Changes in src/moleculelist.cpp [ead4e6:a67d19]

File:

• src/moleculelist.cpp (modified) (52 diffs)

src/moleculelist.cpp

@@ -7 +7 @@
 #include <cstring>
 
-#include "World.hpp"
 #include "atom.hpp"
 #include "bond.hpp"
@@ -20 +19 @@
 #include "memoryallocator.hpp"
 #include "periodentafel.hpp"
+#include "World.hpp"
 
 /*********************************** Functions for class MoleculeListClass *************************/
@@ -25 +25 @@
 /** Constructor for MoleculeListClass.
  */
-MoleculeListClass::MoleculeListClass(World *_world) :
-  world(_world)
+MoleculeListClass::MoleculeListClass()
 {
   // empty lists
@@ -37 +36 @@
 MoleculeListClass::~MoleculeListClass()
 {
-  Log() << Verbose(3) << this << ": Freeing ListOfMolcules." << endl;
+  DoLog(3) && (Log() << Verbose(3) << this << ": Freeing ListOfMolcules." << endl);
   for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
-    Log() << Verbose(4) << "ListOfMolecules: Freeing " << *ListRunner << "." << endl;
-    world->destroyMolecule(*ListRunner);
-  }
-  Log() << Verbose(4) << "Freeing ListOfMolecules." << endl;
+    DoLog(4) && (Log() << Verbose(4) << "ListOfMolecules: Freeing " << *ListRunner << "." << endl);
+    delete (*ListRunner);
+  }
+  DoLog(4) && (Log() << Verbose(4) << "Freeing ListOfMolecules." << endl);
   ListOfMolecules.clear(); // empty list
 };
@@ -52 +51 @@
 void MoleculeListClass::insert(molecule *mol)
 {
-  OBSERVE;
   mol->IndexNr = MaxIndex++;
   ListOfMolecules.push_back(mol);
-  mol->signOn(this);
 };
 
@@ -139 +136 @@
  * \param *out output stream
  */
-void MoleculeListClass::Enumerate(ostream *out)
-{
+void MoleculeListClass::Enumerate(ofstream *out)
+{
+  element* Elemental = NULL;
   atom *Walker = NULL;
-  periodentafel *periode = World::getInstance().getPeriode();
-  std::map<atomicNumber_t,unsigned int> counts;
+  int Counts[MAX_ELEMENTS];
   double size=0;
   Vector Origin;
 
   // header
-  (*out) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
-  (*out) << "-----------------------------------------------" << endl;
+  DoLog(0) && (Log() << Verbose(0) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl);
+  DoLog(0) && (Log() << Verbose(0) << "-----------------------------------------------" << endl);
   if (ListOfMolecules.size() == 0)
-    (*out) << "\tNone" << endl;
+    DoLog(0) && (Log() << Verbose(0) << "\tNone" << endl);
   else {
     Origin.Zero();
     for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
+      // reset element counts
+      for (int j = 0; j<MAX_ELEMENTS;j++)
+        Counts[j] = 0;
       // count atoms per element and determine size of bounding sphere
       size=0.;
@@ -160 +160 @@
       while (Walker->next != (*ListRunner)->end) {
         Walker = Walker->next;
-        counts[Walker->type->getNumber()]++;
+        Counts[Walker->type->Z]++;
         if (Walker->x.DistanceSquared(&Origin) > size)
           size = Walker->x.DistanceSquared(&Origin);
       }
       // output Index, Name, number of atoms, chemical formula
-      (*out) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
-
-      std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
-      for(iter=counts.rbegin(); iter!=counts.rend();++iter){
-        atomicNumber_t Z =(*iter).first;
-        (*out) << periode->FindElement(Z)->getSymbol() << (*iter).second;
+      DoLog(0) && (Log() << Verbose(0) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t");
+      Elemental = (*ListRunner)->elemente->end;
+      while(Elemental->previous != (*ListRunner)->elemente->start) {
+        Elemental = Elemental->previous;
+        if (Counts[Elemental->Z] != 0)
+          DoLog(0) && (Log() << Verbose(0) << Elemental->symbol << Counts[Elemental->Z]);
       }
       // Center and size
-      (*out) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
+      DoLog(0) && (Log() << Verbose(0) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl);
     }
   }
@@ -212 +212 @@
   // remove src
   ListOfMolecules.remove(srcmol);
-  World::getInstance().destroyMolecule(srcmol);
+  delete(srcmol);
   return true;
 };
@@ -314 +314 @@
   Tesselation *TesselStruct = NULL;
   if ((srcmol == NULL) || (mol == NULL)) {
-    eLog() << Verbose(1) << "Either fixed or variable molecule is given as NULL." << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) << "Either fixed or variable molecule is given as NULL." << endl);
     return false;
   }
@@ -322 +322 @@
   FindNonConvexBorder(mol, TesselStruct, (const LinkedCell *&)LCList, 4., NULL);
   if (TesselStruct == NULL) {
-    eLog() << Verbose(1) << "Could not tesselate the fixed molecule." << endl;
+    DoeLog(1) && (eLog()<< Verbose(1) << "Could not tesselate the fixed molecule." << endl);
     return false;
   }
@@ -339 +339 @@
   while (Walker->next != srcmol->end) {
     Walker = Walker->next;
-    Log() << Verbose(2) << "INFO: Current Walker is " << *Walker << "." << endl;
+    DoLog(2) && (Log() << Verbose(2) << "INFO: Current Walker is " << *Walker << "." << endl);
     if (!TesselStruct->IsInnerPoint(Walker->x, LCList)) {
-      CopyAtoms[Walker->nr] = Walker->clone();
+      CopyAtoms[Walker->nr] = new atom(Walker);
       mol->AddAtom(CopyAtoms[Walker->nr]);
       nr++;
@@ -348 +348 @@
     }
   }
-  Log() << Verbose(1) << nr << " of " << srcmol->AtomCount << " atoms have been merged.";
+  DoLog(1) && (Log() << Verbose(1) << nr << " of " << srcmol->AtomCount << " atoms have been merged.");
 
