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  • src/config.cpp

    ra67d19 r4fc93f  
    66
    77#include <stdio.h>
    8 #include <cstring>
    98
    109#include "atom.hpp"
    … …  
    1918#include "molecule.hpp"
    2019#include "periodentafel.hpp"
    21 #include "World.hpp"
    2220
    2321/******************************** Functions for class ConfigFileBuffer **********************/
    … …  
    2927    char number1[8];
    3028    char number2[8];
    31     const char *dummy1, *dummy2;
     29    char *dummy1, *dummy2;
    3230    //Log() << Verbose(0) << s1 << "  " << s2 << endl;
    3331    dummy1 = strchr(s1, '_')+sizeof(char)*5;  // go just after "Ion_Type"
    … …  
    7472  file= new ifstream(filename);
    7573  if (file == NULL) {
    76     DoeLog(1) && (eLog()<< Verbose(1) << "config file " << filename << " missing!" << endl);
     74    eLog() << Verbose(1) << "config file " << filename << " missing!" << endl;
    7775    return;
    7876  }
    … …  
    8583  file->clear();
    8684  file->seekg(file_position, ios::beg);
    87   DoLog(1) && (Log() << Verbose(1) << NoLines-1 << " lines were recognized." << endl);
     85  Log() << Verbose(1) << NoLines-1 << " lines were recognized." << endl;
    8886
    8987  // allocate buffer's 1st dimension
    9088  if (buffer != NULL) {
    91     DoeLog(1) && (eLog()<< Verbose(1) << "FileBuffer->buffer is not NULL!" << endl);
     89    eLog() << Verbose(1) << "FileBuffer->buffer is not NULL!" << endl;
    9290    return;
    9391  } else
    … …  
    105103    lines++;
    106104  } while((!file->eof()) && (lines < NoLines));
    107   DoLog(1) && (Log() << Verbose(1) << lines-1 << " lines were read into the buffer." << endl);
     105  Log() << Verbose(1) << lines-1 << " lines were read into the buffer." << endl;
    108106
    109107  // close and exit
    … …  
    142140void ConfigFileBuffer::MapIonTypesInBuffer(const int NoAtoms)
    143141{
    144   map<const char *, int, IonTypeCompare> IonTypeLineMap;
     142  map<const char *, int, IonTypeCompare> LineList;
    145143  if (LineMapping == NULL) {
    146     DoeLog(0) && (eLog()<< Verbose(0) << "map pointer is NULL: " << LineMapping << endl);
     144    eLog() << Verbose(0) << "map pointer is NULL: " << LineMapping << endl;
    147145    performCriticalExit();
    148146    return;
    … …  
    151149  // put all into hashed map
    152150  for (int i=0; i<NoAtoms; ++i) {
    153     IonTypeLineMap.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
     151    LineList.insert(pair<const char *, int> (buffer[CurrentLine+i], CurrentLine+i));
    154152  }
    155153
    156154  // fill map
    157155  int nr=0;
    158   for (map<const char *, int, IonTypeCompare>::iterator runner = IonTypeLineMap.begin(); runner != IonTypeLineMap.end(); ++runner) {
     156  for (map<const char *, int, IonTypeCompare>::iterator runner = LineList.begin(); runner != LineList.end(); ++runner) {
    159157    if (CurrentLine+nr < NoLines)
    160158      LineMapping[CurrentLine+(nr++)] = runner->second;
    161159    else {
    162       DoeLog(0) && (eLog()<< Verbose(0) << "config::MapIonTypesInBuffer - NoAtoms is wrong: We are past the end of the file!" << endl);
     160      eLog() << Verbose(0) << "config::MapIonTypesInBuffer - NoAtoms is wrong: We are past the end of the file!" << endl;
    163161      performCriticalExit();
    164162    }
    … …  
    250248        Thermostat = None;
    251249      } else {
    252         DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
     250        Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
    253251        Thermostat = None;
    254252      }
    … …  
    258256        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read scaling frequency
    259257      } else {
    260         DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
     258        Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
    261259        Thermostat = None;
    262260      }
    … …  
    266264        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read collision rate
    267265      } else {
    268         DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
     266        Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
    269267        Thermostat = None;
    270268      }
    … …  
    274272        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read gamma
    275273        if (ParseForParameter(verbose,fb,"Thermostat", 0, 3, 1, double_type, &alpha, 1, optional)) {
    276           DoLog(2) && (Log() << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << alpha << "." << endl);
     274          Log() << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << alpha << "." << endl;
    277275        } else {
    278276          alpha = 1.;
    279277        }
    280278      } else {
    281         DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
     279        Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
    282280        Thermostat = None;
    283281      }
    … …  
    287285        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read \tau_T
    288286      } else {
    289         DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
     287        Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
    290288        Thermostat = None;
    291289      }
    … …  
    296294        alpha = 0.;
    297295      } else {
    298         DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
     296        Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
    299297        Thermostat = None;
    300298      }
    301299    } else {
    302       DoLog(1) && (Log() << Verbose(1) << " Warning: thermostat name was not understood!" << endl);
     300      Log() << Verbose(1) << " Warning: thermostat name was not understood!" << endl;
