absorption.cc

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/* Copyright (C) 2000, 2001 Stefan Buehler  <sbuehler@uni-bremen.de>
                            Axel von Engeln <engeln@uni-bremen.de>
 
   This program is free software; you can redistribute it and/or modify it
   under the terms of the GNU General Public License as published by the
   Free Software Foundation; either version 2, or (at your option) any
   later version.
 
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
 
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,
   USA. */
 
#include "arts.h"
#include <map>
#include <cfloat>
#include <algorithm>
#include <cmath>
#include "absorption.h"
#include "math_funcs.h"
#include "auto_md.h"
#include "messages.h"
 
 
std::map<String, Index> SpeciesMap;
 
 
// member fct of isotoperecord, calculates the partition fct at the
// given temperature  from the partition fct coefficients (3rd order
// polynomial in temperature)
Numeric IsotopeRecord::CalculatePartitionFctAtTemp( Numeric
                                                    temperature ) const
{
  Numeric result = 0.;
  Numeric exponent = 1.;
 
  ArrayOfNumeric::const_iterator it;
 
  for (it=mqcoeff.begin(); it != mqcoeff.end(); it++)
    {
      result += *it * exponent;
      exponent *= temperature;
    }
  return result;
}
 
void define_species_map()
{
  extern const Array<SpeciesRecord> species_data;
  extern std::map<String, Index> SpeciesMap;
 
  for ( Index i=0 ; i<species_data.nelem() ; ++i)
    {
      SpeciesMap[species_data[i].Name()] = i;
    }
}
 
 
ostream& operator << (ostream& os, const LineRecord& lr)
{
  // Determine the precision, depending on whether Numeric is double
  // or float:  
  Index precision;
  switch (sizeof(Numeric)) {
  case sizeof(float)  : precision = FLT_DIG; break;
  case sizeof(double) : precision = DBL_DIG; break;
  default: out0 << "Numeric must be double or float\n"; exit(1);
  }
 
  os << "@"
     << " " << lr.Name  ()
     << " "
     << setprecision((int)precision)
     <<        lr.F     ()
     << " " << lr.Psf   ()
     << " " << lr.I0    ()
     << " " << lr.Ti0   ()
     << " " << lr.Elow  ()
     << " " << lr.Agam  ()
     << " " << lr.Sgam  ()
     << " " << lr.Nair  ()
     << " " << lr.Nself ()
     << " " << lr.Tgam  ()
     << " " << lr.Naux  ()
     << " " << lr.dF    ()
     << " " << lr.dI0   ()
     << " " << lr.dAgam ()
     << " " << lr.dSgam ()
     << " " << lr.dNair ()
     << " " << lr.dNself()
     << " " << lr.dPsf  ();  
  
   // Added new lines for the spectroscopic parameters accuracies.
  for ( Index i=0; i<lr.Naux(); ++i )
    os << " " << lr.Aux()[i];
 
  return os;
}
 
 
template<class T>
void extract(T&      x,
             String& line,
             Index  n)
{
  // Initialize output to zero! This is important, because otherwise
  // the output variable could `remember' old values.
  x = T(0);
  
  // This will contain the short subString with the item to extract.
  // Make it a String stream, for easy parsing,
  // extracting subString of width n from line:
  istringstream item( line.substr(0,n) );
 
//  cout << "line = '" << line << "'\n";
//   cout << "line.substr(0,n) = " << line.substr(0,n) << endl;
//   cout << "item = " << item.str() << endl;
 
  // Shorten line by n:
  line.erase(0,n);
//  cout << "line = " << line << endl;
 
  // Convert with the aid of String stream item:
  item >> x;
}
 
 
// This function reads line data in the Hitran 1986-2001 format. For the Hitran
// 2004 data format use ReadFromHitran2004Stream.
//
// 2005/03/29: A check for the right data record length (100 characters) has
//             been added by Hermann Berg (h.berg@utoronto.ca)
//
bool LineRecord::ReadFromHitranStream(istream& is)
{
  // Global species lookup data:
  extern Array<SpeciesRecord> species_data;
 
  // This value is used to flag missing data both in species and
  // isotope lists. Could be any number, it just has to be made sure
  // that it is neither the index of a species nor of an isotope.
  const Index missing = species_data.nelem() + 100;
 
  // We need a species index sorted by HITRAN tag. Keep this in a
  // static variable, so that we have to do this only once.  The ARTS
  // species index is hind[<HITRAN tag>]. 
  //
  // Allow for up to 100 species in HITRAN in the future.
  static Array< Index >        hspec(100);
 
  // This is  an array of arrays for each hitran tag. It contains the
  // ARTS indices of the HITRAN isotopes. 
  static Array< ArrayOfIndex > hiso(100);
 
  // Remeber if this stuff has already been initialized:
  static bool hinit = false;
 
  // Remember, about which missing species we have already issued a
  // warning: 
  static ArrayOfIndex warned_missing;
 
  if ( !hinit )
    {
      // Initialize hspec.
      // The value of missing means that we don't have this species.
      hspec = missing;  // Matpack can set all elements like this.
 
      for ( Index i=0; i<species_data.nelem(); ++i )
        {
          const SpeciesRecord& sr = species_data[i];
 
          // We have to be careful and check for the case that all
          // HITRAN isotope tags are -1 (this species is missing in HITRAN).
 
          if ( 0 < sr.Isotope()[0].HitranTag() )
            {
              // The HITRAN tags are stored as species plus isotope tags
              // (MO and ISO)
              // in the Isotope() part of the species record.
              // We can extract the MO part from any of the isotope tags,
              // so we use the first one. We do this by taking an integer
              // division by 10.
          
              Index mo = sr.Isotope()[0].HitranTag() / 10;
              //          cout << "mo = " << mo << endl;
              hspec[mo] = i; 
          
              // Get a nicer to handle array of HITRAN iso tags:
              Index n_iso = sr.Isotope().nelem();
              ArrayOfIndex iso_tags;
              iso_tags.resize(n_iso);
              for ( Index j=0; j<n_iso; ++j )
                {
                  iso_tags[j] = sr.Isotope()[j].HitranTag();
                }
 
              // Reserve elements for the isotope tags. How much do we
              // need? This depends on the largest HITRAN tag that we know
              // about!
              // Also initialize the tags to missing.
              //          cout << "iso_tags = " << iso_tags << endl;
              //          cout << "static_cast<Index>(max(iso_tags))%10 + 1 = "
              //               << static_cast<Index>(max(iso_tags))%10 + 1 << endl;
              hiso[mo].resize( max(iso_tags)%10 + 1 );
              hiso[mo] = missing; // Matpack can set all elements like this.
 
 
              // Set the isotope tags:
              for ( Index j=0; j<n_iso; ++j )
                {
                  if ( 0 < iso_tags[j] )                                  // ignore -1 elements
                    {
                      // To get the iso tags from HitranTag() we also have to take
                      // modulo 10 to get rid of mo.
                      hiso[mo][iso_tags[j] % 10] = j;
                    }
                }
            }
        }
 
 
      // Print the generated data structures (for debugging):
      out3 << "  HITRAN index table:\n";
      for ( Index i=0; i<hspec.nelem(); ++i )
        {
          if ( missing != hspec[i] )
            {
              // The explicit conversion of Name to a c-String is
              // necessary, because setw does not work correctly for
              // stl Strings.
              out3 << "  mo = " << i << "   Species = "
                   << setw(10) << setiosflags(ios::left)
                   << species_data[hspec[i]].Name().c_str()
                   << "iso = ";
              for ( Index j=1; j<hiso[i].nelem(); ++j )
                {
                  if ( missing==hiso[i][j] )
                    out3 << " " << "m";
                  else
                    out3 << " " << species_data[hspec[i]].Isotope()[hiso[i][j]].Name();
                }
              out3 << "\n";
            }
        }
 
      hinit = true;
    }
 
 
  // This contains the rest of the line to parse. At the beginning the
  // entire line. Line gets shorter and shorter as we continue to
  // extract stuff from the beginning.
  String line;
 
  // The first item is the molecule number:
  Index mo;
 
  // Look for more comments?
  bool comment = true;
 
  while (comment)
    {
      // Return true if eof is reached:
      if (is.eof()) return true;
 
      // Throw runtime_error if stream is bad:
      if (!is) throw runtime_error ("Stream bad.");
 
      // Read line from file into linebuffer:
      getline(is,line);
 
      // It is possible that we were exactly at the end of the file before
      // calling getline. In that case the previous eof() was still false
      // because eof() evaluates only to true if one tries to read after the
      // end of the file. The following check catches this.
      if (line.nelem() == 0 && is.eof()) return true;
 
      // If the catalogue is in dos encoding, throw away the
      // additional carriage return
      if (line[line.nelem () - 1] == 13)
        {
          line.erase (line.nelem () - 1, 1);
        }
 
      // Because of the fixed FORTRAN format, we need to break up the line
      // explicitly in apropriate pieces. Not elegant, but works!
 
      // Extract molecule number:
      mo = 0;
      // Initialization of mo is important, because mo stays the same
      // if line is empty.
      extract(mo,line,2);
      //      cout << "mo = " << mo << endl;
  
      // If mo == 0 this is just a comment line:
      if ( 0 != mo )
        {
          // See if we know this species. Exit with an error if the species is unknown. 
          if ( missing != hspec[mo] )
            {
              comment = false;
 
              // Check if data record has the right number of characters for the
              // in Hitran 1986-2001 format
              Index nChar = line.nelem() + 2; // number of characters in data record;
              if ( nChar != 100 )
                {
                  ostringstream os;
                  os << "Invalid HITRAN 1986-2001 line data record with " << nChar <<
                        " characters (expected: 100)." << endl << line << " n: " << line.nelem ();
                  throw runtime_error(os.str());
                }
 
            }
          else
            {
              // See if this is already in warned_missing, use
              // std::count for that:
              if ( 0 == std::count(warned_missing.begin(),
                                   warned_missing.end(),
                                   mo) )
                {
                  out0 << "Error: HITRAN mo = " << mo << " is not "
                       << "known to ARTS.\n";
                  warned_missing.push_back(mo);
                  exit(1);
                  // SAB 08.08.2000 If you want to make the program
                  // continue anyway, just comment out the exit
                  // line.
                }
            }
        }
    }
 
  // Ok, we seem to have a valid species here.
 
