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  • src/config.cpp

    rb34306 ra67d19  
    7474  file= new ifstream(filename);
    7575  if (file == NULL) {
    76     eLog() << Verbose(1) << "config file " << filename << " missing!" << endl;
     76    DoeLog(1) && (eLog()<< Verbose(1) << "config file " << filename << " missing!" << endl);
    7777    return;
    7878  }
    … …  
    8585  file->clear();
    8686  file->seekg(file_position, ios::beg);
    87   Log() << Verbose(1) << NoLines-1 << " lines were recognized." << endl;
     87  DoLog(1) && (Log() << Verbose(1) << NoLines-1 << " lines were recognized." << endl);
    8888
    8989  // allocate buffer's 1st dimension
    9090  if (buffer != NULL) {
    91     eLog() << Verbose(1) << "FileBuffer->buffer is not NULL!" << endl;
     91    DoeLog(1) && (eLog()<< Verbose(1) << "FileBuffer->buffer is not NULL!" << endl);
    9292    return;
    9393  } else
    … …  
    105105    lines++;
    106106  } while((!file->eof()) && (lines < NoLines));
    107   Log() << Verbose(1) << lines-1 << " lines were read into the buffer." << endl;
     107  DoLog(1) && (Log() << Verbose(1) << lines-1 << " lines were read into the buffer." << endl);
    108108
    109109  // close and exit
    … …  
    144144  map<const char *, int, IonTypeCompare> IonTypeLineMap;
    145145  if (LineMapping == NULL) {
    146     eLog() << Verbose(0) << "map pointer is NULL: " << LineMapping << endl;
     146    DoeLog(0) && (eLog()<< Verbose(0) << "map pointer is NULL: " << LineMapping << endl);
    147147    performCriticalExit();
    148148    return;
    … …  
    160160      LineMapping[CurrentLine+(nr++)] = runner->second;
    161161    else {
    162       eLog() << Verbose(0) << "config::MapIonTypesInBuffer - NoAtoms is wrong: We are past the end of the file!" << endl;
     162      DoeLog(0) && (eLog()<< Verbose(0) << "config::MapIonTypesInBuffer - NoAtoms is wrong: We are past the end of the file!" << endl);
    163163      performCriticalExit();
    164164    }
    … …  
    250250        Thermostat = None;
    251251      } else {
    252         Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
     252        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
    253253        Thermostat = None;
    254254      }
    … …  
    258258        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read scaling frequency
    259259      } else {
    260         Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
     260        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
    261261        Thermostat = None;
    262262      }
    … …  
    266266        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read collision rate
    267267      } else {
    268         Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
     268        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
    269269        Thermostat = None;
    270270      }
    … …  
    274274        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read gamma
    275275        if (ParseForParameter(verbose,fb,"Thermostat", 0, 3, 1, double_type, &alpha, 1, optional)) {
    276           Log() << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << alpha << "." << endl;
     276          DoLog(2) && (Log() << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << alpha << "." << endl);
    277277        } else {
    278278          alpha = 1.;
    279279        }
    280280      } else {
    281         Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
     281        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
    282282        Thermostat = None;
    283283      }
    … …  
    287287        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read \tau_T
    288288      } else {
    289         Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
     289        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
    290290        Thermostat = None;
    291291      }
    … …  
    296296        alpha = 0.;
    297297      } else {
    298         Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
     298        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
    299299        Thermostat = None;
    300300      }
    301301    } else {
    302       Log() << Verbose(1) << " Warning: thermostat name was not understood!" << endl;
     302      DoLog(1) && (Log() << Verbose(1) << " Warning: thermostat name was not understood!" << endl);