    303301      Thermostat = None;
    304302    }
    305303  } else {
    306304    if ((MaxOuterStep > 0) && (TargetTemp != 0))
    307       DoLog(2) && (Log() << Verbose(2) <<  "No thermostat chosen despite finite temperature MD, falling back to None." << endl);
     305      Log() << Verbose(2) <<  "No thermostat chosen despite finite temperature MD, falling back to None." << endl;
    308306    Thermostat = None;
    309307  }
    … …  
    321319
    322320  do {
    323     DoLog(0) && (Log() << Verbose(0) << "===========EDIT CONFIGURATION============================" << endl);
    324     DoLog(0) && (Log() << Verbose(0) << " A - mainname (prefix for all runtime files)" << endl);
    325     DoLog(0) && (Log() << Verbose(0) << " B - Default path (for runtime files)" << endl);
    326     DoLog(0) && (Log() << Verbose(0) << " C - Path of pseudopotential files" << endl);
    327     DoLog(0) && (Log() << Verbose(0) << " D - Number of coefficient sharing processes" << endl);
    328     DoLog(0) && (Log() << Verbose(0) << " E - Number of wave function sharing processes" << endl);
    329     DoLog(0) && (Log() << Verbose(0) << " F - 0: Don't output density for OpenDX, 1: do" << endl);
    330     DoLog(0) && (Log() << Verbose(0) << " G - 0: Don't output physical data, 1: do" << endl);
    331     DoLog(0) && (Log() << Verbose(0) << " H - 0: Don't output densities of each unperturbed orbital for OpenDX, 1: do" << endl);
    332     DoLog(0) && (Log() << Verbose(0) << " I - 0: Don't output current density for OpenDX, 1: do" << endl);
    333     DoLog(0) && (Log() << Verbose(0) << " J - 0: Don't do the full current calculation, 1: do" << endl);
    334     DoLog(0) && (Log() << Verbose(0) << " K - 0: Don't do perturbation calculation to obtain susceptibility and shielding, 1: do" << endl);
    335     DoLog(0) && (Log() << Verbose(0) << " L - 0: Wannier centres as calculated, 1: common centre for all, 2: unite centres according to spread, 3: cell centre, 4: shifted to nearest grid point" << endl);
    336     DoLog(0) && (Log() << Verbose(0) << " M - Absolute begin of unphysical sawtooth transfer for position operator within cell" << endl);
    337     DoLog(0) && (Log() << Verbose(0) << " N - (0,1,2) x,y,z-plane to do two-dimensional current vector cut" << endl);
    338     DoLog(0) && (Log() << Verbose(0) << " O - Absolute position along vector cut axis for cut plane" << endl);
    339     DoLog(0) && (Log() << Verbose(0) << " P - Additional Gram-Schmidt-Orthonormalization to stabilize numerics" << endl);
    340     DoLog(0) && (Log() << Verbose(0) << " Q - Initial integer value of random number generator" << endl);
    341     DoLog(0) && (Log() << Verbose(0) << " R - for perturbation 0, for structure optimization defines upper limit of iterations" << endl);
    342     DoLog(0) && (Log() << Verbose(0) << " T - Output visual after ...th step" << endl);
    343     DoLog(0) && (Log() << Verbose(0) << " U - Output source densities of wave functions after ...th step" << endl);
    344     DoLog(0) && (Log() << Verbose(0) << " X - minimization iterations per wave function, if unsure leave at default value 0" << endl);
    345     DoLog(0) && (Log() << Verbose(0) << " Y - tolerance value for total spread in iterative Jacobi diagonalization" << endl);
    346     DoLog(0) && (Log() << Verbose(0) << " Z - Maximum number of minimization iterations" << endl);
    347     DoLog(0) && (Log() << Verbose(0) << " a - Relative change in total energy to stop min. iteration" << endl);
    348     DoLog(0) && (Log() << Verbose(0) << " b - Relative change in kinetic energy to stop min. iteration" << endl);
    349     DoLog(0) && (Log() << Verbose(0) << " c - Check stop conditions every ..th step during min. iteration" << endl);
    350     DoLog(0) && (Log() << Verbose(0) << " e - Maximum number of minimization iterations during initial level" << endl);
    351     DoLog(0) && (Log() << Verbose(0) << " f - Relative change in total energy to stop min. iteration during initial level" << endl);
    352     DoLog(0) && (Log() << Verbose(0) << " g - Relative change in kinetic energy to stop min. iteration during initial level" << endl);
    353     DoLog(0) && (Log() << Verbose(0) << " h - Check stop conditions every ..th step during min. iteration during initial level" << endl);
     321    Log() << Verbose(0) << "===========EDIT CONFIGURATION============================" << endl;
     322    Log() << Verbose(0) << " A - mainname (prefix for all runtime files)" << endl;
     323    Log() << Verbose(0) << " B - Default path (for runtime files)" << endl;
     324    Log() << Verbose(0) << " C - Path of pseudopotential files" << endl;
     325    Log() << Verbose(0) << " D - Number of coefficient sharing processes" << endl;
     326    Log() << Verbose(0) << " E - Number of wave function sharing processes" << endl;
     327    Log() << Verbose(0) << " F - 0: Don't output density for OpenDX, 1: do" << endl;
     328    Log() << Verbose(0) << " G - 0: Don't output physical data, 1: do" << endl;
     329    Log() << Verbose(0) << " H - 0: Don't output densities of each unperturbed orbital for OpenDX, 1: do" << endl;
     330    Log() << Verbose(0) << " I - 0: Don't output current density for OpenDX, 1: do" << endl;
     331    Log() << Verbose(0) << " J - 0: Don't do the full current calculation, 1: do" << endl;
     332    Log() << Verbose(0) << " K - 0: Don't do perturbation calculation to obtain susceptibility and shielding, 1: do" << endl;
     333    Log() << Verbose(0) << " L - 0: Wannier centres as calculated, 1: common centre for all, 2: unite centres according to spread, 3: cell centre, 4: shifted to nearest grid point" << endl;
     334    Log() << Verbose(0) << " M - Absolute begin of unphysical sawtooth transfer for position operator within cell" << endl;
