Context Navigation

testsuite-analysis-surface-correlation.at@ 49c059

Visit:

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

Last change on this file since 49c059 was 49c059, checked in by Frederik Heber <heber@…>, 14 years ago

Moved DepthFirstSearchAnalysis into functor in Graph/.

Smaller fixes:

molecule::CorrectBondDegree() - does not rely on BondCount which was not necessary anyway.

DFS does not copy atoms or molecules anymore but reinitiates the current molecule structure with present atoms, used new class ConnectedSubgraph for that. New functions:
- UpdateMoleculeStructure() - reinstantiates molecules.
- getMoleculeStructure() - puts molecules into chained list.
adapted because of that:
- DepthFirstSearchAction: uses DFS and CSA functors, also UpdateMoleculeStructure() such that CSA has current structure.
- FragmentationAction: assumes connectivity fully present, DFS created.
- SubgraphDissectionAction: uses DFS and UpdateMoleculeStructure().
- molecule::FragmentMolecule(): no more DFS, instead DFS has to happen beforehand and is given as parameter, used to obtain chained list for compatibility for the moment.
DepthFirstSearchAnalysis::SetNextComponentNumber() bugfix due to wrong assert.

TESTFIXES:

Fragmentation and regression test Fragmentation/FragmentMolecule: FragmentationAction now needs SubgraphDissectionAction beforehand.
shifted id (down by one) due to non-copying (before: one big molecule, copied and split up system started at 1, now it starts at 0):
- (Un)Selection/Atoms/AllAtomsOfMolecule
- Analysis/SurfaceCorrelation
- (Un)Selection/Molecules/MoleculeById (also renamed post-files accordingly)
- (Un)Selection/Molecules/MoleculeByName

Property mode set to 100644

File size: 885 bytes

Line
1	### pair correlation analysis to surface
2
3	AT_SETUP([Analysis - surface correlation])
4	AT_KEYWORDS([analysis,correlation])
5	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/SurfaceCorrelation/pre/test.conf .], 0)
6	AT_CHECK([../../molecuilder -i test.conf -v 3 -I --select-all-molecules --unselect-molecules-by-formula C3H8 --surface-correlation --elements 1 --output-file output.csv --bin-output-file bin_output.csv --bin-start 0 --bin-width 1. --bin-end 20 --molecule-by-id 0], 0, [stdout], [stderr])
7	AT_CHECK([fgrep "Begin of CorrelationToSurface" stdout], 0, [ignore], [ignore])
8	#AT_CHECK([file=output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/SurfaceCorrelation/post/$file], 0, [ignore], [ignore])
9	AT_CHECK([file=bin_output.csv; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Analysis/SurfaceCorrelation/post/$file], 0, [ignore], [ignore])
10	AT_CLEANUP

Note: See TracBrowser for help on using the repository browser.

Download in other formats:

Original Format