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  • src/molecule_fragmentation.cpp

    ra67d19 r49e1ae  
    1818#include "molecule.hpp"
    1919#include "periodentafel.hpp"
    20 #include "World.hpp"
    2120
    2221/************************************* Functions for class molecule *********************************/
    … …  
    4443  }
    4544  FragmentCount = NoNonHydrogen*(1 << (c*order));
    46   DoLog(1) && (Log() << Verbose(1) << "Upper limit for this subgraph is " << FragmentCount << " for " << NoNonHydrogen << " non-H atoms with maximum bond degree of " << c << "." << endl);
     45  Log() << Verbose(1) << "Upper limit for this subgraph is " << FragmentCount << " for " << NoNonHydrogen << " non-H atoms with maximum bond degree of " << c << "." << endl;
    4746  return FragmentCount;
    4847};
    … …  
    6867    } // else it's "-1" or else and thus must not be added
    6968  }
    70   DoLog(1) && (Log() << Verbose(1) << "The scanned KeySet is ");
     69  Log() << Verbose(1) << "The scanned KeySet is ";
    7170  for(KeySet::iterator runner = CurrentSet.begin(); runner != CurrentSet.end(); runner++) {
    72     DoLog(0) && (Log() << Verbose(0) << (*runner) << "\t");
    73   }
    74   DoLog(0) && (Log() << Verbose(0) << endl);
     71    Log() << Verbose(0) << (*runner) << "\t";
     72  }
     73  Log() << Verbose(0) << endl;
    7574  return (status != 0);
    7675};
    … …  
    10099
    101100  // 1st pass: open file and read
    102   DoLog(1) && (Log() << Verbose(1) << "Parsing the KeySet file ... " << endl);
     101  Log() << Verbose(1) << "Parsing the KeySet file ... " << endl;
    103102  sprintf(filename, "%s/%s%s", path, FRAGMENTPREFIX, KEYSETFILE);
    104103  InputFile.open(filename);
    … …  
    113112        testGraphInsert = FragmentList->insert(GraphPair (CurrentSet,pair<int,double>(NumberOfFragments++,1)));  // store fragment number and current factor
    114113        if (!testGraphInsert.second) {
    115           DoeLog(0) && (eLog()<< Verbose(0) << "KeySet file must be corrupt as there are two equal key sets therein!" << endl);
     114          eLog() << Verbose(0) << "KeySet file must be corrupt as there are two equal key sets therein!" << endl;
    116115          performCriticalExit();
    117116        }
    … …  
    122121    InputFile.clear();
    123122    Free(&buffer);
    124     DoLog(1) && (Log() << Verbose(1) << "done." << endl);
     123    Log() << Verbose(1) << "done." << endl;
    125124  } else {
    126     DoLog(1) && (Log() << Verbose(1) << "File " << filename << " not found." << endl);
     125    Log() << Verbose(1) << "File " << filename << " not found." << endl;
    127126    status = false;
    128127  }
    … …  
    154153
    155154  // 2nd pass: open TEFactors file and read
    156   DoLog(1) && (Log() << Verbose(1) << "Parsing the TEFactors file ... " << endl);
     155  Log() << Verbose(1) << "Parsing the TEFactors file ... " << endl;
    157156  sprintf(filename, "%s/%s%s", path, FRAGMENTPREFIX, TEFACTORSFILE);
    158157  InputFile.open(filename);
    … …  
    164163        InputFile >> TEFactor;
    165164        (*runner).second.second = TEFactor;
    166         DoLog(2) && (Log() << Verbose(2) << "Setting " << ++NumberOfFragments << " fragment's TEFactor to " << (*runner).second.second << "." << endl);
     165        Log() << Verbose(2) << "Setting " << ++NumberOfFragments << " fragment's TEFactor to " << (*runner).second.second << "." << endl;
    167166      } else {
    168167        status = false;
    … …  
    172171    // 4. Free and done
    173172    InputFile.close();
    174     DoLog(1) && (Log() << Verbose(1) << "done." << endl);
     173    Log() << Verbose(1) << "done." << endl;
    175174  } else {
    176     DoLog(1) && (Log() << Verbose(1) << "File " << filename << " not found." << endl);
     175    Log() << Verbose(1) << "File " << filename << " not found." << endl;
    177176    status = false;
    178177  }
    … …  
    202201  line += KEYSETFILE;
    203202  output.open(line.c_str(), ios::out);
    204   DoLog(1) && (Log() << Verbose(1) << "Saving key sets of the total graph ... ");
     203  Log() << Verbose(1) << "Saving key sets of the total graph ... ";
    205204  if(output != NULL) {
    206205    for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++) {
    … …  
    212211      output << endl;
    213212    }
    214     DoLog(0) && (Log() << Verbose(0) << "done." << endl);
     213    Log() << Verbose(0) << "done." << endl;
    215214  } else {
    216     DoeLog(0) && (eLog()<< Verbose(0) << "Unable to open " << line << " for writing keysets!" << endl);
     215    eLog() << Verbose(0) << "Unable to open " << line << " for writing keysets!" << endl;
    217216    performCriticalExit();
    218217    status = false;
    … …  
    243242  line += TEFACTORSFILE;
    244243  output.open(line.c_str(), ios::out);
    245   DoLog(1) && (Log() << Verbose(1) << "Saving TEFactors of the total graph ... ");
     244  Log() << Verbose(1) << "Saving TEFactors of the total graph ... ";
    246245  if(output != NULL) {
    247246    for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++)
    248247      output << (*runner).second.second << endl;