     335    Log() << Verbose(0) << " N - (0,1,2) x,y,z-plane to do two-dimensional current vector cut" << endl;
     336    Log() << Verbose(0) << " O - Absolute position along vector cut axis for cut plane" << endl;
     337    Log() << Verbose(0) << " P - Additional Gram-Schmidt-Orthonormalization to stabilize numerics" << endl;
     338    Log() << Verbose(0) << " Q - Initial integer value of random number generator" << endl;
     339    Log() << Verbose(0) << " R - for perturbation 0, for structure optimization defines upper limit of iterations" << endl;
     340    Log() << Verbose(0) << " T - Output visual after ...th step" << endl;
     341    Log() << Verbose(0) << " U - Output source densities of wave functions after ...th step" << endl;
     342    Log() << Verbose(0) << " X - minimization iterations per wave function, if unsure leave at default value 0" << endl;
     343    Log() << Verbose(0) << " Y - tolerance value for total spread in iterative Jacobi diagonalization" << endl;
     344    Log() << Verbose(0) << " Z - Maximum number of minimization iterations" << endl;
     345    Log() << Verbose(0) << " a - Relative change in total energy to stop min. iteration" << endl;
     346    Log() << Verbose(0) << " b - Relative change in kinetic energy to stop min. iteration" << endl;
     347    Log() << Verbose(0) << " c - Check stop conditions every ..th step during min. iteration" << endl;
     348    Log() << Verbose(0) << " e - Maximum number of minimization iterations during initial level" << endl;
     349    Log() << Verbose(0) << " f - Relative change in total energy to stop min. iteration during initial level" << endl;
     350    Log() << Verbose(0) << " g - Relative change in kinetic energy to stop min. iteration during initial level" << endl;
     351    Log() << Verbose(0) << " h - Check stop conditions every ..th step during min. iteration during initial level" << endl;
    354352//    Log() << Verbose(0) << " j - six lower diagonal entries of matrix, defining the unit cell" << endl;
    355     DoLog(0) && (Log() << Verbose(0) << " k - Energy cutoff of plane wave basis in Hartree" << endl);
    356     DoLog(0) && (Log() << Verbose(0) << " l - Maximum number of levels in multi-level-ansatz" << endl);
    357     DoLog(0) && (Log() << Verbose(0) << " m - Factor by which grid nodes increase between standard and upper level" << endl);
    358     DoLog(0) && (Log() << Verbose(0) << " n - 0: Don't use RiemannTensor, 1: Do" << endl);
    359     DoLog(0) && (Log() << Verbose(0) << " o - Factor by which grid nodes increase between Riemann and standard(?) level" << endl);
    360     DoLog(0) && (Log() << Verbose(0) << " p - Number of Riemann levels" << endl);
    361     DoLog(0) && (Log() << Verbose(0) << " r - 0: Don't Use RiemannTensor, 1: Do" << endl);
    362     DoLog(0) && (Log() << Verbose(0) << " s - 0: Doubly occupied orbitals, 1: Up-/Down-Orbitals" << endl);
    363     DoLog(0) && (Log() << Verbose(0) << " t - Number of orbitals (depends pn SpinType)" << endl);
    364     DoLog(0) && (Log() << Verbose(0) << " u - Number of SpinUp orbitals (depends on SpinType)" << endl);
    365     DoLog(0) && (Log() << Verbose(0) << " v - Number of SpinDown orbitals (depends on SpinType)" << endl);
    366     DoLog(0) && (Log() << Verbose(0) << " w - Number of additional, unoccupied orbitals" << endl);
    367     DoLog(0) && (Log() << Verbose(0) << " x - radial cutoff for ewald summation in Bohrradii" << endl);
    368     DoLog(0) && (Log() << Verbose(0) << " y - 0: Don't do structure optimization beforehand, 1: Do" << endl);
    369     DoLog(0) && (Log() << Verbose(0) << " z - 0: Units are in Bohr radii, 1: units are in Aengstrom" << endl);
    370     DoLog(0) && (Log() << Verbose(0) << " i - 0: Coordinates given in file are absolute, 1: ... are relative to unit cell" << endl);
    371     DoLog(0) && (Log() << Verbose(0) << "=========================================================" << endl);
    372     DoLog(0) && (Log() << Verbose(0) << "INPUT: ");
     353    Log() << Verbose(0) << " k - Energy cutoff of plane wave basis in Hartree" << endl;
     354    Log() << Verbose(0) << " l - Maximum number of levels in multi-level-ansatz" << endl;
     355    Log() << Verbose(0) << " m - Factor by which grid nodes increase between standard and upper level" << endl;
     356    Log() << Verbose(0) << " n - 0: Don't use RiemannTensor, 1: Do" << endl;
     357    Log() << Verbose(0) << " o - Factor by which grid nodes increase between Riemann and standard(?) level" << endl;
     358    Log() << Verbose(0) << " p - Number of Riemann levels" << endl;
     359    Log() << Verbose(0) << " r - 0: Don't Use RiemannTensor, 1: Do" << endl;
     360    Log() << Verbose(0) << " s - 0: Doubly occupied orbitals, 1: Up-/Down-Orbitals" << endl;
     361    Log() << Verbose(0) << " t - Number of orbitals (depends pn SpinType)" << endl;
     362    Log() << Verbose(0) << " u - Number of SpinUp orbitals (depends on SpinType)" << endl;
     363    Log() << Verbose(0) << " v - Number of SpinDown orbitals (depends on SpinType)" << endl;
     364    Log() << Verbose(0) << " w - Number of additional, unoccupied orbitals" << endl;
     365    Log() << Verbose(0) << " x - radial cutoff for ewald summation in Bohrradii" << endl;
     366    Log() << Verbose(0) << " y - 0: Don't do structure optimization beforehand, 1: Do" << endl;
     367    Log() << Verbose(0) << " z - 0: Units are in Bohr radii, 1: units are in Aengstrom" << endl;
     368    Log() << Verbose(0) << " i - 0: Coordinates given in file are absolute, 1: ... are relative to unit cell" << endl;
     369    Log() << Verbose(0) << "=========================================================" << endl;
     370    Log() << Verbose(0) << "INPUT: ";
    373371    cin >> choice;
    374372
    375373    switch (choice) {
    376374        case 'A': // mainname