   // go through all bonds and add as well
@@ -354 +354 @@
   while(Binder->next != srcmol->last) {
     Binder = Binder->next;
-    Log() << Verbose(3) << "Adding Bond between " << *CopyAtoms[Binder->leftatom->nr] << " and " << *CopyAtoms[Binder->rightatom->nr]<< "." << endl;
+    DoLog(3) && (Log() << Verbose(3) << "Adding Bond between " << *CopyAtoms[Binder->leftatom->nr] << " and " << *CopyAtoms[Binder->rightatom->nr]<< "." << endl);
     mol->AddBond(CopyAtoms[Binder->leftatom->nr], CopyAtoms[Binder->rightatom->nr], Binder->BondDegree);
   }
@@ -366 +366 @@
 void MoleculeListClass::Output(ofstream *out)
 {
-  Log() << Verbose(1) << "MoleculeList: ";
+  DoLog(1) && (Log() << Verbose(1) << "MoleculeList: ");
   for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
-    Log() << Verbose(0) << *ListRunner << "\t";
-  Log() << Verbose(0) << endl;
+    DoLog(0) && (Log() << Verbose(0) << *ListRunner << "\t");
+  DoLog(0) && (Log() << Verbose(0) << endl);
 };
 
@@ -395 +395 @@
   char *FragmentNumber = NULL;
 
-  Log() << Verbose(1) << "Saving hydrogen saturation correction ... ";
+  DoLog(1) && (Log() << Verbose(1) << "Saving hydrogen saturation correction ... ");
   // 0. parse in fit constant files that should have the same dimension as the final energy files
   // 0a. find dimension of matrices with constants
@@ -405 +405 @@
   input.open(line.c_str());
   if (input == NULL) {
-    Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
+    DoLog(1) && (Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
     return false;
   }
@@ -422 +422 @@
     b++;
   }
-  Log() << Verbose(0) << "I recognized " << a << " columns and " << b << " rows, ";
+  DoLog(0) && (Log() << Verbose(0) << "I recognized " << a << " columns and " << b << " rows, ");
   input.close();
 