    249     DoLog(1) && (Log() << Verbose(1) << "done." << endl);
     248    Log() << Verbose(1) << "done." << endl;
    250249  } else {
    251     DoLog(1) && (Log() << Verbose(1) << "failed to open " << line << "." << endl);
     250    Log() << Verbose(1) << "failed to open " << line << "." << endl;
    252251    status = false;
    253252  }
    … …  
    293292        (*PresentItem).second.first = fabs(Value);
    294293        (*PresentItem).second.second = FragOrder;
    295         DoLog(2) && (Log() << Verbose(2) << "Updated element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl);
     294        Log() << Verbose(2) << "Updated element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl;
    296295      } else {
    297         DoLog(2) && (Log() << Verbose(2) << "Did not update element " <<  (*PresentItem).first << " as " << FragOrder << " is less than or equal to " << (*PresentItem).second.second << "." << endl);
     296        Log() << Verbose(2) << "Did not update element " <<  (*PresentItem).first << " as " << FragOrder << " is less than or equal to " << (*PresentItem).second.second << "." << endl;
    298297      }
    299298    } else {
    300       DoLog(2) && (Log() << Verbose(2) << "Inserted element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl);
     299      Log() << Verbose(2) << "Inserted element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl;
    301300    }
    302301  } else {
    303     DoLog(1) && (Log() << Verbose(1) << "No Fragment under No. " << No << "found." << endl);
     302    Log() << Verbose(1) << "No Fragment under No. " << No << "found." << endl;
    304303  }
    305304};
    … …  
    360359  atom *Walker = mol->start;
    361360  map<double, pair<int,int> > *FinalRootCandidates = new map<double, pair<int,int> > ;
    362   DoLog(1) && (Log() << Verbose(1) << "Root candidate list is: " << endl);
     361  Log() << Verbose(1) << "Root candidate list is: " << endl;
    363362  for(map<int, pair<double,int> >::iterator runner = AdaptiveCriteriaList->begin(); runner != AdaptiveCriteriaList->end(); runner++) {
    364363    Walker = mol->FindAtom((*runner).first);
    … …  
    366365      //if ((*runner).second.second >= Walker->AdaptiveOrder) { // only insert if this is an "active" root site for the current order
    367366      if (!Walker->MaxOrder) {
    368         DoLog(2) && (Log() << Verbose(2) << "(" << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "])" << endl);
     367        Log() << Verbose(2) << "(" << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "])" << endl;
    369368        FinalRootCandidates->insert( make_pair( (*runner).second.first, pair<int,int>((*runner).first, (*runner).second.second) ) );
    370369      } else {
    371         DoLog(2) && (Log() << Verbose(2) << "Excluding (" << *Walker << ", " << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "]), as it has reached its maximum order." << endl);
     370        Log() << Verbose(2) << "Excluding (" << *Walker << ", " << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "]), as it has reached its maximum order." << endl;
    372371      }
    373372    } else {
    374       DoeLog(0) && (eLog()<< Verbose(0) << "Atom No. " << (*runner).second.first << " was not found in this molecule." << endl);
     373      eLog() << Verbose(0) << "Atom No. " << (*runner).second.first << " was not found in this molecule." << endl;
    375374      performCriticalExit();
    376375    }
    … …  
    397396    Walker = mol->FindAtom(No);
    398397    //if (Walker->AdaptiveOrder < MinimumRingSize[Walker->nr]) {
    399       DoLog(2) && (Log() << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to true." << endl);
     398      Log() << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to true." << endl;
    400399      AtomMask[No] = true;
    401400      status = true;
    … …  
    413412void PrintAtomMask(bool *AtomMask, int AtomCount)
    414413{
    415   DoLog(2) && (Log() << Verbose(2) << "              ");
     414  Log() << Verbose(2) << "              ";
    416415  for(int i=0;i<AtomCount;i++)
    417     DoLog(0) && (Log() << Verbose(0) << (i % 10));
    418   DoLog(0) && (Log() << Verbose(0) << endl);
    419   DoLog(2) && (Log() << Verbose(2) << "Atom mask is: ");
     416    Log() << Verbose(0) << (i % 10);
     417  Log() << Verbose(0) << endl;
     418  Log() << Verbose(2) << "Atom mask is: ";
    420419  for(int i=0;i<AtomCount;i++)
    421     DoLog(0) && (Log() << Verbose(0) << (AtomMask[i] ? "t" : "f"));
    422   DoLog(0) && (Log() << Verbose(0) << endl);
     420    Log() << Verbose(0) << (AtomMask[i] ? "t" : "f");
     421  Log() << Verbose(0) << endl;
    423422};
    424423
    … …  
    447446    // transmorph graph keyset list into indexed KeySetList
    448447    if (GlobalKeySetList == NULL) {
    449       DoeLog(1) && (eLog()<< Verbose(1) << "Given global key set list (graph) is NULL!" << endl);
     448      eLog() << Verbose(1) << "Given global key set list (graph) is NULL!" << endl;
    450449      return false;
    451450    }
    … …  
    455454    map<int, pair<double,int> > *AdaptiveCriteriaList = ScanAdaptiveFileIntoMap(path, *IndexKeySetList); // (Root No., (Value, Order)) !