    377           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::mainname << "\t new: ");
     375          Log() << Verbose(0) << "Old: " << config::mainname << "\t new: ";
    378376          cin >> config::mainname;
    379377          break;
    380378        case 'B': // defaultpath
    381           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::defaultpath << "\t new: ");
     379          Log() << Verbose(0) << "Old: " << config::defaultpath << "\t new: ";
    382380          cin >> config::defaultpath;
    383381          break;
    384382        case 'C': // pseudopotpath
    385           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::pseudopotpath << "\t new: ");
     383          Log() << Verbose(0) << "Old: " << config::pseudopotpath << "\t new: ";
    386384          cin >> config::pseudopotpath;
    387385          break;
    388386
    389387        case 'D': // ProcPEGamma
    390           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::ProcPEGamma << "\t new: ");
     388          Log() << Verbose(0) << "Old: " << config::ProcPEGamma << "\t new: ";
    391389          cin >> config::ProcPEGamma;
    392390          break;
    393391        case 'E': // ProcPEPsi
    394           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::ProcPEPsi << "\t new: ");
     392          Log() << Verbose(0) << "Old: " << config::ProcPEPsi << "\t new: ";
    395393          cin >> config::ProcPEPsi;
    396394          break;
    397395        case 'F': // DoOutVis
    398           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoOutVis << "\t new: ");
     396          Log() << Verbose(0) << "Old: " << config::DoOutVis << "\t new: ";
    399397          cin >> config::DoOutVis;
    400398          break;
    401399        case 'G': // DoOutMes
    402           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoOutMes << "\t new: ");
     400          Log() << Verbose(0) << "Old: " << config::DoOutMes << "\t new: ";
    403401          cin >> config::DoOutMes;
    404402          break;
    405403        case 'H': // DoOutOrbitals
    406           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoOutOrbitals << "\t new: ");
     404          Log() << Verbose(0) << "Old: " << config::DoOutOrbitals << "\t new: ";
    407405          cin >> config::DoOutOrbitals;
    408406          break;
    409407        case 'I': // DoOutCurrent
    410           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoOutCurrent << "\t new: ");
     408          Log() << Verbose(0) << "Old: " << config::DoOutCurrent << "\t new: ";
    411409          cin >> config::DoOutCurrent;
    412410          break;
    413411        case 'J': // DoFullCurrent
    414           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoFullCurrent << "\t new: ");
     412          Log() << Verbose(0) << "Old: " << config::DoFullCurrent << "\t new: ";
    415413          cin >> config::DoFullCurrent;
    416414          break;
    417415        case 'K': // DoPerturbation
    418           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoPerturbation << "\t new: ");
     416          Log() << Verbose(0) << "Old: " << config::DoPerturbation << "\t new: ";
    419417          cin >> config::DoPerturbation;
    420418          break;
    421419        case 'L': // CommonWannier
    422           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::CommonWannier << "\t new: ");
     420          Log() << Verbose(0) << "Old: " << config::CommonWannier << "\t new: ";
    423421          cin >> config::CommonWannier;
    424422          break;
    425423        case 'M': // SawtoothStart
    426           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::SawtoothStart << "\t new: ");
     424          Log() << Verbose(0) << "Old: " << config::SawtoothStart << "\t new: ";
    427425          cin >> config::SawtoothStart;
    428426          break;
    429427        case 'N': // VectorPlane
    430           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::VectorPlane << "\t new: ");
     428          Log() << Verbose(0) << "Old: " << config::VectorPlane << "\t new: ";
    431429          cin >> config::VectorPlane;
    432430          break;
    433431        case 'O': // VectorCut
    434           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::VectorCut << "\t new: ");
     432          Log() << Verbose(0) << "Old: " << config::VectorCut << "\t new: ";
    435433          cin >> config::VectorCut;
    436434          break;
    437435        case 'P': // UseAddGramSch
    438           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::UseAddGramSch << "\t new: ");
     436          Log() << Verbose(0) << "Old: " << config::UseAddGramSch << "\t new: ";
    439437          cin >> config::UseAddGramSch;
    440438          break;
    441439        case 'Q': // Seed
    442           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::Seed << "\t new: ");
     440          Log() << Verbose(0) << "Old: " << config::Seed << "\t new: ";
    443441          cin >> config::Seed;
    444442          break;
    445443
    446444        case 'R': // MaxOuterStep
    447           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxOuterStep << "\t new: ");
     445          Log() << Verbose(0) << "Old: " << config::MaxOuterStep << "\t new: ";
    448446          cin >> config::MaxOuterStep;
    449447          break;
    450448        case 'T': // OutVisStep
    451           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::OutVisStep << "\t new: ");
     449          Log() << Verbose(0) << "Old: " << config::OutVisStep << "\t new: ";
    452450          cin >> config::OutVisStep;
    453451          break;
    454452        case 'U': // OutSrcStep
    455           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::OutSrcStep << "\t new: ");
