Changeset 212c179 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, 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:

246e13

Parents:

d0b375b

git-author:

Frederik Heber <heber@…> (10/18/11 13:16:51)

git-committer:

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

Message:

Placed all functions related to BondsPerSPList into own class BondsPerShortestPath.

File:

• src/molecule_fragmentation.cpp (modified) (4 diffs)

src/molecule_fragmentation.cpp

@@ -661 +661 @@
   int RootNr = 0;
   struct UniqueFragments FragmentSearch;
-  class PowerSetGenerator PSG;
 
   DoLog(0) && (Log() << Verbose(0) << "Begin of FragmentBOSSANOVA." << endl);
@@ -702 +701 @@
 
       // initialise Order-dependent entries of UniqueFragments structure
-      FragmentSearch.InitialiseSPList(Order);
+      class PowerSetGenerator PSG(&FragmentSearch, Walker->AdaptiveOrder);
 
       // allocate memory for all lower level orders in this 1D-array of ptrs
@@ -715 +714 @@
 
       // Create list of Graphs of current Bond Order (i.e. F_{ij})
-      FragmentLowerOrdersList[RootNr][0] =  new Graph;
-      FragmentSearch.TEFactor = 1.;
-      FragmentSearch.Leaflet = FragmentLowerOrdersList[RootNr][0];      // set to insertion graph
-      FragmentSearch.setRoot(Walker);
-      NumMoleculesOfOrder[RootNr] = PSG(&FragmentSearch, Walker->AdaptiveOrder, CompleteMolecule);
+      FragmentLowerOrdersList[RootNr][0] = new Graph;
+      FragmentSearch.PrepareForPowersetGeneration(1., FragmentLowerOrdersList[RootNr][0], Walker);
+      NumMoleculesOfOrder[RootNr] = PSG(CompleteMolecule);
 
       // output resulting number
@@ -734 +731 @@
       RootStack.push_back(RootKeyNr); // put back on stack
       RootNr++;
-
-      // free Order-dependent entries of UniqueFragments structure for next loop cycle
-      FragmentSearch.FreeSPList(Order);
     }
   }