@@ -443 +443 @@
     input.open(line.c_str());
     if (input == NULL) {
-      eLog() << Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
+      DoeLog(0) && (eLog()<< Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
       performCriticalExit();
       return false;
@@ -465 +465 @@
   }
   for (int k = 0; k < 3; k++) {
-    Log() << Verbose(0) << "Constants " << k << ":" << endl;
+    DoLog(0) && (Log() << Verbose(0) << "Constants " << k << ":" << endl);
     for (int j = 0; j < b; j++) {
       for (int i = 0; i < a; i++) {
-        Log() << Verbose(0) << FitConstant[k][i][j] << "\t";
+        DoLog(0) && (Log() << Verbose(0) << FitConstant[k][i][j] << "\t");
       }
-      Log() << Verbose(0) << endl;
-    }
-    Log() << Verbose(0) << endl;
+      DoLog(0) && (Log() << Verbose(0) << endl);
+    }
+    DoLog(0) && (Log() << Verbose(0) << endl);
   }
 
@@ -560 +560 @@
   }
   Free(&FitConstant);
-  Log() << Verbose(0) << "done." << endl;
+  DoLog(0) && (Log() << Verbose(0) << "done." << endl);
   return true;
 };
@@ -577 +577 @@
   stringstream line;
   atom *Walker = NULL;
-  periodentafel *periode=World::getInstance().getPeriode();
+  element *runner = NULL;
 
   // open file for the force factors
-  Log() << Verbose(1) << "Saving  force factors ... ";
+  DoLog(1) && (Log() << Verbose(1) << "Saving  force factors ... ");
   line << path << "/" << FRAGMENTPREFIX << FORCESFILE;
   ForcesFile.open(line.str().c_str(), ios::out);
@@ -587 +587 @@
     //output << prefix << "Forces" << endl;
     for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
-      periodentafel::const_iterator elemIter;
-      for(elemIter=periode->begin();elemIter!=periode->end();++elemIter){
-          if ((*ListRunner)->ElementsInMolecule[(*elemIter).first]) { // if this element got atoms
+      runner = (*ListRunner)->elemente->start;
+      while (runner->next != (*ListRunner)->elemente->end) { // go through every element
+        runner = runner->next;
+        if ((*ListRunner)->ElementsInMolecule[runner->Z]) { // if this element got atoms
           Walker = (*ListRunner)->start;
           while (Walker->next != (*ListRunner)->end) { // go through every atom of this element
             Walker = Walker->next;
-            if (Walker->type->getNumber() == (*elemIter).first) {
+            if (Walker->type->Z == runner->Z) {
               if ((Walker->GetTrueFather() != NULL) && (Walker->GetTrueFather() != Walker)) {// if there is a rea
                 //Log() << Verbose(0) << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", it
@@ -607 +608 @@
     }
     ForcesFile.close();
-    Log() << Verbose(1) << "done." << endl;
+    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
   } else {
     status = false;
-    Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
+    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
   }
   ForcesFile.close();
@@ -638 +639 @@
   int FragmentCounter = 0;
   ofstream output;
-
+  double cell_size_backup[6];
+  double * const cell_size = World::get()->cell_size;
+
+  // backup cell_size
+  for (int i=0;i<6;i++)
+    cell_size_backup[i] = cell_size[i];
   // store the fragments as config and as xyz
   for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
@@ -646 +652 @@
       strcpy(PathBackup, path);
     else {
-      eLog() << Verbose(0) << "OutputConfigForListOfFragments: NULL default path obtained from config!" << endl;
+      DoeLog(0) && (eLog()<< Verbose(0) << "OutputConfigForListOfFragments: NULL default path obtained from config!" << endl);
       performCriticalExit();
     }
@@ -657 +663 @@
     sprintf(FragmentName, "%s/%s%s.conf.xyz", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
     outputFragment.open(FragmentName, ios::out);
-    Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...";
+    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...");
     if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
-      Log() << Verbose(0) << " done." << endl;
+      DoLog(0) && (Log() << Verbose(0) << " done." << endl);
     else
-      Log() << Verbose(0) << " failed." << endl;
+      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
     result = result && intermediateResult;
     outputFragment.close();
@@ -667 +673 @@
 
     // list atoms in fragment for debugging
-    Log() << Verbose(2) << "Contained atoms: ";
+    DoLog(2) && (Log() << Verbose(2) << "Contained atoms: ");
     Walker = (*ListRunner)->start;
     while (Walker->next != (*ListRunner)->end) {
       Walker = Walker->next;
-      Log() << Verbose(0) << Walker->Name << " ";
-    }
-    Log() << Verbose(0) << endl;
+      DoLog(0) && (Log() << Verbose(0) << Walker->Name << " ");
+    }
+    DoLog(0) && (Log() << Verbose(0) << endl);
 