    303303      Thermostat = None;
    304304    }
    305305  } else {
    306306    if ((MaxOuterStep > 0) && (TargetTemp != 0))
    307       Log() << Verbose(2) <<  "No thermostat chosen despite finite temperature MD, falling back to None." << endl;
     307      DoLog(2) && (Log() << Verbose(2) <<  "No thermostat chosen despite finite temperature MD, falling back to None." << endl);
    308308    Thermostat = None;
    309309  }
    … …  
    321321
    322322  do {
    323     Log() << Verbose(0) << "===========EDIT CONFIGURATION============================" << endl;
    324     Log() << Verbose(0) << " A - mainname (prefix for all runtime files)" << endl;
    325     Log() << Verbose(0) << " B - Default path (for runtime files)" << endl;
    326     Log() << Verbose(0) << " C - Path of pseudopotential files" << endl;
    327     Log() << Verbose(0) << " D - Number of coefficient sharing processes" << endl;
    328     Log() << Verbose(0) << " E - Number of wave function sharing processes" << endl;
    329     Log() << Verbose(0) << " F - 0: Don't output density for OpenDX, 1: do" << endl;
    330     Log() << Verbose(0) << " G - 0: Don't output physical data, 1: do" << endl;
    331     Log() << Verbose(0) << " H - 0: Don't output densities of each unperturbed orbital for OpenDX, 1: do" << endl;
    332     Log() << Verbose(0) << " I - 0: Don't output current density for OpenDX, 1: do" << endl;
    333     Log() << Verbose(0) << " J - 0: Don't do the full current calculation, 1: do" << endl;
    334     Log() << Verbose(0) << " K - 0: Don't do perturbation calculation to obtain susceptibility and shielding, 1: do" << endl;
    335     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     Log() << Verbose(0) << " M - Absolute begin of unphysical sawtooth transfer for position operator within cell" << endl;
    337     Log() << Verbose(0) << " N - (0,1,2) x,y,z-plane to do two-dimensional current vector cut" << endl;
    338     Log() << Verbose(0) << " O - Absolute position along vector cut axis for cut plane" << endl;
    339     Log() << Verbose(0) << " P - Additional Gram-Schmidt-Orthonormalization to stabilize numerics" << endl;
    340     Log() << Verbose(0) << " Q - Initial integer value of random number generator" << endl;
    341     Log() << Verbose(0) << " R - for perturbation 0, for structure optimization defines upper limit of iterations" << endl;
    342     Log() << Verbose(0) << " T - Output visual after ...th step" << endl;
    343     Log() << Verbose(0) << " U - Output source densities of wave functions after ...th step" << endl;
    344     Log() << Verbose(0) << " X - minimization iterations per wave function, if unsure leave at default value 0" << endl;
    345     Log() << Verbose(0) << " Y - tolerance value for total spread in iterative Jacobi diagonalization" << endl;
    346     Log() << Verbose(0) << " Z - Maximum number of minimization iterations" << endl;
    347     Log() << Verbose(0) << " a - Relative change in total energy to stop min. iteration" << endl;
    348     Log() << Verbose(0) << " b - Relative change in kinetic energy to stop min. iteration" << endl;
    349     Log() << Verbose(0) << " c - Check stop conditions every ..th step during min. iteration" << endl;
    350     Log() << Verbose(0) << " e - Maximum number of minimization iterations during initial level" << endl;
    351     Log() << Verbose(0) << " f - Relative change in total energy to stop min. iteration during initial level" << endl;
    352     Log() << Verbose(0) << " g - Relative change in kinetic energy to stop min. iteration during initial level" << endl;
    353     Log() << Verbose(0) << " h - Check stop conditions every ..th step during min. iteration during initial level" << endl;
     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);
    354354//    Log() << Verbose(0) << " j - six lower diagonal entries of matrix, defining the unit cell" << endl;
    355     Log() << Verbose(0) << " k - Energy cutoff of plane wave basis in Hartree" << endl;
    356     Log() << Verbose(0) << " l - Maximum number of levels in multi-level-ansatz" << endl;
    357     Log() << Verbose(0) << " m - Factor by which grid nodes increase between standard and upper level" << endl;
    358     Log() << Verbose(0) << " n - 0: Don't use RiemannTensor, 1: Do" << endl;
    359     Log() << Verbose(0) << " o - Factor by which grid nodes increase between Riemann and standard(?) level" << endl;
