Ignore:
File:
1 edited

Legend:

Unmodified
Added
Removed

  • src/molecule_fragmentation.cpp

    r49e1ae ra67d19  
    1818#include "molecule.hpp"
    1919#include "periodentafel.hpp"
     20#include "World.hpp"
    2021
    2122/************************************* Functions for class molecule *********************************/
    … …  
    4344  }
    4445  FragmentCount = NoNonHydrogen*(1 << (c*order));
    45   Log() << Verbose(1) << "Upper limit for this subgraph is " << FragmentCount << " for " << NoNonHydrogen << " non-H atoms with maximum bond degree of " << c << "." << endl;
     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);
    4647  return FragmentCount;
    4748};
    … …  
    6768    } // else it's "-1" or else and thus must not be added
    6869  }
    69   Log() << Verbose(1) << "The scanned KeySet is ";
     70  DoLog(1) && (Log() << Verbose(1) << "The scanned KeySet is ");
    7071  for(KeySet::iterator runner = CurrentSet.begin(); runner != CurrentSet.end(); runner++) {
    71     Log() << Verbose(0) << (*runner) << "\t";
    72   }
    73   Log() << Verbose(0) << endl;
     72    DoLog(0) && (Log() << Verbose(0) << (*runner) << "\t");
     73  }
     74  DoLog(0) && (Log() << Verbose(0) << endl);
    7475  return (status != 0);
    7576};
    … …  
    99100
    100101  // 1st pass: open file and read
    101   Log() << Verbose(1) << "Parsing the KeySet file ... " << endl;
     102  DoLog(1) && (Log() << Verbose(1) << "Parsing the KeySet file ... " << endl);
    102103  sprintf(filename, "%s/%s%s", path, FRAGMENTPREFIX, KEYSETFILE);
    103104  InputFile.open(filename);
    … …  
    112113        testGraphInsert = FragmentList->insert(GraphPair (CurrentSet,pair<int,double>(NumberOfFragments++,1)));  // store fragment number and current factor
    113114        if (!testGraphInsert.second) {
    114           eLog() << Verbose(0) << "KeySet file must be corrupt as there are two equal key sets therein!" << endl;
     115          DoeLog(0) && (eLog()<< Verbose(0) << "KeySet file must be corrupt as there are two equal key sets therein!" << endl);
    115116          performCriticalExit();
    116117        }
    … …  
    121122    InputFile.clear();
    122123    Free(&buffer);
    123     Log() << Verbose(1) << "done." << endl;
     124    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    124125  } else {
    125     Log() << Verbose(1) << "File " << filename << " not found." << endl;
     126    DoLog(1) && (Log() << Verbose(1) << "File " << filename << " not found." << endl);
    126127    status = false;
    127128  }
    … …  
    153154
    154155  // 2nd pass: open TEFactors file and read
    155   Log() << Verbose(1) << "Parsing the TEFactors file ... " << endl;
     156  DoLog(1) && (Log() << Verbose(1) << "Parsing the TEFactors file ... " << endl);
    156157  sprintf(filename, "%s/%s%s", path, FRAGMENTPREFIX, TEFACTORSFILE);
    157158  InputFile.open(filename);
    … …  
    163164        InputFile >> TEFactor;
    164165        (*runner).second.second = TEFactor;
    165         Log() << Verbose(2) << "Setting " << ++NumberOfFragments << " fragment's TEFactor to " << (*runner).second.second << "." << endl;
     166        DoLog(2) && (Log() << Verbose(2) << "Setting " << ++NumberOfFragments << " fragment's TEFactor to " << (*runner).second.second << "." << endl);
    166167      } else {
    167168        status = false;
    … …  
    171172    // 4. Free and done
    172173    InputFile.close();
    173     Log() << Verbose(1) << "done." << endl;
     174    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    174175  } else {
    175     Log() << Verbose(1) << "File " << filename << " not found." << endl;
     176    DoLog(1) && (Log() << Verbose(1) << "File " << filename << " not found." << endl);
    176177    status = false;
    177178  }
    … …  
    201202  line += KEYSETFILE;
    202203  output.open(line.c_str(), ios::out);
    203   Log() << Verbose(1) << "Saving key sets of the total graph ... ";
     204  DoLog(1) && (Log() << Verbose(1) << "Saving key sets of the total graph ... ");
    204205  if(output != NULL) {
    205206    for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++) {
    … …  
    211212      output << endl;
    212213    }
    213     Log() << Verbose(0) << "done." << endl;
     214    DoLog(0) && (Log() << Verbose(0) << "done." << endl);
    214215  } else {
    215     eLog() << Verbose(0) << "Unable to open " << line << " for writing keysets!" << endl;
     216    DoeLog(0) && (eLog()<< Verbose(0) << "Unable to open " << line << " for writing keysets!" << endl);
    216217    performCriticalExit();
    217218    status = false;
    … …  
    242243  line += TEFACTORSFILE;
    243244  output.open(line.c_str(), ios::out);
    244   Log() << Verbose(1) << "Saving TEFactors of the total graph ... ";
     245  DoLog(1) && (Log() << Verbose(1) << "Saving TEFactors of the total graph ... ");
    245246  if(output != NULL) {
    246247    for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++)
    247248      output << (*runner).second.second << endl;
    248     Log() << Verbose(1) << "done." << endl;