     453          Log() << Verbose(0) << "Old: " << config::OutSrcStep << "\t new: ";
    456454          cin >> config::OutSrcStep;
    457455          break;
    458456        case 'X': // MaxPsiStep
    459           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxPsiStep << "\t new: ");
     457          Log() << Verbose(0) << "Old: " << config::MaxPsiStep << "\t new: ";
    460458          cin >> config::MaxPsiStep;
    461459          break;
    462460        case 'Y': // EpsWannier
    463           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::EpsWannier << "\t new: ");
     461          Log() << Verbose(0) << "Old: " << config::EpsWannier << "\t new: ";
    464462          cin >> config::EpsWannier;
    465463          break;
    466464
    467465        case 'Z': // MaxMinStep
    468           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxMinStep << "\t new: ");
     466          Log() << Verbose(0) << "Old: " << config::MaxMinStep << "\t new: ";
    469467          cin >> config::MaxMinStep;
    470468          break;
    471469        case 'a': // RelEpsTotalEnergy
    472           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RelEpsTotalEnergy << "\t new: ");
     470          Log() << Verbose(0) << "Old: " << config::RelEpsTotalEnergy << "\t new: ";
    473471          cin >> config::RelEpsTotalEnergy;
    474472          break;
    475473        case 'b': // RelEpsKineticEnergy
    476           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RelEpsKineticEnergy << "\t new: ");
     474          Log() << Verbose(0) << "Old: " << config::RelEpsKineticEnergy << "\t new: ";
    477475          cin >> config::RelEpsKineticEnergy;
    478476          break;
    479477        case 'c': // MaxMinStopStep
    480           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxMinStopStep << "\t new: ");
     478          Log() << Verbose(0) << "Old: " << config::MaxMinStopStep << "\t new: ";
    481479          cin >> config::MaxMinStopStep;
    482480          break;
    483481        case 'e': // MaxInitMinStep
    484           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxInitMinStep << "\t new: ");
     482          Log() << Verbose(0) << "Old: " << config::MaxInitMinStep << "\t new: ";
    485483          cin >> config::MaxInitMinStep;
    486484          break;
    487485        case 'f': // InitRelEpsTotalEnergy
    488           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::InitRelEpsTotalEnergy << "\t new: ");
     486          Log() << Verbose(0) << "Old: " << config::InitRelEpsTotalEnergy << "\t new: ";
    489487          cin >> config::InitRelEpsTotalEnergy;
    490488          break;
    491489        case 'g': // InitRelEpsKineticEnergy
    492           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::InitRelEpsKineticEnergy << "\t new: ");
     490          Log() << Verbose(0) << "Old: " << config::InitRelEpsKineticEnergy << "\t new: ";
    493491          cin >> config::InitRelEpsKineticEnergy;
    494492          break;
    495493        case 'h': // InitMaxMinStopStep
    496           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::InitMaxMinStopStep << "\t new: ");
     494          Log() << Verbose(0) << "Old: " << config::InitMaxMinStopStep << "\t new: ";
    497495          cin >> config::InitMaxMinStopStep;
    498496          break;
    … …  
    500498//        case 'j': // BoxLength
    501499//          Log() << Verbose(0) << "enter lower triadiagonalo form of basis matrix" << endl << endl;
    502 //          double * const cell_size = World::get()->cell_size;
    503500//          for (int i=0;i<6;i++) {
    504501//            Log() << Verbose(0) << "Cell size" << i << ": ";
    505 //            cin >> cell_size[i];
     502//            cin >> mol->cell_size[i];
    506503//          }
    507504//          break;
    508505
    509506        case 'k': // ECut
    510           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::ECut << "\t new: ");
     507          Log() << Verbose(0) << "Old: " << config::ECut << "\t new: ";
    511508          cin >> config::ECut;
    512509          break;
    513510        case 'l': // MaxLevel
    514           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxLevel << "\t new: ");
     511          Log() << Verbose(0) << "Old: " << config::MaxLevel << "\t new: ";
    515512          cin >> config::MaxLevel;
    516513          break;
    517514        case 'm': // RiemannTensor
    518           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RiemannTensor << "\t new: ");
     515          Log() << Verbose(0) << "Old: " << config::RiemannTensor << "\t new: ";
    519516          cin >> config::RiemannTensor;
    520517          break;
    521518        case 'n': // LevRFactor
    522           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::LevRFactor << "\t new: ");
     519          Log() << Verbose(0) << "Old: " << config::LevRFactor << "\t new: ";
    523520          cin >> config::LevRFactor;
    524521          break;
    525522        case 'o': // RiemannLevel
    526           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RiemannLevel << "\t new: ");
     523          Log() << Verbose(0) << "Old: " << config::RiemannLevel << "\t new: ";
    527524          cin >> config::RiemannLevel;
    528525          break;
    529526        case 'p': // Lev0Factor
    530           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::Lev0Factor << "\t new: ");
     527          Log() << Verbose(0) << "Old: " << config::Lev0Factor << "\t new: ";
    531528          cin >> config::Lev0Factor;
    532529          break;
    533530        case 'r': // RTActualUse
    534           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RTActualUse << "\t new: ");
     531          Log() << Verbose(0) << "Old: " << config::RTActualUse << "\t new: ";
