Changeset 555063

Timestamp:

Apr 28, 2008, 1:53:54 PM (17 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:

5b15ab

Parents:

c67e16

Message:

Atoms in the fragments in the configs are again ordered as first labeled during Bond structure recognition

Due to the move to disconnected subgraph recognition an additional "layer" of molecules is inserted. The Atoms are AddCopyAtom()ed into new molecules representing each subgraph and receiving new labels thereby (even if there is just one subgraph in the end). As these labels were used in the sorted "KeySet" sets for adding atoms on the one hand, the KeySet file on the other hand however was created from the molecules directly now with labels from the topmost molecule structure ... : lines in BondFragment configs were swapped with respect to freshly fragmented and parsed from KeySet files.
Do ameloriate this, the StoreFragmentFromKeySet procedure was taken out of FragmentBOSSANOVA() and up into FragmentMolecule(), where the uppermost molecular structure is accessible. At the same time, the topmost labels (via GetTrueFather) are used in the KeySets. Thus, we receive again ordered list of atoms in each fragment config and they match perfectly with those re-created from parsed keyset files (check with diff over all BondFragment*.conf*).

Location:

src

Files:

• molecules.cpp (modified) (10 diffs)
• molecules.hpp (modified) (1 diff)

src/molecules.cpp

@@ -1871 +1871 @@
     } // else it's "-1" or else and thus must not be added
   }
+  *out << Verbose(1) << "The scanned KeySet is ";
+  for(KeySet::iterator runner = CurrentSet.begin(); runner != CurrentSet.end(); runner++) {
+    *out << (*runner) << "\t";
+  }
+  *out << endl;
   return (status != 0);
 };
@@ -2151 +2156 @@
           BondFragments[FragmentCounter] = NULL;
           if (Scheme == ANOVA) {
-            BondFragments[FragmentCounter] = MolecularWalker->Leaf->FragmentBOSSANOVA(out,BottomUpOrder,configuration);
+            Graph *FragmentList = MolecularWalker->Leaf->FragmentBOSSANOVA(out,BottomUpOrder,configuration);
+
+            // allocate memory for the pointer array and transmorph graphs into full molecular fragments
+            int TotalNumberOfMolecules = 0;
+            for(Graph::iterator runner = FragmentList->begin(); runner != FragmentList->end(); runner++)
+              TotalNumberOfMolecules++;
+            BondFragments[FragmentCounter] = new MoleculeListClass(TotalNumberOfMolecules, AtomCount);
+            int k=0;
+            for(Graph::iterator runner = FragmentList->begin(); runner != FragmentList->end(); runner++) {
+              KeySet test = (*runner).first;
+              BondFragments[FragmentCounter]->ListOfMolecules[k] = StoreFragmentFromKeySet(out, test, configuration);
+              BondFragments[FragmentCounter]->TEList[k] = ((*runner).second).second;
+              k++;
+            }
           }  
           if ((Scheme == BottomUp) || (Scheme == Combined)) { // get overlapping subgraphs
@@ -2802 +2820 @@
   // first create the minimal set of atoms from the KeySet
   for(KeySet::iterator runner = Leaflet.begin(); runner != Leaflet.end(); runner++) {
-    FatherOfRunner =  FindAtom((*runner));  // find the id
+    FatherOfRunner = FindAtom((*runner));  // find the id
     SonList[FatherOfRunner->nr] = Leaf->AddCopyAtom(FatherOfRunner);
   }
@@ -3135 +3153 @@
           //if ((!FragmentSearch->UsedList[OtherWalker->nr][i]) && (FragmentSearch->Labels[OtherWalker->nr] > FragmentSearch->Labels[FragmentSearch->Root->nr])) { 
             //*out << Verbose(2+verbosity) << "Not used so far, label " << FragmentSearch->Labels[OtherWalker->nr] << " is bigger than Root's " << FragmentSearch->Labels[FragmentSearch->Root->nr] << "." << endl;
-          *out << Verbose(2+verbosity) << "Adding " << *OtherWalker << "." << endl;
+          *out << Verbose(2+verbosity) << "Adding " << *OtherWalker << " with nr " << OtherWalker->nr << "." << endl;
           TouchedList[TouchedIndex++] = OtherWalker->nr;  // note as added
-          FragmentSearch->FragmentSet->insert( FragmentSearch->FragmentSet->end(), OtherWalker->nr);
+          FragmentSearch->FragmentSet->insert(OtherWalker->GetTrueFather()->nr);
             //FragmentSearch->UsedList[OtherWalker->nr][i] = true;
           //}
@@ -3314 +3332 @@
       }
       Walker = FindAtom(AtomKeyNr);
-      *out << Verbose(0) << "Current Walker is: " << *Walker << " with label " << FragmentSearch.Labels[AtomKeyNr] << " and SP of " << SP << "." << endl;
+      *out << Verbose(0) << "Current Walker is: " << *Walker << " with nr " << Walker->nr << " and label " << FragmentSearch.Labels[AtomKeyNr] << " and SP of " << SP << "." << endl;
       // check for new sp level
       // go through all its bonds
@@ -3326 +3344 @@
 #endif
                                                               ) {  // skip hydrogens and restrict to fragment
-          *out << Verbose(2) << "Current partner is " << *OtherWalker << " in bond " << *Binder << "." << endl;
+          *out << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->nr << " in bond " << *Binder << "." << endl;
           // set the label if not set (and push on root stack as well)
           if (FragmentSearch.Labels[OtherWalker->nr] == -1) {
@@ -3408 +3426 @@
       *out << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.Root << "." << endl;
       FragmentSearch.FragmentSet->clear();  
-      FragmentSearch.FragmentSet->insert(FragmentSearch.Root->nr);
+      FragmentSearch.FragmentSet->insert(FragmentSearch.Root->GetTrueFather()->nr);
       