     // center on edge
@@ -682 +688 @@
       j += k + 1;
       BoxDimension.x[k] = 2.5 * (configuration->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
-      (*ListRunner)->cell_size[j] += BoxDimension.x[k] * 2.;
+      cell_size[j] = BoxDimension.x[k] * 2.;
     }
     (*ListRunner)->Translate(&BoxDimension);
@@ -697 +703 @@
     // and save as config
     sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
-    Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...";
+    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...");
     if ((intermediateResult = configuration->Save(FragmentName, (*ListRunner)->elemente, (*ListRunner))))
-      Log() << Verbose(0) << " done." << endl;
+      DoLog(0) && (Log() << Verbose(0) << " done." << endl);
     else
-      Log() << Verbose(0) << " failed." << endl;
+      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
     result = result && intermediateResult;
 
@@ -709 +715 @@
     // and save as mpqc input file
     sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
-    Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...";
+    DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...");
     if ((intermediateResult = configuration->SaveMPQC(FragmentName, (*ListRunner))))
-      Log() << Verbose(2) << " done." << endl;
+      DoLog(2) && (Log() << Verbose(2) << " done." << endl);
     else
-      Log() << Verbose(0) << " failed." << endl;
+      DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
 
     result = result && intermediateResult;
@@ -720 +726 @@
     Free(&FragmentNumber);
   }
-  Log() << Verbose(0) << " done." << endl;
+  DoLog(0) && (Log() << Verbose(0) << " done." << endl);
 
   // printing final number
-  Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl;
+  DoLog(2) && (Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl);
+
+  // restore cell_size
+  for (int i=0;i<6;i++)
+    cell_size[i] = cell_size_backup[i];
 
   return result;
@@ -746 +756 @@
 void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration)
 {
-  molecule *mol = World::getInstance().createMolecule();
+  molecule *mol = new molecule(periode);
   atom *Walker = NULL;
   atom *Advancer = NULL;
@@ -758 +768 @@
       Walker = Advancer;
       Advancer = Advancer->next;
-      Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl;
+      DoLog(3) && (Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl);
       unlink(Walker);
       Walker->father = Walker;
@@ -771 +781 @@
     }
     // remove the molecule
-    World::getInstance().destroyMolecule(*MolRunner);
+    delete(*MolRunner);
     ListOfMolecules.erase(MolRunner);
   }
 
   // 1. dissect the molecule into connected subgraphs
-  configuration->BG->ConstructBondGraph(mol);
+  if (!configuration->BG->ConstructBondGraph(mol)) {
+    delete (mol);
+    DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
+    return;
+  }
 
   // 2. scan for connected subgraphs
@@ -783 +797 @@
   Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
   delete(BackEdgeStack);
+  if ((Subgraphs == NULL) || (Subgraphs->next == NULL)) {
+    delete (mol);
+    DoeLog(1) && (eLog()<< Verbose(1) << "There are no atoms." << endl);
+    return;
+  }
 
   // 3. dissect (the following construct is needed to have the atoms not in the order of the DFS, but in
@@ -793 +812 @@
   molecule **molecules = Malloc<molecule *>(MolCount, "config::Load() - **molecules");
   for (int i=0;i<MolCount;i++) {
-    molecules[i] = World::getInstance().createMolecule();
+    molecules[i] = (molecule*) new molecule(mol->elemente);
     molecules[i]->ActiveFlag = true;
     strncpy(molecules[i]->name, mol->name, MAXSTRINGSIZE);
@@ -800 +819 @@
       strncat(molecules[i]->name, number, MAXSTRINGSIZE - strlen(mol->name) - 1);
     }
-    cout << "MolName is " << molecules[i]->name << endl;
+    DoLog(1) && (Log() << Verbose(1) << "MolName is " << molecules[i]->name << endl);
     insert(molecules[i]);
   }
@@ -824 +843 @@
     Walker = mol->start->next;
     if ((Walker->nr <0) || (Walker->nr >= mol->AtomCount)) {
-      eLog() << Verbose(0) << "Index of atom " << *Walker << " is invalid!" << endl;
+      DoeLog(0) && (eLog()<< Verbose(0) << "Index of atom " << *Walker << " is invalid!" << endl);
       performCriticalExit();
     }
     FragmentCounter = MolMap[Walker->nr];
     if (FragmentCounter != 0) {
-      Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl;
+      DoLog(3) && (Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl);
       unlink(Walker);
       molecules[FragmentCounter-1]->AddAtom(Walker);    // counting starts at 1
     } else {
-      eLog() << Verbose(0) << "Atom " << *Walker << " not associated to molecule!" << endl;
+      DoeLog(0) && (eLog()<< Verbose(0) << "Atom " << *Walker << " not associated to molecule!" << endl);
       performCriticalExit();
     }
@@ -854 +873 @@
   Free(&MolMap);
   Free(&molecules);
-  Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl);
 };
 