    535532          cin >> config::RTActualUse;
    536533          break;
    537534        case 's': // PsiType
    538           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::PsiType << "\t new: ");
     535          Log() << Verbose(0) << "Old: " << config::PsiType << "\t new: ";
    539536          cin >> config::PsiType;
    540537          break;
    541538        case 't': // MaxPsiDouble
    542           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxPsiDouble << "\t new: ");
     539          Log() << Verbose(0) << "Old: " << config::MaxPsiDouble << "\t new: ";
    543540          cin >> config::MaxPsiDouble;
    544541          break;
    545542        case 'u': // PsiMaxNoUp
    546           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::PsiMaxNoUp << "\t new: ");
     543          Log() << Verbose(0) << "Old: " << config::PsiMaxNoUp << "\t new: ";
    547544          cin >> config::PsiMaxNoUp;
    548545          break;
    549546        case 'v': // PsiMaxNoDown
    550           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::PsiMaxNoDown << "\t new: ");
     547          Log() << Verbose(0) << "Old: " << config::PsiMaxNoDown << "\t new: ";
    551548          cin >> config::PsiMaxNoDown;
    552549          break;
    553550        case 'w': // AddPsis
    554           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::AddPsis << "\t new: ");
     551          Log() << Verbose(0) << "Old: " << config::AddPsis << "\t new: ";
    555552          cin >> config::AddPsis;
    556553          break;
    557554
    558555        case 'x': // RCut
    559           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RCut << "\t new: ");
     556          Log() << Verbose(0) << "Old: " << config::RCut << "\t new: ";
    560557          cin >> config::RCut;
    561558          break;
    562559        case 'y': // StructOpt
    563           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::StructOpt << "\t new: ");
     560          Log() << Verbose(0) << "Old: " << config::StructOpt << "\t new: ";
    564561          cin >> config::StructOpt;
    565562          break;
    566563        case 'z': // IsAngstroem
    567           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::IsAngstroem << "\t new: ");
     564          Log() << Verbose(0) << "Old: " << config::IsAngstroem << "\t new: ";
    568565          cin >> config::IsAngstroem;
    569566          break;
    570567        case 'i': // RelativeCoord
    571           DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RelativeCoord << "\t new: ");
     568          Log() << Verbose(0) << "Old: " << config::RelativeCoord << "\t new: ";
    572569          cin >> config::RelativeCoord;
    573570          break;
    … …  
    648645  }
    649646  strcpy(configname, ptr);
    650   DoLog(0) && (Log() << Verbose(0) << "Found configpath: " << configpath << ", dir slash was found at " << last << ", config name is " << configname << "." << endl);
     647  Log() << Verbose(0) << "Found configpath: " << configpath << ", dir slash was found at " << last << ", config name is " << configname << "." << endl;
    651648  delete[](buffer);
    652649};
    … …  
    659656{
    660657  if (FileBuffer != NULL) {
    661     DoeLog(2) && (eLog()<< Verbose(2) << "deleting present FileBuffer in PrepareFileBuffer()." << endl);
     658    eLog() << Verbose(2) << "deleting present FileBuffer in PrepareFileBuffer()." << endl;
    662659    delete(FileBuffer);
    663660  }
    … …  
    685682
    686683  if (mol == NULL) {
    687     DoeLog(0) && (eLog()<< Verbose(0) << "Molecule is not allocated in LoadMolecule(), exit.");
     684    eLog() << Verbose(0) << "Molecule is not allocated in LoadMolecule(), exit.";
    688685    performCriticalExit();
    689686  }
    … …  
    691688  ParseForParameter(verbose,FileBuffer,"MaxTypes", 0, 1, 1, int_type, &(MaxTypes), 1, critical);
    692689  if (MaxTypes == 0) {
    693     DoeLog(1) && (eLog()<< Verbose(1) << "There are no atoms according to MaxTypes in this config file." << endl);
    694     //performCriticalExit();
     690    eLog() << Verbose(0) << "There are no atoms according to MaxTypes in this config file." << endl;
     691    performCriticalExit();
    695692  } else {
    696693    // prescan number of ions per type
    697     DoLog(0) && (Log() << Verbose(0) << "Prescanning ions per type: " << endl);
     694    Log() << Verbose(0) << "Prescanning ions per type: " << endl;
    698695    int NoAtoms = 0;
    699696    for (int i=0; i < MaxTypes; i++) {
    … …  
    702699      ParseForParameter(verbose,FileBuffer, name, 0, 2, 1, int_type, &Z, 1, critical);
    703700      elementhash[i] = periode->FindElement(Z);
    704       DoLog(1) && (Log() << Verbose(1) << i << ". Z = " << elementhash[i]->Z << " with " << No[i] << " ions." << endl);
     701      Log() << Verbose(1) << i << ". Z = " << elementhash[i]->Z << " with " << No[i] << " ions." << endl;
    705702      NoAtoms += No[i];
    706703    }
    … …  
    710707    sprintf(name,"Ion_Type%i",MaxTypes);
    711708    if (!ParseForParameter(verbose,FileBuffer, (const char*)name, 1, 1, 1, int_type, &value[0], 1, critical)) {
    712       DoeLog(0) && (eLog()<< Verbose(0) << "There are no atoms in the config file!" << endl);
     709      eLog() << Verbose(0) << "There are no atoms in the config file!" << endl;
    713710      performCriticalExit();
    714711      return;
    … …  
    728725      bool status = true;
    729726      while (status) {
    730         DoLog(0) && (Log() << Verbose(0) << "Currently parsing MD step " << repetition << "." << endl);
     727        Log() << Verbose(0) << "Currently parsing MD step " << repetition << "." << endl;
    731728        for (int i=0; i < MaxTypes; i++) {
