% setup structure for a spectroscopic error calculation;
function Q = spectro_sample( Q );
%=== Report levels
%
Q.QP_LEVEL   = 1;
Q.ARTS_LEVEL = 2;

%=== Directories
%
top_dir = '';
%
Q.ARTS           = '/home/home01/cverdes/tmp/arts/src/arts';
Q.OUT             = [top_dir,'OUT/Out'];
Q.SAVE           = [top_dir,'OUT/Out_1'];
Q.TMP_AREA       = '/tmp';
Q.SPECTRO_DIR    = [top_dir,'Input/Spectroscopy'];
Q.CALCGRIDS_DIR  = [top_dir,'Input/CalcGrids'];
Q.SENSOR_DIR     = [top_dir,'Input/Sensor'];
Q.RETRIEVDEF_DIR = [top_dir,'Input/RetrievDef'];
%=== Atmospheres
Q.APRIORI_VMR = ...
    [top_dir,'Input/atmosphere/midlatitude-winter'];
Q.APRIORI_PTZ     = ...
    [top_dir,'Input/atmosphere/midlatitude-winter.tz.aa'];

Q.SETUP_VMR = ...
    ['"Input/atmosphere/midlatitude-winter"'];

Q.SETUP_PTZ     = ...
     ['"Input/atmosphere/midlatitude-winter.tz.aa"'];

%=== Species
%
Q.RETRIEVAL_TAGS   = [ ...
      '"O3",', ...
       '"BrO",', ...
      '"HCl"']; 
Q.SPECIES_KGRIDS   = [ ...
      '"grid_2km.aa",', ...
   '"grid_2km.aa",', ... 
      '"grid_2km.aa"'];
Q.SPECIES_COVMATS  = [ ...
      '"sx.std.aa",', ...
      '"sx.std.aa",', ...
      '"sx.std.aa"'];
%
Q.OTHER_TAGS       = [...
    '"O2-PWR93",', ...
    '"H2O-PWR98",', ...
    '"N2-SelfContMPM93"']
       
%
Q.SPECTRO_TAGS   = [ ...
        '"O3",', ...
       '"HCl"'];

%=== Spectroscopy
%
Q.LINEFORMAT ='Mytran2';
Q.LINEFILE         = 'line_sample.my2';
%
Q.LINESHAPE        = 'Voigt_Kuntz6';
Q.LINESHAPE_FACTOR = 'quadratic'; 
Q.LINESHAPE_CUTOFF = -1;
%
Q.CONTINUA         = 'continua_std';

%=== Hydrostatic eq.
Q.HSE_IN_ON          = 1;
Q.HSE_RETRIEVAL_ON   = 1;
Q.HSE_PREF           = 1.018000e+05 ;
Q.HSE_ZREF           = 0e3;
%
Q.PLATFORM_ALTITUDE  = 820e3;
Q.STEPLENGTH_RTE     =20e3;
%
Q.GROUNDSET_ON       = 1; 
Q.GROUNDATBOTTOM_ON  = 0;
Q.GROUND_ALTITUDE    = 0; 
Q.GROUND_EMISSION    = 1;
%
Q.REFRACTION_ON      = 1;
Q.REFR_METHOD        = 'Boudouris';
Q.REFR_LFAC          = ceil( Q.STEPLENGTH_RTE/2e3 );
%
Q.EMISSION_ON        = 1;


%=== Calculation grids
%
Q.P_ABS     = 'p_abs.aa';
Q.F_MONO    = 'f_mono.aa';
Q.ZA_PENCIL = 'za_pencil.aa';


%=== Sensor
%
Q.F_ORDER     = 1;
Q.ZA_ORDER    = 1;
%
Q.ANTENNA_ON    = 1;
Q.ANTENNA_ZA    = 'za_sensor.aa';
Q.ANTENNA_FILE  = 'ACAP_500.aa';
Q.ANTENNA_ORDER = 1;
Q.ANTENNA_MOVE  = 0.0;
%
Q.DSB_ON        = 0;
Q.DSB_FILE      = '';
Q.DSB_ORDER     = 1;
Q.DSB_FPRIMARY  = 0;
Q.DSB_LO        = 0;
%
Q.BACKEND_ON    = 1;
Q.BACKEND_FREQS = 'f_sensor.aa';
Q.BACKEND_FILE  = 'channel_response_rectangular_50MHz.aa';
Q.BACKEND_ORDER = 1;
%
Q.FREQUENCY_DO = 0;
%Spectroscopic Parameters
%
Q.SPECTRO_DO = 1; 
Q.INTENS_ON = 1;
Q.POSITION_ON = 0;
Q.AGAM_ON = 0;
Q.SGAM_ON = 0;
Q.NAIR_ON =0;
Q.NSELF_ON = 0; 
Q.PSHIFT_ON = 0; 
%
%=== Thermal noise    
%
Q.MEASNOISE_DO     = 2;
Q.MEASNOISE_COVMAT = 'mnoise.aa';
%
Q.CALINOISE_DO   = 0;
Q.CALINOISE_COVMAT = '';

%=== Retrieval/error quantities beside species
%
Q.TEMPERATURE_DO       = 0;
Q.TEMPERATURE_KGRID    = 'grid_3km.aa';
Q.TEMPERATURE_COVMAT   = 'sx.temperature.aa';
Q.TEMPERATURE_FAST     = 0;
%
Q.POINTING_DO          = 0;
Q.POINTING_PDF         = 'uniform'
Q.POINTING_STDV        = 0.2;   
Q.POINTING_DELTA       = 0.001;
%
Q.CONTABS_DO           = 0;
Q.CONTABS_ORDER        = 1;
Q.CONTABS_LIMITS       = [624e9 626.5e9];
Q.CONTABS_KGRID        = 'grid.lowstrato.aa';
Q.CONTABS_COVMAT       = 'sx.std_cont.aa';
Q.CONTABS_REF_SPECIES  = '"O2-PWR93", "H2O-PWR98", "N2-SelfContMPM93"';
%
Q.EGROUND_DO           = 0;
Q.EGROUND_LIMITS       = [400e9 600e9];
Q.EGROUND_COVMAT       = 'sx.eground.aa';
Q.POLYFIT_DO =0;
Q.PPOLYFIT_DO =0;
Q.TB_REFLOADS_DO=0;
Q.PROPCAL_DO=0;

%=== Retrieval parameters
%
Q.RETRIEVAL_METHOD     = 'oem';
%
Q.CLS_SPECIES_POS_ON   = 1;
Q.SPECIES_POSITIVE_ON = 1
Q.CLS_RECALC_ABS_ON    = 1;
Q.CLS_RECALC_WFS_NITER = 1;
Q.CLS_NONLIN_ON        = 1;
%
if Q.CLS_NONLIN_ON
  %
  Q.CLS_GA_START_VALUE      = 1e3;
  Q.CLS_GA_FAC_WHEN_OK      = 2;
  Q.CLS_GA_FAC_WHEN_NOT_OK  = 2;
  Q.CLS_GA_LOWER_TRESHOLD   = 0.1;
  Q.CLS_STOP                = 0.01;
  Q.CLS_GA_UPPER_LIMIT      = 1e15; 
  Q.CLS_MAX_ITER            = 100;
end