@@ -874 +893 @@
   return AtomNo;
 }
-
-/***********
- * Methods Moved here from the menus
- */
-
-void MoleculeListClass::flipChosen() {
-  int j;
-  Log() << Verbose(0) << "Enter index of molecule: ";
-  cin >> j;
-  for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
-    if ((*ListRunner)->IndexNr == j)
-      (*ListRunner)->ActiveFlag = !(*ListRunner)->ActiveFlag;
-}
-
-void MoleculeListClass::createNewMolecule(periodentafel *periode) {
-  OBSERVE;
-  molecule *mol = NULL;
-  mol = World::getInstance().createMolecule();
-  insert(mol);
-};
-
-void MoleculeListClass::loadFromXYZ(periodentafel *periode){
-  molecule *mol = NULL;
-  Vector center;
-  char filename[MAXSTRINGSIZE];
-  Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
-  mol = World::getInstance().createMolecule();
-  do {
-    Log() << Verbose(0) << "Enter file name: ";
-    cin >> filename;
-  } while (!mol->AddXYZFile(filename));
-  mol->SetNameFromFilename(filename);
-  // center at set box dimensions
-  mol->CenterEdge(&center);
-  mol->cell_size[0] = center.x[0];
-  mol->cell_size[1] = 0;
-  mol->cell_size[2] = center.x[1];
-  mol->cell_size[3] = 0;
-  mol->cell_size[4] = 0;
-  mol->cell_size[5] = center.x[2];
-  insert(mol);
-}
-
-void MoleculeListClass::setMoleculeFilename() {
-  char filename[MAXSTRINGSIZE];
-  int nr;
-  molecule *mol = NULL;
-  do {
-    Log() << Verbose(0) << "Enter index of molecule: ";
-    cin >> nr;
-    mol = ReturnIndex(nr);
-  } while (mol == NULL);
-  Log() << Verbose(0) << "Enter name: ";
-  cin >> filename;
-  mol->SetNameFromFilename(filename);
-}
-
-void MoleculeListClass::parseXYZIntoMolecule(){
-  char filename[MAXSTRINGSIZE];
-  int nr;
-  molecule *mol = NULL;
-  mol = NULL;
-  do {
-   Log() << Verbose(0) << "Enter index of molecule: ";
-   cin >> nr;
-   mol = ReturnIndex(nr);
-  } while (mol == NULL);
-  Log() << Verbose(0) << "Format should be XYZ with: ShorthandOfElement\tX\tY\tZ" << endl;
-  do {
-   Log() << Verbose(0) << "Enter file name: ";
-   cin >> filename;
-  } while (!mol->AddXYZFile(filename));
-  mol->SetNameFromFilename(filename);
-};
-
-void MoleculeListClass::eraseMolecule(){
-  int nr;
-  molecule *mol = NULL;
-  Log() << Verbose(0) << "Enter index of molecule: ";
-  cin >> nr;
-  for(MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
-    if (nr == (*ListRunner)->IndexNr) {
-      mol = *ListRunner;
-      ListOfMolecules.erase(ListRunner);
-      World::getInstance().destroyMolecule(mol);
-      break;
-    }
-};
 
 
@@ -1005 +936 @@
   // remove the leaf itself
   if (Leaf != NULL) {
-    World::getInstance().destroyMolecule(Leaf);
+    delete (Leaf);
     Leaf = NULL;
   }
@@ -1051 +982 @@
   int AtomNo;
 