  // Set mspecies from my cool index table:
  mspecies = hspec[mo];
 
  // Extract isotope:
  Index iso;                              
  extract(iso,line,1);
  //  cout << "iso = " << iso << endl;
 
 
  // Set misotope from the other cool index table.
  // We have to be careful to issue an error for unknown iso tags. Iso
  // could be either larger than the size of hiso[mo], or set
  // explicitly to missing. Unfortunately we have to test both cases. 
  misotope = missing;
  if ( iso < hiso[mo].nelem() )
    if ( missing != hiso[mo][iso] )
      misotope = hiso[mo][iso];
 
  // Issue error message if misotope is still missing:
  if (missing == misotope)
    {
      ostringstream os;
      os << "Species: " << species_data[mspecies].Name()
         << ", isotope iso = " << iso
         << " is unknown.";
      throw runtime_error(os.str());
    }
 
  
  // Position.
  {
    // HITRAN position in wavenumbers (cm^-1):
    Numeric v;
    // External constant from constants.cc:
    extern const Numeric SPEED_OF_LIGHT;
    // Conversion from wavenumber to Hz. If you multiply a line
    // position in wavenumber (cm^-1) by this constant, you get the
    // frequency in Hz.
    const Numeric w2Hz = SPEED_OF_LIGHT * 100.;
 
    // Extract HITRAN postion:
    extract(v,line,12);
 
    // ARTS position in Hz:
    mf = v * w2Hz;
//    cout << "mf = " << mf << endl;
  }
 
  // Intensity.
  {
    extern const Numeric SPEED_OF_LIGHT; // in [m/s]
 
    // HITRAN intensity is in cm-1/(molec * cm-2) at 296 Kelvin.
    // It already includes the isotpic ratio.
    // The first cm-1 is the frequency unit (it cancels with the
    // 1/frequency unit of the line shape function). 
    //
    // We need to do the following:
    // 1. Convert frequency from wavenumber to Hz (factor 1e2 * c).
    // 2. Convert [molec * cm-2] to [molec * m-2] (factor 1e-4).
    // 3. Take out the isotopic ratio.
 
    const Numeric hi2arts = 1e-2 * SPEED_OF_LIGHT;
 
    Numeric s;
 
    // Extract HITRAN intensity:
    extract(s,line,10);
    // Convert to ARTS units (Hz / (molec * m-2) ), or shorter: Hz*m^2
    mi0 = s * hi2arts;
    // Take out isotopic ratio:
    mi0 /= species_data[mspecies].Isotope()[misotope].Abundance();  
  }  
  
  // Skip transition probability:
  {
    Numeric r;
    extract(r,line,10);
  }
  
 
  // Air broadening parameters.
  {
    // HITRAN parameter is in cm-1/atm at 296 Kelvin
    // All parameters are HWHM (I hope this is true!)
    Numeric gam;
    // External constant from constants.cc: Converts atm to
    // Pa. Multiply value in atm by this number to get value in Pa. 
    extern const Numeric ATM2PA;
    // External constant from constants.cc:
    extern const Numeric SPEED_OF_LIGHT;
    // Conversion from wavenumber to Hz. If you multiply a value in
    // wavenumber (cm^-1) by this constant, you get the value in Hz.
    const Numeric w2Hz = SPEED_OF_LIGHT * 1e2;
    // Ok, put together the end-to-end conversion that we need:
    const Numeric hi2arts = w2Hz / ATM2PA;
 
    // Extract HITRAN AGAM value:
    extract(gam,line,5);
 
    // ARTS parameter in Hz/Pa:
    magam = gam * hi2arts;
 
    // Extract HITRAN SGAM value:
    extract(gam,line,5);
 
    // ARTS parameter in Hz/Pa:
    msgam = gam * hi2arts;
 
    // If zero, set to agam:
    if (0==msgam)
      msgam = magam;
 
    //    cout << "agam, sgam = " << magam << ", " << msgam << endl;
  }
 
 
  // Lower state energy.
  {
    // HITRAN parameter is in wavenumbers (cm^-1).
    // We have to convert this to the ARTS unit Joule.
 
    // Extract from Catalogue line
    extract(melow,line,10);
 
    // Convert to Joule:
    melow = wavenumber_to_joule(melow);
  }
 
  
  // Temperature coefficient of broadening parameters.
  {
    // This is dimensionless, we can also extract directly.
    extract(mnair,line,4);
 
    // Set self broadening temperature coefficient to the same value:
    mnself = mnair;
//    cout << "mnair = " << mnair << endl;
  }
 
 
  // Pressure shift.
  {
    // HITRAN value in cm^-1 / atm. So the conversion goes exactly as
    // for the broadening parameters.
    Numeric d;
    // External constant from constants.cc: Converts atm to
    // Pa. Multiply value in atm by this number to get value in Pa. 
    extern const Numeric ATM2PA;
    // External constant from constants.cc:
    extern const Numeric SPEED_OF_LIGHT;
    // Conversion from wavenumber to Hz. If you multiply a value in
    // wavenumber (cm^-1) by this constant, you get the value in Hz.
    const Numeric w2Hz = SPEED_OF_LIGHT * 1e2;
    // Ok, put together the end-to-end conversion that we need:
    const Numeric hi2arts = w2Hz / ATM2PA;
 
    // Extract HITRAN value:
    extract(d,line,8);
 
    // ARTS value in Hz/Pa
    mpsf = d * hi2arts;
  }
  // Set the accuracies using the definition of HITRAN 
  // indices. If some are missing, they are set to -1.
 
  //Skip upper state global quanta index
  {
    Index eu;
    extract(eu,line,3);
  }
 
 //Skip lower state global quanta index
  {
    Index el;
    extract(el,line,3);
  }
 
  //Skip upper state local quanta 
  {
    Index eul;
    extract(eul,line,9);
  }
 
  //Skip lower state local quanta 
  {
    Index ell;
    extract(ell,line,9);
  }
 
  // Accuracy index for frequency reference
  {
  Index df;
  // Extract HITRAN value:
  extract(df,line,1);
  // Convert it to ARTS units (Hz)
  convHitranIERF(mdf,df);
  }
 
  // Accuracy index for intensity reference
  {
  Index di0;
  // Extract HITRAN value:
    extract(di0,line,1);
    convHitranIERSH(mdi0,di0);
  }
 
  // Accuracy index for halfwidth reference
  {
    Index dgam;
    // Extract HITRAN value:
    extract(dgam,line,1);
    //Convert to ARTS units (%)
    convHitranIERSH(mdagam,dgam);
    // convHitranIERSH(mdsgam,dgam);
    // convHitranIERSH(mdnair,dgam);
    // convHitranIERSH(mdnself,dgam);
  }
 
  // Accuracy for pressure shift
  // This is missing in HITRAN catalogue and it is set to -1.
    mdpsf =-1;
 
  // These were all the parameters that we can extract from
  // HITRAN. However, we still have to set the reference temperatures
  // to the appropriate value:
 
  // Reference temperature for Intensity in K.
  // (This is fix for HITRAN)
  mti0 = 296.0;
 
  // Reference temperature for AGAM and SGAM in K.
  // (This is also fix for HITRAN)
  mtgam = 296.0;
 
  // That's it!
  return false;
}
 
 
// This function reads line data in the Hitran 2004 format. For the Hitran
// 1986-2004 data format use ReadFromHitranStream().
//
// 2005/03/29: This function was added based on ReadFromHitranStream(). There
//             is a check for the right data record length (160 characters).
//             Hermann Berg (h.berg@utoronto.ca)
//
bool LineRecord::ReadFromHitran2004Stream(istream& is)
{
  // Global species lookup data:
  extern Array<SpeciesRecord> species_data;
 
  // This value is used to flag missing data both in species and
  // isotope lists. Could be any number, it just has to be made sure
  // that it is neither the index of a species nor of an isotope.
  const Index missing = species_data.nelem() + 100;
 
  // We need a species index sorted by HITRAN tag. Keep this in a
  // static variable, so that we have to do this only once.  The ARTS
  // species index is hind[<HITRAN tag>].
  //
  // Allow for up to 100 species in HITRAN in the future.
  static Array< Index >        hspec(100);
 
  // This is  an array of arrays for each hitran tag. It contains the
  // ARTS indices of the HITRAN isotopes.
  static Array< ArrayOfIndex > hiso(100);
 
  // Remeber if this stuff has already been initialized:
  static bool hinit = false;
 
  // Remember, about which missing species we have already issued a
  // warning:
  static ArrayOfIndex warned_missing;
 
  if ( !hinit )
    {
      // Initialize hspec.
      // The value of missing means that we don't have this species.
      hspec = missing;  // Matpack can set all elements like this.
 
      for ( Index i=0; i<species_data.nelem(); ++i )
        {
          const SpeciesRecord& sr = species_data[i];
 
          // We have to be careful and check for the case that all
          // HITRAN isotope tags are -1 (this species is missing in HITRAN).
 
          if ( 0 < sr.Isotope()[0].HitranTag() )
            {
              // The HITRAN tags are stored as species plus isotope tags
              // (MO and ISO)
              // in the Isotope() part of the species record.
              // We can extract the MO part from any of the isotope tags,
              // so we use the first one. We do this by taking an integer
              // division by 10.
 
              Index mo = sr.Isotope()[0].HitranTag() / 10;
              //          cout << "mo = " << mo << endl;
              hspec[mo] = i;
 
              // Get a nicer to handle array of HITRAN iso tags:
              Index n_iso = sr.Isotope().nelem();
              ArrayOfIndex iso_tags;
              iso_tags.resize(n_iso);
              for ( Index j=0; j<n_iso; ++j )
                {
                  iso_tags[j] = sr.Isotope()[j].HitranTag();
                }
 
              // Reserve elements for the isotope tags. How much do we
              // need? This depends on the largest HITRAN tag that we know
              // about!
              // Also initialize the tags to missing.
              //          cout << "iso_tags = " << iso_tags << endl;
              //          cout << "static_cast<Index>(max(iso_tags))%10 + 1 = "
              //               << static_cast<Index>(max(iso_tags))%10 + 1 << endl;
              hiso[mo].resize( max(iso_tags)%10 + 1 );
              hiso[mo] = missing; // Matpack can set all elements like this.
 
