Changeset a564be for src/molecule_fragmentation.cpp

Timestamp:

Dec 6, 2010, 7:37:05 PM (15 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, Candidate_v1.7.0, 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:

4c1230

Parents:

fd19ff

git-author:

Frederik Heber <heber@…> (12/06/10 19:15:03)

git-committer:

Frederik Heber <heber@…> (12/06/10 19:37:05)

Message:

Removed ancient StackClass, replaced by std::deque.

• all PopLast replaced by pop_front.
• all PopFirst replaced by pop_front.
• and we have two remove items in two steps, first get item, then pop.

File:

• src/molecule_fragmentation.cpp (modified) (7 diffs)

src/molecule_fragmentation.cpp

@@ -36 +36 @@
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "Box.hpp"
-#include "stackclass.hpp"
 
 /************************************* Functions for class molecule *********************************/
@@ -613 +612 @@
   fstream File;
   bool FragmentationToDo = true;
-  class StackClass<bond *> *BackEdgeStack = NULL, *LocalBackEdgeStack = NULL;
+  std::deque<bond *> *BackEdgeStack = NULL, *LocalBackEdgeStack = NULL;
   bool CheckOrder = false;
   Graph **FragmentList = NULL;
@@ -656 +655 @@
     MolecularWalker->FillBondStructureFromReference(this, ListOfAtoms, false);  // we want to keep the created ListOfLocalAtoms
     DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
-    LocalBackEdgeStack = new StackClass<bond *> (MolecularWalker->Leaf->BondCount);
+    LocalBackEdgeStack = new std::deque<bond *>; // (MolecularWalker->Leaf->BondCount);
 //    // check the list of local atoms for debugging
 //    Log() << Verbose(0) << "ListOfLocalAtoms for this subgraph is:" << endl;
@@ -884 +883 @@
 
 
-/** Looks through a StackClass<atom *> and returns the likeliest removal candiate.
+/** Looks through a std::deque<atom *> and returns the likeliest removal candiate.
  * \param *out output stream for debugging messages
  * \param *&Leaf KeySet to look through
@@ -1743 +1742 @@
   double tmp;
   Vector Translationvector;
-  //class StackClass<atom *> *CompStack = NULL;
-  class StackClass<atom *> *AtomStack = new StackClass<atom *>(getAtomCount());
+  //std::deque<atom *> *CompStack = NULL;
+  std::deque<atom *> *AtomStack = new std::deque<atom *>; // (getAtomCount());
   bool flag = true;
 
@@ -1785 +1784 @@
       for (int i=getAtomCount();i--;)
         ColorList[i] = white;
-      AtomStack->Push(Binder->leftatom);
-      while (!AtomStack->IsEmpty()) {
-        Walker = AtomStack->PopFirst();
+      AtomStack->push_front(Binder->leftatom);
+      while (!AtomStack->empty()) {
+        Walker = AtomStack->front();
+        AtomStack->pop_front();
         //Log() << Verbose (3) << "Current Walker is: " << *Walker << "." << endl;
         ColorList[Walker->nr] = black;    // mark as explored
@@ -1795 +1795 @@
             OtherWalker = (*Runner)->GetOtherAtom(Walker);
             if (ColorList[OtherWalker->nr] == white) {
-              AtomStack->Push(OtherWalker); // push if yet unexplored
+              AtomStack->push_front(OtherWalker); // push if yet unexplored
             }
           }