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  • src/moleculelist.cpp

    ra67d19 r6a7f78c  
    44 *
    55 */
    6 
    7 #include <cstring>
    86
    97#include "atom.hpp"
    … …  
    1917#include "memoryallocator.hpp"
    2018#include "periodentafel.hpp"
    21 #include "World.hpp"
    2219
    2320/*********************************** Functions for class MoleculeListClass *************************/
    … …  
    3633MoleculeListClass::~MoleculeListClass()
    3734{
    38   DoLog(3) && (Log() << Verbose(3) << this << ": Freeing ListOfMolcules." << endl);
     35  Log() << Verbose(3) << this << ": Freeing ListOfMolcules." << endl;
    3936  for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
    40     DoLog(4) && (Log() << Verbose(4) << "ListOfMolecules: Freeing " << *ListRunner << "." << endl);
     37    Log() << Verbose(4) << "ListOfMolecules: Freeing " << *ListRunner << "." << endl;
    4138    delete (*ListRunner);
    4239  }
    43   DoLog(4) && (Log() << Verbose(4) << "Freeing ListOfMolecules." << endl);
     40  Log() << Verbose(4) << "Freeing ListOfMolecules." << endl;
    4441  ListOfMolecules.clear(); // empty list
    4542};
    … …  
    145142
    146143  // header
    147   DoLog(0) && (Log() << Verbose(0) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl);
    148   DoLog(0) && (Log() << Verbose(0) << "-----------------------------------------------" << endl);
     144  Log() << Verbose(0) << "Index\tName\t\tAtoms\tFormula\tCenter\tSize" << endl;
     145  Log() << Verbose(0) << "-----------------------------------------------" << endl;
    149146  if (ListOfMolecules.size() == 0)
    150     DoLog(0) && (Log() << Verbose(0) << "\tNone" << endl);
     147    Log() << Verbose(0) << "\tNone" << endl;
    151148  else {
    152149    Origin.Zero();
    … …  
    165162      }
    166163      // output Index, Name, number of atoms, chemical formula
    167       DoLog(0) && (Log() << Verbose(0) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t");
     164      Log() << Verbose(0) << ((*ListRunner)->ActiveFlag ? "*" : " ") << (*ListRunner)->IndexNr << "\t" << (*ListRunner)->name << "\t\t" << (*ListRunner)->AtomCount << "\t";
    168165      Elemental = (*ListRunner)->elemente->end;
    169166      while(Elemental->previous != (*ListRunner)->elemente->start) {
    170167        Elemental = Elemental->previous;
    171168        if (Counts[Elemental->Z] != 0)
    172           DoLog(0) && (Log() << Verbose(0) << Elemental->symbol << Counts[Elemental->Z]);
     169          Log() << Verbose(0) << Elemental->symbol << Counts[Elemental->Z];
    173170      }
    174171      // Center and size
    175       DoLog(0) && (Log() << Verbose(0) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl);
     172      Log() << Verbose(0) << "\t" << (*ListRunner)->Center << "\t" << sqrt(size) << endl;
    176173    }
    177174  }
    … …  
    314311  Tesselation *TesselStruct = NULL;
    315312  if ((srcmol == NULL) || (mol == NULL)) {
    316     DoeLog(1) && (eLog()<< Verbose(1) << "Either fixed or variable molecule is given as NULL." << endl);
     313    eLog() << Verbose(1) << "Either fixed or variable molecule is given as NULL." << endl;
    317314    return false;
    318315  }
    … …  
    322319  FindNonConvexBorder(mol, TesselStruct, (const LinkedCell *&)LCList, 4., NULL);
    323320  if (TesselStruct == NULL) {
    324     DoeLog(1) && (eLog()<< Verbose(1) << "Could not tesselate the fixed molecule." << endl);
     321    eLog() << Verbose(1) << "Could not tesselate the fixed molecule." << endl;
    325322    return false;
    326323  }
    … …  
    339336  while (Walker->next != srcmol->end) {
    340337    Walker = Walker->next;
    341     DoLog(2) && (Log() << Verbose(2) << "INFO: Current Walker is " << *Walker << "." << endl);