     249    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    249250  } else {
    250     Log() << Verbose(1) << "failed to open " << line << "." << endl;
     251    DoLog(1) && (Log() << Verbose(1) << "failed to open " << line << "." << endl);
    251252    status = false;
    252253  }
    … …  
    292293        (*PresentItem).second.first = fabs(Value);
    293294        (*PresentItem).second.second = FragOrder;
    294         Log() << Verbose(2) << "Updated element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl;
     295        DoLog(2) && (Log() << Verbose(2) << "Updated element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl);
    295296      } else {
    296         Log() << Verbose(2) << "Did not update element " <<  (*PresentItem).first << " as " << FragOrder << " is less than or equal to " << (*PresentItem).second.second << "." << endl;
     297        DoLog(2) && (Log() << Verbose(2) << "Did not update element " <<  (*PresentItem).first << " as " << FragOrder << " is less than or equal to " << (*PresentItem).second.second << "." << endl);
    297298      }
    298299    } else {
    299       Log() << Verbose(2) << "Inserted element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl;
     300      DoLog(2) && (Log() << Verbose(2) << "Inserted element (" <<  (*PresentItem).first << ",[" << (*PresentItem).second.first << "," << (*PresentItem).second.second << "])." << endl);
    300301    }
    301302  } else {
    302     Log() << Verbose(1) << "No Fragment under No. " << No << "found." << endl;
     303    DoLog(1) && (Log() << Verbose(1) << "No Fragment under No. " << No << "found." << endl);
    303304  }
    304305};
    … …  
    359360  atom *Walker = mol->start;
    360361  map<double, pair<int,int> > *FinalRootCandidates = new map<double, pair<int,int> > ;
    361   Log() << Verbose(1) << "Root candidate list is: " << endl;
     362  DoLog(1) && (Log() << Verbose(1) << "Root candidate list is: " << endl);
    362363  for(map<int, pair<double,int> >::iterator runner = AdaptiveCriteriaList->begin(); runner != AdaptiveCriteriaList->end(); runner++) {
    363364    Walker = mol->FindAtom((*runner).first);
    … …  
    365366      //if ((*runner).second.second >= Walker->AdaptiveOrder) { // only insert if this is an "active" root site for the current order
    366367      if (!Walker->MaxOrder) {
    367         Log() << Verbose(2) << "(" << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "])" << endl;
     368        DoLog(2) && (Log() << Verbose(2) << "(" << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "])" << endl);
    368369        FinalRootCandidates->insert( make_pair( (*runner).second.first, pair<int,int>((*runner).first, (*runner).second.second) ) );
    369370      } else {
    370         Log() << Verbose(2) << "Excluding (" << *Walker << ", " << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "]), as it has reached its maximum order." << endl;
     371        DoLog(2) && (Log() << Verbose(2) << "Excluding (" << *Walker << ", " << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "]), as it has reached its maximum order." << endl);
    371372      }
    372373    } else {
    373       eLog() << Verbose(0) << "Atom No. " << (*runner).second.first << " was not found in this molecule." << endl;
     374      DoeLog(0) && (eLog()<< Verbose(0) << "Atom No. " << (*runner).second.first << " was not found in this molecule." << endl);
    374375      performCriticalExit();
    375376    }
    … …  
    396397    Walker = mol->FindAtom(No);
    397398    //if (Walker->AdaptiveOrder < MinimumRingSize[Walker->nr]) {
    398       Log() << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to true." << endl;
     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);
    399400      AtomMask[No] = true;
    400401      status = true;
    … …  
    412413void PrintAtomMask(bool *AtomMask, int AtomCount)
    413414{
    414   Log() << Verbose(2) << "              ";
     415  DoLog(2) && (Log() << Verbose(2) << "              ");
    415416  for(int i=0;i<AtomCount;i++)
    416     Log() << Verbose(0) << (i % 10);
    417   Log() << Verbose(0) << endl;
    418   Log() << Verbose(2) << "Atom mask is: ";
     417    DoLog(0) && (Log() << Verbose(0) << (i % 10));
     418  DoLog(0) && (Log() << Verbose(0) << endl);
     419  DoLog(2) && (Log() << Verbose(2) << "Atom mask is: ");
    419420  for(int i=0;i<AtomCount;i++)
    420     Log() << Verbose(0) << (AtomMask[i] ? "t" : "f");
    421   Log() << Verbose(0) << endl;
     421    DoLog(0) && (Log() << Verbose(0) << (AtomMask[i] ? "t" : "f"));
     422  DoLog(0) && (Log() << Verbose(0) << endl);
    422423};
    423424
    … …  
    446447    // transmorph graph keyset list into indexed KeySetList
    447448    if (GlobalKeySetList == NULL) {
    448       eLog() << Verbose(1) << "Given global key set list (graph) is NULL!" << endl;
     449      DoeLog(1) && (eLog()<< Verbose(1) << "Given global key set list (graph) is NULL!" << endl);
    449450      return false;
    450451    }
    … …  
    454455    map<int, pair<double,int> > *AdaptiveCriteriaList = ScanAdaptiveFileIntoMap(path, *IndexKeySetList); // (Root No., (Value, Order)) !