    456455    if (AdaptiveCriteriaList->empty()) {
    457       DoeLog(2) && (eLog()<< Verbose(2) << "Unable to parse file, incrementing all." << endl);
     456      eLog() << Verbose(2) << "Unable to parse file, incrementing all." << endl;
    458457      while (Walker->next != end) {
    459458        Walker = Walker->next;
    … …  
    493492    if (!status) {
    494493      if (Order == 0)
    495         DoLog(1) && (Log() << Verbose(1) << "Single stepping done." << endl);
     494        Log() << Verbose(1) << "Single stepping done." << endl;
    496495      else
    497         DoLog(1) && (Log() << Verbose(1) << "Order at every site is already equal or above desired order " << Order << "." << endl);
     496        Log() << Verbose(1) << "Order at every site is already equal or above desired order " << Order << "." << endl;
    498497    }
    499498  }
    … …  
    512511{
    513512  if (SortIndex != NULL) {
    514     DoLog(1) && (Log() << Verbose(1) << "SortIndex is " << SortIndex << " and not NULL as expected." << endl);
     513    Log() << Verbose(1) << "SortIndex is " << SortIndex << " and not NULL as expected." << endl;
    515514    return false;
    516515  }
    … …  
    563562  bool *AtomMask = NULL;
    564563
    565   DoLog(0) && (Log() << Verbose(0) << endl);
     564  Log() << Verbose(0) << endl;
    566565#ifdef ADDHYDROGEN
    567   DoLog(0) && (Log() << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl);
     566  Log() << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl;
    568567#else
    569   DoLog(0) && (Log() << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl);
     568  Log() << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl;
    570569#endif
    571570
    … …  
    593592    // fill the bond structure of the individually stored subgraphs
    594593  MolecularWalker->FillBondStructureFromReference(this, FragmentCounter, ListOfLocalAtoms, false);  // we want to keep the created ListOfLocalAtoms
    595     DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
     594    Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
    596595    LocalBackEdgeStack = new StackClass<bond *> (MolecularWalker->Leaf->BondCount);
    597596//    // check the list of local atoms for debugging
    … …  
    602601//      else
    603602//        Log() << Verbose(0) << "\t" << ListOfLocalAtoms[FragmentCounter][i]->Name;
    604     DoLog(0) && (Log() << Verbose(0) << "Gathering local back edges for subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
     603    Log() << Verbose(0) << "Gathering local back edges for subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
    605604    MolecularWalker->Leaf->PickLocalBackEdges(ListOfLocalAtoms[FragmentCounter++], BackEdgeStack, LocalBackEdgeStack);
    606     DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
     605    Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
    607606    MolecularWalker->Leaf->CyclicStructureAnalysis(LocalBackEdgeStack, MinimumRingSize);
    608     DoLog(0) && (Log() << Verbose(0) << "Done with Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
     607    Log() << Verbose(0) << "Done with Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
    609608    delete(LocalBackEdgeStack);
    610609  }
    … …  
    637636    while (MolecularWalker->next != NULL) {
    638637      MolecularWalker = MolecularWalker->next;
    639       DoLog(1) && (Log() << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl);
     638      Log() << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl;
    640639      //MolecularWalker->Leaf->OutputListOfBonds(out);  // output atom::ListOfBonds for debugging
    641640      if (MolecularWalker->Leaf->first->next != MolecularWalker->Leaf->last) {
    642641        // call BOSSANOVA method
    643         DoLog(0) && (Log() << Verbose(0) << endl << " ========== BOND ENERGY of subgraph " << FragmentCounter << " ========================= " << endl);
     642        Log() << Verbose(0) << endl << " ========== BOND ENERGY of subgraph " << FragmentCounter << " ========================= " << endl;
    644643        MolecularWalker->Leaf->FragmentBOSSANOVA(FragmentList[FragmentCounter], RootStack[FragmentCounter], MinimumRingSize);
    645644      } else {
    646         DoeLog(1) && (eLog()<< Verbose(1) << "Subgraph " << MolecularWalker << " has no atoms!" << endl);
     645        eLog() << Verbose(1) << "Subgraph " << MolecularWalker << " has no atoms!" << endl;
    647646      }
    648647      FragmentCounter++;  // next fragment list
    649648    }