     338    Log() << Verbose(2) << "INFO: Current Walker is " << *Walker << "." << endl;
    342339    if (!TesselStruct->IsInnerPoint(Walker->x, LCList)) {
    343340      CopyAtoms[Walker->nr] = new atom(Walker);
    … …  
    348345    }
    349346  }
    350   DoLog(1) && (Log() << Verbose(1) << nr << " of " << srcmol->AtomCount << " atoms have been merged.");
     347  Log() << Verbose(1) << nr << " of " << srcmol->AtomCount << " atoms have been merged.";
    351348
    352349  // go through all bonds and add as well
    … …  
    354351  while(Binder->next != srcmol->last) {
    355352    Binder = Binder->next;
    356     DoLog(3) && (Log() << Verbose(3) << "Adding Bond between " << *CopyAtoms[Binder->leftatom->nr] << " and " << *CopyAtoms[Binder->rightatom->nr]<< "." << endl);
     353    Log() << Verbose(3) << "Adding Bond between " << *CopyAtoms[Binder->leftatom->nr] << " and " << *CopyAtoms[Binder->rightatom->nr]<< "." << endl;
    357354    mol->AddBond(CopyAtoms[Binder->leftatom->nr], CopyAtoms[Binder->rightatom->nr], Binder->BondDegree);
    358355  }
    … …  
    366363void MoleculeListClass::Output(ofstream *out)
    367364{
    368   DoLog(1) && (Log() << Verbose(1) << "MoleculeList: ");
     365  Log() << Verbose(1) << "MoleculeList: ";
    369366  for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++)
    370     DoLog(0) && (Log() << Verbose(0) << *ListRunner << "\t");
    371   DoLog(0) && (Log() << Verbose(0) << endl);
     367    Log() << Verbose(0) << *ListRunner << "\t";
     368  Log() << Verbose(0) << endl;
    372369};
    373370
    … …  
    395392  char *FragmentNumber = NULL;
    396393
    397   DoLog(1) && (Log() << Verbose(1) << "Saving hydrogen saturation correction ... ");
     394  Log() << Verbose(1) << "Saving hydrogen saturation correction ... ";
    398395  // 0. parse in fit constant files that should have the same dimension as the final energy files
    399396  // 0a. find dimension of matrices with constants
    … …  
    405402  input.open(line.c_str());
    406403  if (input == NULL) {
    407     DoLog(1) && (Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
     404    eLog() << Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
     405    performCriticalExit();
    408406    return false;
    409407  }
    … …  
    422420    b++;
    423421  }
    424   DoLog(0) && (Log() << Verbose(0) << "I recognized " << a << " columns and " << b << " rows, ");
     422  Log() << Verbose(0) << "I recognized " << a << " columns and " << b << " rows, ";
    425423  input.close();
    426424
    … …  
    443441    input.open(line.c_str());
    444442    if (input == NULL) {
    445       DoeLog(0) && (eLog()<< Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
     443      eLog() << Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl;
    446444      performCriticalExit();
    447445      return false;
    … …  
    465463  }
    466464  for (int k = 0; k < 3; k++) {
    467     DoLog(0) && (Log() << Verbose(0) << "Constants " << k << ":" << endl);
     465    Log() << Verbose(0) << "Constants " << k << ":" << endl;
    468466    for (int j = 0; j < b; j++) {
    469467      for (int i = 0; i < a; i++) {
    470         DoLog(0) && (Log() << Verbose(0) << FitConstant[k][i][j] << "\t");
     468        Log() << Verbose(0) << FitConstant[k][i][j] << "\t";
    471469      }
    472       DoLog(0) && (Log() << Verbose(0) << endl);
    473     }
    474     DoLog(0) && (Log() << Verbose(0) << endl);
     470      Log() << Verbose(0) << endl;
     471    }
     472    Log() << Verbose(0) << endl;
    475473  }
    476474
    … …  
    560558  }
    561559  Free(&FitConstant);
    562   DoLog(0) && (Log() << Verbose(0) << "done." << endl);
     560  Log() << Verbose(0) << "done." << endl;
    563561  return true;
    564562};
    … …  
    580578