    455456    if (AdaptiveCriteriaList->empty()) {
    456       eLog() << Verbose(2) << "Unable to parse file, incrementing all." << endl;
     457      DoeLog(2) && (eLog()<< Verbose(2) << "Unable to parse file, incrementing all." << endl);
    457458      while (Walker->next != end) {
    458459        Walker = Walker->next;
    … …  
    492493    if (!status) {
    493494      if (Order == 0)
    494         Log() << Verbose(1) << "Single stepping done." << endl;
     495        DoLog(1) && (Log() << Verbose(1) << "Single stepping done." << endl);
    495496      else
    496         Log() << Verbose(1) << "Order at every site is already equal or above desired order " << Order << "." << endl;
     497        DoLog(1) && (Log() << Verbose(1) << "Order at every site is already equal or above desired order " << Order << "." << endl);
    497498    }
    498499  }
    … …  
    511512{
    512513  if (SortIndex != NULL) {
    513     Log() << Verbose(1) << "SortIndex is " << SortIndex << " and not NULL as expected." << endl;
     514    DoLog(1) && (Log() << Verbose(1) << "SortIndex is " << SortIndex << " and not NULL as expected." << endl);
    514515    return false;
    515516  }
    … …  
    562563  bool *AtomMask = NULL;
    563564
    564   Log() << Verbose(0) << endl;
     565  DoLog(0) && (Log() << Verbose(0) << endl);
    565566#ifdef ADDHYDROGEN
    566   Log() << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl;
     567  DoLog(0) && (Log() << Verbose(0) << "I will treat hydrogen special and saturate dangling bonds with it." << endl);
    567568#else
    568   Log() << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl;
     569  DoLog(0) && (Log() << Verbose(0) << "Hydrogen is treated just like the rest of the lot." << endl);
    569570#endif
    570571
    … …  
    592593    // fill the bond structure of the individually stored subgraphs
    593594  MolecularWalker->FillBondStructureFromReference(this, FragmentCounter, ListOfLocalAtoms, false);  // we want to keep the created ListOfLocalAtoms
    594     Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     595    DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
    595596    LocalBackEdgeStack = new StackClass<bond *> (MolecularWalker->Leaf->BondCount);
    596597//    // check the list of local atoms for debugging
    … …  
    601602//      else
    602603//        Log() << Verbose(0) << "\t" << ListOfLocalAtoms[FragmentCounter][i]->Name;
    603     Log() << Verbose(0) << "Gathering local back edges for subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     604    DoLog(0) && (Log() << Verbose(0) << "Gathering local back edges for subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
    604605    MolecularWalker->Leaf->PickLocalBackEdges(ListOfLocalAtoms[FragmentCounter++], BackEdgeStack, LocalBackEdgeStack);
    605     Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     606    DoLog(0) && (Log() << Verbose(0) << "Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
    606607    MolecularWalker->Leaf->CyclicStructureAnalysis(LocalBackEdgeStack, MinimumRingSize);
    607     Log() << Verbose(0) << "Done with Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl;
     608    DoLog(0) && (Log() << Verbose(0) << "Done with Analysing the cycles of subgraph " << MolecularWalker->Leaf << " with nr. " << FragmentCounter << "." << endl);
    608609    delete(LocalBackEdgeStack);
    609610  }
    … …  
    636637    while (MolecularWalker->next != NULL) {
    637638      MolecularWalker = MolecularWalker->next;
    638       Log() << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl;
     639      DoLog(1) && (Log() << Verbose(1) << "Fragmenting subgraph " << MolecularWalker << "." << endl);
    639640      //MolecularWalker->Leaf->OutputListOfBonds(out);  // output atom::ListOfBonds for debugging
    640641      if (MolecularWalker->Leaf->first->next != MolecularWalker->Leaf->last) {
    641642        // call BOSSANOVA method
    642         Log() << Verbose(0) << endl << " ========== BOND ENERGY of subgraph " << FragmentCounter << " ========================= " << endl;
     643        DoLog(0) && (Log() << Verbose(0) << endl << " ========== BOND ENERGY of subgraph " << FragmentCounter << " ========================= " << endl);
    643644        MolecularWalker->Leaf->FragmentBOSSANOVA(FragmentList[FragmentCounter], RootStack[FragmentCounter], MinimumRingSize);
