Changeset ec7511 for tests/Fragmentations

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.

Location:

tests/Fragmentations

Files:

• Fragmenting/anthracene/pre/anthracene.pdb (added)
• Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at (added)
• Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at (added)
• Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at (added)
• Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at (added)
• Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at (added)
• Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at (added)
• Fragmenting/coronene/pre/coronene.pdb (added)
• Fragmenting/coronene/testsuite-fragmenting-coronene-order1.at (added)
• Fragmenting/coronene/testsuite-fragmenting-coronene-order2.at (added)
• Fragmenting/coronene/testsuite-fragmenting-coronene-order3.at (added)
• Fragmenting/coronene/testsuite-fragmenting-coronene-order4.at (added)
• Fragmenting/coronene/testsuite-fragmenting-coronene-order5.at (added)
• Fragmenting/coronene/testsuite-fragmenting-coronene-order6.at (added)
• Fragmenting/naphthalene/pre/naphthalene.pdb (added)
• Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order1.at (added)
• Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order2.at (added)
• Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order3.at (added)
• Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order4.at (added)
• Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order5.at (added)
• Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order6.at (added)
• Fragmenting/phenanthrene/pre/phenanthrene.pdb (added)
• Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order1.at (added)
• Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order2.at (added)
• Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order3.at (added)
• Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order4.at (added)
• Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order5.at (added)
• Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order6.at (added)
• Makefile.am (modified) (6 diffs)
• testsuite.at (modified) (4 diffs)

tests/Fragmentations/Makefile.am

@@ -13 +13 @@
         $(srcdir)/Fragmenting/1_2-dimethylbenzene \
         $(srcdir)/Fragmenting/2-methylcyclohexanone \
+        $(srcdir)/Fragmenting/anthracene \
         $(srcdir)/Fragmenting/benzene \
         $(srcdir)/Fragmenting/cholesterol \
+        $(srcdir)/Fragmenting/coronene \
         $(srcdir)/Fragmenting/cycloheptane \
         $(srcdir)/Fragmenting/dimethyl_bromomalonate \
@@ -20 +22 @@
         $(srcdir)/Fragmenting/heptan \
         $(srcdir)/Fragmenting/isoleucine \
+        $(srcdir)/Fragmenting/naphthalene \
         $(srcdir)/Fragmenting/neohexane \
         $(srcdir)/Fragmenting/N_N-dimethylacetamide \
+        $(srcdir)/Fragmenting/phenanthrene \
         $(srcdir)/Fragmenting/proline \
         $(srcdir)/Fragmenting/putrescine \
@@ -44 +48 @@
         Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order3.at \
         Fragmenting/2-methylcyclohexanone/testsuite-fragmenting-2-methylcyclohexanone-order4.at \
+        Fragmenting/anthracene/testsuite-fragmenting-anthracene-order1.at \
+        Fragmenting/anthracene/testsuite-fragmenting-anthracene-order2.at \
+        Fragmenting/anthracene/testsuite-fragmenting-anthracene-order3.at \
+        Fragmenting/anthracene/testsuite-fragmenting-anthracene-order4.at \
+        Fragmenting/anthracene/testsuite-fragmenting-anthracene-order5.at \
+        Fragmenting/anthracene/testsuite-fragmenting-anthracene-order6.at \
         Fragmenting/benzene/testsuite-fragmenting-benzene-order1.at \
         Fragmenting/benzene/testsuite-fragmenting-benzene-order2.at \
@@ -54 +64 @@
         Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order3.at \
         Fragmenting/cholesterol/testsuite-fragmenting-cholesterol-order4.at \
+        Fragmenting/coronene/testsuite-fragmenting-coronene-order1.at \
+        Fragmenting/coronene/testsuite-fragmenting-coronene-order2.at \
+        Fragmenting/coronene/testsuite-fragmenting-coronene-order3.at \
+        Fragmenting/coronene/testsuite-fragmenting-coronene-order4.at \
+        Fragmenting/coronene/testsuite-fragmenting-coronene-order5.at \
+        Fragmenting/coronene/testsuite-fragmenting-coronene-order6.at \
         Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order1.at \
         Fragmenting/cycloheptane/testsuite-fragmenting-cycloheptane-order2.at \
@@ -82 +98 @@
         Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order5.at \
         Fragmenting/isoleucine/testsuite-fragmenting-isoleucine-order6.at \
+        Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order1.at \
+        Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order2.at \
+        Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order3.at \
+        Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order4.at \
+        Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order5.at \
+        Fragmenting/naphthalene/testsuite-fragmenting-naphthalene-order6.at \
         Fragmenting/neohexane/testsuite-fragmenting-neohexane-order1.at \
         Fragmenting/neohexane/testsuite-fragmenting-neohexane-order2.at \
@@ -94 +116 @@
         Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order5.at \
         Fragmenting/N_N-dimethylacetamide/testsuite-fragmenting-N_N-dimethylacetamide-order6.at \
+        Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order1.at \
+        Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order2.at \
+        Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order3.at \
+        Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order4.at \
+        Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order5.at \
+        Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order6.at \
         Fragmenting/proline/testsuite-fragmenting-proline-order1.at \
         Fragmenting/proline/testsuite-fragmenting-proline-order2.at \

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