 
              // Set the isotope tags:
              for ( Index j=0; j<n_iso; ++j )
                {
                  if ( 0 < iso_tags[j] )                                  // ignore -1 elements
                    {
                      // To get the iso tags from HitranTag() we also have to take
                      // modulo 10 to get rid of mo.
                      hiso[mo][iso_tags[j] % 10] = j;
                    }
                }
            }
        }
 
 
      // Print the generated data structures (for debugging):
      out3 << "  HITRAN index table:\n";
      for ( Index i=0; i<hspec.nelem(); ++i )
        {
          if ( missing != hspec[i] )
            {
              // The explicit conversion of Name to a c-String is
              // necessary, because setw does not work correctly for
              // stl Strings.
              out3 << "  mo = " << i << "   Species = "
                   << setw(10) << setiosflags(ios::left)
                   << species_data[hspec[i]].Name().c_str()
                   << "iso = ";
              for ( Index j=1; j<hiso[i].nelem(); ++j )
                {
                  if ( missing==hiso[i][j] )
                    out3 << " " << "m";
                  else
                    out3 << " " << species_data[hspec[i]].Isotope()[hiso[i][j]].Name();
                }
              out3 << "\n";
            }
        }
 
      hinit = true;
    }
 
 
  // This contains the rest of the line to parse. At the beginning the
  // entire line. Line gets shorter and shorter as we continue to
  // extract stuff from the beginning.
  String line;
 
  // The first item is the molecule number:
  Index mo;
 
  // Look for more comments?
  bool comment = true;
 
  while (comment)
    {
      // Return true if eof is reached:
      if (is.eof()) return true;
 
      // Throw runtime_error if stream is bad:
      if (!is) throw runtime_error ("Stream bad.");
 
      // Read line from file into linebuffer:
      getline(is,line);
 
      // It is possible that we were exactly at the end of the file before
      // calling getline. In that case the previous eof() was still false
      // because eof() evaluates only to true if one tries to read after the
      // end of the file. The following check catches this.
      if (line.nelem() == 0 && is.eof()) return true;
 
      // If the catalogue is in dos encoding, throw away the
      // additional carriage return
      if (line[line.nelem () - 1] == 13)
        {
          line.erase (line.nelem () - 1, 1);
        }
 
      // Because of the fixed FORTRAN format, we need to break up the line
      // explicitly in apropriate pieces. Not elegant, but works!
 
      // Extract molecule number:
      mo = 0;
      // Initialization of mo is important, because mo stays the same
      // if line is empty.
      extract(mo,line,2);
      //      cout << "mo = " << mo << endl;
 
      // If mo == 0 this is just a comment line:
      if ( 0 != mo )
        {
          // See if we know this species. Exit with an error if the species is unknown.
          if ( missing != hspec[mo] )
            {
              comment = false;
              
              // Check if data record has the right number of characters for the
              // in Hitran 2004 format
              Index nChar = line.nelem() + 2; // number of characters in data record;
              if ( nChar != 160 )
                {
                  ostringstream os;
                  os << "Invalid HITRAN 2004 line data record with " << nChar <<
                        " characters (expected: 160).";
                  throw runtime_error(os.str());
                }
                
            }
          else
            {
              // See if this is already in warned_missing, use
              // std::count for that:
              if ( 0 == std::count(warned_missing.begin(),
                                   warned_missing.end(),
                                   mo) )
                {
                  out0 << "Warning: HITRAN molecule number mo = " << mo << " is not "
                       << "known to ARTS.\n";
                  warned_missing.push_back(mo);
               }
            }
        }
    }
 
  // Ok, we seem to have a valid species here.
 
  // Set mspecies from my cool index table:
  mspecies = hspec[mo];
 
  // Extract isotope:
  Index iso;
  extract(iso,line,1);
  //  cout << "iso = " << iso << endl;
 
 
  // Set misotope from the other cool index table.
  // We have to be careful to issue an error for unknown iso tags. Iso
  // could be either larger than the size of hiso[mo], or set
  // explicitly to missing. Unfortunately we have to test both cases.
  misotope = missing;
  if ( iso < hiso[mo].nelem() )
    if ( missing != hiso[mo][iso] )
      misotope = hiso[mo][iso];
 
  // Issue error message if misotope is still missing:
  if (missing == misotope)
    {
      ostringstream os;
      os << "Species: " << species_data[mspecies].Name()
         << ", isotope iso = " << iso
         << " is unknown.";
      throw runtime_error(os.str());
    }
 
 
  // Position.
  {
    // HITRAN position in wavenumbers (cm^-1):
    Numeric v;
    // External constant from constants.cc:
    extern const Numeric SPEED_OF_LIGHT;
    // Conversion from wavenumber to Hz. If you multiply a line
    // position in wavenumber (cm^-1) by this constant, you get the
    // frequency in Hz.
    const Numeric w2Hz = SPEED_OF_LIGHT * 100.;
 
    // Extract HITRAN postion:
    extract(v,line,12);
 
    // ARTS position in Hz:
    mf = v * w2Hz;
//    cout << "mf = " << mf << endl;
  }
 
  // Intensity.
  {
    extern const Numeric SPEED_OF_LIGHT; // in [m/s]
 
    // HITRAN intensity is in cm-1/(molec * cm-2) at 296 Kelvin.
    // It already includes the isotpic ratio.
    // The first cm-1 is the frequency unit (it cancels with the
    // 1/frequency unit of the line shape function).
    //
    // We need to do the following:
    // 1. Convert frequency from wavenumber to Hz (factor 1e2 * c).
    // 2. Convert [molec * cm-2] to [molec * m-2] (factor 1e-4).
    // 3. Take out the isotopic ratio.
 
    const Numeric hi2arts = 1e-2 * SPEED_OF_LIGHT;
 
    Numeric s;
 
    // Extract HITRAN intensity:
    extract(s,line,10);
    // Convert to ARTS units (Hz / (molec * m-2) ), or shorter: Hz*m^2
    mi0 = s * hi2arts;
    // Take out isotopic ratio:
    mi0 /= species_data[mspecies].Isotope()[misotope].Abundance();
  }
 
  // Skip Einstein coefficient
  {
    Numeric r;
    extract(r,line,10);
  }
 
 
  // Air broadening parameters.
  {
    // HITRAN parameter is in cm-1/atm at 296 Kelvin
    // All parameters are HWHM (I hope this is true!)
    Numeric gam;
    // External constant from constants.cc: Converts atm to
    // Pa. Multiply value in atm by this number to get value in Pa.
    extern const Numeric ATM2PA;
    // External constant from constants.cc:
    extern const Numeric SPEED_OF_LIGHT;
    // Conversion from wavenumber to Hz. If you multiply a value in
    // wavenumber (cm^-1) by this constant, you get the value in Hz.
    const Numeric w2Hz = SPEED_OF_LIGHT * 1e2;
    // Ok, put together the end-to-end conversion that we need:
    const Numeric hi2arts = w2Hz / ATM2PA;
 
    // Extract HITRAN AGAM value:
    extract(gam,line,5);
 
    // ARTS parameter in Hz/Pa:
    magam = gam * hi2arts;
 
    // Extract HITRAN SGAM value:
    extract(gam,line,5);
 
    // ARTS parameter in Hz/Pa:
    msgam = gam * hi2arts;
 
    // If zero, set to agam:
    if (0==msgam)
      msgam = magam;
 
    //    cout << "agam, sgam = " << magam << ", " << msgam << endl;
  }
 
 
  // Lower state energy.
  {
    // HITRAN parameter is in wavenumbers (cm^-1).
    // We have to convert this to the ARTS unit Joule.
 
    // Extract from Catalogue line
    extract(melow,line,10);
 
    // Convert to Joule:
    melow = wavenumber_to_joule(melow);
  }
 
 
  // Temperature coefficient of broadening parameters.
  {
    // This is dimensionless, we can also extract directly.
    extract(mnair,line,4);
 
    // Set self broadening temperature coefficient to the same value:
    mnself = mnair;
//    cout << "mnair = " << mnair << endl;
  }
 
 
  // Pressure shift.
  {
    // HITRAN value in cm^-1 / atm. So the conversion goes exactly as
    // for the broadening parameters.
    Numeric d;
    // External constant from constants.cc: Converts atm to
    // Pa. Multiply value in atm by this number to get value in Pa.
    extern const Numeric ATM2PA;
    // External constant from constants.cc:
    extern const Numeric SPEED_OF_LIGHT;
    // Conversion from wavenumber to Hz. If you multiply a value in
    // wavenumber (cm^-1) by this constant, you get the value in Hz.
    const Numeric w2Hz = SPEED_OF_LIGHT * 1e2;
    // Ok, put together the end-to-end conversion that we need:
    const Numeric hi2arts = w2Hz / ATM2PA;
 
    // Extract HITRAN value:
    extract(d,line,8);
 
    // ARTS value in Hz/Pa
    mpsf = d * hi2arts;
  }
  // Set the accuracies using the definition of HITRAN
  // indices. If some are missing, they are set to -1.
 
  //Skip upper state global quanta index
  {
    Index eu;
    extract(eu,line,15);
  }
 
  //Skip lower state global quanta index
  {
    Index el;
    extract(el,line,15);
  }
 
  //Skip upper state local quanta
  {
    Index eul;
    extract(eul,line,15);
  }
 
  //Skip lower state local quanta
  {
    Index ell;
    extract(ell,line,15);
  }
 
  // Accuracy index for frequency
  {
    Index df;
    // Extract HITRAN value:
    extract(df,line,1);
    // Convert it to ARTS units (Hz)
    convHitranIERF(mdf,df);
  }
 
  // Accuracy index for intensity
  {
    Index di0;
    // Extract HITRAN value:
    extract(di0,line,1);
    //Convert to ARTS units (%)
    convHitranIERSH(mdi0,di0);
  }
 
  // Accuracy index for air-broadened halfwidth
  {
    Index dagam;
    // Extract HITRAN value:
    extract(dagam,line,1);
    //Convert to ARTS units (%)
    convHitranIERSH(mdagam,dagam);
  }
 
  // Accuracy index for self-broadened half-width
  {
    Index dsgam;
    // Extract HITRAN value:
    extract(dsgam,line,1);
    //Convert to ARTS units (%)
    convHitranIERSH(mdsgam,dsgam);
  }
  
  // Accuracy index for temperature-dependence exponent for agam
  {
    Index dnair;
    // Extract HITRAN value:
    extract(dnair,line,1);
    //Convert to ARTS units (%)
    convHitranIERSH(mdnair,dnair);
  }
 
  // Accuracy index for temperature-dependence exponent for sgam
  // This is missing in HITRAN catalogue and is set to -1.
    mdnself =-1;
 
  // Accuracy index for pressure shift
  {
    Index dpsf;
    // Extract HITRAN value (given in cm-1):
    extract(dpsf,line,1);
    // Convert it to ARTS units (Hz)
    convHitranIERF(mdpsf,dpsf);
    // ARTS wants this error in %
    mdpsf = mdpsf / mf;
  }
 