    650649  }
    651   DoLog(2) && (Log() << Verbose(2) << "CheckOrder is " << CheckOrder << "." << endl);
     650  Log() << Verbose(2) << "CheckOrder is " << CheckOrder << "." << endl;
    652651  delete[](RootStack);
    653652  delete[](AtomMask);
    … …  
    680679  for(Graph::iterator runner = TotalGraph.begin(); runner != TotalGraph.end(); runner++) {
    681680    KeySet test = (*runner).first;
    682     DoLog(0) && (Log() << Verbose(0) << "Fragment No." << (*runner).second.first << " with TEFactor " << (*runner).second.second << "." << endl);
     681    Log() << Verbose(0) << "Fragment No." << (*runner).second.first << " with TEFactor " << (*runner).second.second << "." << endl;
    683682    BondFragments->insert(StoreFragmentFromKeySet(test, configuration));
    684683    k++;
    685684  }
    686   DoLog(0) && (Log() << Verbose(0) << k << "/" << BondFragments->ListOfMolecules.size() << " fragments generated from the keysets." << endl);
     685  Log() << Verbose(0) << k << "/" << BondFragments->ListOfMolecules.size() << " fragments generated from the keysets." << endl;
    687686
    688687  // ===== 9. Save fragments' configuration and keyset files et al to disk ===
    … …  
    691690    CreateMappingLabelsToConfigSequence(SortIndex);
    692691
    693     DoLog(1) && (Log() << Verbose(1) << "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs" << endl);
     692    Log() << Verbose(1) << "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs" << endl;
    694693    if (BondFragments->OutputConfigForListOfFragments(configuration, SortIndex))
    695       DoLog(1) && (Log() << Verbose(1) << "All configs written." << endl);
     694      Log() << Verbose(1) << "All configs written." << endl;
    696695    else
    697       DoLog(1) && (Log() << Verbose(1) << "Some config writing failed." << endl);
     696      Log() << Verbose(1) << "Some config writing failed." << endl;
    698697
    699698    // store force index reference file
    … …  
    704703
    705704    // store Adjacency file
    706     char *filename = Malloc<char> (MAXSTRINGSIZE, "molecule::FragmentMolecule - *filename");
    707     strcpy(filename, FRAGMENTPREFIX);
    708     strcat(filename, ADJACENCYFILE);
    709     StoreAdjacencyToFile(configuration->configpath, filename);
    710     Free(&filename);
     705    StoreAdjacencyToFile(configuration->configpath);
    711706
    712707    // store Hydrogen saturation correction file
    … …  
    720715
    721716    // free memory for bond part
    722     DoLog(1) && (Log() << Verbose(1) << "Freeing bond memory" << endl);
     717    Log() << Verbose(1) << "Freeing bond memory" << endl;
    723718    delete(FragmentList); // remove bond molecule from memory
    724719    Free(&SortIndex);
    725720  } else {
    726     DoLog(1) && (Log() << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl);
     721    Log() << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl;
    727722  }
    728723  delete(BondFragments);
    729   DoLog(0) && (Log() << Verbose(0) << "End of bond fragmentation." << endl);
     724  Log() << Verbose(0) << "End of bond fragmentation." << endl;
    730725
    731726  return ((int)(!FragmentationToDo)+1);    // 1 - continue, 2 - stop (no fragmentation occured)
    … …  
    746741  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
    747742  file.open(line.str().c_str());
    748   DoLog(1) && (Log() << Verbose(1) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl);
     743  Log() << Verbose(1) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl;
    749744  if (file != NULL) {
    750745    ActOnAllAtoms( &atom::OutputOrder, &file );
    751746    file.close();
    752     DoLog(1) && (Log() << Verbose(1) << "done." << endl);
     747    Log() << Verbose(1) << "done." << endl;
    753748    return true;
    754749  } else {
    755     DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
     750    Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
    756751    return false;
    757752  }
    … …  
    774769  ifstream file;
    775770
    776   DoLog(1) && (Log() << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl);
     771  Log() << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl;
    777772  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
    778773  file.open(line.str().c_str());
    … …  
    795790    SetAtomValueToIndexedArray( MaxArray, &atom::nr, &atom::MaxOrder );
    796791
    797     DoLog(1) && (Log() << Verbose(1) << "done." << endl);
     792    Log() << Verbose(1) << "done." << endl;
    798793    status = true;