    360     Log() << Verbose(0) << " p - Number of Riemann levels" << endl;
    361     Log() << Verbose(0) << " r - 0: Don't Use RiemannTensor, 1: Do" << endl;
    362     Log() << Verbose(0) << " s - 0: Doubly occupied orbitals, 1: Up-/Down-Orbitals" << endl;
    363     Log() << Verbose(0) << " t - Number of orbitals (depends pn SpinType)" << endl;
    364     Log() << Verbose(0) << " u - Number of SpinUp orbitals (depends on SpinType)" << endl;
    365     Log() << Verbose(0) << " v - Number of SpinDown orbitals (depends on SpinType)" << endl;
    366     Log() << Verbose(0) << " w - Number of additional, unoccupied orbitals" << endl;
    367     Log() << Verbose(0) << " x - radial cutoff for ewald summation in Bohrradii" << endl;
    368     Log() << Verbose(0) << " y - 0: Don't do structure optimization beforehand, 1: Do" << endl;
    369     Log() << Verbose(0) << " z - 0: Units are in Bohr radii, 1: units are in Aengstrom" << endl;
    370     Log() << Verbose(0) << " i - 0: Coordinates given in file are absolute, 1: ... are relative to unit cell" << endl;
    371     Log() << Verbose(0) << "=========================================================" << endl;
    372     Log() << Verbose(0) << "INPUT: ";
     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: ");
    373373    cin >> choice;
    374374
    375375    switch (choice) {
    376376        case 'A': // mainname
    377           Log() << Verbose(0) << "Old: " << config::mainname << "\t new: ";
     377          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::mainname << "\t new: ");
    378378          cin >> config::mainname;
    379379          break;
    380380        case 'B': // defaultpath
    381           Log() << Verbose(0) << "Old: " << config::defaultpath << "\t new: ";
     381          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::defaultpath << "\t new: ");
    382382          cin >> config::defaultpath;
    383383          break;
    384384        case 'C': // pseudopotpath
    385           Log() << Verbose(0) << "Old: " << config::pseudopotpath << "\t new: ";
     385          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::pseudopotpath << "\t new: ");
    386386          cin >> config::pseudopotpath;
    387387          break;
    388388
    389389        case 'D': // ProcPEGamma
    390           Log() << Verbose(0) << "Old: " << config::ProcPEGamma << "\t new: ";
     390          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::ProcPEGamma << "\t new: ");
    391391          cin >> config::ProcPEGamma;
    392392          break;
    393393        case 'E': // ProcPEPsi
    394           Log() << Verbose(0) << "Old: " << config::ProcPEPsi << "\t new: ";
     394          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::ProcPEPsi << "\t new: ");
    395395          cin >> config::ProcPEPsi;
    396396          break;
    397397        case 'F': // DoOutVis
    398           Log() << Verbose(0) << "Old: " << config::DoOutVis << "\t new: ";
     398          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoOutVis << "\t new: ");
    399399          cin >> config::DoOutVis;
    400400          break;
    401401        case 'G': // DoOutMes
    402           Log() << Verbose(0) << "Old: " << config::DoOutMes << "\t new: ";
     402          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoOutMes << "\t new: ");
    403403          cin >> config::DoOutMes;
    404404          break;
    405405        case 'H': // DoOutOrbitals
    406           Log() << Verbose(0) << "Old: " << config::DoOutOrbitals << "\t new: ";
     406          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoOutOrbitals << "\t new: ");
    407407          cin >> config::DoOutOrbitals;
    408408          break;
    409409        case 'I': // DoOutCurrent
    410           Log() << Verbose(0) << "Old: " << config::DoOutCurrent << "\t new: ";
     410          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoOutCurrent << "\t new: ");
    411411          cin >> config::DoOutCurrent;
    412412          break;
    413413        case 'J': // DoFullCurrent
    414           Log() << Verbose(0) << "Old: " << config::DoFullCurrent << "\t new: ";
     414          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoFullCurrent << "\t new: ");
    415415          cin >> config::DoFullCurrent;
    416416          break;
    417417        case 'K': // DoPerturbation
    418           Log() << Verbose(0) << "Old: " << config::DoPerturbation << "\t new: ";
