Changeset 88ada9

Timestamp:

Apr 17, 2013, 6:56:53 PM (12 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:

1f693d

Parents:

c8bbf2

git-author:

Frederik Heber <heber@…> (03/18/13 21:08:17)

git-committer:

Frederik Heber <heber@…> (04/17/13 18:56:53)

Message:

Enhanced BondedParticle::CorrectBondDegree() to first fill up valency.

• in order to get 1,3,1,3 for simple polyine chains, we now have an extra rule to rather pick the candidate closer to fulfilling his valency.

File:

• src/Atom/atom_bondedparticle.cpp (modified) (2 diffs)

src/Atom/atom_bondedparticle.cpp

@@ -356 +356 @@
   int OtherNoBonds = 0;
   int FalseBondDegree = 0;
+  int CandidateDeltaNoBonds = -1;
   atom *OtherWalker = NULL;
   bond::ptr CandidateBond;
 
   NoBonds = CountBonds();
-  //LOG(3, "Walker " << *this << ": " << (int)this->type->NoValenceOrbitals << " > " << NoBonds << "?");
-  if ((int)(getType()->getNoValenceOrbitals()) > NoBonds) { // we have a mismatch, check all bonding partners for mismatch
+  LOG(3, "Walker " << *this << ": " << (int)this->getType()->getNoValenceOrbitals() << " > " << NoBonds << "?");
+  const int DeltaNoBonds = (int)(getType()->getNoValenceOrbitals()) - NoBonds;
+  if (DeltaNoBonds > 0) { // we have a mismatch, check all bonding partners for mismatch
     const BondList& ListOfBonds = getListOfBonds();
     for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner)) {
       OtherWalker = (*Runner)->GetOtherAtom(this);
       OtherNoBonds = OtherWalker->CountBonds();
-      //LOG(3, "OtherWalker " << *OtherWalker << ": " << (int)OtherWalker->type->NoValenceOrbitals << " > " << OtherNoBonds << "?");
-      if ((int)(OtherWalker->getType()->getNoValenceOrbitals()) > OtherNoBonds) { // check if possible candidate
+      const int OtherDeltaNoBonds = (int)(OtherWalker->getType()->getNoValenceOrbitals()) - OtherNoBonds;
+      LOG(3, "OtherWalker " << *OtherWalker << ": " << (int)OtherWalker->getType()->getNoValenceOrbitals() << " > " << OtherNoBonds << "?");
+      if (OtherDeltaNoBonds > 0) { // check if possible candidate
         const BondList& OtherListOfBonds = OtherWalker->getListOfBonds();
-        if ((CandidateBond == NULL) || (ListOfBonds.size() > OtherListOfBonds.size())) { // pick the one with fewer number of bonds first
+        if ((CandidateBond == NULL)
+            || (ListOfBonds.size() > OtherListOfBonds.size()) // pick the one with fewer number of bonds first
+            || ((CandidateDeltaNoBonds < 0) || (CandidateDeltaNoBonds > OtherDeltaNoBonds)) ) // pick the one closer to fulfilling its valence first
+        {
+          CandidateDeltaNoBonds = OtherDeltaNoBonds;
           CandidateBond = (*Runner);
-          //LOG(3, "New candidate is " << *CandidateBond << ".");
+          LOG(3, "New candidate is " << *CandidateBond << ".");
         }
       }
@@ -377 +384 @@
     if ((CandidateBond != NULL)) {
       CandidateBond->BondDegree++;
-      //LOG(2, "Increased bond degree for bond " << *CandidateBond << ".");
+      LOG(2, "Increased bond degree for bond " << *CandidateBond << ".");
     } else {
       ELOG(2, "Could not find correct degree for atom " << *this << ".");