Changeset a03d25 for src/molecule_fragmentation.cpp

Timestamp:

Oct 25, 2011, 12:08:03 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:

f6d1d0

Parents:

d9a032

git-author:

Frederik Heber <heber@…> (10/18/11 11:53:21)

git-committer:

Frederik Heber <heber@…> (10/25/11 12:08:03)

Message:

Placed all routines working on UniqueFragments struct inside this class.

• changed struct to class.

File:

• src/molecule_fragmentation.cpp (modified) (8 diffs)

src/molecule_fragmentation.cpp

@@ -31 +31 @@
 #include "Element/periodentafel.hpp"
 #include "Fragmentation/fragmentation_helpers.hpp"
+#include "Fragmentation/UniqueFragments.hpp"
 #include "Graph/BondGraph.hpp"
 #include "Graph/CheckAgainstAdjacencyFile.hpp"
@@ -732 +733 @@
           DoLog(0) && (Log() << Verbose(0) << (*runner) << " ");
         DoLog(0) && (Log() << Verbose(0) << endl);
-        InsertFragmentIntoGraph(FragmentSearch);
+        FragmentSearch->InsertFragmentIntoGraph();
       }
 
@@ -769 +770 @@
   DoLog(0) && (Log() << Verbose(0) << "Begin of PowerSetGenerator with order " << Order << " at Root " << *FragmentSearch.Root << "." << endl);
 
-  SetSPList(Order, FragmentSearch);
+  FragmentSearch.SetSPList(Order);
 
   // do a BFS search to fill the SP lists and label the found vertices
-  FillSPListandLabelVertices(Order, FragmentSearch, this, RestrictedKeySet);
+  FragmentSearch.FillSPListandLabelVertices(Order, RestrictedKeySet);
 
   // outputting all list for debugging
-  OutputSPList(Order, FragmentSearch);
+  FragmentSearch.OutputSPList(Order);
 
   // creating fragments with the found edge sets  (may be done in reverse order, faster)
-  int SP = CountNumbersInBondsList(Order, FragmentSearch);
+  int SP = FragmentSearch.CountNumbersInBondsList(Order);
   DoLog(0) && (Log() << Verbose(0) << "Total number of edges is " << SP << "." << endl);
   if (SP >= (Order-1)) {
@@ -804 +805 @@
 
   // free'ing the bonds lists
-  ResetSPList(Order, FragmentSearch);
+  FragmentSearch.ResetSPList(Order);
 
   // return list
@@ -856 +857 @@
   }
 
-  // initialise the fragments structure
-  FragmentSearch.FragmentCounter = 0;
-  FragmentSearch.FragmentSet = new KeySet;
-  FragmentSearch.Root = FindAtom(RootKeyNr);
-  FragmentSearch.ShortestPathList = new int[getAtomCount()];
-  for (int i=getAtomCount();i--;) {
-    FragmentSearch.ShortestPathList[i] = -1;
-  }
+  FragmentSearch.Init(FindAtom(RootKeyNr), getAtomCount());
 
   // Construct the complete KeySet which we need for topmost level only (but for all Roots)
@@ -890 +884 @@
 
       // initialise Order-dependent entries of UniqueFragments structure
-      InitialiseSPList(Order, FragmentSearch);
+      FragmentSearch.InitialiseSPList(Order);
 
       // allocate memory for all lower level orders in this 1D-array of ptrs
@@ -924 +918 @@
 
       // free Order-dependent entries of UniqueFragments structure for next loop cycle
-      FreeSPList(Order, FragmentSearch);
+      FragmentSearch.FreeSPList(Order);
     }
   }
@@ -932 +926 @@
 
   // cleanup FragmentSearch structure
-  delete[](FragmentSearch.ShortestPathList);
-  delete(FragmentSearch.FragmentSet);
+  FragmentSearch.Cleanup();
 
   // now, FragmentLowerOrdersList is complete, it looks - for BondOrder 5 - as this (number is the ANOVA Order of the terms therein)