     418          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::DoPerturbation << "\t new: ");
    419419          cin >> config::DoPerturbation;
    420420          break;
    421421        case 'L': // CommonWannier
    422           Log() << Verbose(0) << "Old: " << config::CommonWannier << "\t new: ";
     422          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::CommonWannier << "\t new: ");
    423423          cin >> config::CommonWannier;
    424424          break;
    425425        case 'M': // SawtoothStart
    426           Log() << Verbose(0) << "Old: " << config::SawtoothStart << "\t new: ";
     426          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::SawtoothStart << "\t new: ");
    427427          cin >> config::SawtoothStart;
    428428          break;
    429429        case 'N': // VectorPlane
    430           Log() << Verbose(0) << "Old: " << config::VectorPlane << "\t new: ";
     430          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::VectorPlane << "\t new: ");
    431431          cin >> config::VectorPlane;
    432432          break;
    433433        case 'O': // VectorCut
    434           Log() << Verbose(0) << "Old: " << config::VectorCut << "\t new: ";
     434          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::VectorCut << "\t new: ");
    435435          cin >> config::VectorCut;
    436436          break;
    437437        case 'P': // UseAddGramSch
    438           Log() << Verbose(0) << "Old: " << config::UseAddGramSch << "\t new: ";
     438          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::UseAddGramSch << "\t new: ");
    439439          cin >> config::UseAddGramSch;
    440440          break;
    441441        case 'Q': // Seed
    442           Log() << Verbose(0) << "Old: " << config::Seed << "\t new: ";
     442          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::Seed << "\t new: ");
    443443          cin >> config::Seed;
    444444          break;
    445445
    446446        case 'R': // MaxOuterStep
    447           Log() << Verbose(0) << "Old: " << config::MaxOuterStep << "\t new: ";
     447          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxOuterStep << "\t new: ");
    448448          cin >> config::MaxOuterStep;
    449449          break;
    450450        case 'T': // OutVisStep
    451           Log() << Verbose(0) << "Old: " << config::OutVisStep << "\t new: ";
     451          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::OutVisStep << "\t new: ");
    452452          cin >> config::OutVisStep;
    453453          break;
    454454        case 'U': // OutSrcStep
    455           Log() << Verbose(0) << "Old: " << config::OutSrcStep << "\t new: ";
     455          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::OutSrcStep << "\t new: ");
    456456          cin >> config::OutSrcStep;
    457457          break;
    458458        case 'X': // MaxPsiStep
    459           Log() << Verbose(0) << "Old: " << config::MaxPsiStep << "\t new: ";
     459          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxPsiStep << "\t new: ");
    460460          cin >> config::MaxPsiStep;
    461461          break;
    462462        case 'Y': // EpsWannier
    463           Log() << Verbose(0) << "Old: " << config::EpsWannier << "\t new: ";
     463          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::EpsWannier << "\t new: ");
    464464          cin >> config::EpsWannier;
    465465          break;
    466466
    467467        case 'Z': // MaxMinStep
    468           Log() << Verbose(0) << "Old: " << config::MaxMinStep << "\t new: ";
     468          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxMinStep << "\t new: ");
    469469          cin >> config::MaxMinStep;
    470470          break;
    471471        case 'a': // RelEpsTotalEnergy
    472           Log() << Verbose(0) << "Old: " << config::RelEpsTotalEnergy << "\t new: ";
     472          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RelEpsTotalEnergy << "\t new: ");
    473473          cin >> config::RelEpsTotalEnergy;
    474474          break;
    475475        case 'b': // RelEpsKineticEnergy
    476           Log() << Verbose(0) << "Old: " << config::RelEpsKineticEnergy << "\t new: ";
     476          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RelEpsKineticEnergy << "\t new: ");
    477477          cin >> config::RelEpsKineticEnergy;