    799794  } else {
    800     DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
     795    Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
    801796    status = false;
    802797  }
    … …  
    804799  Free(&MaxArray);
    805800
    806   DoLog(1) && (Log() << Verbose(1) << "End of ParseOrderAtSiteFromFile" << endl);
     801  Log() << Verbose(1) << "End of ParseOrderAtSiteFromFile" << endl;
    807802  return status;
    808803};
    … …  
    821816  int SP, Removal;
    822817
    823   DoLog(2) && (Log() << Verbose(2) << "Looking for removal candidate." << endl);
     818  Log() << Verbose(2) << "Looking for removal candidate." << endl;
    824819  SP = -1; //0;  // not -1, so that Root is never removed
    825820  Removal = -1;
    … …  
    848843
    849844  Leaf->BondDistance = mol->BondDistance;
     845  for(int i=NDIM*2;i--;)
     846    Leaf->cell_size[i] = mol->cell_size[i];
    850847
    851848  // first create the minimal set of atoms from the KeySet
    … …  
    906903      }
    907904    } else {
    908       DoeLog(1) && (eLog()<< Verbose(1) << "Son " << Runner->Name << " has father " << FatherOfRunner->Name << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl);
     905      eLog() << Verbose(1) << "Son " << Runner->Name << " has father " << FatherOfRunner->Name << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl;
    909906    }
    910907    if ((LonelyFlag) && (Leaf->AtomCount > 1)) {
    911       DoLog(0) && (Log() << Verbose(0) << *Runner << "has got bonds only to hydrogens!" << endl);
     908      Log() << Verbose(0) << *Runner << "has got bonds only to hydrogens!" << endl;
    912909    }
    913910#ifdef ADDHYDROGEN
    … …  
    10561053    TouchedList[j] = -1;
    10571054  }
    1058   DoLog(2) && (Log() << Verbose(2) << "Remaining local nr.s on snake stack are: ");
     1055  Log() << Verbose(2) << "Remaining local nr.s on snake stack are: ";
    10591056  for(KeySet::iterator runner = FragmentSet->begin(); runner != FragmentSet->end(); runner++)
    1060     DoLog(0) && (Log() << Verbose(0) << (*runner) << " ");
    1061   DoLog(0) && (Log() << Verbose(0) << endl);
     1057    Log() << Verbose(0) << (*runner) << " ";
     1058  Log() << Verbose(0) << endl;
    10621059  TouchedIndex = 0; // set Index to 0 for list of atoms added on this level
    10631060};
    … …  
    11361133        Log() << Verbose(1+verbosity) << "Enough items on stack for a fragment!" << endl;
    11371134        // store fragment as a KeySet
    1138         DoLog(2) && (Log() << Verbose(2) << "Found a new fragment[" << FragmentSearch->FragmentCounter << "], local nr.s are: ");
     1135        Log() << Verbose(2) << "Found a new fragment[" << FragmentSearch->FragmentCounter << "], local nr.s are: ";
    11391136        for(KeySet::iterator runner = FragmentSearch->FragmentSet->begin(); runner != FragmentSearch->FragmentSet->end(); runner++)
    1140           DoLog(0) && (Log() << Verbose(0) << (*runner) << " ");
    1141         DoLog(0) && (Log() << Verbose(0) << endl);
     1137          Log() << Verbose(0) << (*runner) << " ";
     1138        Log() << Verbose(0) << endl;
    11421139        //if (!CheckForConnectedSubgraph(FragmentSearch->FragmentSet))
    1143           //DoeLog(1) && (eLog()<< Verbose(1) << "The found fragment is not a connected subgraph!" << endl);
     1140          //eLog() << Verbose(1) << "The found fragment is not a connected subgraph!" << endl;
    11441141        InsertFragmentIntoGraph(FragmentSearch);
    11451142      }
    … …  
    12211218{
    12221219  bond *Binder = NULL;
    1223   DoLog(0) && (Log() << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl);
     1220  Log() << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl;
    12241221  for(int i=Order;i--;) {
    1225     DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << ": ");
     1222    Log() << Verbose(1) << "Current SP level is " << i << ": ";
    12261223    Binder = FragmentSearch.BondsPerSPList[2*i];
    12271224    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
    … …  
    12341231    cleanup(FragmentSearch.BondsPerSPList[2*i], FragmentSearch.BondsPerSPList[2*i+1]);
    12351232    // also start and end node
    1236     DoLog(0) && (Log() << Verbose(0) << "cleaned." << endl);
     1233    Log() << Verbose(0) << "cleaned." << endl;
    12371234  }
    12381235};
    … …  
    12641261  int SP = -1;
    12651262
    1266   DoLog(0) && (Log() << Verbose(0) << "Starting BFS analysis ..." << endl);
     1263  Log() << Verbose(0) << "Starting BFS analysis ..." << endl;
