Changeset 0763ce

Timestamp:

Feb 10, 2015, 2:09:38 PM (10 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:

c17aa8

Parents:

cd5aa0

git-author:

Frederik Heber <heber@…> (01/25/15 13:31:53)

git-committer:

Frederik Heber <heber@…> (02/10/15 14:09:38)

Message:

Added BondGraph::checkBondDegree, FragmentationAction only resets degrees when incorrect.

• this fixes the bug where the molecular dynamics actions would flip the double bonds in an aromatic ring during the simulation steps because the bond degrees are reset even though the bond graph is present and should be re-used.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAction.cpp (modified) (1 diff)
• Graph/BondGraph.cpp (modified) (1 diff)
• Graph/BondGraph.hpp (modified) (2 diffs)
• World.cpp (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -129 +129 @@
     BondGraph *BG = World::getInstance().getBondGraph();
     World::AtomComposite Set = World::getInstance().getAllAtoms(AtomsBySelection());
-    BG->CorrectBondDegree(Set);
+    // check whether bond graph is correct
+    if (!BG->checkBondDegree(Set))
+      BG->CorrectBondDegree(Set);
+    else
+      LOG(1, "INFO: Bond degrees all valid, not correcting.");
   }
 

src/Graph/BondGraph.cpp

@@ -473 +473 @@
 }
 
+bool BondGraph::checkBondDegree(const deltaatoms_t &allatoms) const
+{
+  deltaatoms_t deltaatoms;
+  return (gatherAllDeltaAtoms(allatoms, deltaatoms) == 0);
+}
+
 
 int BondGraph::calculateBondDegree(const deltaatoms_t &allatoms) const

src/Graph/BondGraph.hpp

@@ -359 +359 @@
   }
 
+  /** Checks whether the bond degree for each atom on the set matches with its valency.
+   *
+   * @param Set Range with atoms
+   * @return true - bond degrees match valency, false - bond degree correction is needed
+   */
+  template <class container_type,
+            class iterator_type,
+            class const_iterator_type>
+  bool checkBondDegree(
+      AtomSetMixin<container_type,iterator_type,const_iterator_type> &Set) const
+  {
+    std::set<atom *> allatoms;
+    for(iterator_type AtomRunner = Set.begin(); AtomRunner != Set.end(); ++AtomRunner)
+      allatoms.insert(*AtomRunner);
+    return checkBondDegree(allatoms);
+  }
+
   /** correct bond degree by comparing valence and bond degree.
    * correct Bond degree of each bond by checking both bond partners for a mismatch between valence and current sum of bond degrees,
@@ -472 +489 @@
   }
 
+  bool checkBondDegree(const std::set<atom *> &allatoms) const;
+
   /** Calculates the bond degree for each atom on the set.
    *

src/World.cpp

@@ -228 +228 @@
     const atom * const Walker = (*bonditer)->leftatom;
     const atom * const OtherWalker = (*bonditer)->rightatom;
-    const_cast<atom *>(Walker)->addBond(_deststep, const_cast<atom *>(OtherWalker));
+    bond::ptr const _bond =
+        const_cast<atom *>(Walker)->addBond(_deststep, const_cast<atom *>(OtherWalker));
+    _bond->setDegree((*bonditer)->getDegree());
   }
 }