    478478          break;
    479479        case 'c': // MaxMinStopStep
    480           Log() << Verbose(0) << "Old: " << config::MaxMinStopStep << "\t new: ";
     480          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxMinStopStep << "\t new: ");
    481481          cin >> config::MaxMinStopStep;
    482482          break;
    483483        case 'e': // MaxInitMinStep
    484           Log() << Verbose(0) << "Old: " << config::MaxInitMinStep << "\t new: ";
     484          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxInitMinStep << "\t new: ");
    485485          cin >> config::MaxInitMinStep;
    486486          break;
    487487        case 'f': // InitRelEpsTotalEnergy
    488           Log() << Verbose(0) << "Old: " << config::InitRelEpsTotalEnergy << "\t new: ";
     488          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::InitRelEpsTotalEnergy << "\t new: ");
    489489          cin >> config::InitRelEpsTotalEnergy;
    490490          break;
    491491        case 'g': // InitRelEpsKineticEnergy
    492           Log() << Verbose(0) << "Old: " << config::InitRelEpsKineticEnergy << "\t new: ";
     492          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::InitRelEpsKineticEnergy << "\t new: ");
    493493          cin >> config::InitRelEpsKineticEnergy;
    494494          break;
    495495        case 'h': // InitMaxMinStopStep
    496           Log() << Verbose(0) << "Old: " << config::InitMaxMinStopStep << "\t new: ";
     496          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::InitMaxMinStopStep << "\t new: ");
    497497          cin >> config::InitMaxMinStopStep;
    498498          break;
    … …  
    508508
    509509        case 'k': // ECut
    510           Log() << Verbose(0) << "Old: " << config::ECut << "\t new: ";
     510          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::ECut << "\t new: ");
    511511          cin >> config::ECut;
    512512          break;
    513513        case 'l': // MaxLevel
    514           Log() << Verbose(0) << "Old: " << config::MaxLevel << "\t new: ";
     514          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxLevel << "\t new: ");
    515515          cin >> config::MaxLevel;
    516516          break;
    517517        case 'm': // RiemannTensor
    518           Log() << Verbose(0) << "Old: " << config::RiemannTensor << "\t new: ";
     518          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RiemannTensor << "\t new: ");
    519519          cin >> config::RiemannTensor;
    520520          break;
    521521        case 'n': // LevRFactor
    522           Log() << Verbose(0) << "Old: " << config::LevRFactor << "\t new: ";
     522          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::LevRFactor << "\t new: ");
    523523          cin >> config::LevRFactor;
    524524          break;
    525525        case 'o': // RiemannLevel
    526           Log() << Verbose(0) << "Old: " << config::RiemannLevel << "\t new: ";
     526          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RiemannLevel << "\t new: ");
    527527          cin >> config::RiemannLevel;
    528528          break;
    529529        case 'p': // Lev0Factor
    530           Log() << Verbose(0) << "Old: " << config::Lev0Factor << "\t new: ";
     530          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::Lev0Factor << "\t new: ");
    531531          cin >> config::Lev0Factor;
    532532          break;
    533533        case 'r': // RTActualUse
    534           Log() << Verbose(0) << "Old: " << config::RTActualUse << "\t new: ";
     534          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RTActualUse << "\t new: ");
    535535          cin >> config::RTActualUse;
    536536          break;
    537537        case 's': // PsiType
    538           Log() << Verbose(0) << "Old: " << config::PsiType << "\t new: ";
     538          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::PsiType << "\t new: ");
    539539          cin >> config::PsiType;
    540540          break;
    541541        case 't': // MaxPsiDouble
    542           Log() << Verbose(0) << "Old: " << config::MaxPsiDouble << "\t new: ";
     542          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::MaxPsiDouble << "\t new: ");
    543543          cin >> config::MaxPsiDouble;
    544544          break;
    545545        case 'u': // PsiMaxNoUp
