Changeset 266237 for src/molecule_fragmentation.cpp

Timestamp:

Oct 18, 2009, 2:51:38 PM (16 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:

174e0e

Parents:

b8b75d

git-author:

Frederik Heber <heber@…> (10/18/09 14:15:37)

git-committer:

Frederik Heber <heber@…> (10/18/09 14:51:38)

Message:

Huge refactoring: molecule::ListOfBondsPerAtom and molecule::NumberOfBondsPerAtom removed, atom::ListOfBonds introduced. Unit Test for ListOfBonds manipulation introduced.

• changes to class atom:
  • ~atom(): removes all bonds it is part of and unlink()s
  • new functions: CountBonds() - counts bonds times BondDegree, OutputGraphInfo() - graph data is output, OutputComponentNumber() - output of component numbers, OutputAdjacency() - indices of this and its neighbours, CorrectBondDegree() - corrects bond degree incrementally (by at most one) -- all since ListOfBonds is now local info
  • OutputBondOfAtom() - does not need ListOfBondsPerAtom, ... as ListOfBonds is now local info
  • new functions for ListOfBonds access: RegisterBond(), UnregisterBond(), UnregisterAllBonds() (the latter only remove from the list, do not delete, as molecule still has a global list of all bonds and does deletion.)

• changes to class bond:
  • ~bond() uses unlink(), uses UnregisterBond() on leftatom and rightatom
  • removed unused bond::GetFirstBond() and bond::GetLastBond()
  • GetOtherAtom() has now const parameter

• changes to builder.cpp: removed CreateListOfBondsPerAtom() calls, as the creation of the global arrays is not necessary anymore

• changes to LinkedCell: LinkedCell::CheckBounds(int[NDIM]) does not admonish out of bonds as this is not desired for the local offset which may become out of bounds.

• changes to lists.hpp templates: BUGFIX: unlink() now sets ->next and ->previous to NULL, cleanup() uses removedwithoutcheck()

• new templates for molecule.hpp: SumPerAtom() allows for summation of the return value of atom:...() member fiunctions. This is needed e.g. for atom::CorrectBondDegree()

• changes to MoleculeListClass:
  • changes due to ListOfBondsPerAtom -> atom::ListOfBonds: AddHydrogenCorrection(), FillBondStructureFromReference()

• changes to class molecule:
  • changes due to ListOfBondsPerAtom -> atom::ListOfBonds: GuesstimateFragmentCount(), FragmentMolecule(), FillSPListandLabelVertices(), ScanForPeriodicCorrection(), DeterminePeriodicCenter(), CyclicStructureAnalysis(), InitComponentNumbers(), FindNextUnused(), CheckAdjacencyFileAgainstMolecule(), PickLocalBackEdges(), BreadthFirstSearchAdd(), BuildInducedSubgraph(), CheckForConnectedSubgraph(), molecule(), ~molecule(), AddHydrogenReplacementAtom(), RemoveBonds(), OutputListOfBonds(), removed CreateListOfBondsPerAtom()
  • due to removal of CreateListOfBonds(): FragmentMolecule(), CreateAdjacencyListFromDbondFile(), CreateAdjacencyList(), SetNextComponentNumber()
  • ActOnAllAtoms() used: CreateAdjacencyList() - uses atom::OutputBondOfAtom(), StoreAdjacencyToFile() - uses atom::OutputAdjacency(),
  • SumPerAtom() used: CorrectBondDegree() - uses atom::CorrectBondDegree(),
  • function removed: molecule::CountAtomsBonds() - shifted to atom::CountBonds(), OutputComponentNumber() - shifted to atom::OutputComponentNumber()
  • CountCyclicBonds() - manipulates molecule::NoCyclicBonds directly.
  • rewritten DepthFirstSearchAnalysis() - refactored to CyclicBondAnalysis(), OutputGraphInfoPerAtom(), OutputGraphInfoPerBond()
  • rewritten RemoveAtom() - uses RemoveBonds()
  • FIX: rewritten CleanupMolecule() - cleanup was wrong order, now is first bonds, then atoms
  • rewritten BreadthFirstSearchAdd() - uses molecule::CopyBond() (equal code was present multiple(!) times before)
  • new functions CyclicBondAnalysis(), OutputGraphInfoPerAtom(), OutputGraphInfoPerBond(), CopyBond()

• New UnitTest for ListOfBonds:
  • tests AddBond(), RemoveAtom(), RemoveBond(), RemoveBonds() and simple deletion of atoms or bonds, where afterwards chain lists of bonds should remain intact.

