Context Navigation

testsuite-analysis-dipole-angular-correlation.at@ 4b8630

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 4b8630 was 4b8630, checked in by Frederik Heber <heber@…>, 13 years ago

World::setTime() now updates bond structure of system and related changes to DipoleAngularCorrelation.

extended regression test Analysis/DipoleAngularCorrelation with xyz example whose bond structure is updated per time step.
FIX: DepthFirstSearchAnalysis::operator() did not reset bonds to unused.
FIX: DipoleAngularCorrelationAction has to work on atoms not molecules as the latter are subject to changes due to changing bond structure.
FIX: DipoleAngularCorrelation() re-calculates current set of molecules from the select atoms and stores first atom in values file, not molecule name.

Property mode set to 100644

File size: 2.5 KB

Rev	Line
[4fc828]	1	### dipole angular correlation analysis
	2
	3	AT_SETUP([Analysis - dipole angular correlation on PDBs with CONECT])
	4	AT_KEYWORDS([analysis dipole correlation pdb dipole-angular-correlation])
	5	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.pdb .], 0)
[4b8630]	6	AT_CHECK([../../molecuilder -v 4 -i watermulti_X.pdb -o pdb --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values_X.dat --bin-output-file water_histogram_X.dat], 0, [stdout], [stderr])
[4fc828]	7	AT_CHECK([file=water_histogram_X.dat; diff $file ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/post/$file], 0, [ignore], [ignore])
	8	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.pdb .], 0)
[4b8630]	9	AT_CHECK([../../molecuilder -v 4 -i watermulti_Y.pdb -o pdb --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values_Y.dat --bin-output-file water_histogram_Y.dat], 0, [stdout], [stderr])
	10	AT_CHECK([file=water_histogram_Y.dat; diff $file ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/post/$file], 0, [ignore], [ignore])
	11	AT_CLEANUP
	12
	13	AT_SETUP([Analysis - dipole angular correlation on XYZs])
	14	AT_KEYWORDS([analysis dipole correlation xyz dipole-angular-correlation])
	15	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_X.xyz .], 0)
	16	AT_CHECK([../../molecuilder -v 4 -i watermulti_X.xyz -o xyz -I --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values_X.dat --bin-output-file water_histogram_X.dat], 0, [stdout], [stderr])
	17	AT_CHECK([file=water_histogram_X.dat; diff $file ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/post/$file], 0, [ignore], [ignore])
	18	AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/pre/watermulti_Y.xyz .], 0)
	19	AT_CHECK([../../molecuilder -v 4 -i watermulti_Y.xyz -o xyz -I --select-molecules-by-formula H2O --select-molecules-atoms --dipole-angular-correlation --bin-start -5 --bin-width 10. --bin-end 184.5 --output-file water_values_Y.dat --bin-output-file water_histogram_Y.dat], 0, [stdout], [stderr])
[4fc828]	20	AT_CHECK([file=water_histogram_Y.dat; diff $file ${abs_top_srcdir}/tests/regression/Analysis/DipoleAngularCorrelation/post/$file], 0, [ignore], [ignore])
	21	AT_CLEANUP
	22

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

Download in other formats:

Original Format