    546           Log() << Verbose(0) << "Old: " << config::PsiMaxNoUp << "\t new: ";
     546          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::PsiMaxNoUp << "\t new: ");
    547547          cin >> config::PsiMaxNoUp;
    548548          break;
    549549        case 'v': // PsiMaxNoDown
    550           Log() << Verbose(0) << "Old: " << config::PsiMaxNoDown << "\t new: ";
     550          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::PsiMaxNoDown << "\t new: ");
    551551          cin >> config::PsiMaxNoDown;
    552552          break;
    553553        case 'w': // AddPsis
    554           Log() << Verbose(0) << "Old: " << config::AddPsis << "\t new: ";
     554          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::AddPsis << "\t new: ");
    555555          cin >> config::AddPsis;
    556556          break;
    557557
    558558        case 'x': // RCut
    559           Log() << Verbose(0) << "Old: " << config::RCut << "\t new: ";
     559          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RCut << "\t new: ");
    560560          cin >> config::RCut;
    561561          break;
    562562        case 'y': // StructOpt
    563           Log() << Verbose(0) << "Old: " << config::StructOpt << "\t new: ";
     563          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::StructOpt << "\t new: ");
    564564          cin >> config::StructOpt;
    565565          break;
    566566        case 'z': // IsAngstroem
    567           Log() << Verbose(0) << "Old: " << config::IsAngstroem << "\t new: ";
     567          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::IsAngstroem << "\t new: ");
    568568          cin >> config::IsAngstroem;
    569569          break;
    570570        case 'i': // RelativeCoord
    571           Log() << Verbose(0) << "Old: " << config::RelativeCoord << "\t new: ";
     571          DoLog(0) && (Log() << Verbose(0) << "Old: " << config::RelativeCoord << "\t new: ");
    572572          cin >> config::RelativeCoord;
    573573          break;
    … …  
    648648  }
    649649  strcpy(configname, ptr);
    650   Log() << Verbose(0) << "Found configpath: " << configpath << ", dir slash was found at " << last << ", config name is " << configname << "." << endl;
     650  DoLog(0) && (Log() << Verbose(0) << "Found configpath: " << configpath << ", dir slash was found at " << last << ", config name is " << configname << "." << endl);
    651651  delete[](buffer);
    652652};
    … …  
    659659{
    660660  if (FileBuffer != NULL) {
    661     eLog() << Verbose(2) << "deleting present FileBuffer in PrepareFileBuffer()." << endl;
     661    DoeLog(2) && (eLog()<< Verbose(2) << "deleting present FileBuffer in PrepareFileBuffer()." << endl);
    662662    delete(FileBuffer);
    663663  }
    … …  
    685685
    686686  if (mol == NULL) {
    687     eLog() << Verbose(0) << "Molecule is not allocated in LoadMolecule(), exit.";
     687    DoeLog(0) && (eLog()<< Verbose(0) << "Molecule is not allocated in LoadMolecule(), exit.");
    688688    performCriticalExit();
    689689  }
    … …  
    691691  ParseForParameter(verbose,FileBuffer,"MaxTypes", 0, 1, 1, int_type, &(MaxTypes), 1, critical);
    692692  if (MaxTypes == 0) {
    693     eLog() << Verbose(1) << "There are no atoms according to MaxTypes in this config file." << endl;
     693    DoeLog(1) && (eLog()<< Verbose(1) << "There are no atoms according to MaxTypes in this config file." << endl);
    694694    //performCriticalExit();
    695695  } else {
    696696    // prescan number of ions per type
    697     Log() << Verbose(0) << "Prescanning ions per type: " << endl;
     697    DoLog(0) && (Log() << Verbose(0) << "Prescanning ions per type: " << endl);
    698698    int NoAtoms = 0;
    699699    for (int i=0; i < MaxTypes; i++) {
    … …  
    702702      ParseForParameter(verbose,FileBuffer, name, 0, 2, 1, int_type, &Z, 1, critical);
    703703      elementhash[i] = periode->FindElement(Z);
    704       Log() << Verbose(1) << i << ". Z = " << elementhash[i]->Z << " with " << No[i] << " ions." << endl;
     704      DoLog(1) && (Log() << Verbose(1) << i << ". Z = " << elementhash[i]->Z << " with " << No[i] << " ions." << endl);
    705705      NoAtoms += No[i];
    706706    }
    … …  
    710710    sprintf(name,"Ion_Type%i",MaxTypes);
    711711    if (!ParseForParameter(verbose,FileBuffer, (const char*)name, 1, 1, 1, int_type, &value[0], 1, critical)) {