    644645      } else {
    645         eLog() << Verbose(1) << "Subgraph " << MolecularWalker << " has no atoms!" << endl;
     646        DoeLog(1) && (eLog()<< Verbose(1) << "Subgraph " << MolecularWalker << " has no atoms!" << endl);
    646647      }
    647648      FragmentCounter++;  // next fragment list
    648649    }
    649650  }
    650   Log() << Verbose(2) << "CheckOrder is " << CheckOrder << "." << endl;
     651  DoLog(2) && (Log() << Verbose(2) << "CheckOrder is " << CheckOrder << "." << endl);
    651652  delete[](RootStack);
    652653  delete[](AtomMask);
    … …  
    679680  for(Graph::iterator runner = TotalGraph.begin(); runner != TotalGraph.end(); runner++) {
    680681    KeySet test = (*runner).first;
    681     Log() << Verbose(0) << "Fragment No." << (*runner).second.first << " with TEFactor " << (*runner).second.second << "." << endl;
     682    DoLog(0) && (Log() << Verbose(0) << "Fragment No." << (*runner).second.first << " with TEFactor " << (*runner).second.second << "." << endl);
    682683    BondFragments->insert(StoreFragmentFromKeySet(test, configuration));
    683684    k++;
    684685  }
    685   Log() << Verbose(0) << k << "/" << BondFragments->ListOfMolecules.size() << " fragments generated from the keysets." << endl;
     686  DoLog(0) && (Log() << Verbose(0) << k << "/" << BondFragments->ListOfMolecules.size() << " fragments generated from the keysets." << endl);
    686687
    687688  // ===== 9. Save fragments' configuration and keyset files et al to disk ===
    … …  
    690691    CreateMappingLabelsToConfigSequence(SortIndex);
    691692
    692     Log() << Verbose(1) << "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs" << endl;
     693    DoLog(1) && (Log() << Verbose(1) << "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs" << endl);
    693694    if (BondFragments->OutputConfigForListOfFragments(configuration, SortIndex))
    694       Log() << Verbose(1) << "All configs written." << endl;
     695      DoLog(1) && (Log() << Verbose(1) << "All configs written." << endl);
    695696    else
    696       Log() << Verbose(1) << "Some config writing failed." << endl;
     697      DoLog(1) && (Log() << Verbose(1) << "Some config writing failed." << endl);
    697698
    698699    // store force index reference file
    … …  
    703704
    704705    // store Adjacency file
    705     StoreAdjacencyToFile(configuration->configpath);
     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);
    706711
    707712    // store Hydrogen saturation correction file
    … …  
    715720
    716721    // free memory for bond part
    717     Log() << Verbose(1) << "Freeing bond memory" << endl;
     722    DoLog(1) && (Log() << Verbose(1) << "Freeing bond memory" << endl);
    718723    delete(FragmentList); // remove bond molecule from memory
    719724    Free(&SortIndex);
    720725  } else {
    721     Log() << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl;
     726    DoLog(1) && (Log() << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl);
    722727  }
    723728  delete(BondFragments);
    724   Log() << Verbose(0) << "End of bond fragmentation." << endl;
     729  DoLog(0) && (Log() << Verbose(0) << "End of bond fragmentation." << endl);
    725730
    726731  return ((int)(!FragmentationToDo)+1);    // 1 - continue, 2 - stop (no fragmentation occured)
    … …  
    741746  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
    742747  file.open(line.str().c_str());
    743   Log() << Verbose(1) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl;
     748  DoLog(1) && (Log() << Verbose(1) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl);
    744749  if (file != NULL) {
    745750    ActOnAllAtoms( &atom::OutputOrder, &file );
    746751    file.close();
    747     Log() << Verbose(1) << "done." << endl;
     752    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    748753    return true;
    749754  } else {
    750     Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
     755    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
    751756    return false;
    752757  }
    … …  
    769774  ifstream file;
    770775
    771   Log() << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl;
     776  DoLog(1) && (Log() << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl);