-  Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl);
   // fill ListOfLocalAtoms if NULL was given
   if (!FillListOfLocalAtoms(ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
-    Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl;
+    DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
     return false;
   }
 
   if (status) {
-    Log() << Verbose(1) << "Creating adjacency list for subgraph " << Leaf << "." << endl;
+    DoLog(1) && (Log() << Verbose(1) << "Creating adjacency list for subgraph " << Leaf << "." << endl);
     // remove every bond from the list
     bond *Binder = NULL;
@@ -1080 +1011 @@
             Leaf->AddBond(Walker, OtherWalker, (*Runner)->BondDegree);
         } else {
-          Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << FragmentCounter << "][" << (*Runner)->GetOtherAtom(Walker->GetTrueFather())->nr << "] is NULL!" << endl;
+          DoLog(1) && (Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << FragmentCounter << "][" << (*Runner)->GetOtherAtom(Walker->GetTrueFather())->nr << "] is NULL!" << endl);
           status = false;
         }
@@ -1093 +1024 @@
       Free(&ListOfLocalAtoms);
   }
-  Log() << Verbose(1) << "End of FillBondStructureFromReference." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "End of FillBondStructureFromReference." << endl);
   return status;
 };
@@ -1126 +1057 @@
         next->FillRootStackForSubgraphs(RootStack, AtomMask, ++FragmentCounter);
     } else {
-      Log() << Verbose(1) << "Rootstack[" << FragmentCounter << "] is NULL." << endl;
+      DoLog(1) && (Log() << Verbose(1) << "Rootstack[" << FragmentCounter << "] is NULL." << endl);
       return false;
     }
@@ -1132 +1063 @@
     return true;
   } else {
-    Log() << Verbose(1) << "Rootstack is NULL." << endl;
+    DoLog(1) && (Log() << Verbose(1) << "Rootstack is NULL." << endl);
     return false;
   }
@@ -1182 +1113 @@
   int KeySetCounter = 0;
 
-  Log() << Verbose(1) << "Begin of AssignKeySetsToFragment." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "Begin of AssignKeySetsToFragment." << endl);
   // fill ListOfLocalAtoms if NULL was given
   if (!FillListOfLocalAtoms(ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
-    Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl;
+    DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
     return false;
   }
@@ -1213 +1144 @@
     delete (TempSet);
     if (KeySetCounter == 0) {// if there are no keysets, delete the list
-      Log() << Verbose(1) << "KeySetCounter is zero, deleting FragmentList." << endl;
+      DoLog(1) && (Log() << Verbose(1) << "KeySetCounter is zero, deleting FragmentList." << endl);
       delete (FragmentList[FragmentCounter]);
     } else
-      Log() << Verbose(1) << KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << "." << endl;
+      DoLog(1) && (Log() << Verbose(1) << KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << "." << endl);
     FragmentCounter++;
     if (next != NULL)
@@ -1222 +1153 @@
     FragmentCounter--;
   } else
-    Log() << Verbose(1) << "KeySetList is NULL or empty." << endl;
+    DoLog(1) && (Log() << Verbose(1) << "KeySetList is NULL or empty." << endl);
 
   if ((FreeList) && (ListOfLocalAtoms != NULL)) {
@@ -1230 +1161 @@
       Free(&ListOfLocalAtoms);
   }
-  Log() << Verbose(1) << "End of AssignKeySetsToFragment." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "End of AssignKeySetsToFragment." << endl);
   return status;
 };
@@ -1243 +1174 @@
 void MoleculeLeafClass::TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph)
 {
-  Log() << Verbose(1) << "Begin of TranslateIndicesToGlobalIDs." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "Begin of TranslateIndicesToGlobalIDs." << endl);
   KeySet *TempSet = new KeySet;
   if (FragmentList[FragmentCounter] != NULL) {
@@ -1254 +1185 @@
     delete (TempSet);
   } else {
-    Log() << Verbose(1) << "FragmentList is NULL." << endl;
+    DoLog(1) && (Log() << Verbose(1) << "FragmentList is NULL." << endl);
   }
   if (next != NULL)
     next->TranslateIndicesToGlobalIDs(FragmentList, ++FragmentCounter, TotalNumberOfKeySets, TotalGraph);
   FragmentCounter--;
-  Log() << Verbose(1) << "End of TranslateIndicesToGlobalIDs." << endl;
+  DoLog(1) && (Log() << Verbose(1) << "End of TranslateIndicesToGlobalIDs." << endl);
 };