    712       eLog() << Verbose(0) << "There are no atoms in the config file!" << endl;
     712      DoeLog(0) && (eLog()<< Verbose(0) << "There are no atoms in the config file!" << endl);
    713713      performCriticalExit();
    714714      return;
    … …  
    728728      bool status = true;
    729729      while (status) {
    730         Log() << Verbose(0) << "Currently parsing MD step " << repetition << "." << endl;
     730        DoLog(0) && (Log() << Verbose(0) << "Currently parsing MD step " << repetition << "." << endl);
    731731        for (int i=0; i < MaxTypes; i++) {
    732732          sprintf(name,"Ion_Type%i",i+1);
    … …  
    794794      }
    795795      repetition--;
    796       Log() << Verbose(0) << "Found " << repetition << " trajectory steps." << endl;
     796      DoLog(0) && (Log() << Verbose(0) << "Found " << repetition << " trajectory steps." << endl);
    797797      if (repetition <= 1)  // if onyl one step, desactivate use of trajectories
    798798        mol->MDSteps = 0;
    … …  
    806806              ParseForParameter(verbose,FileBuffer, "Ion_Type1_1", 0, 3, 1, double_type, &value[2], repetition, (repetition == 0) ? critical : optional))
    807807        repetition++;
    808       Log() << Verbose(0) << "I found " << repetition << " times the keyword Ion_Type1_1." << endl;
     808      DoLog(0) && (Log() << Verbose(0) << "I found " << repetition << " times the keyword Ion_Type1_1." << endl);
    809809      // parse in molecule coordinates
    810810      for (int i=0; i < MaxTypes; i++) {
    … …  
    855855  ifstream *file = new ifstream(filename);
    856856  if (file == NULL) {
    857     eLog() << Verbose(1) << "config file " << filename << " missing!" << endl;
     857    DoeLog(1) && (eLog()<< Verbose(1) << "config file " << filename << " missing!" << endl);
    858858    return;
    859859  }
    … …  
    10631063    BG = new BondGraph(IsAngstroem);
    10641064    if (BG->LoadBondLengthTable(BondGraphFileName)) {
    1065       Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
     1065      DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
    10661066    } else {
    1067       eLog() << Verbose(1) << "Bond length table loading failed." << endl;
     1067      DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
    10681068    }
    10691069  }
    … …  
    10941094  ifstream *file = new ifstream(filename);
    10951095  if (file == NULL) {
    1096     eLog() << Verbose(1) << "config file " << filename << " missing!" << endl;
     1096    DoeLog(1) && (eLog()<< Verbose(1) << "config file " << filename << " missing!" << endl);
    10971097    return;
    10981098  }
    … …  
    12541254  BG = new BondGraph(IsAngstroem);
    12551255  if (BG->LoadBondLengthTable(BondGraphFileName)) {
    1256     Log() << Verbose(0) << "Bond length table loaded successfully." << endl;
     1256    DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
    12571257  } else {
    1258     Log() << Verbose(0) << "Bond length table loading failed." << endl;
     1258    DoLog(0) && (Log() << Verbose(0) << "Bond length table loading failed." << endl);
    12591259  }
    12601260
    … …  
    12631263  for (i=MAX_ELEMENTS;i--;)
    12641264    elementhash[i] = NULL;
    1265   Log() << Verbose(0) << "Parsing Ions ..." << endl;
     1265  DoLog(0) && (Log() << Verbose(0) << "Parsing Ions ..." << endl);
    12661266  No=0;
    12671267  found = 0;
    12681268  while (getline(*file,zeile,'\n')) {
    12691269    if (zeile.find("Ions_Data") == 0) {
    1270       Log() << Verbose(1) << "found Ions_Data...begin parsing" << endl;
     1270      DoLog(1) && (Log() << Verbose(1) << "found Ions_Data...begin parsing" << endl);
    12711271      found ++;
    12721272    }
    … …  
    12821282      input >> b;     // element mass
    12831283      elementhash[No] = periode->FindElement(Z);
    1284       Log() << Verbose(1) << "AtomNo: " << AtomNo << "\tZ: " << Z << "\ta:" << a << "\tl:"  << l << "\b:" << b << "\tElement:" << elementhash[No] << "\t:" << endl;
     1284      DoLog(1) && (Log() << Verbose(1) << "AtomNo: " << AtomNo << "\tZ: " << Z << "\ta:" << a << "\tl:"  << l << "\b:" << b << "\tElement:" << elementhash[No] << "\t:" << endl);
    12851285      for(i=0;i<AtomNo;i++) {
    12861286        if (!getline(*file,zeile,'\n')) {// parse on and on
    1287           Log() << Verbose(2) << "Error: Too few items in ionic list of element" << elementhash[No] << "." << endl << "Exiting." << endl;