    581579  // open file for the force factors
    582   DoLog(1) && (Log() << Verbose(1) << "Saving  force factors ... ");
     580  Log() << Verbose(1) << "Saving  force factors ... ";
    583581  line << path << "/" << FRAGMENTPREFIX << FORCESFILE;
    584582  ForcesFile.open(line.str().c_str(), ios::out);
    … …  
    608606    }
    609607    ForcesFile.close();
    610     DoLog(1) && (Log() << Verbose(1) << "done." << endl);
     608    Log() << Verbose(1) << "done." << endl;
    611609  } else {
    612610    status = false;
    613     DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
     611    Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
    614612  }
    615613  ForcesFile.close();
    … …  
    639637  int FragmentCounter = 0;
    640638  ofstream output;
    641   double cell_size_backup[6];
    642   double * const cell_size = World::get()->cell_size;
    643 
    644   // backup cell_size
    645   for (int i=0;i<6;i++)
    646     cell_size_backup[i] = cell_size[i];
     639
    647640  // store the fragments as config and as xyz
    648641  for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
    … …  
    652645      strcpy(PathBackup, path);
    653646    else {
    654       DoeLog(0) && (eLog()<< Verbose(0) << "OutputConfigForListOfFragments: NULL default path obtained from config!" << endl);
     647      eLog() << Verbose(0) << "OutputConfigForListOfFragments: NULL default path obtained from config!" << endl;
    655648      performCriticalExit();
    656649    }
    … …  
    663656    sprintf(FragmentName, "%s/%s%s.conf.xyz", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
    664657    outputFragment.open(FragmentName, ios::out);
    665     DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...");
     658    Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...";
    666659    if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
    667       DoLog(0) && (Log() << Verbose(0) << " done." << endl);
     660      Log() << Verbose(0) << " done." << endl;
    668661    else
    669       DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
     662      Log() << Verbose(0) << " failed." << endl;
    670663    result = result && intermediateResult;
    671664    outputFragment.close();
    … …  
    673666
    674667    // list atoms in fragment for debugging
    675     DoLog(2) && (Log() << Verbose(2) << "Contained atoms: ");
     668    Log() << Verbose(2) << "Contained atoms: ";
    676669    Walker = (*ListRunner)->start;
    677670    while (Walker->next != (*ListRunner)->end) {
    678671      Walker = Walker->next;
    679       DoLog(0) && (Log() << Verbose(0) << Walker->Name << " ");
    680     }
    681     DoLog(0) && (Log() << Verbose(0) << endl);
     672      Log() << Verbose(0) << Walker->Name << " ";
     673    }
     674    Log() << Verbose(0) << endl;
    682675
    683676    // center on edge
    … …  
    688681      j += k + 1;
    689682      BoxDimension.x[k] = 2.5 * (configuration->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
    690       cell_size[j] = BoxDimension.x[k] * 2.;
     683      (*ListRunner)->cell_size[j] += BoxDimension.x[k] * 2.;
    691684    }
    692685    (*ListRunner)->Translate(&BoxDimension);
    … …  
    703696    // and save as config
    704697    sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
    705     DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...");
     698    Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...";
    706699    if ((intermediateResult = configuration->Save(FragmentName, (*ListRunner)->elemente, (*ListRunner))))
    707       DoLog(0) && (Log() << Verbose(0) << " done." << endl);
     700      Log() << Verbose(0) << " done." << endl;
    708701    else
    709       DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