    772777  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
    773778  file.open(line.str().c_str());
    … …  
    790795    SetAtomValueToIndexedArray( MaxArray, &atom::nr, &atom::MaxOrder );
    791796
    792     Log() << Verbose(1) << "done." << endl;
     797    DoLog(1) && (Log() << Verbose(1) << "done." << endl);
    793798    status = true;
    794799  } else {
    795     Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
     800    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
    796801    status = false;
    797802  }
    … …  
    799804  Free(&MaxArray);
    800805
    801   Log() << Verbose(1) << "End of ParseOrderAtSiteFromFile" << endl;
     806  DoLog(1) && (Log() << Verbose(1) << "End of ParseOrderAtSiteFromFile" << endl);
    802807  return status;
    803808};
    … …  
    816821  int SP, Removal;
    817822
    818   Log() << Verbose(2) << "Looking for removal candidate." << endl;
     823  DoLog(2) && (Log() << Verbose(2) << "Looking for removal candidate." << endl);
    819824  SP = -1; //0;  // not -1, so that Root is never removed
    820825  Removal = -1;
    … …  
    843848
    844849  Leaf->BondDistance = mol->BondDistance;
    845   for(int i=NDIM*2;i--;)
    846     Leaf->cell_size[i] = mol->cell_size[i];
    847850
    848851  // first create the minimal set of atoms from the KeySet
    … …  
    903906      }
    904907    } else {
    905       eLog() << Verbose(1) << "Son " << Runner->Name << " has father " << FatherOfRunner->Name << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl;
     908      DoeLog(1) && (eLog()<< Verbose(1) << "Son " << Runner->Name << " has father " << FatherOfRunner->Name << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl);
    906909    }
    907910    if ((LonelyFlag) && (Leaf->AtomCount > 1)) {
    908       Log() << Verbose(0) << *Runner << "has got bonds only to hydrogens!" << endl;
     911      DoLog(0) && (Log() << Verbose(0) << *Runner << "has got bonds only to hydrogens!" << endl);
    909912    }
    910913#ifdef ADDHYDROGEN
    … …  
    10531056    TouchedList[j] = -1;
    10541057  }
    1055   Log() << Verbose(2) << "Remaining local nr.s on snake stack are: ";
     1058  DoLog(2) && (Log() << Verbose(2) << "Remaining local nr.s on snake stack are: ");
    10561059  for(KeySet::iterator runner = FragmentSet->begin(); runner != FragmentSet->end(); runner++)
    1057     Log() << Verbose(0) << (*runner) << " ";
    1058   Log() << Verbose(0) << endl;
     1060    DoLog(0) && (Log() << Verbose(0) << (*runner) << " ");
     1061  DoLog(0) && (Log() << Verbose(0) << endl);
    10591062  TouchedIndex = 0; // set Index to 0 for list of atoms added on this level
    10601063};
    … …  
    11331136        Log() << Verbose(1+verbosity) << "Enough items on stack for a fragment!" << endl;
    11341137        // store fragment as a KeySet
    1135         Log() << Verbose(2) << "Found a new fragment[" << FragmentSearch->FragmentCounter << "], local nr.s are: ";
     1138        DoLog(2) && (Log() << Verbose(2) << "Found a new fragment[" << FragmentSearch->FragmentCounter << "], local nr.s are: ");
    11361139        for(KeySet::iterator runner = FragmentSearch->FragmentSet->begin(); runner != FragmentSearch->FragmentSet->end(); runner++)
    1137           Log() << Verbose(0) << (*runner) << " ";
    1138         Log() << Verbose(0) << endl;
     1140          DoLog(0) && (Log() << Verbose(0) << (*runner) << " ");
     1141        DoLog(0) && (Log() << Verbose(0) << endl);
    11391142        //if (!CheckForConnectedSubgraph(FragmentSearch->FragmentSet))
    1140           //eLog() << Verbose(1) << "The found fragment is not a connected subgraph!" << endl;
     1143          //DoeLog(1) && (eLog()<< Verbose(1) << "The found fragment is not a connected subgraph!" << endl);
    11411144        InsertFragmentIntoGraph(FragmentSearch);
    11421145      }
    … …  
    12181221{
    12191222  bond *Binder = NULL;
    1220   Log() << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl;
     1223  DoLog(0) && (Log() << Verbose(0) << "Free'ing all found lists. and resetting index lists" << endl);
    12211224  for(int i=Order;i--;) {
    1222     Log() << Verbose(1) << "Current SP level is " << i << ": ";
     1225    DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << ": ");
    12231226    Binder = FragmentSearch.BondsPerSPList[2*i];
