Changeset 3738f0 for src/unittests

Timestamp:

Mar 1, 2011, 12:49:28 PM (15 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:

0cbad2

Parents:

ce5f05

git-author:

Frederik Heber <heber@…> (02/26/11 00:10:05)

git-committer:

Frederik Heber <heber@…> (03/01/11 12:49:28)

Message:

Moved molecule::CreateAdjacencyList over to class BondGraph.

to make this possible we had to:

• enhance AtomSet such that individual const_ and iterator are templated.
• FIX: FragmentationCreateAdjacencyAction needs to call BondGraph::SetMaxDistanceToMaxOfCovalentRadii() before getMaxDistance() is valid.
• new function molecule::getAtomSet() which copies the internal atomSet to a vector AtomSetMixin and delivers. This is needed as PointCloudAdaptor needs a reference to a AtomSetMixin and we don't want to expose the internal set.

other changes:

• the following Actions do not create adjacency beforehand anymore:
  • DepthFirstSearchAction
  • MoleculeSaveAdjacencyAction
  • MoleculeSaveBondsAction
• changes to BondGraph:
  • removed CreateAdjacencyForMolecule()
  • removed SetMaxDistanceToMaxOfCovalentRadii()
  • new function CreateAdjacency on LinkedCell reference
• new BondGraph functions that work on AtomSetMixin reference: CreateAdjacency(), cleanAdjacencyList(), CorrectBondDegree(), resetBondDegree(), calculateBondDegree()

TESTFIXES:

• the regression test for all Actions mentioned above that don't create adjacency themselves anymore needed to be prepended with --select-all-atoms --create-adjacency.

Location:

src/unittests

Files:

• AnalysisBondsUnitTest.cpp (modified) (1 diff)
• BondGraphUnitTest.cpp (modified) (3 diffs)
• CountBondsUnitTest.cpp (modified) (1 diff)

src/unittests/AnalysisBondsUnitTest.cpp

@@ -109 +109 @@
   CPPUNIT_ASSERT_EQUAL( 1.5, BG->GetBondLength(5,5) );
 
-  BG->CreateAdjacencyForMolecule(TestMolecule);
+  molecule::atomVector Set = TestMolecule->getAtomSet();
+  BG->CreateAdjacency(Set);
 };
 

src/unittests/BondGraphUnitTest.cpp

@@ -139 +139 @@
 };
 
-/** UnitTest for BondGraphTest::CreateAdjacencyForMolecule().
+/** UnitTest for BondGraphTest::CreateAdjacency().
  */
 void BondGraphTest::ConstructGraphFromTableTest()
@@ -147 +147 @@
   Runner++;
   CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(test) );
-  CPPUNIT_ASSERT_EQUAL( true , BG->CreateAdjacencyForMolecule(TestMolecule) );
+  molecule::atomVector Set = TestMolecule->getAtomSet();
+  BG->CreateAdjacency(Set);
+  CPPUNIT_ASSERT( TestMolecule->getBondCount() != 0);
   CPPUNIT_ASSERT_EQUAL( true , (*Walker)->IsBondedTo(WorldTime::getTime(), (*Runner)) );
 };
 
-/** UnitTest for BondGraphTest::CreateAdjacencyForMolecule().
+/** UnitTest for BondGraphTest::CreateAdjacency().
  */
 void BondGraphTest::ConstructGraphFromCovalentRadiiTest()
@@ -157 +159 @@
 
   CPPUNIT_ASSERT_EQUAL( false , BG->LoadBondLengthTable(dummy) );
-  CPPUNIT_ASSERT_EQUAL( true , BG->CreateAdjacencyForMolecule(TestMolecule) );
+  molecule::atomVector Set = TestMolecule->getAtomSet();
+  BG->CreateAdjacency(Set);
+  CPPUNIT_ASSERT( TestMolecule->getBondCount() != 0);
 
   // this cannot be assured using dynamic IDs

src/unittests/CountBondsUnitTest.cpp

@@ -112 +112 @@
 
   // construct bond graphs
-  CPPUNIT_ASSERT_EQUAL( true , BG->CreateAdjacencyForMolecule(TestMolecule1) );
-  CPPUNIT_ASSERT_EQUAL( true , BG->CreateAdjacencyForMolecule(TestMolecule2) );
+  molecule::atomVector Set1 = TestMolecule1->getAtomSet();
+  BG->CreateAdjacency(Set1);
+  CPPUNIT_ASSERT( TestMolecule1->getBondCount() != 0);
+  molecule::atomVector Set2 = TestMolecule2->getAtomSet();
+  BG->CreateAdjacency(Set2);
+  CPPUNIT_ASSERT( TestMolecule2->getBondCount() != 0);
 //  TestMolecule1->Output((ofstream *)&cout);
 //  TestMolecule1->OutputBondsList(std::cout);