    12671264  for (SP = 0; SP < (Order-1); SP++) {
    1268     DoLog(1) && (Log() << Verbose(1) << "New SP level reached: " << SP << ", creating new SP list with " << FragmentSearch.BondsPerSPCount[SP] << " item(s)");
     1265    Log() << Verbose(1) << "New SP level reached: " << SP << ", creating new SP list with " << FragmentSearch.BondsPerSPCount[SP] << " item(s)";
    12691266    if (SP > 0) {
    1270       DoLog(0) && (Log() << Verbose(0) << ", old level closed with " << FragmentSearch.BondsPerSPCount[SP-1] << " item(s)." << endl);
     1267      Log() << Verbose(0) << ", old level closed with " << FragmentSearch.BondsPerSPCount[SP-1] << " item(s)." << endl;
    12711268      FragmentSearch.BondsPerSPCount[SP] = 0;
    12721269    } else
    1273       DoLog(0) && (Log() << Verbose(0) << "." << endl);
     1270      Log() << Verbose(0) << "." << endl;
    12741271
    12751272    RemainingWalkers = FragmentSearch.BondsPerSPCount[SP];
    … …  
    12811278      Predecessor = CurrentEdge->leftatom;    // ... and leftatom is predecessor
    12821279      AtomKeyNr = Walker->nr;
    1283       DoLog(0) && (Log() << Verbose(0) << "Current Walker is: " << *Walker << " with nr " << Walker->nr << " and SP of " << SP << ", with " << RemainingWalkers << " remaining walkers on this level." << endl);
     1280      Log() << Verbose(0) << "Current Walker is: " << *Walker << " with nr " << Walker->nr << " and SP of " << SP << ", with " << RemainingWalkers << " remaining walkers on this level." << endl;
    12841281      // check for new sp level
    12851282      // go through all its bonds
    1286       DoLog(1) && (Log() << Verbose(1) << "Going through all bonds of Walker." << endl);
     1283      Log() << Verbose(1) << "Going through all bonds of Walker." << endl;
    12871284      for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
    12881285        OtherWalker = (*Runner)->GetOtherAtom(Walker);
    … …  
    12921289  #endif
    12931290                                                              ) {  // skip hydrogens and restrict to fragment
    1294           DoLog(2) && (Log() << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->nr << " in bond " << *(*Runner) << "." << endl);
     1291          Log() << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->nr << " in bond " << *(*Runner) << "." << endl;
    12951292          // set the label if not set (and push on root stack as well)
    12961293          if ((OtherWalker != Predecessor) && (OtherWalker->GetTrueFather()->nr > RootKeyNr)) { // only pass through those with label bigger than Root's
    12971294            FragmentSearch.ShortestPathList[OtherWalker->nr] = SP+1;
    1298             DoLog(3) && (Log() << Verbose(3) << "Set Shortest Path to " << FragmentSearch.ShortestPathList[OtherWalker->nr] << "." << endl);
     1295            Log() << Verbose(3) << "Set Shortest Path to " << FragmentSearch.ShortestPathList[OtherWalker->nr] << "." << endl;
    12991296            // add the bond in between to the SP list
    13001297            Binder = new bond(Walker, OtherWalker); // create a new bond in such a manner, that bond::rightatom is always the one more distant
    13011298            add(Binder, FragmentSearch.BondsPerSPList[2*(SP+1)+1]);
    13021299            FragmentSearch.BondsPerSPCount[SP+1]++;
    1303             DoLog(3) && (Log() << Verbose(3) << "Added its bond to SP list, having now " << FragmentSearch.BondsPerSPCount[SP+1] << " item(s)." << endl);
     1300            Log() << Verbose(3) << "Added its bond to SP list, having now " << FragmentSearch.BondsPerSPCount[SP+1] << " item(s)." << endl;
    13041301          } else {
    13051302            if (OtherWalker != Predecessor)
    1306               DoLog(3) && (Log() << Verbose(3) << "Not passing on, as index of " << *OtherWalker << " " << OtherWalker->GetTrueFather()->nr << " is smaller than that of Root " << RootKeyNr << "." << endl);
     1303              Log() << Verbose(3) << "Not passing on, as index of " << *OtherWalker << " " << OtherWalker->GetTrueFather()->nr << " is smaller than that of Root " << RootKeyNr << "." << endl;
    13071304            else
    1308               DoLog(3) && (Log() << Verbose(3) << "This is my predecessor " << *Predecessor << "." << endl);
     1305              Log() << Verbose(3) << "This is my predecessor " << *Predecessor << "." << endl;
    13091306          }
    13101307        } else Log() << Verbose(2) << "Is not in the restricted keyset or skipping hydrogen " << *OtherWalker << "." << endl;
    … …  
    13221319{