  // These were all the parameters that we can extract from
  // HITRAN 2004. However, we still have to set the reference temperatures
  // to the appropriate value:
 
  // Reference temperature for Intensity in K.
  // (This is fix for HITRAN 2004)
  mti0 = 296.0;
 
  // Reference temperature for AGAM and SGAM in K.
  // (This is also fix for HITRAN 2004)
  mtgam = 296.0;
 
  // That's it!
  return false;
}
 
 
bool LineRecord::ReadFromMytran2Stream(istream& is)
{
  // Global species lookup data:
  extern Array<SpeciesRecord> species_data;
 
  // This value is used to flag missing data both in species and
  // isotope lists. Could be any number, it just has to be made sure
  // that it is neither the index of a species nor of an isotope.
  const Index missing = species_data.nelem() + 100;
 
  // We need a species index sorted by MYTRAN tag. Keep this in a
  // static variable, so that we have to do this only once.  The ARTS
  // species index is hind[<MYTRAN tag>]. The value of
  // missing means that we don't have this species.
  //
  // Allow for up to 100 species in MYTRAN in the future.
  static Array< Index >        hspec(100,missing);      
 
  // This is  an array of arrays for each mytran tag. It contains the
  // ARTS indices of the MYTRAN isotopes. 
  static Array< ArrayOfIndex > hiso(100);
 
  // Remeber if this stuff has already been initialized:
  static bool hinit = false;
 
  // Remember, about which missing species we have already issued a
  // warning: 
  static ArrayOfIndex warned_missing;
 
  if ( !hinit )
    {
      for ( Index i=0; i<species_data.nelem(); ++i )
        {
          const SpeciesRecord& sr = species_data[i];
 
          // We have to be careful and check for the case that all
          // MYTRAN isotope tags are -1 (this species is missing in MYTRAN).
 
          if ( 0 < sr.Isotope()[0].MytranTag() )
            {
              // The MYTRAN tags are stored as species plus isotope tags
              // (MO and ISO)
              // in the Isotope() part of the species record.
              // We can extract the MO part from any of the isotope tags,
              // so we use the first one. We do this by taking an integer
              // division by 10.
          
              Index mo = sr.Isotope()[0].MytranTag() / 10;
              //          cout << "mo = " << mo << endl;
              hspec[mo] = i; 
          
              // Get a nicer to handle array of MYTRAN iso tags:
              Index n_iso = sr.Isotope().nelem();
              ArrayOfIndex iso_tags;
              iso_tags.resize(n_iso);
              for ( Index j=0; j<n_iso; ++j )
                {
                  iso_tags[j] = sr.Isotope()[j].MytranTag();
                }
 
              // Reserve elements for the isotope tags. How much do we
              // need? This depends on the largest MYTRAN tag that we know
              // about!
              // Also initialize the tags to missing.
              //          cout << "iso_tags = " << iso_tags << endl;
              //          cout << "static_cast<Index>(max(iso_tags))%10 + 1 = "
              //               << static_cast<Index>(max(iso_tags))%10 + 1 << endl;
              hiso[mo].resize( max(iso_tags)%10 + 1 );
              hiso[mo] = missing; // Matpack can set all elements like this.
 
              // Set the isotope tags:
              for ( Index j=0; j<n_iso; ++j )
                {
                  if ( 0 < iso_tags[j] )                                  // ignore -1 elements
                    {
                      // To get the iso tags from MytranTag() we also have to take
                      // modulo 10 to get rid of mo.
                      //                  cout << "iso_tags[j] % 10 = " << iso_tags[j] % 10 << endl;
                      hiso[mo][iso_tags[j] % 10] = j;
                    }
                }
            }
        }
      
//      cout << "hiso = " << hiso << endl << "***********" << endl;
 
 
      // Print the generated data structures (for debugging):
      out3 << "  MYTRAN index table:\n";
      for ( Index i=0; i<hspec.nelem(); ++i )
        {
          if ( missing != hspec[i] )
            {
              // The explicit conversion of Name to a c-String is
              // necessary, because setw does not work correctly for
              // stl Strings.
              out3 << "  mo = " << i << "   Species = "
                   << setw(10) << setiosflags(ios::left)
                   << species_data[hspec[i]].Name().c_str()
                   << "iso = ";
              for ( Index j=1; j<hiso[i].nelem(); ++j )
                {
                  if ( missing==hiso[i][j] )
                    out3 << " " << "m";
                  else
                    out3 << " " << species_data[hspec[i]].Isotope()[hiso[i][j]].Name();
                }
              out3 << "\n";
            }
        }
 
      hinit = true;
    }
 
 
  // This contains the rest of the line to parse. At the beginning the
  // entire line. Line gets shorter and shorter as we continue to
  // extract stuff from the beginning.
  String line;
 
  // The first item is the molecule number:
  Index mo;
 
  // Look for more comments?
  bool comment = true;
 
  while (comment)
    {
      // Return true if eof is reached:
      if (is.eof()) return true;
 
      // Throw runtime_error if stream is bad:
      if (!is) throw runtime_error ("Stream bad.");
 
      // Read line from file into linebuffer:
      getline(is,line);
 
      // It is possible that we were exactly at the end of the file before
      // calling getline. In that case the previous eof() was still false
      // because eof() evaluates only to true if one tries to read after the
      // end of the file. The following check catches this.
      if (line.nelem() == 0 && is.eof()) return true;
 
      // Because of the fixed FORTRAN format, we need to break up the line
      // explicitly in apropriate pieces. Not elegant, but works!
 
      // Extract molecule number:
      mo = 0;
      // Initialization of mo is important, because mo stays the same
      // if line is empty.
      extract(mo,line,2);
      //           cout << "mo = " << mo << endl;
  
      // If mo == 0 this is just a comment line:
      if ( 0 != mo )
        {
          // See if we know this species. We will give an error if a
          // species is not known. 
          if ( missing != hspec[mo] )       comment = false ;
          else
            {
              // See if this is already in warned_missing, use
              // std::count for that:
              if ( 0 == std::count(warned_missing.begin(),
                                   warned_missing.end(),
                                   mo) )
                {
                  out0 << "Error: MYTRAN mo = " << mo << " is not "
                       << "known to ARTS.\n";
                  warned_missing.push_back(mo);
                  exit(1);
                  // SAB 08.08.2000 If you want to make the program
                  // continue anyway, just comment out the exit
                  // line.
                }
            }
        }
    }
 
  // Ok, we seem to have a valid species here.
 
  // Set mspecies from my cool index table:
  mspecies = hspec[mo];
 
  // Extract isotope:
  Index iso;                              
  extract(iso,line,1);
  //  cout << "iso = " << iso << endl;
 
 
  // Set misotope from the other cool index table.
  // We have to be careful to issue an error for unknown iso tags. Iso
  // could be either larger than the size of hiso[mo], or set
  // explicitly to missing. Unfortunately we have to test both cases. 
  misotope = missing;
  if ( iso < hiso[mo].nelem() )
    if ( missing != hiso[mo][iso] )
      misotope = hiso[mo][iso];
 
  // Issue error message if misotope is still missing:
  if (missing == misotope)
    {
      ostringstream os;
      os << "Species: " << species_data[mspecies].Name()
         << ", isotope iso = " << iso
         << " is unknown.";
      throw runtime_error(os.str());
    }
 
  
  // Position.
  {
    // MYTRAN position in MHz:
    Numeric v;
 
    // Extract MYTRAN postion:
    extract(v,line,13);
 
    // ARTS position in Hz:
    mf = v * 1E6;
    //    cout << "mf = " << mf << endl;
  }
 
  // Accuracy for line position
  {
    // Extract MYTRAN postion accuracy:
    Numeric df;
    extract(df,line,8);
    //  ARTS accuracy of line position  in Hz:
    mdf = df * 1E6;
  } 
  
  // Intensity.
  {
    extern const Numeric SPEED_OF_LIGHT; // in [m/s]
 
    // MYTRAN2 intensity is in cm-1/(molec * cm-2) at 296 Kelvin.
    // (just like HITRAN, only isotopic ratio is not included)
    // The first cm-1 is the frequency unit (it cancels with the
    // 1/frequency unit of the line shape function). 
    //
    // We need to do the following:
    // 1. Convert frequency from wavenumber to Hz (factor 1e2 * c)
    // 2. Convert [molec * cm-2] to [molec * m-2] (factor 1e-4)
 
    const Numeric hi2arts = 1e-2 * SPEED_OF_LIGHT;
 
    Numeric s;
 
    // Extract HITRAN intensity:
    extract(s,line,10);
 
    // Convert to ARTS units (Hz / (molec * m-2) ), or shorter: Hz*m^2
    mi0 = s * hi2arts;
  }
 
  
  // Air broadening parameters.
  {
    // MYTRAN parameter is in MHz/Torr at reference temperature
    // All parameters are HWHM
    Numeric gam;
    // External constant from constants.cc: Converts torr to
    // Pa. Multiply value in torr by this number to get value in Pa. 
    extern const Numeric TORR2PA;
 
    // Extract HITRAN AGAM value:
    extract(gam,line,5);
 
    // ARTS parameter in Hz/Pa:
    magam = gam * 1E6 / TORR2PA;
 
    // Extract MYTRAN SGAM value:
    extract(gam,line,5);
 
    // ARTS parameter in Hz/Pa:
    msgam = gam * 1E6 / TORR2PA;
 
//    cout << "agam, sgam = " << magam << ", " << msgam << endl;
  }
 
 
  // Lower state energy.
  {
    // MYTRAN parameter is in wavenumbers (cm^-1).
    // We have to convert this to the ARTS unit Joule.
 
    // Extract from Catalogue line
    extract(melow,line,10);
 
    // Convert to Joule:
    melow = wavenumber_to_joule(melow);
  }
 
  
  // Temperature coefficient of broadening parameters.
  {
    // This is dimensionless, we can also extract directly.
    extract(mnair,line,4);
 
    // Extract the self broadening parameter:
    extract(mnself,line,4);
//    cout << "mnair = " << mnair << endl;
  }
 
  
  // Reference temperature for broadening parameter in K:
  {
    // correct units, extract directly
    extract(mtgam,line,7);
  }
 
 
  // Pressure shift.
  {
    // MYTRAN value in MHz/Torr
    Numeric d;
    // External constant from constants.cc: Converts torr to
    // Pa. Multiply value in torr by this number to get value in Pa. 
    extern const Numeric TORR2PA;
 
    // Extract MYTRAN value:
    extract(d,line,9);
 
    // ARTS value in Hz/Pa
    mpsf = d * 1E6 / TORR2PA;
  }
  // Set the accuracies using the definition of MYTRAN accuracy
  // indices. If some are missing, they are set to -1.
 
