Changeset f7307f

Timestamp:

Oct 26, 2012, 1:24:01 PM (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:

ed9da4

Parents:

f96874

git-author:

Frederik Heber <heber@…> (09/07/12 10:16:11)

git-committer:

Frederik Heber <heber@…> (10/26/12 13:24:01)

Message:

Using ListOfLocalAtoms_t now also as SonList.

Location:

src/Fragmentation

Files:

• Fragmentation.cpp (modified) (7 diffs)
• Fragmentation.hpp (modified) (1 diff)

src/Fragmentation/Fragmentation.cpp

@@ -434 +434 @@
 {
   Info info(__func__);
-  atom **SonList = new atom*[mol->getAtomCount()+1];
+  ListOfLocalAtoms_t SonList;
   molecule *Leaf = World::getInstance().createMolecule();
-
-  for(int i=0;i<=mol->getAtomCount();i++)
-    SonList[i] = NULL;
 
   StoreFragmentFromKeySet_Init(mol, Leaf, Leaflet, SonList);
@@ -446 +443 @@
 
   //Leaflet->Leaf->ScanForPeriodicCorrection(out);
-  delete[](SonList);
   return Leaf;
 };
@@ -660 +656 @@
  * \param *Leaf fragment molecule
  * \param &Leaflet pointer to KeySet structure
- * \param **SonList calloc'd list which atom of \a *Leaf is a son of which atom in \a *mol
+ * \param SonList calloc'd list which atom of \a *Leaf is a son of which atom in \a *mol
  * \return number of atoms in fragment
  */
-int Fragmentation::StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, atom **SonList)
+int Fragmentation::StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList)
 {
   atom *FatherOfRunner = NULL;
@@ -671 +667 @@
   for(KeySet::iterator runner = Leaflet.begin(); runner != Leaflet.end(); runner++) {
     FatherOfRunner = mol->FindAtom((*runner));  // find the id
-    SonList[FatherOfRunner->getNr()] = Leaf->AddCopyAtom(FatherOfRunner);
+    SonList.insert( std::make_pair(FatherOfRunner->getNr(), Leaf->AddCopyAtom(FatherOfRunner) ) );
     size++;
   }
@@ -683 +679 @@
  * \param *Leaf fragment molecule
  * \param IsAngstroem whether we have Ansgtroem or bohrradius
- * \param **SonList list which atom of \a *Leaf is a son of which atom in \a *mol
- */
-void Fragmentation::CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, atom **SonList, bool IsAngstroem)
+ * \param SonList list which atom of \a *Leaf is a son of which atom in \a *mol
+ */
+void Fragmentation::CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem)
 {
   bool LonelyFlag = false;
@@ -697 +693 @@
     FatherOfRunner = (*iter)->father;
     ASSERT(FatherOfRunner,"Atom without father found");
-    if (SonList[FatherOfRunner->getNr()] != NULL)  {  // check if this, our father, is present in list
+    if (SonList.find(FatherOfRunner->getNr()) != SonList.end())  {  // check if this, our father, is present in list
       // create all bonds
       const BondList& ListOfBonds = FatherOfRunner->getListOfBonds();
@@ -704 +700 @@
           ++BondRunner) {
         OtherFather = (*BondRunner)->GetOtherAtom(FatherOfRunner);
-        if (SonList[OtherFather->getNr()] != NULL) {
+        if (SonList.find(OtherFather->getNr()) != SonList.end()) {
 //          LOG(2, "INFO: Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->getNr()]
 //              << " is bound to " << *OtherFather << ", whose son is "

src/Fragmentation/Fragmentation.hpp

@@ -54 +54 @@
   // storing fragments
   molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
-  int StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, atom **SonList);
-  void CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, atom **SonList, bool IsAngstroem);
+  int StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList);
+  void CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem);
 
 private: