Changeset 72d90e

Timestamp:

Mar 1, 2011, 10:16:39 AM (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:

e7350d4

Parents:

f71baf

git-author:

Frederik Heber <heber@…> (02/18/11 14:24:43)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:39)

Message:

New function BondGraph::getMinMaxDistance().

• Covalent and BondLengthMatrix criteria are hidden behind that depending on whether the bond length matrix is set or not.
• now private:
  • BondGraph::CovalentMinMaxDistance()
  • BondGraph::BondLengthMatrixMinMaxDistance()
• adapted:
  • FragmentationConstructBondGraphAction
  • FragmentationDepthFirstSearchAction
  • FragmentationFragmentationAction

Location:

src

Files:

• Actions/FragmentationAction/ConstructBondGraphAction.cpp (modified) (1 diff)
• Actions/FragmentationAction/DepthFirstSearchAction.cpp (modified) (1 diff)
• Actions/FragmentationAction/FragmentationAction.cpp (modified) (1 diff)
• bondgraph.cpp (modified) (2 diffs)
• bondgraph.hpp (modified) (2 diffs)

src/Actions/FragmentationAction/ConstructBondGraphAction.cpp

@@ -135 +135 @@
                           ASSERT(OtherWalker,"TesselPoint that was not an atom retrieved from LinkedNode");
                           //Log() << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
-                          BG->CovalentMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
+                          BG->getMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
                           const double distance = domain.periodicDistanceSquared(OtherWalker->getPosition(),Walker->getPosition());
                           const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);

src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

@@ -53 +53 @@
   std::deque<bond *> *LocalBackEdgeStack = NULL;
   BondGraph *BG = World::getInstance().getBondGraph();
-  if (BG != NULL)
-    mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::BondLengthMatrixMinMaxDistance, BG);
-  else
-    mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
+  mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::getMinMaxDistance, BG);
   Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
   if (Subgraphs != NULL) {

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -55 +55 @@
     DoLog(0) && (Log() << Verbose(0) << "Creating connection matrix..." << endl);
     start = clock();
-    mol->CreateAdjacencyList(params.distance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
+    mol->CreateAdjacencyList(params.distance, configuration->GetIsAngstroem(), &BondGraph::getMinMaxDistance, World::getInstance().getBondGraph());
     DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
     if (mol->hasBondStructure()) {

src/bondgraph.cpp

@@ -113 +113 @@
     return false;
 
-  if (BondLengthMatrix == NULL) { // no bond length matrix parsed?
-    SetMaxDistanceToMaxOfCovalentRadii(mol);
-    mol->CreateAdjacencyList(max_distance, IsAngstroem, &BondGraph::CovalentMinMaxDistance, this);
-  } else
-    mol->CreateAdjacencyList(max_distance, IsAngstroem, &BondGraph::BondLengthMatrixMinMaxDistance, this);
+  SetMaxDistanceToMaxOfCovalentRadii(mol);
+  mol->CreateAdjacencyList(max_distance, IsAngstroem, &BondGraph::getMinMaxDistance, this);
 
   return status;
@@ -193 +190 @@
 void BondGraph::BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
 {
+  ASSERT(BondLengthMatrix != NULL,
+      "BondGraph::BondLengthMatrixMinMaxDistance() called without NULL BondLengthMatrix.");
+  MinDistance = GetBondLength(Walker->getType()->getAtomicNumber()-1, OtherWalker->getType()->getAtomicNumber()-1);
+  MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
+  MaxDistance = MinDistance + BondThreshold;
+  MinDistance -= BondThreshold;
+};
+
+void BondGraph::getMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
+{
   if (BondLengthMatrix == NULL) {// safety measure if no matrix has been parsed yet
-    DoeLog(2) && (eLog()<< Verbose(2) << "BondLengthMatrixMinMaxDistance() called without having parsed the bond length matrix yet!" << endl);
+    LOG(2, "INFO: Using Covalent radii criterion for [min,max] distances.");
     CovalentMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
   } else {
-    MinDistance = GetBondLength(Walker->getType()->getAtomicNumber()-1, OtherWalker->getType()->getAtomicNumber()-1);
-    MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
-    MaxDistance = MinDistance + BondThreshold;
-    MinDistance -= BondThreshold;
-  }
-};
+    LOG(2, "INFO: Using Covalent radii criterion for [min,max] distances.");
+    BondLengthMatrixMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
+  }
+}

src/bondgraph.hpp

@@ -41 +41 @@
   double SetMaxDistanceToMaxOfCovalentRadii(const molecule * const mol);
 
-  void BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
-  void CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
+
+  /** Returns bond criterion for given pair based on a bond length matrix.
+   * This calls either the covalent or the bond matrix criterion.
+   * \param *Walker first BondedParticle
+   * \param *OtherWalker second BondedParticle
+   * \param &MinDistance lower bond bound on return
+   * \param &MaxDistance upper bond bound on return
+   * \param IsAngstroem whether units are in angstroem or bohr radii
+   */
+  void getMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
 
   double getMaxDistance() const;
@@ -48 +56 @@
 private:
   static const double BondThreshold;
+
+  void BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
+
+  void CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);
 
   MatrixContainer *BondLengthMatrix;