  //Skip upper state global quanta index
  {
    Index eu;
    extract(eu,line,3);
  }
 
 //Skip lower state global quanta index
  {
    Index el;
    extract(el,line,3);
  }
 
  //Skip upper state local quanta 
  {
    Index eul;
    extract(eul,line,9);
  }
 
  //Skip lower state local quanta 
  {
    Index ell;
    extract(ell,line,9);
  }
 // Accuracy index for intensity
  {
  Index di0;
  // Extract MYTRAN value:
  extract(di0,line,1);
  //convert to ARTS units (%)
  convMytranIER(mdi0,di0);
  }
 
  // Accuracy index for AGAM
  {
  Index dgam;
  // Extract MYTRAN value:
  extract(dgam,line,1);
  //convert to ARTS units (%)
  convMytranIER(mdagam,dgam);
  }
 
  // Accuracy index for NAIR 
  {
  Index dnair;
  // Extract MYTRAN value:
  extract(dnair,line,1); 
  //convert to ARTS units (%);
  convMytranIER(mdnair,dnair);
  }
 
 
  // These were all the parameters that we can extract from
  // MYTRAN. However, we still have to set the reference temperatures
  // to the appropriate value:
 
  // Reference temperature for Intensity in K.
  // (This is fix for MYTRAN2)
  mti0 = 296.0;
 
  // It is important that you intialize here all the new parameters that
  // you added to the line record. (This applies to all the reading
  // functions, also for ARTS, JPL, and HITRAN format.) Parameters
  // should be either set from the catalogue, or set to -1.)
 
  // That's it!
  return false;
}
 
 
bool LineRecord::ReadFromJplStream(istream& is)
{
  // Global species lookup data:
  extern Array<SpeciesRecord> species_data;
 
  // We need a species index sorted by JPL tag. Keep this in a
  // static variable, so that we have to do this only once.  The ARTS
  // species index is JplMap[<JPL tag>]. We need Index in this map,
  // because the tag array within the species data is an Index array.
  static map<Index, SpecIsoMap> JplMap;
 
  // Remeber if this stuff has already been initialized:
  static bool hinit = false;
 
  if ( !hinit )
    {
 
      out3 << "  JPL index table:\n";
 
      for ( Index i=0; i<species_data.nelem(); ++i )
        {
          const SpeciesRecord& sr = species_data[i];
 
 
          for ( Index j=0; j<sr.Isotope().nelem(); ++j)
            {
              
              for (Index k=0; k<sr.Isotope()[j].JplTags().nelem(); ++k)
                {
 
                  SpecIsoMap indicies(i,j);
 
                  JplMap[sr.Isotope()[j].JplTags()[k]] = indicies;
 
                  // Print the generated data structures (for debugging):
                  // The explicit conversion of Name to a c-String is
                  // necessary, because setw does not work correctly for
                  // stl Strings.
                  const Index& i1 = JplMap[sr.Isotope()[j].JplTags()[k]].Speciesindex();
                  const Index& i2 = JplMap[sr.Isotope()[j].JplTags()[k]].Isotopeindex();
                                         
                  out3 << "  JPL TAG = " << sr.Isotope()[j].JplTags()[k] << "   Species = "
                       << setw(10) << setiosflags(ios::left)
                       << species_data[i1].Name().c_str()
                       << "iso = " 
                       << species_data[i1].Isotope()[i2].Name().c_str()
                       << "\n";
                }
 
            }
        }
      hinit = true;
    }
 
 
  // This contains the rest of the line to parse. At the beginning the
  // entire line. Line gets shorter and shorter as we continue to
  // extract stuff from the beginning.
  String line;
 
 
  // Look for more comments?
  bool comment = true;
 
  while (comment)
    {
      // Return true if eof is reached:
      if (is.eof()) return true;
 
      // Throw runtime_error if stream is bad:
      if (!is) throw runtime_error ("Stream bad.");
 
      // Read line from file into linebuffer:
      getline(is,line);
 
      // It is possible that we were exactly at the end of the file before
      // calling getline. In that case the previous eof() was still false
      // because eof() evaluates only to true if one tries to read after the
      // end of the file. The following check catches this.
      if (line.nelem() == 0 && is.eof()) return true;
 
      // Because of the fixed FORTRAN format, we need to break up the line
      // explicitly in apropriate pieces. Not elegant, but works!
 
      // Extract center frequency:
      // Initialization of v is important, because v stays the same
      // if line is empty.
      // JPL position in MHz:
      Numeric v = 0.0;
      
      // Extract JPL position:
      extract(v,line,13);
        
      // check for empty line
      if (v != 0.0)
        {
          // ARTS position in Hz:
          mf = v * 1E6;
          
          comment = false;
        }
    }
 
  // Accuracy for line position 
  {
    Numeric df;
    extract(df,line,8);
    //convert to ARTS units (Hz)
    mdf = df * 1E6; 
  } 
  
  // Intensity.
  {
    // JPL has log (10) of intensity in nm2 MHz at 300 Kelvin.
    //
    // We need to do the following:
    // 1. take 10^intensity 
    // 2. convert to cm-1/(molecule * cm-2): devide by c * 1e10
    // 3. Convert frequency from wavenumber to Hz (factor 1e2 * c)
    // 4. Convert [molec * cm-2] to [molec * m-2] (factor 1e-4)
 
    Numeric s;
 
    // Extract JPL intensity:
    extract(s,line,8);
 
    // remove log
    s = pow(10,s);
 
    // Convert to ARTS units (Hz / (molec * m-2) ), or shorter: Hz*m^2
    mi0 = s / 1E12;
  }
 
  // Degrees of freedom
  {
    Index dr;
 
    // Extract degrees of freedom
    extract(dr,line,2);
  }
 
  // Lower state energy.
  {
    // JPL parameter is in wavenumbers (cm^-1).
    // We have to convert this to the ARTS unit Joule.
 
    // Extract from Catalogue line
    extract(melow,line,10);
 
    // Convert to Joule:
    melow = wavenumber_to_joule(melow);
  }
 
  // Upper state degeneracy
  {
    Index gup;
 
    // Extract upper state degeneracy
    extract(gup,line,3);
  }
 
  // Tag number
  Index tag;
  {
    // Extract Tag number
    extract(tag,line,7);
 
    // make sure tag is not negative (damned jpl cat):
    tag = tag > 0 ? tag : -tag;
  }
 
  // ok, now for the cool index map:
 
  // is this tag valid?
  const map<Index, SpecIsoMap>::const_iterator i = JplMap.find(tag);
  if ( i == JplMap.end() )
    {
      ostringstream os;
      os << "JPL Tag: " << tag << " is unknown.";
      throw runtime_error(os.str());
    }
 
  SpecIsoMap id = i->second;
 
 
  // Set mspecies:
  mspecies = id.Speciesindex();
 
  // Set misotope:
  misotope = id.Isotopeindex();
 
  // Air broadening parameters: unknown to jpl, use old iup forward
  // model default values, which is mostly set to 0.0025 GHz/hPa, even
  // though for some lines the pressure broadening is given explicitly
  // in the program code. The explicitly given values are ignored and
  // only the default value is set. Self broadening was in general not
  // considered in the old forward model.
  {
    // ARTS parameter in Hz/Pa:
    magam = 2.5E4;
 
    // ARTS parameter in Hz/Pa:
    msgam = magam;
  }
 
 
  // Temperature coefficient of broadening parameters. Was set to 0.75
  // in old forward model, even though for some lines the parameter is
  // given explicitly in the program code. The explicitly given values
  // are ignored and only the default value is set. Self broadening
  // not considered.
  {
    mnair = 0.75;
    mnself = 0.0;
  }
 
  
  // Reference temperature for broadening parameter in K, was
  // generally set to 300 K in old forward model, with the exceptions
  // as already mentioned above:
  {
    mtgam = 300.0;
  }
 
 
  // Pressure shift: not given in JPL, set to 0
  {
    mpsf = 0.0;
  }
 
 
  // These were all the parameters that we can extract from
  // JPL. However, we still have to set the reference temperatures
  // to the appropriate value:
 
  // Reference temperature for Intensity in K.
  // (This is fix for JPL)
  mti0 = 300.0;
 
  // That's it!
  return false;
}
 
 
bool LineRecord::ReadFromArtsStream(istream& is)
{
  // Global species lookup data:
  extern Array<SpeciesRecord> species_data;
 
  // We need a species index sorted by Arts identifier. Keep this in a
  // static variable, so that we have to do this only once.  The ARTS
  // species index is ArtsMap[<Arts String>]. 
  static map<String, SpecIsoMap> ArtsMap;
 
  // Remeber if this stuff has already been initialized:
  static bool hinit = false;
 
  if ( !hinit )
    {
 
      out3 << "  ARTS index table:\n";
 
      for ( Index i=0; i<species_data.nelem(); ++i )
        {
          const SpeciesRecord& sr = species_data[i];
 
 
          for ( Index j=0; j<sr.Isotope().nelem(); ++j)
            {
              
              SpecIsoMap indicies(i,j);
              String buf = sr.Name()+"-"+sr.Isotope()[j].Name();
              
              ArtsMap[buf] = indicies;
              
              // Print the generated data structures (for debugging):
              // The explicit conversion of Name to a c-String is
              // necessary, because setw does not work correctly for
              // stl Strings.
              const Index& i1 = ArtsMap[buf].Speciesindex();
              const Index& i2 = ArtsMap[buf].Isotopeindex();
                                         
              out3 << "  Arts Identifier = " << buf << "   Species = "
                   << setw(10) << setiosflags(ios::left)
                   << species_data[i1].Name().c_str()
                   << "iso = " 
                   << species_data[i1].Isotope()[i2].Name().c_str()
                   << "\n";
 
            }
        }
      hinit = true;
    }
 
 
  // This always contains the rest of the line to parse. At the
  // beginning the entire line. Line gets shorter and shorter as we
  // continue to extract stuff from the beginning.
  String line;
 
  // Look for more comments?
  bool comment = true;
 
  while (comment)
    {
      // Return true if eof is reached:
      if (is.eof()) return true;
 
      // Throw runtime_error if stream is bad:
      if (!is) throw runtime_error ("Stream bad.");
 
