Changeset 108968

Timestamp:

Apr 3, 2012, 8:00:19 AM (13 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:

e791dc

Parents:

08a0f52

git-author:

Frederik Heber <heber@…> (03/13/12 17:37:53)

git-committer:

Frederik Heber <heber@…> (04/03/12 08:00:19)

Message:

FIX: Rewrite of BondGraph's CreateAdjacency() and getMaxPossibleBondDistance().

• getMaxPossibleBondDistance() is not templated anymore but expects simply a set of atomicNumber_t.
• new helper function BondGraph::getElementSetFromNumbers() which converts a set of atomicNumber_t into a set of elements.
• createAdjacency now prepares initially the set of atomicNumber_t and from it the set of elements such that no further element lookups are necessary except once for each atom's element.

Location:

src/Graph

Files:

• BondGraph.cpp (modified) (1 diff)
• BondGraph.hpp (modified) (6 diffs)

src/Graph/BondGraph.cpp

@@ -179 +179 @@
 }
 
+std::set< const element *> BondGraph::getElementSetFromNumbers(const std::set<atomicNumber_t> &Set) const
+{
+  std::set< const element *> PresentElements;
+  for(std::set<atomicNumber_t>::const_iterator iter = Set.begin(); iter != Set.end(); ++iter)
+    PresentElements.insert( World::getInstance().getPeriode()->FindElement(*iter) );
+  return PresentElements;
+}
+
 Box &BondGraph::getDomain() const
 {

src/Graph/BondGraph.hpp

@@ -19 +19 @@
 
 #include <iosfwd>
+#include <set>
 
 #include <boost/serialization/array.hpp>
@@ -75 +76 @@
   void CleanupBondLengthTable();
 
+  /** Internal helper to convert a set of atomicNumber_t to element refs.
+   *
+   * @param Set set of atomicNumber_t
+   * @return set of element refs
+   */
+  std::set< const element *> getElementSetFromNumbers(const std::set<atomicNumber_t> &Set) const;
+
   /** Determines the maximum of all element::CovalentRadius for elements present in \a &Set.
    *
@@ -80 +88 @@
    * e.g. to be used for LinkedCell_deprecated or others.
    *
-   * \param &Set AtomSetMixin with all particles to consider
-   */
-  template <class container_type,
-            class iterator_type,
-            class const_iterator_type>
+   * \param &PresentElements set of elements whose maximal pair to find
+   */
   double getMaxPossibleBondDistance(
-      const AtomSetMixin<container_type,iterator_type,const_iterator_type> &Set) const
+      const std::set< const element *> &PresentElements) const
   {
     double max_distance = 0.;
-    // get all elements
-    std::set< const element *> PresentElements;
-    for(const_iterator_type AtomRunner = Set.begin(); AtomRunner != Set.end(); ++AtomRunner) {
-      PresentElements.insert( (*AtomRunner)->getType() );
-    }
+
     // create all element combinations
     for (std::set< const element *>::const_iterator iter = PresentElements.begin();
@@ -114 +115 @@
    * e.g. to be used for LinkedCell_deprecated or others.
    *
-   * \param &Set AtomSetMixin with all particles to consider
-   */
-  template <class container_type,
-            class iterator_type,
-            class const_iterator_type>
+   * \param Walker element first element in the pair
+   * \param &PresentElements set of elements whose maximal pair to find
+   */
   double getMaxPossibleBondDistance(
       const element * const Walker,
-      const AtomSetMixin<container_type,iterator_type,const_iterator_type> &Set) const
+      const std::set< const element *> &PresentElements) const
   {
     double max_distance = 0.;
-    // get all elements
-    std::set< const element *> PresentElements;
-    for(const_iterator_type AtomRunner = Set.begin(); AtomRunner != Set.end(); ++AtomRunner) {
-      PresentElements.insert( (*AtomRunner)->getType() );
-    }
+
     // create all element combinations
     for (std::set< const element *>::const_iterator iter = PresentElements.begin();
@@ -182 +177 @@
     cleanAdjacencyList(Set);
 
+    // gather set of all present elements
+    std::set<atomicNumber_t> elements;
+    for(typename AtomSetMixin<container_type,iterator_type,const_iterator_type>::iterator iter = Set.begin();
+        iter != Set.end(); ++iter) {
+      const atom * const Walker = dynamic_cast<const atom *>(*iter);
+      ASSERT(Walker != NULL,
+          "BondGraph::CreateAdjacency() - TesselPoint "
+          +(*iter)->getName()+" that was not an atom retrieved from given set");
+      elements.insert( Walker->getElementNo() );
+    }
+    // get all elements
+    std::set< const element *> PresentElements = getElementSetFromNumbers(elements);
+
     // count atoms in molecule = dimension of matrix (also give each unique name and continuous numbering)
     const unsigned int counter = Set.size();
     if (counter > 1) {
       LOG(1, "STATUS: Setting max bond distance.");
-      LinkedCell::LinkedCell_View LC = getLinkedCell(getMaxPossibleBondDistance(Set));
+      LinkedCell::LinkedCell_View LC = getLinkedCell(getMaxPossibleBondDistance(PresentElements));
 
       LOG(1, "STATUS: Creating LinkedCell structure for given " << counter << " atoms.");
@@ -205 +213 @@
         // obtain all possible neighbors
         LinkedCell::LinkedList ListOfNeighbors = LC.getAllNeighbors(
-            getMaxPossibleBondDistance(Walker->getType(), Set),
+            getMaxPossibleBondDistance(Walker->getType(), PresentElements),
             Walker->getPosition());
         if (!ListOfNeighbors.empty()) {