     1287          DoLog(2) && (Log() << Verbose(2) << "Error: Too few items in ionic list of element" << elementhash[No] << "." << endl << "Exiting." << endl);
    12881288          // return 1;
    12891289        } else {
    … …  
    14331433    return result;
    14341434  } else {
    1435     eLog() << Verbose(1) << "Cannot open output file:" << filename << endl;
     1435    DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open output file:" << filename << endl);
    14361436    return false;
    14371437  }
    … …  
    14551455    output = new ofstream(fname->str().c_str(), ios::out);
    14561456    if (output == NULL) {
    1457       eLog() << Verbose(1) << "Cannot open mpqc output file:" << fname << endl;
     1457      DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open mpqc output file:" << fname << endl);
    14581458      delete(fname);
    14591459      return false;
    … …  
    14981498    output = new ofstream(fname->str().c_str(), ios::out);
    14991499    if (output == NULL) {
    1500       eLog() << Verbose(1) << "Cannot open mpqc hessian output file:" << fname << endl;
     1500      DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open mpqc hessian output file:" << fname << endl);
    15011501      delete(fname);
    15021502      return false;
    … …  
    15541554  f = fopen(name, "w" );
    15551555  if (f == NULL) {
    1556     eLog() << Verbose(1) << "Cannot open pdb output file:" << name << endl;
     1556    DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open pdb output file:" << name << endl);
    15571557    return false;
    15581558  }
    … …  
    16091609  f = fopen(name, "w" );
    16101610  if (f == NULL) {
    1611     eLog() << Verbose(1) << "Cannot open pdb output file:" << name << endl;
     1611    DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open pdb output file:" << name << endl);
    16121612    Free(&elementNo);
    16131613    return false;
    … …  
    16461646/** Stores all atoms in a TREMOLO data input file.
    16471647 * 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!
    16481649 * \param *filename name of file (without ".in" suffix!)
    16491650 * \param *mol pointer to molecule
    … …  
    16581659  output = new ofstream(fname->str().c_str(), ios::out);
    16591660  if (output == NULL) {
    1660     eLog() << Verbose(1) << "Cannot open tremolo output file:" << fname << endl;
     1661    DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open tremolo output file:" << fname << endl);
    16611662    delete(fname);
    16621663    return false;
    … …  
    17001701/** Stores all atoms from all molecules in a TREMOLO data input file.
    17011702 * 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!
    17021704 * \param *filename name of file (without ".in" suffix!)
    17031705 * \param *MolList pointer to MoleculeListClass containing all atoms
    … …  
    17121714  output = new ofstream(fname->str().c_str(), ios::out);
    17131715  if (output == NULL) {
    1714     eLog() << Verbose(1) << "Cannot open tremolo output file:" << fname << endl;
     1716    DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open tremolo output file:" << fname << endl);
    17151717    delete(fname);
    17161718    return false;
    … …  
    17521754      while (Walker->next != (*MolWalker)->end) {
    17531755        Walker = Walker->next;
    1754         *output << AtomNo << "\t";
     1756        *output << AtomNo+1 << "\t";
    17551757        *output << Walker->Name << "\t";
    17561758        *output << (*MolWalker)->name << "\t";
    1757         *output << MolCounter << "\t";
     1759        *output << MolCounter+1 << "\t";
    17581760        *output << Walker->node->x[0] << "\t" << Walker->node->x[1] << "\t" << Walker->node->x[2] << "\t";
    17591761        *output << (double)Walker->type->Valence << "\t";
    17601762        *output << Walker->type->symbol << "\t";
    17611763        for (BondList::iterator runner = Walker->ListOfBonds.begin(); runner != Walker->ListOfBonds.end(); runner++)
    1762           *output << LocalNotoGlobalNoMap[MolCounter][ (*runner)->GetOtherAtom(Walker)->nr ] << "\t";
     1764          *output << LocalNotoGlobalNoMap[MolCounter][ (*runner)->GetOtherAtom(Walker)->nr ]+1 << "\t";
    17631765        for(int i=Walker->ListOfBonds.size(); i < MaxNeighbours; i++)
    17641766          *output << "-\t";
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