      // Read line from file into linebuffer:
      getline(is,line);
 
      // It is possible that we were exactly at the end of the file before
      // calling getline. In that case the previous eof() was still false
      // because eof() evaluates only to true if one tries to read after the
      // end of the file. The following check catches this.
      if (line.nelem() == 0 && is.eof()) return true;
 
      // @ as first character marks catalogue entry
      char c;
      extract(c,line,1);
      
      // check for empty line
      if (c == '@')
        {
          comment = false;
        }
    }
 
 
  // read the arts identifier String
  istringstream icecream(line);
 
  String artsid;
  icecream >> artsid;
 
  if (artsid.length() != 0)
    {
 
      // ok, now for the cool index map:
      // is this arts identifier valid?
      const map<String, SpecIsoMap>::const_iterator i = ArtsMap.find(artsid);
      if ( i == ArtsMap.end() )
        {
          ostringstream os;
          os << "ARTS Tag: " << artsid << " is unknown.";
          throw runtime_error(os.str());
        }
 
      SpecIsoMap id = i->second;
 
 
      // Set mspecies:
      mspecies = id.Speciesindex();
 
      // Set misotope:
      misotope = id.Isotopeindex();
 
 
      // Extract center frequency:
      icecream >> mf;
 
 
      // Extract pressure shift:
      icecream >> mpsf;
  
      // Extract intensity:
      icecream >> mi0;
 
 
      // Extract reference temperature for Intensity in K:
      icecream >> mti0;
 
 
      // Extract lower state energy:
      icecream >> melow;
 
 
      // Extract air broadening parameters:
      icecream >> magam;
      icecream >> msgam;
 
      // Extract temperature coefficient of broadening parameters:
      icecream >> mnair;
      icecream >> mnself;
 
  
      // Extract reference temperature for broadening parameter in K:
      icecream >> mtgam;
 
      // Extract the aux parameters:
      Index naux;
      icecream >> naux;
 
      // resize the aux array and read it
      maux.resize(naux);
 
      for (Index i = 0; i<naux; i++)
        {
          icecream >> maux[i];
          //cout << "maux" << i << " = " << maux[i] << "\n";
        }
 
      // Extract accuracies:
      try
        {
          icecream >> mdf;
          icecream >> mdi0;
          icecream >> mdagam;
          icecream >> mdsgam;
          icecream >> mdnair;
          icecream >> mdnself;
          icecream >> mdpsf;
        }
      catch (runtime_error x)
        {
          // Nothing to do here, the accuracies are optional, so we
          // just set them to -1 and continue reading the next line of
          // the catalogue
          mdf      = -1;
          mdi0     = -1;
          mdagam   = -1;
          mdsgam   = -1;
          mdnair   = -1;
          mdnself  = -1;
          mdpsf    = -1;            
        }
    }
 
  // That's it!
  return false;
}
 
 
 
OneTag::OneTag(String def) 
{
  // Species lookup data:
  extern const Array<SpeciesRecord> species_data;
  // The species map. This is used to find the species id.
  extern std::map<String, Index> SpeciesMap;
  // Name of species and isotope (aux variables):
  String name, isoname;
  // Aux index:
  Index n;
 
 
  // Set frequency limits to default values (no limits):
  mlf = -1;
  muf = -1;
 
  // We cannot set a default value for the isotope, because the
  // default should be `ALL' and the value for `ALL' depends on the
  // species. 
    
 
  // Extract the species name:
  n    = (Index)def.find('-');    // find the '-'
  if (n != def.npos )
    {
      name = def.substr(0,n);      // Extract before '-'
      def.erase(0,n+1);             // Remove from def
    }
  else
    {
      // n==def.npos means that def does not contain a '-'. In that
      // case we assume that it contains just a species name and
      // nothing else
      name = def;
      def  = "";
    }
 
 
//  cout << "name / def = " << name << " / " << def << endl;
 
  // Look for species name in species map:
  map<String, Index>::const_iterator mi = SpeciesMap.find(name);
  if ( mi != SpeciesMap.end() )
    {
      // Ok, we've found the species. Set mspecies.
      mspecies = mi->second;
    }
  else
    {
      ostringstream os;
      os << "Species " << name << " is not a valid species.";
      throw runtime_error(os.str());
    }
 
  // Get a reference to the relevant Species Record:
  const SpeciesRecord& spr = species_data[mspecies];
 
  if ( 0 == def.nelem() )
    {
      // This means that there is nothing else to parse. Apparently
      // the user wants all isotopes and no frequency limits.
      // Frequency defaults are already set. Set isotope defaults:
      misotope = spr.Isotope().nelem();
      // This means all isotopes.
 
      return;
    }
    
  // Extract the isotope name:
  n    = (Index)def.find('-');    // find the '-'
  if (n != def.npos )
    {
      isoname = def.substr(0,n);          // Extract before '-'
      def.erase(0,n+1);             // Remove from def
    }
  else
    {
      // n==def.npos means that def does not contain a '-'. In that
      // case we assume that it contains just the isotope name and
      // nothing else.
      isoname = def;
      def  = "";
    }
    
  // Check for joker:
  if ( "*" == isoname )
    {
      // The user wants all isotopes. Set this accordingly:
      misotope = spr.Isotope().nelem();
    }
  else
    {
      // Make an array containing the isotope names:
      ArrayOfString ins;
      for ( Index i=0; i<spr.Isotope().nelem(); ++i )
        ins.push_back( spr.Isotope()[i].Name() );
 
      // Use the find algorithm from the STL to find the isotope ID. It
      // returns an iterator, so to get the index we take the
      // difference to the begin() iterator.
      misotope = (Index)(find( ins.begin(),
                       ins.end(),
                       isoname ) - ins.begin());
 
      // Check if we found a matching isotope:
      if ( misotope >= ins.nelem() ) 
        {
          ostringstream os;
          os << "Isotope " << isoname << " is not a valid isotope for "
             << "species " << name << ".\n"
             << "Valid isotopes are:";
          for ( Index i=0; i<ins.nelem(); ++i )
            os << " " << ins[i];
          throw runtime_error(os.str());
        }
    }
 
  if ( 0 == def.nelem() )
    {
      // This means that there is nothing else to parse. Apparently
      // the user wants no frequency limits.  Frequency defaults are
      // already set, so we can return directly.
 
      return;
    }
 
 
  // Look for the two frequency limits:
  
  // Extract first frequency
  n    = (Index)def.find('-');    // find the '-'
  if (n != def.npos )
    {
      // Frequency as a String:
      String fname;
      fname = def.substr(0,n);              // Extract before '-'
      def.erase(0,n+1);               // Remove from def
 
      // Check for joker:
      if ( "*" == fname )
        {
          // The default for mlf is already -1, meaning `ALL'.
          // So there is nothing to do here.
        }
      else
        {
          // Convert to Numeric:
          istringstream is(fname);
          is >> mlf;
        }
    }
  else
    {
      // n==def.npos means that def does not contain a '-'. In this
      // case that is not allowed!
      throw runtime_error("You must either speciefy both frequency limits\n"
                          "(at least with jokers), or none.");
    }
 
 
  // Now there should only be the upper frequency left in def.
  // Check for joker:
  if ( "*" == def )
    {
      // The default for muf is already -1, meaning `ALL'.
      // So there is nothing to do here.
    }
  else
    {
      // Convert to Numeric:
      istringstream is(def);
      is >> muf;
    }
}
 
 
String OneTag::Name() const 
{
  // Species lookup data:
  extern const Array<SpeciesRecord> species_data;
  // A reference to the relevant record of the species data:
  const  SpeciesRecord& spr = species_data[mspecies];
  // For return value:
  ostringstream os;
 
  // First the species name:
  os << spr.Name() << "-";
 
  // Now the isotope. Can be a single isotope or ALL.
  if ( misotope == spr.Isotope().nelem() )
    {
      // One larger than allowed means all isotopes!
      os << "*-";
    }
  else
    {
      os << spr.Isotope()[misotope].Name() << "-";
    }
 
  // Now the frequency limits, if there are any. For this we first
  // need to determine the floating point precision.
 
  // Determine the precision, depending on whether Numeric is double
  // or float:  
  Index precision;
  switch (sizeof(Numeric)) {
  case sizeof(float)  : precision = FLT_DIG; break;
  case sizeof(double) : precision = DBL_DIG; break;
  default: out0 << "Numeric must be double or float\n"; exit(1);
  }
 
  if ( 0 > mlf )
    {
      // mlf < 0 means no lower limit.
      os << "*-";
    }
  else
    {
      os << setprecision((int)precision);
      os << mlf << "-";
    }
 
  if ( 0 > muf )
    {
      // muf < 0 means no upper limit.
      os << "*";
    }
  else
    {
      os << setprecision((int)precision);
      os << muf;
    }
 
  return os.str();
}
 
ostream& operator << (ostream& os, const OneTag& ot)
{
  return os << ot.Name();
}
 
 
 
void get_tagindex_for_Strings( 
                              ArrayOfIndex&   tags1_index, 
                              const TagGroups&      tags1, 
                              const ArrayOfString&  tags2_Strings )
{
  const Index   n1 = tags1.nelem();
  const Index   n2 = tags2_Strings.nelem();
     TagGroups   tags2;                // Internal tag names for tag_Strings
        Index   i1, i2, nj, j, found, ok;
 
  tags1_index.resize(n2);
  //  cout << "tags2_Strings: " << tags2_Strings << "\n";
  tgsDefine( tags2, tags2_Strings );
 
  for ( i2=0; i2<n2; i2++ )
  {
    found = 0;
    for ( i1=0; (i1<n1) && !found; i1++ )
    {
      nj = tags2[i2].nelem(); 
      if ( nj  == tags1[i1].nelem() )
      {
        ok = 1;
        for ( j=0; j<nj; j++ )
        {
          if ( tags2[i2][j].Name() != tags1[i1][j].Name() )
            ok = 0;
        }
        if ( ok )
        {
          found = 1;
          tags1_index[i2] = i1;
        }
      }
    } 
    if ( !found )
    {
      ostringstream os;
      os << "The tag String \"" << tags2_Strings[i2] << 
            "\" does not match any of the given tags.\n";
      throw runtime_error(os.str());
    }
  }
}
 
 
void get_tag_group_index_for_tag_group( Index&               tgs1_index, 
                                        const TagGroups&      tgs1, 
                                        const Array<OneTag>&  tg2 )
{
  bool found = false;
 
  for ( Index i=0;
        i<tgs1.nelem() && !found;
        ++i )
    {
      // Is at least the size correct?
      if ( tg2.nelem() == tgs1[i].nelem() )
        {
          bool ok = true;
 
          for ( Index j=0; j<tg2.nelem(); ++j )
            {
              if ( tg2[j].Name() != tgs1[i][j].Name() )
                ok = false;
            }
 
          if ( ok )
            {
              found = true;
              tgs1_index = i;
            }
        }
    }
 
  if ( !found )
    {
      ostringstream os;
      os << "The tag String \"" << tg2 << 
        "\" does not match any of the given tags.\n";
      throw runtime_error(os.str());
    }
}
 