Signed-off-by: Frederik Heber <heber@…>

File:

• src/molecule_fragmentation.cpp (modified) (14 diffs)

src/molecule_fragmentation.cpp

@@ -31 +31 @@
 int molecule::GuesstimateFragmentCount(ofstream *out, int order)
 {
-  int c = 0;
+  size_t c = 0;
   int FragmentCount;
   // get maximum bond degree
@@ -37 +37 @@
   while (Walker->next != end) {
     Walker = Walker->next;
-    c = (NumberOfBondsPerAtom[Walker->nr] > c) ? NumberOfBondsPerAtom[Walker->nr] : c;
+    c = (Walker->ListOfBonds.size() > c) ? Walker->ListOfBonds.size() : c;
   }
   FragmentCount = NoNonHydrogen*(1 << (c*order));
@@ -564 +564 @@
 
   // ===== 1. Check whether bond structure is same as stored in files ====
-
-  // fill the adjacency list
-  CreateListOfBondsPerAtom(out);
 
   // create lookup table for Atom::nr
@@ -630 +627 @@
       MolecularWalker = MolecularWalker->next;
       *out << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl;
-      //MolecularWalker->Leaf->OutputListOfBonds(out);  // output ListOfBondsPerAtom for debugging
+      //MolecularWalker->Leaf->OutputListOfBonds(out);  // output atom::ListOfBonds for debugging
       if (MolecularWalker->Leaf->first->next != MolecularWalker->Leaf->last) {
         // call BOSSANOVA method
@@ -879 +876 @@
     if (SonList[FatherOfRunner->nr] != NULL)  {  // check if this, our father, is present in list
       // create all bonds
-      for (int i=0;i<mol->NumberOfBondsPerAtom[FatherOfRunner->nr];i++) { // go through every bond of father
-        OtherFather = mol->ListOfBondsPerAtom[FatherOfRunner->nr][i]->GetOtherAtom(FatherOfRunner);
+      for (BondList::const_iterator BondRunner = FatherOfRunner->ListOfBonds.begin(); BondRunner != FatherOfRunner->ListOfBonds.end(); (++BondRunner)) {
+        OtherFather = (*BondRunner)->GetOtherAtom(FatherOfRunner);
 //        *out << Verbose(2) << "Father " << *FatherOfRunner << " of son " << *SonList[FatherOfRunner->nr] << " is bound to " << *OtherFather;
         if (SonList[OtherFather->nr] != NULL) {
@@ -887 +884 @@
 //            *out << Verbose(3) << "Adding Bond: ";
 //            *out <<
-            Leaf->AddBond(Runner, SonList[OtherFather->nr], mol->ListOfBondsPerAtom[FatherOfRunner->nr][i]->BondDegree);
+            Leaf->AddBond(Runner, SonList[OtherFather->nr], (*BondRunner)->BondDegree);
 //            *out << "." << endl;
             //NumBonds[Runner->nr]++;
@@ -898 +895 @@
 #ifdef ADDHYDROGEN
           //*out << Verbose(3) << "Adding Hydrogen to " << Runner->Name << " and a bond in between." << endl;
-          if(!Leaf->AddHydrogenReplacementAtom(out, mol->ListOfBondsPerAtom[FatherOfRunner->nr][i], Runner, FatherOfRunner, OtherFather, mol->ListOfBondsPerAtom[FatherOfRunner->nr],mol->NumberOfBondsPerAtom[FatherOfRunner->nr], IsAngstroem))
+          if(!Leaf->AddHydrogenReplacementAtom(out, (*BondRunner), Runner, FatherOfRunner, OtherFather, IsAngstroem))
             exit(1);
 #endif
-          //NumBonds[Runner->nr] += ListOfBondsPerAtom[FatherOfRunner->nr][i]->BondDegree;
+          //NumBonds[Runner->nr] += Binder->BondDegree;
         }
       }
@@ -936 +933 @@
   CreateInducedSubgraphOfFragment(out, this, Leaf, SonList, IsAngstroem);
 