    13231320  bond *Binder = NULL;
    1324   DoLog(0) && (Log() << Verbose(0) << "Printing all found lists." << endl);
     1321  Log() << Verbose(0) << "Printing all found lists." << endl;
    13251322  for(int i=1;i<Order;i++) {    // skip the root edge in the printing
    13261323    Binder = FragmentSearch.BondsPerSPList[2*i];
    1327     DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << "." << endl);
     1324    Log() << Verbose(1) << "Current SP level is " << i << "." << endl;
    13281325    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
    13291326      Binder = Binder->next;
    1330       DoLog(2) && (Log() << Verbose(2) << *Binder << endl);
     1327      Log() << Verbose(2) << *Binder << endl;
    13311328    }
    13321329  }
    … …  
    13721369  int Counter = FragmentSearch.FragmentCounter; // mark current value of counter
    13731370
    1374   DoLog(0) && (Log() << Verbose(0) << endl);
    1375   DoLog(0) && (Log() << Verbose(0) << "Begin of PowerSetGenerator with order " << Order << " at Root " << *FragmentSearch.Root << "." << endl);
     1371  Log() << Verbose(0) << endl;
     1372  Log() << Verbose(0) << "Begin of PowerSetGenerator with order " << Order << " at Root " << *FragmentSearch.Root << "." << endl;
    13761373
    13771374  SetSPList(Order, FragmentSearch);
    … …  
    13851382  // creating fragments with the found edge sets  (may be done in reverse order, faster)
    13861383  int SP = CountNumbersInBondsList(Order, FragmentSearch);
    1387   DoLog(0) && (Log() << Verbose(0) << "Total number of edges is " << SP << "." << endl);
     1384  Log() << Verbose(0) << "Total number of edges is " << SP << "." << endl;
    13881385  if (SP >= (Order-1)) {
    13891386    // start with root (push on fragment stack)
    1390     DoLog(0) && (Log() << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.Root << ", local nr is " << FragmentSearch.Root->nr << "." << endl);
     1387    Log() << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.Root << ", local nr is " << FragmentSearch.Root->nr << "." << endl;
    13911388    FragmentSearch.FragmentSet->clear();
    1392     DoLog(0) && (Log() << Verbose(0) << "Preparing subset for this root and calling generator." << endl);
     1389    Log() << Verbose(0) << "Preparing subset for this root and calling generator." << endl;
    13931390
    13941391    // prepare the subset and call the generator
    … …  
    14001397    Free(&BondsList);
    14011398  } else {
    1402     DoLog(0) && (Log() << Verbose(0) << "Not enough total number of edges to build " << Order << "-body fragments." << endl);
     1399    Log() << Verbose(0) << "Not enough total number of edges to build " << Order << "-body fragments." << endl;
    14031400  }
    14041401
    14051402  // as FragmentSearch structure is used only once, we don't have to clean it anymore
    14061403  // remove root from stack
    1407   DoLog(0) && (Log() << Verbose(0) << "Removing root again from stack." << endl);
     1404  Log() << Verbose(0) << "Removing root again from stack." << endl;
    14081405  FragmentSearch.FragmentSet->erase(FragmentSearch.Root->nr);
    14091406
    … …  
    14121409
    14131410  // return list
    1414   DoLog(0) && (Log() << Verbose(0) << "End of PowerSetGenerator." << endl);
     1411  Log() << Verbose(0) << "End of PowerSetGenerator." << endl;
    14151412  return (FragmentSearch.FragmentCounter - Counter);
    14161413};
    … …  
    14581455  atom *Walker = NULL;
    14591456
    1460   DoLog(0) && (Log() << Verbose(0) << "Combining the lists of all orders per order and finally into a single one." << endl);
     1457  Log() << Verbose(0) << "Combining the lists of all orders per order and finally into a single one." << endl;
    14611458  if (FragmentList == NULL) {
    14621459    FragmentList = new Graph;
    … …  
    14911488void FreeAllOrdersList(Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
    14921489{
    1493   DoLog(1) && (Log() << Verbose(1) << "Free'ing the lists of all orders per order." << endl);
     1490  Log() << Verbose(1) << "Free'ing the lists of all orders per order." << endl;
    14941491  int RootNr = 0;
    14951492  int RootKeyNr = 0;
    … …  
    15441541  struct UniqueFragments FragmentSearch;
    15451542
    1546   DoLog(0) && (Log() << Verbose(0) << "Begin of FragmentBOSSANOVA." << endl);
     1543  Log() << Verbose(0) << "Begin of FragmentBOSSANOVA." << endl;
    15471544
    15481545  // FragmentLowerOrdersList is a 2D-array of pointer to MoleculeListClass objects, one dimension represents the ANOVA expansion of a single order (i.e. 5)