 
String get_tag_group_name( const Array<OneTag>& tg )
{
  String name;
  Index i;
  
  for ( i=0; i<tg.nelem()-1; ++i )
    {
      name += tg[i].Name() + ", ";
    }
  name += tg[i].Name();
 
  return name;
}
 
 
void write_lines_to_stream(ostream& os,
                           const ArrayOfLineRecord& lines)
{
  // We need this dummy line record, so that we can get the catalogue
  // version tag from dummy.Version, even if the line list is empty.
  LineRecord dummy;
 
  // Output version String first, followed by number of lines:
  os << dummy.Version() << " " << lines.nelem() << "\n";
 
  // Now output the line data:
  for ( Index i=0; i<lines.nelem(); ++i )
    {
      //      out3 << lines[i] << "\n";
      os << lines[i] << "\n";
    }
}
 
 
 
bool is_sorted( ConstVectorView   x )
{
  if( x.nelem() > 1 )
    {
      for( Index i=1; i<x.nelem(); i++ )
        {
          if( x[i] < x[i-1] )
            return false;
        }
    }
  return true;
}
 
 
void xsec_species( MatrixView               xsec,
                   ConstVectorView          f_mono,
                   ConstVectorView          p_abs,
                   ConstVectorView          t_abs,
                   ConstVectorView          h2o_abs,
                   ConstVectorView          vmr,
                   const ArrayOfLineRecord& lines,
                   const Index              ind_ls,
                   const Index              ind_lsn,
                   const Numeric            cutoff)
{
  // Make lineshape and species lookup data visible:
  extern const Array<LineshapeRecord> lineshape_data;
  extern const Array<LineshapeNormRecord> lineshape_norm_data;
 
  // speed of light constant
  extern const Numeric SPEED_OF_LIGHT;
 
  // Boltzmann constant
  extern const Numeric BOLTZMAN_CONST;
 
  // Avogadros constant
  extern const Numeric AVOGADROS_NUMB;
 
  // Planck constant
  extern const Numeric PLANCK_CONST;
 
  // sqrt(ln(2))
  // extern const Numeric SQRT_NAT_LOG_2;
 
  // Constant within the Doppler Broadening calculation:
  static const Numeric doppler_const = sqrt( 2.0 * BOLTZMAN_CONST *
                                             AVOGADROS_NUMB) / SPEED_OF_LIGHT; 
 
  // dimension of f_mono, lines
  Index nf = f_mono.nelem();
  Index nl = lines.nelem();
 
  // Define the vector for the line shape function and the
  // normalization factor of the lineshape here, so that we don't need
  // so many free store allocations.  the last element is used to
  // calculate the value at the cutoff frequency
  Vector ls(nf+1);
  Vector fac(nf+1);
 
  bool cut = (cutoff != -1) ? true : false;
 
  // Check that the frequency grid is sorted in the case of lineshape
  // with cutoff. Duplicate frequency values are allowed.
  if (cut)
    {
      if ( ! is_sorted( f_mono ) )
        {
          ostringstream os;
          os << "If you use a lineshape function with cutoff, your\n"
             << "frequency grid *f_mono* must be sorted.\n"
             << "(Duplicate values are allowed.)";
          throw runtime_error(os.str());
        }
    }
  
  // Check that all temperatures are non-negative
  bool negative = false;
  
  for (Index i = 0; !negative && i < t_abs.nelem (); i++)
    {
      if (t_abs[i] < 0.)
        negative = true;
    }
  
  if (negative)
    {
      ostringstream os;
      os << "t_abs contains at least one negative temperature value.\n"
         << "This is not allowed.";
      throw runtime_error(os.str());
    }
  
  // We need a local copy of f_mono which is 1 element longer, because
  // we append a possible cutoff to it.
  // The initialization of this has to be inside the line loop!
  Vector f_local( nf + 1 );
 
  // Voigt generally needs a different frequency grid. If we allocate
  // that in the outer loop, instead of in voigt, we don't have the
  // free store allocation at each lineshape call. Calculation is
  // still done in the voigt routine itself, this is just an auxillary
  // parameter, passed to lineshape. For selected lineshapes (e.g.,
  // Rosenkranz) it is used additionally to pass parameters needed in
  // the lineshape (e.g., overlap, ...). Consequently we have to
  // assure that aux has a dimension not less then the number of
  // parameters passed.
  Index ii = (nf+1 < 10) ? 10 : nf+1;
  Vector aux(ii);
 
  // Check that p_abs, t_abs, and h2o_abs all have the same
  // dimension. This could be a user error, so we throw a
  // runtime_error.  FIXME: why do we do this for each tag? wouldn't a
  // check in abscalc be sufficient?
 
  if ( t_abs.nelem() != p_abs.nelem() )
    {
      ostringstream os;
      os << "Variable t_abs must have the same dimension as p_abs.\n"
         << "t_abs.nelem() = " << t_abs.nelem() << '\n'
         << "p_abs.nelem() = " << p_abs.nelem();
      throw runtime_error(os.str());
    }
 
  if ( vmr.nelem() != p_abs.nelem() )
    {
      ostringstream os;
      os << "Variable vmr must have the same dimension as p_abs.\n"
         << "vmr.nelem() = " << vmr.nelem() << '\n'
         << "p_abs.nelem() = " << p_abs.nelem();
      throw runtime_error(os.str());
    }
 
  if ( h2o_abs.nelem() != p_abs.nelem() )
    {
      ostringstream os;
      os << "Variable h2o_abs must have the same dimension as p_abs.\n"
         << "h2o_abs.nelem() = " << h2o_abs.nelem() << '\n'
         << "p_abs.nelem() = " << p_abs.nelem();
      throw runtime_error(os.str());
    }
 
 
  // Check that the dimension of xsec is indeed [f_mono.nelem(),
  // p_abs.nelem()]:
  if ( xsec.nrows() != nf || xsec.ncols() != p_abs.nelem() )
    {
      ostringstream os;
      os << "Variable xsec must have dimensions [f_mono.nelem(),p_abs.nelem()].\n"
         << "[xsec.nrows(),xsec.ncols()] = [" << xsec.nrows()
         << ", " << xsec.ncols() << "]\n"
         << "f_mono.nelem() = " << nf << '\n'
         << "p_abs.nelem() = " << p_abs.nelem();
      throw runtime_error(os.str());
    }
 
 
  // Loop all pressures:
  for ( Index i=0; i<p_abs.nelem(); ++i )
    {
 
      // store variables p_abs[i] and t_abs[i],
      // this is slightly faster
      Numeric p_i = p_abs[i];
      Numeric t_i = t_abs[i];
 
    
      //out3 << "  p = " << p_i << " Pa\n";
 
      // Calculate total number density from pressure and temperature.
      // n = n0*T0/p0 * p/T or n = p/kB/t, ideal gas law
      Numeric n = p_i / BOLTZMAN_CONST / t_i;
 
      // For the pressure broadening, we also need the partial pressure:
      const Numeric p_partial = p_i * vmr[i];
 
 
      // Loop all lines:
      for ( Index l=0; l< nl; ++l )
        {
          // Copy f_mono to the beginning of f_local. There is one
          // element left at the end of f_local.  
          // THIS HAS TO BE INSIDE THE LINE LOOP, BECAUSE THE CUTOFF
          // FREQUENCY IS ALWAYS PUT IN A DIFFERENT PLACE!
          f_local[Range(0,nf)] = f_mono;
 
          // This will hold the actual number of frequencies to add to
          // xsec later on:
          Index nfl = nf;
 
          // This will hold the actual number of frequencies for the
          // call to the lineshape functions later on:
          Index nfls = nf;      
 
          // The baseline to substract for cutoff frequency
          Numeric base=0.0;
 
          // lines[l] is used several times, this construct should be
          // faster (Oliver Lemke)
          LineRecord l_l = lines[l];  // which line are we dealing with
          // Center frequency in vacuum:
          Numeric F0 = l_l.F();
 
          // Intensity is already in the right units (Hz*m^2). It also
          // includes already the isotopic ratio. Needs only to be
          // coverted to the actual temperature and multiplied by total
          // number density and lineshape.
          Numeric intensity = l_l.I0();
 
          // Lower state energy is already in the right unit (Joule).
          Numeric e_lower = l_l.Elow();
 
          // Upper state energy:
          Numeric e_upper = e_lower + F0 * PLANCK_CONST;
 
          // Get the ratio of the partition function.
          // This will throw a runtime error if no data exists.
          // Important: This function needs both the reference
          // temperature and the actual temperature, because the
          // reference temperature can be different for each line,
          // even of the same species.
          Numeric part_fct_ratio =
            l_l.IsotopeData().CalculatePartitionFctRatio( l_l.Ti0(),
                                                          t_i );
 
          // Boltzmann factors
          Numeric nom = exp(- e_lower / ( BOLTZMAN_CONST * t_i ) ) - 
            exp(- e_upper / ( BOLTZMAN_CONST * t_i ) );
 
          Numeric denom = exp(- e_lower / ( BOLTZMAN_CONST * l_l.Ti0() ) ) - 
            exp(- e_upper / ( BOLTZMAN_CONST * l_l.Ti0() ) );
 
 
          // intensity at temperature
          // (calculate the line intensity according to the standard 
          // expression given in HITRAN)
          intensity *= part_fct_ratio * nom / denom;
 
          if (lineshape_norm_data[ind_lsn].Name() == "quadratic")
            {
              // in case of the quadratic normalization factor use the 
              // so called 'microwave approximation' of the line intensity 
              // given by 
              // P. W. Rosenkranz, Chapter 2, Eq.(2.16), in M. A. Janssen, 
              // Atmospheric Remote Sensing by Microwave Radiometry, 
              // John Wiley & Sons, Inc., 1993
              Numeric mafac = (PLANCK_CONST * F0) / (2.000e0 * BOLTZMAN_CONST * t_i);
              intensity     = intensity * mafac / sinh(mafac);
            }
 
