Ignore:
Timestamp:
Aug 20, 2014, 12:59:22 PM (10 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:
4c9101
Parents:
83cc3e
git-author:
Frederik Heber <heber@…> (08/20/14 12:01:24)
git-committer:
Frederik Heber <heber@…> (08/20/14 12:59:22)
Message:

FIX: Fragmentations tests used -I and not --correct-bonddegree in case of pdb files.

  • this bond graph was always recalculated and not taken from the parsed file.
Location:
tests/Fragmentations/Fragmenting/phenanthrene
Files:
6 edited

Legend:

Unmodified
Added
Removed

  • tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order1.at

    r83cc3e r2cb77c  
    3333AT_CHECK([chmod u+w $file], 0)
    3434
    35 AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 1 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
     35AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 1 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
    3636AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
    3737AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

  • tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order2.at

    r83cc3e r2cb77c  
    3333AT_CHECK([chmod u+w $file], 0)
    3434
    35 AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 2 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
     35AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 2 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
    3636AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
    3737AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

  • tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order3.at

    r83cc3e r2cb77c  
    3333AT_CHECK([chmod u+w $file], 0)
    3434
    35 AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 3 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
     35AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 3 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
    3636AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
    3737AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

  • tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order4.at

    r83cc3e r2cb77c  
    3333AT_CHECK([chmod u+w $file], 0)
    3434
    35 AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 4 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
     35AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 4 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
    3636AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
    3737AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

  • tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order5.at

    r83cc3e r2cb77c  
    3333AT_CHECK([chmod u+w $file], 0)
    3434
    35 AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 5 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
     35AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 5 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
    3636AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
    3737AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])

  • tests/Fragmentations/Fragmenting/phenanthrene/testsuite-fragmenting-phenanthrene-order6.at

    r83cc3e r2cb77c  
    3333AT_CHECK([chmod u+w $file], 0)
    3434
    35 AT_CHECK([../../molecuilder -i $file -I --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 6 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
     35AT_CHECK([../../molecuilder -i $file --correct-bonddegree --select-molecule-by-id 0 --select-molecules-atoms -f $FILENAME --order 6 --distance $DISTANCE --DoCyclesFull 1  --output-types mpqc pcp pdb], 0, [stdout], [stderr])
    3636AT_CHECK([ls ${FILENAME}*.conf | wc -l | awk '{print $1}'], 0, [stdout], [ignore])
    3737AT_CHECK([test $FragNo == `cat stdout`], 0, [ignore], [ignore])
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