       if (FragmentSearch.FragmentSet->size() == (unsigned int) Order) {
@@ -3681 +3699 @@
  * \param ANOVAOrder ANOVA expansion is truncated above this order
  * \param *configuration configuration for writing config files for each fragment
- * \return pointer to MoleculeListClass with all the fragments or NULL if something went wrong.
- */
-MoleculeListClass * molecule::FragmentBOSSANOVA(ofstream *out, int ANOVAOrder, config *configuration)
+ * \return pointer to Graph list
+ */
+Graph * molecule::FragmentBOSSANOVA(ofstream *out, int ANOVAOrder, config *configuration)
 {
   Graph *FragmentList = NULL, ***FragmentLowerOrdersList = NULL;
-  MoleculeListClass *FragmentMoleculeList = NULL;
+  //MoleculeListClass *FragmentMoleculeList = NULL;
   int Order, NumLevels, NumMolecules, TotalNumMolecules = 0, *NumMoleculesOfOrder = NULL;
   int counter = 0;
@@ -3702 +3720 @@
   while (Walker->next != end) {
     Walker = Walker->next;
-    CompleteMolecule.insert(Walker->nr);
+    CompleteMolecule.insert(Walker->GetTrueFather()->nr);
   } 
 
@@ -3775 +3793 @@
   Free((void **)&FragmentLowerOrdersList, "molecule::FragmentBOSSANOVA: ***FragmentLowerOrdersList");
   Free((void **)&NumMoleculesOfOrder, "molecule::FragmentBOSSANOVA: *NumMoleculesOfOrder");
-  // allocate memory for the pointer array and transmorph graphs into full molecular fragments
-  FragmentMoleculeList = new MoleculeListClass(TotalNumMolecules, AtomCount);
-  int k=0;
-  for(Graph::iterator runner = FragmentList->begin(); runner != FragmentList->end(); runner++) {
-    KeySet test = (*runner).first;
-    FragmentMoleculeList->ListOfMolecules[k] = StoreFragmentFromKeySet(out, test, configuration);
-    FragmentMoleculeList->TEList[k] = ((*runner).second).second;
-    k++;
-  }
   
   *out << Verbose(0) << "End of FragmentBOSSANOVA." << endl;
-  delete(FragmentList); 
-  return FragmentMoleculeList;
+  return FragmentList;
 };
 

src/molecules.hpp

@@ -532 +532 @@
   void FragmentMoleculeByBond(ofstream *out, bond *Bond, molecule **LeftFragment, molecule **RightFragment, bool IsAngstroem, enum CutCyclicBond CutCyclic);
   /// -# BOSSANOVA
-        MoleculeListClass * FragmentBOSSANOVA(ofstream *out, int ANOVAOrder, config *configuration);
+  Graph * FragmentBOSSANOVA(ofstream *out, int ANOVAOrder, config *configuration);
         int CreateListOfUniqueFragmentsOfOrder(ofstream *out, int Order, Graph *ListOfGraph, KeySet Fragment, double TEFactor, config *configuration);
   bool BuildInducedSubgraph(ofstream *out, const molecule *Father);