 
          // 2. Get pressure broadened line width:
          // (Agam is in Hz/Pa, p_abs is in Pa, gamma is in Hz)
          const Numeric theta = l_l.Tgam() / t_i;
          const Numeric theta_Nair = pow(theta, l_l.Nair());
 
          Numeric gamma
            = l_l.Agam() * theta_Nair  * (p_i - p_partial)
            + l_l.Sgam() * pow(theta, l_l.Nself()) * p_partial;
 
          // 3. Doppler broadening without the sqrt(ln(2)) factor, which
          // seems to be redundant FIXME: verify .
          Numeric sigma = F0 * doppler_const * 
            sqrt( t_i / l_l.IsotopeData().Mass());
 
          // 3.a. Put in pressure shift.
          // The T dependence is connected to that of agam by:
          // n_shift = .25 + 1.5 * n_agam
          // Theta has been initialized above.
          F0 += l_l.Psf() * p_i * 
              std::pow( theta , (Numeric).25 + (Numeric)1.5*l_l.Nair() );
 
          // 4. the rosenkranz lineshape for oxygen calculates the
          // pressure broadening, overlap, ... differently. Therefore
          // all required parameters are passed in the aux array, the
          // given order must agree with how they are accessed in the
          // used lineshape (currently only the Rosenkranz routines are
          // using this method of passing parameters). Parameters are
          // always passed, because the Rosenkranz lineshape function
          // can be used without overlap correction, which is then just
          // set to 0. I know, this is not very nice, but I suggested to
          // put the oxygen absorption into a different workspace
          // method, but nobody listened to me, Schnief.
          aux[0] = theta;
          aux[1] = theta_Nair;
          aux[2] = p_i;
          aux[3] = vmr[i];
          aux[4] = h2o_abs[i];
          aux[5] = l_l.Agam();
          aux[6] = l_l.Nair();
          // is overlap available, otherwise pass zero
          if (l_l.Naux() > 1)
            {
              aux[7] = l_l.Aux()[0];
              aux[8] = l_l.Aux()[1];
              //            cout << "aux7, aux8: " << aux[7] << " " << aux[8] << "\n";
            }
          else
            {
              aux[7] = 0.0;
              aux[8] = 0.0;
            }
 
 
          // Indices pointing at begin/end frequencies of f_mono or at
          // the elements that have to be calculated in case of cutoff
          Index i_f_min = 0;            
          Index i_f_max = nf-1;         
 
          // cutoff ?
          if ( cut )
            {
              // Check whether we have elements in ls that can be
              // ignored at lower frequencies of f_mono.
              //
              // Loop through all frequencies, finding min value and
              // set all values to zero on that way.
              while ( i_f_min < nf && (F0 - cutoff) > f_mono[i_f_min] )
                {
                  //              ls[i_f_min] = 0;
                  ++i_f_min;
                }
              
 
              // Check whether we have elements in ls that can be
              // ignored at higher frequencies of f_mono.
              //
              // Loop through all frequencies, finding max value and
              // set all values to zero on that way.
              while ( i_f_max >= 0 && (F0 + cutoff) < f_mono[i_f_max] )
                {
                  //              ls[i_f_max] = 0;
                  --i_f_max;
                }
              
              // Append the cutoff frequency to f_local:
              ++i_f_max;
              f_local[i_f_max] = F0 + cutoff;
 
              // Number of frequencies to calculate:
              nfls = i_f_max - i_f_min + 1; // Add one because indices
              // are pointing to first and
              // last valid element. This
              // is for the lineshape
              // calls. 
              nfl = nfls -1;              // This is for xsec.
            }
          else
            {
              // Nothing to do here. Note that nfl and nfls are both still set to nf.
            }
 
          //      cout << "nf, nfl, nfls = " << nf << ", " << nfl << ", " << nfls << ".\n";
        
          // Maybe there are no frequencies left to compute?  Note that
          // the number that counts here is nfl, since only these are
          // the `real' frequencies, for which xsec is changed. nfls
          // will always be at least one, because it contains the cutoff.
          if ( nfl > 0 )
            {
              // Calculate the line shape:
              lineshape_data[ind_ls].Function()(ls,
                                                aux,F0,gamma,sigma,
                                                f_local[Range(i_f_min,nfls)],
                                                nfls);
 
              // Calculate the chosen normalization factor:
              lineshape_norm_data[ind_lsn].Function()(fac,F0,
                                                      f_local[Range(i_f_min,nfls)],
                                                      t_i,nfls);
 
              // Get a handle on the range of xsec that we want to change.
              // We use nfl here, which could be one less than nfls.
              VectorView this_xsec = xsec(Range(i_f_min,nfl),i);
 
              // Get handles on the range of ls and fac that we need.
              VectorView this_ls  = ls[Range(0,nfl)];
              VectorView this_fac = fac[Range(0,nfl)];
 
              // cutoff ?
              if ( cut )
                {
                  // The index nfls-1 should be exactly the index pointing
                  // to the value at the cutoff frequency.
                  base = ls[nfls-1];
 
                  // Subtract baseline from xsec. 
                  // this_xsec -= base;
                  this_ls -= base;
                }
 
              // Add line to xsec. 
              {
                // To make the loop a bit faster, precompute all constant
                // factors. These are:
                // 1. Total number density of the air.
                // 2. Line intensity.
                // 3. Isotopic ratio.
                //
                // The isotopic ratio must be applied here, since we are
                // summing up lines belonging to different isotopes.
 
                const Numeric factors = n * intensity * l_l.IsotopeData().Abundance();
 
                // We have to do:
                // xsec(j,i) += factors * ls[j1] * fac[j1];
                //
                // We use ls as a dummy to compute the product, then add it
                // to this_xsec.
 
                // FIXME: Maybe try if this is faster with a good
                // old-fashioned simple loop.
 
                this_ls *= this_fac;
                this_ls *= factors;
                this_xsec += this_ls;
              }
            }
        }
    }
}
 
 
 
 
//======================================================================
//             Functions related to refraction
//======================================================================
 
 
 
void refr_index_BoudourisDryAir (
                                Vector&   refr_index,
                                ConstVectorView   p_abs,
                                ConstVectorView   t_abs )
{
  const Index   n = p_abs.nelem();
  refr_index.resize( n );
 
  assert ( n == t_abs.nelem() );
 
  // N = 77.593e-2 * p / t ppm
  for ( Index i=0; i<n; i++ )
    refr_index[i] = 1.0 + 77.593e-8 * p_abs[i] / t_abs[i];
}
 
 
 
 
void refr_index_Boudouris (
                          Vector&   refr_index,
                          ConstVectorView   p_abs,
                          ConstVectorView   t_abs,
                          ConstVectorView   h2o_abs )
{
  const Index   n = p_abs.nelem();
  refr_index.resize( n );
 
  assert ( n == t_abs.nelem() );
  assert ( n == h2o_abs.nelem() );
 
  Numeric   e;     // Partial pressure of water in Pa
  Numeric   p;     // Partial pressure of the dry air: p = p_tot - e 
 
  for ( Index i=0; i<n; i++ )
  {
    e = p_abs[i] * h2o_abs[i];
    p = p_abs[i] - e;
 
    refr_index[i] = 1.0 + 77.593e-8 * p / t_abs[i] + 
                          72e-8 * e / t_abs[i] +
                          3.754e-3 * e / (t_abs[i]*t_abs[i]);
  }
}
 
Numeric wavenumber_to_joule(Numeric e)
{
  // Planck constant [Js]
  extern const Numeric PLANCK_CONST;
 
  // Speed of light [m/s]
  extern const Numeric SPEED_OF_LIGHT;
 
  // Constant to convert lower state energy from cm^-1 to J
  static const Numeric lower_energy_const = PLANCK_CONST * SPEED_OF_LIGHT * 1E2;
 
  return e*lower_energy_const; 
}
 
//======================================================================
//        Functions to convert the accuracy index to ARTS units
//======================================================================
 
// ********* for HITRAN database *************
//convert HITRAN index for line position accuracy to ARTS
//units (Hz).
 
void convHitranIERF(     
                    Numeric&     mdf,
              const Index&       df 
                    )
{
  switch ( df )
    {
    case 0:
      { 
        mdf = -1;
        break; 
      }
    case 1:
      {
        mdf = 30*1E9;
        break; 
      }
    case 2:
      {
        mdf = 3*1E9;
        break; 
      }
    case 3:
      {
        mdf = 300*1E6;
        break; 
      }
    case 4:
      {
        mdf = 30*1E6;
        break; 
      }
    case 5:
      {
        mdf = 3*1E6;
        break; 
      }
    case 6:
      {
        mdf = 0.3*1E6;
        break; 
      }
    }
}
                    
//convert HITRAN index for intensity and halfwidth accuracy to ARTS
//units (relative difference).
void convHitranIERSH(     
                    Numeric&     mdh,
              const Index&       dh 
                    )
{
  switch ( dh )
    {
    case 0:
      { 
        mdh = -1;
        break; 
      }
    case 1:
      {
        mdh = -1;
        break; 
      }
    case 2:
      {
        mdh = -1;
        break; 
      }
    case 3:
      {
        mdh = 30;
        break; 
      }
    case 4:
      {
        mdh = 20;
        break; 
      }
    case 5:
      {
        mdh = 10;
        break; 
      }
    case 6:
      {
        mdh =5;
        break; 
      }
    case 7:
      {
        mdh =2;
        break; 
      }
    case 8:
      {
        mdh =1;
        break; 
      }
    }
  mdh=mdh/100;              
}
 
// ********* for MYTRAN database ************* 
//convert MYTRAN index for intensity and halfwidth accuracy to ARTS
//units (relative difference).
void convMytranIER(     
                    Numeric&     mdh,
              const Index  &      dh 
                    )
{
  switch ( dh )
    {
    case 0:
      { 
        mdh = 200;
        break; 
      }
    case 1:
      {
        mdh = 100;
        break; 
      }
    case 2:
      {
        mdh = 50;
        break; 
      }
    case 3:
      {
        mdh = 30;
        break; 
      }
    case 4:
      {
        mdh = 20;
        break; 
      }
    case 5:
      {
        mdh = 10;
        break; 
      }
    case 6:
      {
        mdh =5;
        break; 
      }
    case 7:
      {
        mdh = 2;
        break; 
      }
    case 8:
      {
        mdh = 1;
        break; 
      }
    case 9:
      {
        mdh = 0.5;
        break; 
      }
    }
  mdh=mdh/100;              
}