    12241227    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
    … …  
    12311234    cleanup(FragmentSearch.BondsPerSPList[2*i], FragmentSearch.BondsPerSPList[2*i+1]);
    12321235    // also start and end node
    1233     Log() << Verbose(0) << "cleaned." << endl;
     1236    DoLog(0) && (Log() << Verbose(0) << "cleaned." << endl);
    12341237  }
    12351238};
    … …  
    12611264  int SP = -1;
    12621265
    1263   Log() << Verbose(0) << "Starting BFS analysis ..." << endl;
     1266  DoLog(0) && (Log() << Verbose(0) << "Starting BFS analysis ..." << endl);
    12641267  for (SP = 0; SP < (Order-1); SP++) {
    1265     Log() << Verbose(1) << "New SP level reached: " << SP << ", creating new SP list with " << FragmentSearch.BondsPerSPCount[SP] << " item(s)";
     1268    DoLog(1) && (Log() << Verbose(1) << "New SP level reached: " << SP << ", creating new SP list with " << FragmentSearch.BondsPerSPCount[SP] << " item(s)");
    12661269    if (SP > 0) {
    1267       Log() << Verbose(0) << ", old level closed with " << FragmentSearch.BondsPerSPCount[SP-1] << " item(s)." << endl;
     1270      DoLog(0) && (Log() << Verbose(0) << ", old level closed with " << FragmentSearch.BondsPerSPCount[SP-1] << " item(s)." << endl);
    12681271      FragmentSearch.BondsPerSPCount[SP] = 0;
    12691272    } else
    1270       Log() << Verbose(0) << "." << endl;
     1273      DoLog(0) && (Log() << Verbose(0) << "." << endl);
    12711274
    12721275    RemainingWalkers = FragmentSearch.BondsPerSPCount[SP];
    … …  
    12781281      Predecessor = CurrentEdge->leftatom;    // ... and leftatom is predecessor
    12791282      AtomKeyNr = Walker->nr;
    1280       Log() << Verbose(0) << "Current Walker is: " << *Walker << " with nr " << Walker->nr << " and SP of " << SP << ", with " << RemainingWalkers << " remaining walkers on this level." << endl;
     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);
    12811284      // check for new sp level
    12821285      // go through all its bonds
    1283       Log() << Verbose(1) << "Going through all bonds of Walker." << endl;
     1286      DoLog(1) && (Log() << Verbose(1) << "Going through all bonds of Walker." << endl);
    12841287      for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
    12851288        OtherWalker = (*Runner)->GetOtherAtom(Walker);
    … …  
    12891292  #endif
    12901293                                                              ) {  // skip hydrogens and restrict to fragment
    1291           Log() << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->nr << " in bond " << *(*Runner) << "." << endl;
     1294          DoLog(2) && (Log() << Verbose(2) << "Current partner is " << *OtherWalker << " with nr " << OtherWalker->nr << " in bond " << *(*Runner) << "." << endl);
    12921295          // set the label if not set (and push on root stack as well)
    12931296          if ((OtherWalker != Predecessor) && (OtherWalker->GetTrueFather()->nr > RootKeyNr)) { // only pass through those with label bigger than Root's
    12941297            FragmentSearch.ShortestPathList[OtherWalker->nr] = SP+1;
    1295             Log() << Verbose(3) << "Set Shortest Path to " << FragmentSearch.ShortestPathList[OtherWalker->nr] << "." << endl;
     1298            DoLog(3) && (Log() << Verbose(3) << "Set Shortest Path to " << FragmentSearch.ShortestPathList[OtherWalker->nr] << "." << endl);
    12961299            // add the bond in between to the SP list
    12971300            Binder = new bond(Walker, OtherWalker); // create a new bond in such a manner, that bond::rightatom is always the one more distant
    12981301            add(Binder, FragmentSearch.BondsPerSPList[2*(SP+1)+1]);
    12991302            FragmentSearch.BondsPerSPCount[SP+1]++;
    1300             Log() << Verbose(3) << "Added its bond to SP list, having now " << FragmentSearch.BondsPerSPCount[SP+1] << " item(s)." << endl;
     1303            DoLog(3) && (Log() << Verbose(3) << "Added its bond to SP list, having now " << FragmentSearch.BondsPerSPCount[SP+1] << " item(s)." << endl);
    13011304          } else {
    13021305            if (OtherWalker != Predecessor)
    1303               Log() << Verbose(3) << "Not passing on, as index of " << *OtherWalker << " " << OtherWalker->GetTrueFather()->nr << " is smaller than that of Root " << RootKeyNr << "." << endl;
