Changeset 0ec7fe

Timestamp:

Mar 1, 2011, 1:17:08 PM (14 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:

111f4a

Parents:

300220

git-author:

Frederik Heber <heber@…> (02/28/11 15:11:16)

git-committer:

Frederik Heber <heber@…> (03/01/11 13:17:08)

Message:

Removed BondGraph::max_distance along with getter and setter.

• SetMaxDistanceFromCovalentDistance() was nonsense and prone to faults and misunderstandings.
• instead getMaxPossibleBondDistance() returns upper cutoff limit based on a given atomset.

Location:

src

Files:

• Actions/FragmentationAction/CreateAdjacencyAction.cpp (modified) (1 diff)
• bondgraph.cpp (modified) (3 diffs)
• bondgraph.hpp (modified) (3 diffs)

src/Actions/FragmentationAction/CreateAdjacencyAction.cpp

@@ -59 +59 @@
   BondGraph *BG = World::getInstance().getBondGraph();
   ASSERT(BG != NULL, "FragmentationCreateAdjacencyAction: BondGraph is NULL.");
-  BG->SetMaxDistanceToMaxOfCovalentRadii(AtomSetMixin<std::vector<atom *> >(World::getInstance().getSelectedAtoms()));
-  double BondDistance = BG->getMaxDistance();
+  double BondDistance = BG->getMaxPossibleBondDistance(AtomSetMixin<std::vector<atom *> >(World::getInstance().getSelectedAtoms()));
   bool IsAngstroem = configuration->GetIsAngstroem();
 

src/bondgraph.cpp

@@ -42 +42 @@
 BondGraph::BondGraph(bool IsA) :
     BondLengthMatrix(NULL),
-    max_distance(0),
     IsAngstroem(IsA)
 {}
@@ -73 +72 @@
     status = false;
   }
-
-  // find greatest distance
-  max_distance=0;
-  if (status) {
-    for(int i=0;i<TempContainer->RowCounter[0];i++)
-      for(int j=i;j<TempContainer->ColumnCounter[0];j++)
-        if (TempContainer->Matrix[0][i][j] > max_distance)
-          max_distance = TempContainer->Matrix[0][i][j];
-  }
-  max_distance += BondThreshold;
 
   if (status) // set to not NULL only if matrix was parsed
@@ -105 +94 @@
     return (BondLengthMatrix->Matrix[0][firstZ][secondZ]);
   }
-}
-
-double BondGraph::getMaxDistance() const
-{
-  return max_distance;
 }
 

src/bondgraph.hpp

@@ -68 +68 @@
   /** Determines the maximum of all element::CovalentRadius for elements present in \a &Set.
    *
-   * Sets BondGraph::max_distance
-   *
-   * \param &Set PointCloud with all particles
-   */
-  template <class container_type,
-            class iterator_type,
-            class const_iterator_type>
-  double SetMaxDistanceToMaxOfCovalentRadii(const AtomSetMixin<container_type,iterator_type,const_iterator_type> &Set)
-  {
-    max_distance = 0.;
-
+   * I.e. the function returns a sensible cutoff criteria for bond recognition,
+   * e.g. to be used for LinkedCell or others.
+   *
+   * \param &Set AtomSetMixin with all particles to consider
+   */
+  template <class container_type,
+            class iterator_type,
+            class const_iterator_type>
+  double getMaxPossibleBondDistance(
+      const AtomSetMixin<container_type,iterator_type,const_iterator_type> &Set) const
+  {
+    double max_distance = 0.;
+    // get all elements
+    std::set< const element *> PresentElements;
     for(const_iterator_type AtomRunner = Set.begin(); AtomRunner != Set.end(); ++AtomRunner) {
-      const double radius = (*AtomRunner)->getType()->getCovalentRadius();
-      if (radius > max_distance)
-        max_distance = radius;
-    }
-    max_distance *= 2.;
-    max_distance += BondThreshold;
-
+      PresentElements.insert( (*AtomRunner)->getType() );
+    }
+    // create all element combinations
+    for (std::set< const element *>::const_iterator iter = PresentElements.begin();
+        iter != PresentElements.end();
+        ++iter) {
+      for (std::set< const element *>::const_iterator otheriter = iter;
+          otheriter != PresentElements.end();
+          ++otheriter) {
+        range<double> MinMaxDistance(0.,0.);
+        getMinMaxDistance((*iter),(*otheriter), MinMaxDistance, IsAngstroem);
+        if (MinMaxDistance.last > max_distance)
+          max_distance = MinMaxDistance.last;
+      }
+    }
     return max_distance;
   }
-
-  /** Returns the upper limit on possible bond distances.
-   *
-   * Is set by SetMaxDistanceToMaxOfCovalentRadii(), is needed e.g. as cutoff
-   * for linked-cell.
-   *
-   * \return maximum possible bond distance
-   */
-  double getMaxDistance() const;
 
   /** Returns bond criterion for given pair based on a bond length matrix.
@@ -142 +144 @@
     if (counter > 1) {
       LOG(1, "STATUS: Setting max bond distance.");
-      SetMaxDistanceToMaxOfCovalentRadii(Set);
+      const double max_distance = getMaxPossibleBondDistance(Set);
 
       LOG(1, "STATUS: Creating LinkedCell structure for given " << counter << " atoms.");
@@ -399 +401 @@
   //!> Matrix with bond lenth per two elements
   MatrixContainer *BondLengthMatrix;
-  //!> maximum distance over all bonds possible
-  double max_distance;
   //!> distance units are angstroem (true), bohr radii (false)
   bool IsAngstroem;