     702      Log() << Verbose(0) << " failed." << endl;
    710703    result = result && intermediateResult;
    711704
    … …  
    715708    // and save as mpqc input file
    716709    sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
    717     DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...");
     710    Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...";
    718711    if ((intermediateResult = configuration->SaveMPQC(FragmentName, (*ListRunner))))
    719       DoLog(2) && (Log() << Verbose(2) << " done." << endl);
     712      Log() << Verbose(2) << " done." << endl;
    720713    else
    721       DoLog(0) && (Log() << Verbose(0) << " failed." << endl);
     714      Log() << Verbose(0) << " failed." << endl;
    722715
    723716    result = result && intermediateResult;
    … …  
    726719    Free(&FragmentNumber);
    727720  }
    728   DoLog(0) && (Log() << Verbose(0) << " done." << endl);
     721  Log() << Verbose(0) << " done." << endl;
    729722
    730723  // printing final number
    731   DoLog(2) && (Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl);
    732 
    733   // restore cell_size
    734   for (int i=0;i<6;i++)
    735     cell_size[i] = cell_size_backup[i];
     724  Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl;
    736725
    737726  return result;
    … …  
    751740/** Dissects given \a *mol into connected subgraphs and inserts them as new molecules but with old atoms into \a this.
    752741 * \param *out output stream for debugging
    753  * \param *periode periodentafel
     742 * \param *mol molecule with atoms to dissect
    754743 * \param *configuration config with BondGraph
    755744 */
    756 void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration)
    757 {
    758   molecule *mol = new molecule(periode);
    759   atom *Walker = NULL;
    760   atom *Advancer = NULL;
    761   bond *Binder = NULL;
    762   bond *Stepper = NULL;
    763   // 0. gather all atoms into single molecule
    764   for (MoleculeList::iterator MolRunner = ListOfMolecules.begin(); !ListOfMolecules.empty(); MolRunner = ListOfMolecules.begin()) {
    765     // shift all atoms to new molecule
    766     Advancer = (*MolRunner)->start->next;
    767     while (Advancer != (*MolRunner)->end) {
    768       Walker = Advancer;
    769       Advancer = Advancer->next;
    770       DoLog(3) && (Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl);
    771       unlink(Walker);
    772       Walker->father = Walker;
    773       mol->AddAtom(Walker);    // counting starts at 1
    774     }
    775     // remove all bonds
    776     Stepper = (*MolRunner)->first->next;
    777     while (Stepper != (*MolRunner)->last) {
    778       Binder = Stepper;
    779       Stepper = Stepper->next;
    780       delete(Binder);
    781     }
    782     // remove the molecule
    783     delete(*MolRunner);
    784     ListOfMolecules.erase(MolRunner);
    785   }
    786 
     745void MoleculeListClass::DissectMoleculeIntoConnectedSubgraphs(molecule * const mol, config * const configuration)
     746{
    787747  // 1. dissect the molecule into connected subgraphs
    788   if (!configuration->BG->ConstructBondGraph(mol)) {
    789     delete (mol);
    790     DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
    791     return;
    792   }
     748  configuration->BG->ConstructBondGraph(mol);
    793749
    794750  // 2. scan for connected subgraphs
    … …  
    797753  Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
    798754  delete(BackEdgeStack);
    799   if ((Subgraphs == NULL) || (Subgraphs->next == NULL)) {
    800     delete (mol);
    801     DoeLog(1) && (eLog()<< Verbose(1) << "There are no atoms." << endl);
    802     return;
    803   }
    804755
