Changeset 3738f0 for src/molecule_fragmentation.cpp

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, Candidate_v1.7.0, 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.

File:

• src/molecule_fragmentation.cpp (modified) (2 diffs)

src/molecule_fragmentation.cpp

@@ -667 +667 @@
       iter != World::getInstance().moleculeEnd();
       ++iter) {
-      // reset bond degree to 1
-    for (molecule::iterator atomiter = (*iter)->begin();
-        atomiter != (*iter)->end();
-        ++atomiter) {
-      const BondList& ListOfBonds = (*atomiter)->getListOfBonds();
-      for (BondList::const_iterator bonditer = ListOfBonds.begin();
-          bonditer != ListOfBonds.end();
-          ++bonditer) {
-        (*bonditer)->BondDegree = 1;
-      }
-    }
     // correct bond degree
-    (*iter)->CorrectBondDegree();
+    molecule::atomVector Set = (*iter)->getAtomSet();
+    World::getInstance().getBondGraph()->CorrectBondDegree(Set);
   }
 
@@ -748 +738 @@
       MolecularWalker = MolecularWalker->next;
       DoLog(1) && (Log() << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl);
-      //MolecularWalker->Leaf->OutputListOfBonds(out);  // output atom::ListOfBonds for debugging
       if (MolecularWalker->Leaf->hasBondStructure()) {
         // call BOSSANOVA method