    732729          sprintf(name,"Ion_Type%i",i+1);
    … …  
    794791      }
    795792      repetition--;
    796       DoLog(0) && (Log() << Verbose(0) << "Found " << repetition << " trajectory steps." << endl);
     793      Log() << Verbose(0) << "Found " << repetition << " trajectory steps." << endl;
    797794      if (repetition <= 1)  // if onyl one step, desactivate use of trajectories
    798795        mol->MDSteps = 0;
    … …  
    806803              ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 3, 1, double_type, &value[2], repetition, (repetition == 0) ? critical : optional))
    807804        repetition++;
    808       DoLog(0) && (Log() << Verbose(0) << "I found " << repetition << " times the keyword Ion_Type1_1." << endl);
     805      Log() << Verbose(0) << "I found " << repetition << " times the keyword Ion_Type1_1." << endl;
    809806      // parse in molecule coordinates
    810807      for (int i=0; i < MaxTypes; i++) {
    … …  
    855852  ifstream *file = new ifstream(filename);
    856853  if (file == NULL) {
    857     DoeLog(1) && (eLog()<< Verbose(1) << "config file " << filename << " missing!" << endl);
     854    eLog() << Verbose(1) << "config file " << filename << " missing!" << endl;
    858855    return;
    859856  }
    … …  
    967964  // Unit cell and magnetic field
    968965  ParseForParameter(verbose,FileBuffer, "BoxLength", 0, 3, 3, lower_trigrid, BoxLength, 1, critical); /* Lattice->RealBasis */
    969   double * const cell_size = World::get()->cell_size;
    970   cell_size[0] = BoxLength[0];
    971   cell_size[1] = BoxLength[3];
    972   cell_size[2] = BoxLength[4];
    973   cell_size[3] = BoxLength[6];
    974   cell_size[4] = BoxLength[7];
    975   cell_size[5] = BoxLength[8];
     966  mol->cell_size[0] = BoxLength[0];
     967  mol->cell_size[1] = BoxLength[3];
     968  mol->cell_size[2] = BoxLength[4];
     969  mol->cell_size[3] = BoxLength[6];
     970  mol->cell_size[4] = BoxLength[7];
     971  mol->cell_size[5] = BoxLength[8];
    976972  //if (1) fprintf(stderr,"\n");
    977973
    … …  
    10631059    BG = new BondGraph(IsAngstroem);
    10641060    if (BG->LoadBondLengthTable(BondGraphFileName)) {
    1065       DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
     1061      Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
    10661062    } else {
    1067       DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
     1063      eLog() << Verbose(1) << "Bond length table loading failed." << endl;
    10681064    }
    10691065  }
    … …  
    10781074  // don't do this here ...
    10791075  //MolList->DissectMoleculeIntoConnectedSubgraphs(mol,this);
    1080   //delete(mol);
    1081 
     1076
     1077  delete(mol);
    10821078  delete(FileBuffer);
    10831079};
    … …  
    10941090  ifstream *file = new ifstream(filename);
    10951091  if (file == NULL) {
    1096     DoeLog(1) && (eLog()<< Verbose(1) << "config file " << filename << " missing!" << endl);
     1092    eLog() << Verbose(1) << "config file " << filename << " missing!" << endl;
    10971093    return;
    10981094  }
    … …  
    11721168
    11731169  ParseForParameter(verbose,file, "BoxLength", 0, 3, 3, lower_trigrid, BoxLength, 1, critical); /* Lattice->RealBasis */
    1174   double * const cell_size = World::get()->cell_size;
    1175   cell_size[0] = BoxLength[0];
    1176   cell_size[1] = BoxLength[3];
    1177   cell_size[2] = BoxLength[4];
    1178   cell_size[3] = BoxLength[6];
    1179   cell_size[4] = BoxLength[7];
    1180   cell_size[5] = BoxLength[8];
     1170  mol->cell_size[0] = BoxLength[0];
     1171  mol->cell_size[1] = BoxLength[3];
     1172  mol->cell_size[2] = BoxLength[4];
     1173  mol->cell_size[3] = BoxLength[6];
     1174  mol->cell_size[4] = BoxLength[7];
     1175  mol->cell_size[5] = BoxLength[8];
    11811176  if (1) fprintf(stderr,"\n");
    11821177  config::DoPerturbation = 0;
    … …  
    12541249  BG = new BondGraph(IsAngstroem);
    12551250  if (BG->LoadBondLengthTable(BondGraphFileName)) {
    1256     DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
     1251    Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
    12571252  } else {
    1258     DoLog(0) && (Log() << Verbose(0) << "Bond length table loading failed." << endl);
     1253    Log() << Verbose(0) << "Bond length table loading failed." << endl;
    12591254  }
    12601255
    … …  
    12631258  for (i=MAX_ELEMENTS;i--;)
    12641259    elementhash[i] = NULL;
    1265   DoLog(0) && (Log() << Verbose(0) << "Parsing Ions ..." << endl);
     1260  Log() << Verbose(0) << "Parsing Ions ..." << endl;
    12661261  No=0;
    12671262  found = 0;
    12681263  while (getline(*file,zeile,'\n')) {
    12691264    if (zeile.find("Ions_Data") == 0) {
    1270       DoLog(1) && (Log() << Verbose(1) << "found Ions_Data...begin parsing" << endl);
     1265      Log() << Verbose(1) << "found Ions_Data...begin parsing" << endl;
    12711266      found ++;
    12721267    }
    … …  
    12821277      input >> b;     // element mass
    12831278      elementhash[No] = periode->FindElement(Z);
    1284       DoLog(1) && (Log() << Verbose(1) << "AtomNo: " << AtomNo << "\tZ: " << Z << "\ta:" << a << "\tl:"  << l << "\b:" << b << "\tElement:" << elementhash[No] << "\t:" << endl);
     1279      Log() << Verbose(1) << "AtomNo: " << AtomNo << "\tZ: " << Z << "\ta:" << a << "\tl:"  << l << "\b:" << b << "\tElement:" << elementhash[No] << "\t:" << endl;
    12851280      for(i=0;i<AtomNo;i++) {
    12861281        if (!getline(*file,zeile,'\n')) {// parse on and on
    1287           DoLog(2) && (Log() << Verbose(2) << "Error: Too few items in ionic list of element" << elementhash[No] << "." << endl << "Exiting." << endl);
     1282          Log() << Verbose(2) << "Error: Too few items in ionic list of element" << elementhash[No] << "." << endl << "Exiting." << endl;
