Changeset 826e8c for tests/regression/Molecules/SaveAdjacency/post/test.adj

Timestamp:

Feb 22, 2012, 11:29:04 AM (13 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:

153985

Parents:

cbcda6

git-author:

Frederik Heber <heber@…> (02/06/12 17:46:56)

git-committer:

Frederik Heber <heber@…> (02/22/12 11:29:04)

Message:

Introduced new LinkedCell into BondGraph.

• new convenience functions BondGraph::getDomain(), ::getLinkedCell(), ::getTime() to have World dependency not in header file (circular include).
• new function BondGraph::getMaxPossibleBondDistance() where one element is given.
• dropped BondGraph::CreateAdjacency(LC_deprecated) as functionality is better placed directly into templated version directly.
• rewrote templated BondGraph::CreateAdjacency that now makes use of LinkedCell_View::getAllNeighbours().
• FIX: BondGraph::CreateAdjacency() created bonds for atom's fathers, not for atoms.
• TESTFIX: New LinkedCell construct in BondGraph::CreateAdjacency changes order of ids in adjacency file:
  • ids are now in order (unlike to before), hence we simply use the new file in the regression test.
  • this is actually a fault of the test, not of the code as order of ids is not guaranteed in the file anyway.
• TESTFIX: Removed XFAILs from regression test Graph/SubgraphDissection- BoundaryCondition.
• TESTFIX: CountBondsUnitTest use two molecules that are on top of each other: This causes mess with changed LinkedCell BondGraph recognition, and we even actually need just one molecule for the testing.

File:

• tests/regression/Molecules/SaveAdjacency/post/test.adj (modified) (1 diff)

tests/regression/Molecules/SaveAdjacency/post/test.adj

@@ -8 +8 @@
 7       11      
 8       11      
-9       1       10      2       3       
-10      9       11      4       5       
+9       1       2       3       10      
+10      4       5       9       11      
 11      6       7       8       10