Changeset ec7511 for tests/Fragmentations/testsuite.at

Timestamp:

Apr 29, 2014, 12:42:43 PM (11 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

237f93

Parents:

4b10fd

git-author:

Frederik Heber <heber@…> (11/11/13 09:49:19)

git-committer:

Frederik Heber <heber@…> (04/29/14 12:42:43)

Message:

FIX: CyclicStructureAnalysis falsely used DFS, skipped some cycles.

• FIX: CyclicStructureAnalysis did use DFS instead of BFS for finding cycles. Note that CyclicStructureAnalysis with coronene would find supercycles and not the smaller interconnected ones.
• FIX: Cycles were skipped when all bonds marked cyclic, not enough. In interconnected aromatic rings, bonds may very well be marked as cyclic from earlier extraction of cycles and yet the specific cycle might not have been found yet (e.g. coronene). In this case we now check whether this particular cycle has already been extracted and only skip if so.
• TESTFIX: added new fragmentation regression tests on some metallic systems.
• this is mainly for regression on bond graph detection and cycle analysis.

File:

• tests/Fragmentations/testsuite.at (modified) (4 diffs)

tests/Fragmentations/testsuite.at

@@ -62 +62 @@
 m4_include(Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at)
 
+# fragmentation of anthracene
+m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at)
+m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at)
+m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at)
+m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at)
+m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at)
+m4_include(Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at)
+
 # fragmentation of benzene
 m4_include(Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at)
@@ -75 +83 @@
 m4_include(Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at)
 m4_include(Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at)
+
+# fragmentation of coronene
+m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order1.at)
+m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order2.at)
+m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order3.at)
+m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order4.at)
+m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order5.at)
+m4_include(Fragmenting/coronene/testsuite-fragmenting-coronene-order6.at)
 
 # fragmentation of cycloheptane
@@ -114 +130 @@
 m4_include(Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at)
 
+# fragmentation of naphthalene
+m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order1.at)
+m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order2.at)
+m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order3.at)
+m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order4.at)
+m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order5.at)
+m4_include(Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order6.at)
+
 # fragmentation of neohexane
 m4_include(Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at)
@@ -129 +153 @@
 m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at)
 m4_include(Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at)
+
+# fragmentation of phenanthrene
+m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order1.at)
+m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order2.at)
+m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order3.at)
+m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order4.at)
+m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order5.at)
+m4_include(Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order6.at)
 
 # fragmentation of proline