    12881283          // return 1;
    12891284        } else {
    … …  
    13161311  // bring MaxTypes up to date
    13171312  mol->CountElements();
    1318   const double * const cell_size = World::get()->cell_size;
    13191313  ofstream * const output = new ofstream(filename, ios::out);
    13201314  if (output != NULL) {
    … …  
    13871381    *output << endl;
    13881382    *output << "BoxLength\t\t\t# (Length of a unit cell)" << endl;
    1389     *output << cell_size[0] << "\t" << endl;
    1390     *output << cell_size[1] << "\t" << cell_size[2] << "\t" << endl;
    1391     *output << cell_size[3] << "\t" << cell_size[4] << "\t" << cell_size[5] << "\t" << endl;
     1383    *output << mol->cell_size[0] << "\t" << endl;
     1384    *output << mol->cell_size[1] << "\t" << mol->cell_size[2] << "\t" << endl;
     1385    *output << mol->cell_size[3] << "\t" << mol->cell_size[4] << "\t" << mol->cell_size[5] << "\t" << endl;
    13921386    // FIXME
    13931387    *output << endl;
    … …  
    14331427    return result;
    14341428  } else {
    1435     DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open output file:" << filename << endl);
     1429    eLog() << Verbose(1) << "Cannot open output file:" << filename << endl;
    14361430    return false;
    14371431  }
    … …  
    14551449    output = new ofstream(fname->str().c_str(), ios::out);
    14561450    if (output == NULL) {
    1457       DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open mpqc output file:" << fname << endl);
     1451      eLog() << Verbose(1) << "Cannot open mpqc output file:" << fname << endl;
    14581452      delete(fname);
    14591453      return false;
    … …  
    14981492    output = new ofstream(fname->str().c_str(), ios::out);
    14991493    if (output == NULL) {
    1500       DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open mpqc hessian output file:" << fname << endl);
     1494      eLog() << Verbose(1) << "Cannot open mpqc hessian output file:" << fname << endl;
    15011495      delete(fname);
    15021496      return false;
    … …  
    15541548  f = fopen(name, "w" );
    15551549  if (f == NULL) {
    1556     DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open pdb output file:" << name << endl);
     1550    eLog() << Verbose(1) << "Cannot open pdb output file:" << name << endl;
    15571551    return false;
    15581552  }
    … …  
    16091603  f = fopen(name, "w" );
    16101604  if (f == NULL) {
    1611     DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open pdb output file:" << name << endl);
     1605    eLog() << Verbose(1) << "Cannot open pdb output file:" << name << endl;
    16121606    Free(&elementNo);
    16131607    return false;
    … …  
    16461640/** Stores all atoms in a TREMOLO data input file.
    16471641 * Note that this format cannot be parsed again.
    1648  * Note that TREMOLO does not like Id starting at 0, but at 1. Atoms with Id 0 are discarded!
    16491642 * \param *filename name of file (without ".in" suffix!)
    16501643 * \param *mol pointer to molecule
    … …  
    16591652  output = new ofstream(fname->str().c_str(), ios::out);
    16601653  if (output == NULL) {
    1661     DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open tremolo output file:" << fname << endl);
     1654    eLog() << Verbose(1) << "Cannot open tremolo output file:" << fname << endl;
    16621655    delete(fname);
    16631656    return false;
    … …  
    17011694/** Stores all atoms from all molecules in a TREMOLO data input file.
    17021695 * Note that this format cannot be parsed again.
    1703  * Note that TREMOLO does not like Id starting at 0, but at 1. Atoms with Id 0 are discarded!
    17041696 * \param *filename name of file (without ".in" suffix!)
    17051697 * \param *MolList pointer to MoleculeListClass containing all atoms
    … …  
    17141706  output = new ofstream(fname->str().c_str(), ios::out);
    17151707  if (output == NULL) {
    1716     DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open tremolo output file:" << fname << endl);
     1708    eLog() << Verbose(1) << "Cannot open tremolo output file:" << fname << endl;
    17171709    delete(fname);
    17181710    return false;
    … …  
    17541746      while (Walker->next != (*MolWalker)->end) {
    17551747        Walker = Walker->next;
    1756         *output << AtomNo+1 << "\t";
     1748        *output << AtomNo << "\t";
    17571749        *output << Walker->Name << "\t";
    17581750        *output << (*MolWalker)->name << "\t";
    1759         *output << MolCounter+1 << "\t";
     1751        *output << MolCounter << "\t";
    17601752        *output << Walker->node->x[0] << "\t" << Walker->node->x[1] << "\t" << Walker->node->x[2] << "\t";
    17611753        *output << (double)Walker->type->Valence << "\t";
    17621754        *output << Walker->type->symbol << "\t";
    17631755        for (BondList::iterator runner = Walker->ListOfBonds.begin(); runner != Walker->ListOfBonds.end(); runner++)
    1764           *output << LocalNotoGlobalNoMap[MolCounter][ (*runner)->GetOtherAtom(Walker)->nr ]+1 << "\t";
     1756          *output << LocalNotoGlobalNoMap[MolCounter][ (*runner)->GetOtherAtom(Walker)->nr ] << "\t";
    17651757        for(int i=Walker->ListOfBonds.size(); i < MaxNeighbours; i++)
    17661758          *output << "-\t";
    … …  
    21312123              }
    21322124              line++;
    2133             } while ((dummy1 != NULL) && ((dummy1[0] == '#') || (dummy1[0] == '\n')));
     2125            } while (dummy1 != NULL && (dummy1[0] == '#') || (dummy1[0] == '\n'));
    21342126            dummy = dummy1;
    21352127          } else { // simple int, strings or doubles start in the same line
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