    805756  // 3. dissect (the following construct is needed to have the atoms not in the order of the DFS, but in
    … …  
    819770      strncat(molecules[i]->name, number, MAXSTRINGSIZE - strlen(mol->name) - 1);
    820771    }
    821     DoLog(1) && (Log() << Verbose(1) << "MolName is " << molecules[i]->name << endl);
     772    cout << "MolName is " << molecules[i]->name << endl;
    822773    insert(molecules[i]);
    823774  }
    … …  
    827778  int *MolMap = Calloc<int>(mol->AtomCount, "config::Load() - *MolMap");
    828779  MoleculeLeafClass *MolecularWalker = Subgraphs;
    829   Walker = NULL;
     780  atom *Walker = NULL;
    830781  while (MolecularWalker->next != NULL) {
    831782    MolecularWalker = MolecularWalker->next;
    … …  
    843794    Walker = mol->start->next;
    844795    if ((Walker->nr <0) || (Walker->nr >= mol->AtomCount)) {
    845       DoeLog(0) && (eLog()<< Verbose(0) << "Index of atom " << *Walker << " is invalid!" << endl);
     796      eLog() << Verbose(0) << "Index of atom " << *Walker << " is invalid!" << endl;
    846797      performCriticalExit();
    847798    }
    848799    FragmentCounter = MolMap[Walker->nr];
    849800    if (FragmentCounter != 0) {
    850       DoLog(3) && (Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl);
     801      Log() << Verbose(3) << "Re-linking " << *Walker << "..." << endl;
    851802      unlink(Walker);
    852803      molecules[FragmentCounter-1]->AddAtom(Walker);    // counting starts at 1
    853804    } else {
    854       DoeLog(0) && (eLog()<< Verbose(0) << "Atom " << *Walker << " not associated to molecule!" << endl);
     805      eLog() << Verbose(0) << "Atom " << *Walker << " not associated to molecule!" << endl;
    855806      performCriticalExit();
    856807    }
    857808  }
    858809  // 4d. we don't need to redo bonds, as they are connected subgraphs and still maintain their ListOfBonds, but we have to remove them from first..last list
    859   Binder = mol->first;
     810  bond *Binder = mol->first;
    860811  while (mol->first->next != mol->last) {
    861812    Binder = mol->first->next;
    … …  
    873824  Free(&MolMap);
    874825  Free(&molecules);
    875   DoLog(1) && (Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl);
     826  Log() << Verbose(1) << "I scanned " << FragmentCounter << " molecules." << endl;
    876827};
    877828
    … …  
    982933  int AtomNo;
    983934
    984   DoLog(1) && (Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl);
     935  Log() << Verbose(1) << "Begin of FillBondStructureFromReference." << endl;
    985936  // fill ListOfLocalAtoms if NULL was given
    986937  if (!FillListOfLocalAtoms(ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
    987     DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
     938    Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl;
    988939    return false;
    989940  }
    990941
    991942  if (status) {
    992     DoLog(1) && (Log() << Verbose(1) << "Creating adjacency list for subgraph " << Leaf << "." << endl);
     943    Log() << Verbose(1) << "Creating adjacency list for subgraph " << Leaf << "." << endl;
    993944    // remove every bond from the list
    994945    bond *Binder = NULL;
    … …  
    1011962            Leaf->AddBond(Walker, OtherWalker, (*Runner)->BondDegree);
    1012963        } else {
    1013           DoLog(1) && (Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << FragmentCounter << "][" << (*Runner)->GetOtherAtom(Walker->GetTrueFather())->nr << "] is NULL!" << endl);
     964          Log() << Verbose(1) << "OtherWalker = ListOfLocalAtoms[" << FragmentCounter << "][" << (*Runner)->GetOtherAtom(Walker->GetTrueFather())->nr << "] is NULL!" << endl;
    1014965          status = false;
    1015966        }
    … …  
    1024975      Free(&ListOfLocalAtoms);
    1025976  }
