Changeset 00ef5c

Timestamp:

Aug 25, 2010, 4:10:54 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

5cd333c

Parents:

14b65e

Message:

Removed several calls to molecule::ActOnEachAtom() from molecule_graph.cpp

• Added a function to initialize the DFS inside the molecule

Location:

src

Files:

• molecule.hpp (modified) (1 diff)
• molecule_graph.cpp (modified) (6 diffs)

src/molecule.hpp

@@ -339 +339 @@
 
   private:
+  void init_DFS(struct DFSAccounting&) const;
   int last_atom;      //!< number given to last atom
   mutable internal_iterator InternalPointer;  //!< internal pointer for PointCloud

src/molecule_graph.cpp

@@ -285 +285 @@
     do {
       OldNo = No;
-      No = SumPerAtom( &atom::CorrectBondDegree );
+      No=0;
+      BOOST_FOREACH(atom *atom,atoms){
+        No+=atom->CorrectBondDegree();
+      }
     } while (OldNo != No);
     DoLog(0) && (Log() << Verbose(0) << " done." << endl);
@@ -515 +518 @@
   DFS.BackStepping = false;
   mol->ResetAllBondsToUnused();
-  mol->SetAtomValueToValue(-1, &atom::GraphNr);
-  mol->ActOnAllAtoms(&atom::InitComponentNr);
   DFS.BackEdgeStack->ClearStack();
 }
@@ -531 +532 @@
 }
 ;
+
+void molecule::init_DFS(struct DFSAccounting &DFS) const{
+  DepthFirstSearchAnalysis_Init(DFS, this);
+  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::resetGraphNr));
+  for_each(atoms.begin(),atoms.end(),mem_fun(&atom::InitComponentNr));
+}
 
 /** Performs a Depth-First search on this molecule.
@@ -554 +561 @@
     return SubGraphs;
   DoLog(0) && (Log() << Verbose(0) << "Begin of DepthFirstSearchAnalysis" << endl);
-  DepthFirstSearchAnalysis_Init(DFS, this);
+  init_DFS(DFS);
 
   for (molecule::const_iterator iter = begin(); iter != end();) {
@@ -1060 +1067 @@
   if (AdjacencyFile.good()) {
     AdjacencyFile << "m\tn" << endl;
-    ActOnAllAtoms(&atom::OutputAdjacency, &AdjacencyFile);
+    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputAdjacency),&AdjacencyFile));
     AdjacencyFile.close();
     DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);
@@ -1092 +1099 @@
   if (BondFile.good()) {
     BondFile << "m\tn" << endl;
-    ActOnAllAtoms(&atom::OutputBonds, &BondFile);
+    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputBonds),&BondFile));
     BondFile.close();
     DoLog(1) && (Log() << Verbose(1) << "\t... done." << endl);