Changeset 339910 for src/Fragmentation/fragmentation_helpers.cpp

Timestamp:

Dec 3, 2012, 9:49:30 AM (12 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:

de0af2

Parents:

b9401e

git-author:

Frederik Heber <heber@…> (09/19/12 14:32:32)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:49:30)

Message:

Fragmentation now operates on a single molecule.

• FragmentMolecule() does not continue on Subgraphs.
• shifted remaining functionality from MoleculeLeafClass to Fragmentation.
• FragmentList, KeySets, and RootStack are all just instances not arrays anymore.

File:

• src/Fragmentation/fragmentation_helpers.cpp (modified) (3 diffs)

src/Fragmentation/fragmentation_helpers.cpp

@@ -77 +77 @@
 
 /** Combines all KeySets from all orders into single ones (with just unique entries).
- * \param *out output stream for debugging
- * \param *&FragmentList list to fill
+ * \param &FragmentList list to fill
  * \param ***FragmentLowerOrdersList
  * \param &RootStack stack with all root candidates (unequal to each atom in complete molecule if adaptive scheme is applied)
  * \param *mol molecule with atoms and bonds
  */
-int CombineAllOrderListIntoOne(Graph *&FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
+int CombineAllOrderListIntoOne(Graph &FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
 {
   int RootNr = 0;
@@ -93 +92 @@
 
   LOG(0, "Combining the lists of all orders per order and finally into a single one.");
-  if (FragmentList == NULL) {
-    FragmentList = new Graph;
-    counter = 0;
-  } else {
-    counter = FragmentList->size();
-  }
+  counter = FragmentList.size();
 
   StartNr = RootStack.back();
@@ -108 +102 @@
     for(int i=0;i<NumLevels;i++) {
       if (FragmentLowerOrdersList[RootNr][i] != NULL) {
-        (*FragmentList).InsertGraph((*FragmentLowerOrdersList[RootNr][i]), &counter);
+        FragmentList.InsertGraph((*FragmentLowerOrdersList[RootNr][i]), &counter);
       }
     }