    1026   DoLog(1) && (Log() << Verbose(1) << "End of FillBondStructureFromReference." << endl);
     977  Log() << Verbose(1) << "End of FillBondStructureFromReference." << endl;
    1027978  return status;
    1028979};
    … …  
    10571008        next->FillRootStackForSubgraphs(RootStack, AtomMask, ++FragmentCounter);
    10581009    } else {
    1059       DoLog(1) && (Log() << Verbose(1) << "Rootstack[" << FragmentCounter << "] is NULL." << endl);
     1010      Log() << Verbose(1) << "Rootstack[" << FragmentCounter << "] is NULL." << endl;
    10601011      return false;
    10611012    }
    … …  
    10631014    return true;
    10641015  } else {
    1065     DoLog(1) && (Log() << Verbose(1) << "Rootstack is NULL." << endl);
     1016    Log() << Verbose(1) << "Rootstack is NULL." << endl;
    10661017    return false;
    10671018  }
    … …  
    11131064  int KeySetCounter = 0;
    11141065
    1115   DoLog(1) && (Log() << Verbose(1) << "Begin of AssignKeySetsToFragment." << endl);
     1066  Log() << Verbose(1) << "Begin of AssignKeySetsToFragment." << endl;
    11161067  // fill ListOfLocalAtoms if NULL was given
    11171068  if (!FillListOfLocalAtoms(ListOfLocalAtoms, FragmentCounter, reference->AtomCount, FreeList)) {
    1118     DoLog(1) && (Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl);
     1069    Log() << Verbose(1) << "Filling of ListOfLocalAtoms failed." << endl;
    11191070    return false;
    11201071  }
    … …  
    11441095    delete (TempSet);
    11451096    if (KeySetCounter == 0) {// if there are no keysets, delete the list
    1146       DoLog(1) && (Log() << Verbose(1) << "KeySetCounter is zero, deleting FragmentList." << endl);
     1097      Log() << Verbose(1) << "KeySetCounter is zero, deleting FragmentList." << endl;
    11471098      delete (FragmentList[FragmentCounter]);
    11481099    } else
    1149       DoLog(1) && (Log() << Verbose(1) << KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << "." << endl);
     1100      Log() << Verbose(1) << KeySetCounter << " keysets were assigned to subgraph " << FragmentCounter << "." << endl;
    11501101    FragmentCounter++;
    11511102    if (next != NULL)
    … …  
    11531104    FragmentCounter--;
    11541105  } else
    1155     DoLog(1) && (Log() << Verbose(1) << "KeySetList is NULL or empty." << endl);
     1106    Log() << Verbose(1) << "KeySetList is NULL or empty." << endl;
    11561107
    11571108  if ((FreeList) && (ListOfLocalAtoms != NULL)) {
    … …  
    11611112      Free(&ListOfLocalAtoms);
    11621113  }
    1163   DoLog(1) && (Log() << Verbose(1) << "End of AssignKeySetsToFragment." << endl);
     1114  Log() << Verbose(1) << "End of AssignKeySetsToFragment." << endl;
    11641115  return status;
    11651116};
    … …  
    11741125void MoleculeLeafClass::TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph)
    11751126{
    1176   DoLog(1) && (Log() << Verbose(1) << "Begin of TranslateIndicesToGlobalIDs." << endl);
     1127  Log() << Verbose(1) << "Begin of TranslateIndicesToGlobalIDs." << endl;
    11771128  KeySet *TempSet = new KeySet;
    11781129  if (FragmentList[FragmentCounter] != NULL) {
    … …  
    11851136    delete (TempSet);
    11861137  } else {
    1187     DoLog(1) && (Log() << Verbose(1) << "FragmentList is NULL." << endl);
     1138    Log() << Verbose(1) << "FragmentList is NULL." << endl;
    11881139  }
    11891140  if (next != NULL)
    11901141    next->TranslateIndicesToGlobalIDs(FragmentList, ++FragmentCounter, TotalNumberOfKeySets, TotalGraph);
    11911142  FragmentCounter--;
    1192   DoLog(1) && (Log() << Verbose(1) << "End of TranslateIndicesToGlobalIDs." << endl);
     1143  Log() << Verbose(1) << "End of TranslateIndicesToGlobalIDs." << endl;
    11931144};
    11941145
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