     1306              DoLog(3) && (Log() << Verbose(3) << "Not passing on, as index of " << *OtherWalker << " " << OtherWalker->GetTrueFather()->nr << " is smaller than that of Root " << RootKeyNr << "." << endl);
    13041307            else
    1305               Log() << Verbose(3) << "This is my predecessor " << *Predecessor << "." << endl;
     1308              DoLog(3) && (Log() << Verbose(3) << "This is my predecessor " << *Predecessor << "." << endl);
    13061309          }
    13071310        } else Log() << Verbose(2) << "Is not in the restricted keyset or skipping hydrogen " << *OtherWalker << "." << endl;
    … …  
    13191322{
    13201323  bond *Binder = NULL;
    1321   Log() << Verbose(0) << "Printing all found lists." << endl;
     1324  DoLog(0) && (Log() << Verbose(0) << "Printing all found lists." << endl);
    13221325  for(int i=1;i<Order;i++) {    // skip the root edge in the printing
    13231326    Binder = FragmentSearch.BondsPerSPList[2*i];
    1324     Log() << Verbose(1) << "Current SP level is " << i << "." << endl;
     1327    DoLog(1) && (Log() << Verbose(1) << "Current SP level is " << i << "." << endl);
    13251328    while (Binder->next != FragmentSearch.BondsPerSPList[2*i+1]) {
    13261329      Binder = Binder->next;
    1327       Log() << Verbose(2) << *Binder << endl;
     1330      DoLog(2) && (Log() << Verbose(2) << *Binder << endl);
    13281331    }
    13291332  }
    … …  
    13691372  int Counter = FragmentSearch.FragmentCounter; // mark current value of counter
    13701373
    1371   Log() << Verbose(0) << endl;
    1372   Log() << Verbose(0) << "Begin of PowerSetGenerator with order " << Order << " at Root " << *FragmentSearch.Root << "." << endl;
     1374  DoLog(0) && (Log() << Verbose(0) << endl);
     1375  DoLog(0) && (Log() << Verbose(0) << "Begin of PowerSetGenerator with order " << Order << " at Root " << *FragmentSearch.Root << "." << endl);
    13731376
    13741377  SetSPList(Order, FragmentSearch);
    … …  
    13821385  // creating fragments with the found edge sets  (may be done in reverse order, faster)
    13831386  int SP = CountNumbersInBondsList(Order, FragmentSearch);
    1384   Log() << Verbose(0) << "Total number of edges is " << SP << "." << endl;
     1387  DoLog(0) && (Log() << Verbose(0) << "Total number of edges is " << SP << "." << endl);
    13851388  if (SP >= (Order-1)) {
    13861389    // start with root (push on fragment stack)
    1387     Log() << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.Root << ", local nr is " << FragmentSearch.Root->nr << "." << endl;
     1390    DoLog(0) && (Log() << Verbose(0) << "Starting fragment generation with " << *FragmentSearch.Root << ", local nr is " << FragmentSearch.Root->nr << "." << endl);
    13881391    FragmentSearch.FragmentSet->clear();
    1389     Log() << Verbose(0) << "Preparing subset for this root and calling generator." << endl;
     1392    DoLog(0) && (Log() << Verbose(0) << "Preparing subset for this root and calling generator." << endl);
    13901393
    13911394    // prepare the subset and call the generator
    … …  
    13971400    Free(&BondsList);
    13981401  } else {
    1399     Log() << Verbose(0) << "Not enough total number of edges to build " << Order << "-body fragments." << endl;
     1402    DoLog(0) && (Log() << Verbose(0) << "Not enough total number of edges to build " << Order << "-body fragments." << endl);
    14001403  }
    14011404
    14021405  // as FragmentSearch structure is used only once, we don't have to clean it anymore
    14031406  // remove root from stack
    1404   Log() << Verbose(0) << "Removing root again from stack." << endl;
     1407  DoLog(0) && (Log() << Verbose(0) << "Removing root again from stack." << endl);
    14051408  FragmentSearch.FragmentSet->erase(FragmentSearch.Root->nr);
    14061409
    … …  
    14091412
    14101413  // return list
    1411   Log() << Verbose(0) << "End of PowerSetGenerator." << endl;
     1414  DoLog(0) && (Log() << Verbose(0) << "End of PowerSetGenerator." << endl);
    14121415  return (FragmentSearch.FragmentCounter - Counter);
    14131416};
    … …  
    14551458  atom *Walker = NULL;
    14561459
    1457   Log() << Verbose(0) << "Combining the lists of all orders per order and finally into a single one." << endl;
     1460  DoLog(0) && (Log() << Verbose(0) << "Combining the lists of all orders per order and finally into a single one." << endl);