-  Leaf->CreateListOfBondsPerAtom(out);
   //Leaflet->Leaf->ScanForPeriodicCorrection(out);
   Free(&SonList);
@@ -981 +977 @@
     if (bit) {  // if bit is set, we add this bond partner
       OtherWalker = BondsSet[j]->rightatom;  // rightatom is always the one more distant, i.e. the one to add
-      //*out << Verbose(1+verbosity) << "Current Bond is " << ListOfBondsPerAtom[Walker->nr][CurrentCombination] << ", checking on " << *OtherWalker << "." << endl;
+      //*out << Verbose(1+verbosity) << "Current Bond is " << BondsSet[j] << ", checking on " << *OtherWalker << "." << endl;
       *out << Verbose(2+verbosity) << "Adding " << *OtherWalker << " with nr " << OtherWalker->nr << "." << endl;
       TestKeySetInsert = FragmentSet->insert(OtherWalker->nr);
@@ -1089 +1085 @@
   NumCombinations = 1 << SetDimension;
 
-  // Hier muessen von 1 bis NumberOfBondsPerAtom[Walker->nr] alle Kombinationen
-  // von Endstuecken (aus den Bonds) hinzugefuegt werden und fuer verbleibende ANOVAOrder
-  // rekursiv GraphCrawler in der naechsten Ebene aufgerufen werden
+  // here for all bonds of Walker all combinations of end pieces (from the bonds)
+  // have to be added and for the remaining ANOVA order GraphCrawler be called
+  // recursively for the next level
 
   *out << Verbose(1+verbosity) << "Begin of SPFragmentGenerator." << endl;
@@ -1258 +1254 @@
   atom *OtherWalker = NULL;
   atom *Predecessor = NULL;
+  bond *CurrentEdge = NULL;
   bond *Binder = NULL;
-  bond *CurrentEdge = NULL;
   int RootKeyNr = FragmentSearch.Root->GetTrueFather()->nr;
   int RemainingWalkers = -1;
@@ -1285 +1281 @@
       // go through all its bonds
       *out << Verbose(1) << "Going through all bonds of Walker." << endl;
-      for (int i=0;i<mol->NumberOfBondsPerAtom[AtomKeyNr];i++) {
-        Binder = mol->ListOfBondsPerAtom[AtomKeyNr][i];
-        OtherWalker = Binder->GetOtherAtom(Walker);
+      for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
+        OtherWalker = (*Runner)->GetOtherAtom(Walker);
         if ((RestrictedKeySet.find(OtherWalker->nr) != RestrictedKeySet.end())
   #ifdef ADDHYDROGEN
@@ -1293 +1288 @@
   #endif
                                                               ) {  // skip hydrogens and restrict to fragment
-          *out << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->nr << " in bond " << *Binder << "." << endl;
+          *out << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->nr << " in bond " << *(*Runner) << "." << endl;
           // set the label if not set (and push on root stack as well)
           if ((OtherWalker != Predecessor) && (OtherWalker->GetTrueFather()->nr > RootKeyNr)) { // only pass through those with label bigger than Root's
@@ -1712 +1707 @@
         ColorList[Walker->nr] = black;    // mark as explored
         Walker->x.AddVector(&Translationvector); // translate
-        for (int i=0;i<NumberOfBondsPerAtom[Walker->nr];i++) {  // go through all binding partners
-          if (ListOfBondsPerAtom[Walker->nr][i] != Binder) {
-            OtherWalker = ListOfBondsPerAtom[Walker->nr][i]->GetOtherAtom(Walker);
+        for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
+          if ((*Runner) != Binder) {
+            OtherWalker = (*Runner)->GetOtherAtom(Walker);
             if (ColorList[OtherWalker->nr] == white) {
               AtomStack->Push(OtherWalker); // push if yet unexplored