIX: Made integration tests for structure optimization of water ... Wed, 20 Jun 2018 08:21:14 GMT Frederik Heber [e72d94] * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-methane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-water.at (modified) TESTFIX: threshold check in integration tests on structure ... Wed, 20 Jun 2018 08:21:13 GMT Frederik Heber [31baf0] * tests/integration/testsuite-integration.at (modified) TESTFIX: Readded missing Structure Optimization integration tests. ... Wed, 20 Jun 2018 08:20:42 GMT Frederik Heber [6a5921] * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-ethane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-methane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-water.at (modified) TESTS: Deactivated temporarily all tests related to bond graph ... Thu, 12 Apr 2018 10:03:28 GMT Frederik Heber [4fc0ea] * tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) * tests/integration/MolecularDynamics/post/ethane.ekin (modified) * tests/integration/MolecularDynamics/post/ethane_initial_steps.data (modified) * tests/integration/MolecularDynamics/post/methane.ekin (modified) * tests/integration/MolecularDynamics/post/methane_initial_steps.data (modified) * tests/integration/MolecularDynamics/post/water-system.ekin (modified) * tests/integration/MolecularDynamics/post/water-system_initial_steps.data (modified) * tests/integration/MolecularDynamics/post/water.ekin (modified) * tests/integration/MolecularDynamics/post/water_initial_steps.data (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-ethane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-methane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water-system.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at (modified) * tests/regression/Domain/RepeatBox/post/ec.data (modified) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) * tests/regression/Filling/FillSurface/post/tensid-undo.data (modified) * tests/regression/Filling/FillSurface/post/tensid.data (modified) * tests/regression/Filling/FillSurface/testsuite-fill-surface-micelle.at (modified) * tests/regression/Filling/RegularGrid/post/solved_single_sles.data (modified) * tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid.at (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/alkane-3.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) * tests/regression/Molecules/Copy/post/tensid.data (modified) * tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) * tests/regression/Parser/Tremolo-Potentials/post/argon.data (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-load.at (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/argon.data (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/output.data (modified) * tests/regression/Parser/Tremolo-SetAtomdata/post/undo.data (modified) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-resetatomdata.at (modified) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at (modified) * tests/regression/Parser/Tremolo/post/argon.data (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load.at (modified) TESTFIX: Changes to various regression and Python tests because of ... Wed, 11 Apr 2018 06:30:51 GMT Frederik Heber [fba720] * src/Parser/TremoloParser.cpp (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-ethane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-methane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water-system.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at (modified) * tests/regression/Domain/RepeatBox/testsuite-domain-repeat-box.at (modified) * tests/regression/Filling/FillSurface/testsuite-fill-surface-micelle.at (modified) * tests/regression/Filling/RegularGrid/testsuite-fill-regular-grid.at (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) * tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at (modified) * tests/regression/Parser/Tremolo-Potentials/testsuite-parser-tremolo-potentials-load.at (modified) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-resetatomdata.at (modified) * tests/regression/Parser/Tremolo-SetAtomdata/testsuite-parser-tremolo-setatomdata.at (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load.at (modified) Increased output precision in tremolo's data files to 10 digits. - ... Wed, 11 Apr 2018 06:30:10 GMT Frederik Heber [cd91bd] * tests/Python/AllActions/moltest.py (modified) * tests/Python/AllActions/moltest_check.py (modified) * tests/Python/AllActions/options.dat (modified) * tests/Python/AllActions/testsuite-python-allactions.at (modified) * tests/Python/AllActions/testsuite-python-options_dat.at (modified) * tests/Python/BoxMaker/testsuite-python-boxmaker.at (modified) * tests/Python/ReturnValueActions/testsuite-python-returnvalueactions.at (modified) * tests/regression/Options/DryRun/post/session.py (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) * tests/regression/Options/Session/post/complextest.py (modified) * tests/regression/Options/Session/post/test.py (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) TESTFIX: Changes to test scripts because now keyword arguments are ... Wed, 11 Apr 2018 06:30:10 GMT Frederik Heber [e7ad08] * doc/userguide/userguide.xml (modified) * src/Actions/Action.hpp (modified) * src/Actions/Action_impl_pre.hpp (modified) * src/Actions/Action_impl_python.hpp (modified) * src/Actions/MakroAction_impl_pre.hpp (modified) * tests/Python/AllActions/testsuite-python-options_dat.at (modified) * tests/regression/Options/DryRun/testsuite-options-dryrun-storesession.at (modified) * tests/regression/Options/Session/testsuite-options-load-session-python.at (modified) * tests/regression/Options/Session/testsuite-options-store-session-python.at (modified) Python interface now converts dashes in tokens to underscores, store- ... Tue, 10 Apr 2018 06:43:31 GMT Frederik Heber [8450da] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) ForceAnnealing functions now have better readable time step ... Tue, 10 Apr 2018 06:43:31 GMT Frederik Heber [90ece9] * tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) TESTFIX: Fixes to Python tests due to changed anneal() and modified ... Tue, 10 Apr 2018 06:43:31 GMT Frederik Heber [441d40] * tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_bondgraph.data (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) TESTFIX: bondgraph annealing is working better than expected. Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [038ccd] * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/post/two_carbon_test_no-bondgraph.data (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) * tests/regression/Molecules/ForceAnnealing/post/test.conf (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) TESTFIX: Needed to change ForceAnnealing Python and regression test ... Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [be729b] * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) ForceAnnealing::anneal() now only once reduces deltat. - TESTFIX: ... Tue, 10 Apr 2018 06:43:30 GMT Frederik Heber [77d0cd] * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (modified) ForceAnnealing now uses BondVectors to optimize the structure from ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [075357] * tests/Python/ForceAnnealing/post/five_carbon_test_bondgraph.data (added) * tests/Python/ForceAnnealing/post/five_carbon_test_no-bondgraph.data (added) * tests/Python/ForceAnnealing/post/two_carbon_test_bondgraph.data (added) * tests/Python/ForceAnnealing/post/two_carbon_test_no-bondgraph.data (added) * tests/Python/ForceAnnealing/pre/ising_model_chain.py (added) * tests/Python/ForceAnnealing/testsuite-python-forceannealing-ising.at (added) * tests/Python/Makefile.am (modified) * tests/Python/numpy_check.py (added) * tests/Python/testsuite.at (modified) TEST: Adding Python test on ForceAnnealing using an Ising model with ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [41de6e] * tests/regression/Molecules/ForceAnnealing/post/test.conf (modified) * tests/regression/Molecules/ForceAnnealing/pre/test.forces (modified) TESTFIX: ForceAnnealing regression test used zero force. - all ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [c87d6e] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo.conf (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo2.conf (added) * tests/regression/Molecules/ForceAnnealing/pre/test2.conf (added) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) ForceAnnealingAction's Undo removes trajectory item if it was added. ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [6145577] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Actions/UndoRedoHelpers.cpp (modified) * src/Actions/UndoRedoHelpers.hpp (modified) * src/Atom/AtomicInfo.cpp (modified) * src/Atom/AtomicInfo.hpp (modified) * tests/regression/Molecules/ForceAnnealing/post/test-undo.conf (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) FIX: ForceAnnealingAction's Undo is again working. - ... Tue, 10 Apr 2018 06:43:12 GMT Frederik Heber [efd020] * src/Actions/FragmentationAction/StructuralOptimizationAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) Readded step-world-time to StructuralOptimization. - adapted ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [2bb3be] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * tests/regression/Molecules/ForceAnnealing/post/test.conf (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) Removed DoOutput param from ForceAnnealing. - TESTFIX: Modifying ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [866dec] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/OBC/alkane-3.data (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/PBC/alkane-3.data (modified) ForceAnnealing no longer resets forces, AnalyseFragmentResults now ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [b2acca] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/AllActions/options.dat (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) ForceAnnealing can now be used either atom- or bond-centered. - new ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [56b4c6] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/AllActions/options.dat (modified) Added damping-factor as another option to ForceAnnealing for proper ... Tue, 10 Apr 2018 06:43:11 GMT Frederik Heber [cdfb6f] * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/Python/AllActions/options.dat (modified) ForceAnnealing now shifts atoms in the bond graph to anneal forces, ... Tue, 10 Apr 2018 06:42:56 GMT Frederik Heber [1e58bb] * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs-mpqc-jobs.at (modified) * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs-vmg-jobs.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-ethane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-methane.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water-system.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at (modified) * tests/integration/PotentialFitting/testsuite-integration-potentialfitting-water.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-ethane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-methane.at (modified) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-water.at (modified) * tests/integration/molecuilder_poolworker.in (modified) FIX: Integration tests now abort safely when one of the programs ... Wed, 04 Apr 2018 16:59:48 GMT Frederik Heber [322d58] * doc/userguide/userguide.xml (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.cpp (modified) * src/Actions/MoleculeAction/ForceAnnealingAction.def (modified) * src/Dynamics/ForceAnnealing.hpp (modified) * tests/GuiChecks/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) * tests/integration/testsuite-integration.at (modified) * tests/regression/Molecules/ForceAnnealing/testsuite-molecules-force-annealing.at (modified) ForceAnnealing now uses step width according to Barzilai-Borwein ... Wed, 04 Apr 2018 16:59:37 GMT Frederik Heber [9b32071] * tests/CodeChecks/Makefile.am (modified) * tests/CodeChecks/testsuite-testsuite-integration-unique-ports.at (added) * tests/CodeChecks/testsuite.at (modified) TESTS: Added CodeCheck on uniqueness of ports in integration tests. Wed, 04 Apr 2018 16:59:36 GMT Frederik Heber [53a85a] * tests/integration/Makefile.am (modified) * tests/integration/PotentialFitting/pre/water.pdb (added) * tests/integration/PotentialFitting/testsuite-integration-potentialfitting-water.at (added) * tests/integration/PotentialFitting/testsuite-integration-potentialfitting.at (added) * tests/integration/testsuite-integration.at (modified) Added integration test on Potential Fitting for water. - we fit ... Wed, 04 Apr 2018 16:59:36 GMT Frederik Heber [167523] * tests/integration/Makefile.am (modified) * tests/integration/StructureOptimization/pre/ethane.pdb (added) * tests/integration/StructureOptimization/pre/methane.pdb (added) * tests/integration/StructureOptimization/pre/water.pdb (added) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-ethane.at (added) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-methane.at (added) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization-water.at (added) * tests/integration/StructureOptimization/testsuite-integration-structureoptimization.at (added) * tests/integration/testsuite-integration.at (modified) Added integration tests on Structure Optimization. - we use the ... Wed, 04 Apr 2018 16:59:24 GMT Frederik Heber [37fe17] * data/molecules/methane.pdb (added) * tests/integration/Makefile.am (modified) * tests/integration/MolecularDynamics/post/ethane.ekin (added) * tests/integration/MolecularDynamics/post/ethane_initial_steps.data (added) * tests/integration/MolecularDynamics/post/methane.ekin (added) * tests/integration/MolecularDynamics/post/methane_initial_steps.data (added) * tests/integration/MolecularDynamics/post/water-system.ekin (added) * tests/integration/MolecularDynamics/post/water-system_initial_steps.data (added) * tests/integration/MolecularDynamics/pre/ethane.pdb (added) * tests/integration/MolecularDynamics/pre/methane.pdb (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-ethane.at (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-methane.at (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water-system.at (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at (modified) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics.at (modified) TESTS: Added MD tests on methane, ethane, and water-filled system. Wed, 04 Apr 2018 16:59:24 GMT Frederik Heber [0aae02] * tests/integration/Makefile.am (modified) * tests/integration/MolecularDynamics/post/water.ekin (added) * tests/integration/MolecularDynamics/post/water_initial_steps.data (added) * tests/integration/MolecularDynamics/pre/water.pdb (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics-water.at (added) * tests/integration/MolecularDynamics/testsuite-integration-moleculardynamics.at (added) * tests/integration/testsuite-integration.at (modified) Added integration test molecular dynamics of a water molecule. - we ... Wed, 04 Apr 2018 16:59:24 GMT Frederik Heber [775f3f] * tests/Tesselations/Convex/1_2-dimethoxyethane/testsuite-1_2-dimethoxyethane.at (modified) * tests/Tesselations/Convex/1_2-dimethylbenzene/testsuite-1_2-dimethylbenzene.at (modified) * tests/Tesselations/Convex/2-methylcyclohexanone/testsuite-2-methylcyclohexanone.at (modified) * tests/Tesselations/Convex/N_N-dimethylacetamide/testsuite-N_N-dimethylacetamide.at (modified) * tests/Tesselations/Convex/amylose/testsuite-amylose.at (modified) * tests/Tesselations/Convex/benzene/testsuite-benzene.at (modified) * tests/Tesselations/Convex/cholesterol/testsuite-cholesterol.at (modified) * tests/Tesselations/Convex/cycloheptane/testsuite-cycloheptane.at (modified) * tests/Tesselations/Convex/dimethyl_bromomalonate/testsuite-dimethyl_bromomalonate.at (modified) * tests/Tesselations/Convex/glucose/testsuite-glucose.at (modified) * tests/Tesselations/Convex/heptan/testsuite-heptan.at (modified) * tests/Tesselations/Convex/isoleucine/testsuite-isoleucine.at (modified) * tests/Tesselations/Convex/neohexane/testsuite-neohexane.at (modified) * tests/Tesselations/Convex/proline/testsuite-proline.at (modified) * tests/Tesselations/Convex/putrescine/testsuite-putrescine.at (modified) * tests/Tesselations/Convex/tartaric_acid/testsuite-tartaric_acid.at (modified) TESTFIX: Convex Tesselation did not specify nonconvex-file which they ... Wed, 04 Apr 2018 16:59:24 GMT Frederik Heber [6491d3] * tests/integration/FragmentJobs/pre/ethane.pdb (moved) * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs-mpqc-jobs.at (moved) * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs-vmg-jobs.at (moved) * tests/integration/FragmentJobs/testsuite-integration-fragmentjobs.at (added) * tests/integration/Makefile.am (modified) * tests/integration/testsuite-integration.at (modified) Moved fragment jobs integration test into subfolder. Wed, 12 Jul 2017 19:12:47 GMT Frederik Heber [d86d97] * src/Actions/FragmentationAction/ParseFragmentResultsAction.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.cpp (modified) * src/UIElements/Views/Qt4/QtFragmentList.hpp (modified) * tests/regression/DiffFragmentResultContainer.cpp (modified) FIX: FragmentResultsContainer is no longer purged during run. - so ... Wed, 12 Jul 2017 19:12:47 GMT Frederik Heber [9a1e099] * tests/regression/Fragmentation/DiffFragmentResultContainer/pre/alkane_results.dat (added) * tests/regression/Fragmentation/DiffFragmentResultContainer/pre/water_results.dat (added) * tests/regression/Fragmentation/DiffFragmentResultContainer/testsuite-fragmentation-difffragmenresultcontainer.at (added) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Makefile.am (modified) Added regression test on DiffFragmentResultContainer. Wed, 12 Jul 2017 19:12:43 GMT Frederik Heber [4c6f0d] * src/Actions/FragmentationAction/FragmentationAutomationAction.def (modified) * tests/GuiChecks/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (modified) * tests/regression/Fragmentation/FragmentationAutomation/testsuite-fragmentation-fragmentation-automation.at (modified) FIX: server-port was invalid. - now, we use empty string as param ... Wed, 12 Jul 2017 19:11:51 GMT Frederik Heber [b10593] * configure.ac (modified) * tests/GuiChecks/Atoms/RandomPerturbation/testsuite-atoms-random-perturbation.at (added) * tests/GuiChecks/Atoms/testsuite-atoms.at (modified) * tests/GuiChecks/Fragmentation/ParseSaveFragmentResults/testsuite-fragmentation-parse-save-fragment-results.at (modified) * tests/GuiChecks/Geometry/testsuite-geometry-common.at (modified) * tests/GuiChecks/Makefile.am (modified) * tests/GuiChecks/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (added) * tests/GuiChecks/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at (modified) * tests/GuiChecks/Molecules/StretchBond/testsuite-molecules-stretch-bond-cyclic_bond.at (added) * tests/GuiChecks/Molecules/testsuite-molecules.at (modified) * tests/GuiChecks/Parser/Tremolo/testsuite-parser-tremolo-load-multiple-timesteps.at (added) * tests/GuiChecks/Parser/testsuite-parser.at (modified) * tests/GuiChecks/Selection/Atoms/AtomByName/testsuite-selection-select-atoms-by-name.at (added) * tests/GuiChecks/Selection/Atoms/AtomByName/testsuite-selection-unselect-atoms-by-name.at (added) * tests/GuiChecks/Selection/Atoms/testsuite-selection-atoms.at (modified) * tests/GuiChecks/WorldTime/StepWorldTime/testsuite-worldtime-step-world-time.at (modified) * tests/GuiChecks/atlocal.in (modified) * tests/GuiChecks/difffragmentresultcontainer.in (added) Recreated all GuiChecks. - GuiChecks lacked ... Wed, 12 Jul 2017 19:11:50 GMT Frederik Heber [ecacf0] * tests/regression/Makefile.am (modified) FIX: regression test Makefile.am lacked difffragmentresultcontainer ... Wed, 12 Jul 2017 19:11:50 GMT Frederik Heber [a9db89] * tests/regression/Geometry/testsuite-geometry-common.at (modified) FIX: regression test Geometry common still used position instead of ... Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [92d0e6] * tests/Examples/ManyWaysTranslateAtom/testsuite-examples-many-ways-translate-atom.at (modified) ManyWaysToTranslateAtom: Added stretch-bond test. Wed, 12 Jul 2017 19:10:32 GMT Frederik Heber [d1134d] * src/Actions/MoleculeAction/RotateAroundBondAction.cpp (modified) * tests/regression/Molecules/RotateAroundBond/post/benzene_90degree.pdb (added) * tests/regression/Molecules/RotateAroundBond/pre/benzene.pdb (added) * tests/regression/Molecules/RotateAroundBond/testsuite-molecules-rotate-around-bond.at (modified) FIX: rotate-around-bond now rotates only one side of mol's bond ... Wed, 12 Jul 2017 19:10:31 GMT Frederik Heber [3b74fa] * src/Actions/MoleculeAction/StretchBondAction.cpp (modified) * src/Actions/MoleculeAction/StretchBondAction.def (modified) * tests/regression/Makefile.am (modified) * tests/regression/Molecules/StretchBond/post/benzene.pdb (added) * tests/regression/Molecules/StretchBond/pre/benzene.pdb (added) * tests/regression/Molecules/StretchBond/testsuite-molecules-stretch-bond-cyclic_bond.at (added) * tests/regression/Molecules/testsuite-molecules.at (modified) Rewrite of StretchBondAction to take bondgraph into account. - i.e. ... Wed, 12 Jul 2017 19:10:21 GMT Frederik Heber [f56e14] * tests/Examples/Makefile.am (modified) * tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz (added) * tests/Examples/ManyWaysTranslateAtom/pre/water.xyz (added) * tests/Examples/ManyWaysTranslateAtom/testsuite-examples-many-ways-translate-atom.at (added) * tests/Examples/testsuite-examples.at (modified) Added Examples testcase for the many ways to translate an atom blog ... Wed, 12 Jul 2017 19:10:07 GMT Frederik Heber [33af20] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiple-timesteps.at (modified) TremoloParser::save() now supports multiple time steps. - TESTS: ... Wed, 12 Jul 2017 19:10:07 GMT Frederik Heber [220d2c] * src/Parser/TremoloParser.cpp (modified) * src/Parser/TremoloParser.hpp (modified) * tests/regression/Makefile.am (modified) * tests/regression/Parser/Tremolo/post/water_multipletimesteps.data (added) * tests/regression/Parser/Tremolo/post/water_multipletimesteps_fail.data (added) * tests/regression/Parser/Tremolo/pre/water_multipletimesteps.data (added) * tests/regression/Parser/Tremolo/pre/water_multipletimesteps_fail.data (added) * tests/regression/Parser/Tremolo/testsuite-parser-tremolo-load-multiple-timesteps.at (added) * tests/regression/Parser/testsuite-parser.at (modified) TremoloParser::load() can deal with multiple time steps. - TESTS: ... Mon, 03 Jul 2017 15:06:31 GMT Frederik Heber [3f6aac] * doc/userguide/userguide.xml (modified) * src/Actions/GlobalListOfActions.hpp (modified) * src/Actions/Makefile.am (modified) * src/Actions/SelectionAction/Atoms/AtomByNameAction.cpp (added) * src/Actions/SelectionAction/Atoms/AtomByNameAction.def (added) * src/Actions/SelectionAction/Atoms/AtomByNameAction.hpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.cpp (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.def (added) * src/Actions/SelectionAction/Atoms/NotAtomByNameAction.hpp (added) * tests/Python/AllActions/options.dat (modified) * tests/regression/Makefile.am (modified) * tests/regression/Selection/Atoms/AtomByName/post/ethane-H5_missing.pdb (added) * tests/regression/Selection/Atoms/AtomByName/pre/ethane.pdb (added) * tests/regression/Selection/Atoms/AtomByName/testsuite-selection-select-atoms-by-name.at (added) * tests/regression/Selection/Atoms/AtomByName/testsuite-selection-unselect-atoms-by-name.at (added) * tests/regression/Selection/Atoms/testsuite-selection-atoms.at (modified) Added (Un)selectAtomByName. - Descriptor for AtomByName was already ...