    14581461  if (FragmentList == NULL) {
    14591462    FragmentList = new Graph;
    … …  
    14881491void FreeAllOrdersList(Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol)
    14891492{
    1490   Log() << Verbose(1) << "Free'ing the lists of all orders per order." << endl;
     1493  DoLog(1) && (Log() << Verbose(1) << "Free'ing the lists of all orders per order." << endl);
    14911494  int RootNr = 0;
    14921495  int RootKeyNr = 0;
    … …  
    15411544  struct UniqueFragments FragmentSearch;
    15421545
    1543   Log() << Verbose(0) << "Begin of FragmentBOSSANOVA." << endl;
     1546  DoLog(0) && (Log() << Verbose(0) << "Begin of FragmentBOSSANOVA." << endl);
    15441547
    15451548  // FragmentLowerOrdersList is a 2D-array of pointer to MoleculeListClass objects, one dimension represents the ANOVA expansion of a single order (i.e. 5)
    … …  
    15911594
    15921595      // create top order where nothing is reduced
    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 << "
     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 << "
    15951598
    15961599      // Create list of Graphs of current Bond Order (i.e. F_{ij})
    … …  
    16021605
    16031606      // output resulting number
    1604       Log() << Verbose(1) << "Number of resulting KeySets is: " << NumMoleculesOfOrder[RootNr] << "." << endl;
     1607      DoLog(1) && (Log() << Verbose(1) << "Number of resulting KeySets is: " << NumMoleculesOfOrder[RootNr] << "." << endl);
    16051608      if (NumMoleculesOfOrder[RootNr] != 0) {
    16061609        NumMolecules = 0;
    … …  
    16191622    }
    16201623  }
    1621   Log() << Verbose(0) << "==============================================================================================================" << endl;
    1622   Log() << Verbose(1) << "Total number of resulting molecules is: " << TotalNumMolecules << "." << endl;
    1623   Log() << Verbose(0) << "==============================================================================================================" << endl;
     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);
    16241627
    16251628  // cleanup FragmentSearch structure
    … …  
    16391642  Free(&NumMoleculesOfOrder);
    16401643
    1641   Log() << Verbose(0) << "End of FragmentBOSSANOVA." << endl;
     1644  DoLog(0) && (Log() << Verbose(0) << "End of FragmentBOSSANOVA." << endl);
    16421645};
    16431646
    … …  
    16541657  atom *Walker = NULL;
    16551658  atom *OtherWalker = NULL;
     1659  double * const cell_size = World::get()->cell_size;
    16561660  double *matrix = ReturnFullMatrixforSymmetric(cell_size);
    16571661  enum Shading *ColorList = NULL;
    … …  
    16621666  bool flag = true;
    16631667
    1664   Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl;
     1668  DoLog(2) && (Log() << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl);
    16651669
    16661670  ColorList = Calloc<enum Shading>(AtomCount, "molecule::ScanForPeriodicCorrection: *ColorList");
    … …  
    16801684          OtherBinder = Binder->next; // note down binding partner for later re-insertion
    16811685          unlink(Binder);   // unlink bond
    1682           Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl;
     1686          DoLog(2) && (Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl);
    16831687          flag = true;
    16841688          break;
    … …  
    16961700      //Log() << Verbose(3) << "Translation vector is ";
    16971701      Translationvector.Output();
    1698       Log() << Verbose(0) << endl;
     1702      DoLog(0) && (Log() << Verbose(0) << endl);
    16991703      // apply to all atoms of first component via BFS
    17001704      for (int i=AtomCount;i--;)
    … …  
    17181722      link(Binder, OtherBinder);
    17191723    } else {
    1720       Log() << Verbose(3) << "No corrections for this fragment." << endl;
     1724      DoLog(3) && (Log() << Verbose(3) << "No corrections for this fragment." << endl);
    17211725    }
    17221726    //delete(CompStack);
    … …  
    17271731  Free(&ColorList);
    17281732  Free(&matrix);
    1729   Log() << Verbose(2) << "End of ScanForPeriodicCorrection." << endl;
    1730 };
     1733  DoLog(2) && (Log() << Verbose(2) << "End of ScanForPeriodicCorrection." << endl);
     1734};
Note: See TracChangeset for help on using the changeset viewer.