    … …  
    15941591
    15951592      // create top order where nothing is reduced
    1596       DoLog(0) && (Log() << Verbose(0) << "==============================================================================================================" << endl);
    1597       DoLog(0) && (Log() << Verbose(0) << "Creating KeySets of Bond Order " << Order << " for " << *Walker << ", " << (RootStack.size()-RootNr) << " Roots remaining." << endl); // , NumLevels is " << NumLevels << "
     1593      Log() << Verbose(0) << "==============================================================================================================" << endl;
     1594      Log() << Verbose(0) << "Creating KeySets of Bond Order " << Order << " for " << *Walker << ", " << (RootStack.size()-RootNr) << " Roots remaining." << endl; // , NumLevels is " << NumLevels << "
    15981595
    15991596      // Create list of Graphs of current Bond Order (i.e. F_{ij})
    … …  
    16051602
    16061603      // output resulting number
    1607       DoLog(1) && (Log() << Verbose(1) << "Number of resulting KeySets is: " << NumMoleculesOfOrder[RootNr] << "." << endl);
     1604      Log() << Verbose(1) << "Number of resulting KeySets is: " << NumMoleculesOfOrder[RootNr] << "." << endl;
    16081605      if (NumMoleculesOfOrder[RootNr] != 0) {
    16091606        NumMolecules = 0;
    … …  
    16221619    }
    16231620  }
    1624   DoLog(0) && (Log() << Verbose(0) << "==============================================================================================================" << endl);
    1625   DoLog(1) && (Log() << Verbose(1) << "Total number of resulting molecules is: " << TotalNumMolecules << "." << endl);
    1626   DoLog(0) && (Log() << Verbose(0) << "==============================================================================================================" << endl);
     1621  Log() << Verbose(0) << "==============================================================================================================" << endl;
     1622  Log() << Verbose(1) << "Total number of resulting molecules is: " << TotalNumMolecules << "." << endl;
     1623  Log() << Verbose(0) << "==============================================================================================================" << endl;
    16271624
    16281625  // cleanup FragmentSearch structure
    … …  
    16421639  Free(&NumMoleculesOfOrder);
    16431640
    1644   DoLog(0) && (Log() << Verbose(0) << "End of FragmentBOSSANOVA." << endl);
     1641  Log() << Verbose(0) << "End of FragmentBOSSANOVA." << endl;
    16451642};
    16461643
    … …  
    16571654  atom *Walker = NULL;
    16581655  atom *OtherWalker = NULL;
    1659   double * const cell_size = World::get()->cell_size;
    16601656  double *matrix = ReturnFullMatrixforSymmetric(cell_size);
    16611657  enum Shading *ColorList = NULL;
    … …  
    16661662  bool flag = true;
    16671663
    1668   DoLog(2) && (Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl);
     1664  Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl;
    16691665
    16701666  ColorList = Calloc<enum Shading>(AtomCount, "molecule::ScanForPeriodicCorrection: *ColorList");
    … …  
    16841680          OtherBinder = Binder->next; // note down binding partner for later re-insertion
    16851681          unlink(Binder);   // unlink bond
    1686           DoLog(2) && (Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl);
     1682          Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl;
    16871683          flag = true;
    16881684          break;
    … …  
    17001696      //Log() << Verbose(3) << "Translation vector is ";
    17011697      Translationvector.Output();
    1702       DoLog(0) && (Log() << Verbose(0) << endl);
     1698      Log() << Verbose(0) << endl;
    17031699      // apply to all atoms of first component via BFS
    17041700      for (int i=AtomCount;i--;)
    … …  
    17221718      link(Binder, OtherBinder);
    17231719    } else {
    1724       DoLog(3) && (Log() << Verbose(3) << "No corrections for this fragment." << endl);
     1720      Log() << Verbose(3) << "No corrections for this fragment." << endl;
    17251721    }
    17261722    //delete(CompStack);
    … …  
    17311727  Free(&ColorList);
    17321728  Free(&matrix);
    1733   DoLog(2) && (Log() << Verbose(2) << "End of ScanForPeriodicCorrection." << endl);
    1734 };
     1729  Log() << Verbose(2) << "End of ScanForPeriodicCorrection." << endl;
     1730};
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