#DEFINITIONS:  -*-sh-*-
#
# This control file demonstrates a simple ARTS 1D clear sky calculation.
# Calculation of brightness temperature and optical depth as an auxilary variable is included. 
#
# You can choose different species and change the sensor position and sensor line of soght (los)

Arts2 {

INCLUDE "general/general.arts"
INCLUDE "general/continua.arts"
INCLUDE "general/agendas.arts"
INCLUDE "general/planet_earth.arts"

# Agenda for scalar gas absorption calculation
Copy(abs_xsec_agenda, abs_xsec_agenda__noCIA)

# (standard) emission calculation
Copy( iy_main_agenda, iy_main_agenda__Emission )

# cosmic background radiation
Copy( iy_space_agenda, iy_space_agenda__CosmicBackground )

# standard surface agenda (i.e., make use of surface_rtprop_agenda)
Copy( iy_surface_agenda, iy_surface_agenda__UseSurfaceRtprop )

# Planck as blackbody radiation
Copy( blackbody_radiation_agenda, blackbody_radiation_agenda__Planck )

# on-the-fly absorption
Copy( propmat_clearsky_agenda, propmat_clearsky_agenda__OnTheFly )

# sensor-only path
Copy( ppath_agenda, ppath_agenda__FollowSensorLosPath )

# no refraction
Copy( ppath_step_agenda, ppath_step_agenda__GeometricPath )

# Number of Stokes components to be computed
#
IndexSet( stokes_dim, 1 )

# Clearsky = No scattering
#
cloudboxOff



#########################################################################

# A pressure grid rougly matching 0 to 80 km, in steps of 2 km.
# ---
VectorNLogSpace( p_grid, 200, 1013e2, 10 )


# Definition of species:
# you can take out and add again one of the species to see what effect it has on radiative transfer in the atmosphere. 
# ---
abs_speciesSet( species=
            ["N2",
             "O2",
             "H2O"] )


# Read a line file and a matching small frequency grid
# ---
abs_linesReadFromSplitArtscat(abs_lines, abs_species, "spectroscopy/Perrin/",150e9, 200e9)
#abs_linesReadFromHitran(abs_lines,"/scratch/uni/u237/data/catalogue/hitran/hitran2012/HITRAN2012.par",10e9,250e9 )

# Sort the line file according to species
# ---
abs_lines_per_speciesCreateFromLines

# Atmospheric scenario
# ---
AtmRawRead(t_field_raw, z_field_raw, vmr_field_raw, abs_species, "planets/Earth/Fascod/midlatitude-summer/midlatitude-summer")

# Non reflecting surface
# ---
VectorSetConstant( surface_scalar_reflectivity, 1, 0.4 )
Copy( surface_rtprop_agenda, surface_rtprop_agenda__Specular_NoPol_ReflFix_SurfTFromt_surface )

# Create a frequency grid
VectorNLinSpace(f_grid, 200, 150e+9, 200e+9)

# No sensor properties
# ---
sensorOff


# We select here to use Planck brightness temperatures
# ---
StringSet( iy_unit, "PlanckBT" )


# Extract optical depth as auxiliary variables
# ---
ArrayOfStringSet( iy_aux_vars, [ "Pressure", "Absorption, summed"] )

# Create vector container for the optical depth
VectorCreate( odepth )


#########################################################################

# Atmosphere and surface
# ---
AtmosphereSet1D
AtmFieldsCalc
Extract( z_surface, z_field, 0 )
Extract( t_surface, t_field, 0 )

# Definition of sensor position and line of sight (LOS)
# ---
 VectorSet( rte_pos, [800e3])	# 10e3 for sensor in z = 10 km
 MatrixSet( sensor_pos, [800e3])
 MatrixSet( sensor_los, [180] )
 VectorSet( rte_los, [180] )		# zenith angle 	0�. looking up
#							180� looking nadir
 VectorSet( rte_pos2, [] )
 MatrixSet( sensor_description_amsu,
           [  89.00e9, 0.90e9, 1000e6 ;
      	     150.00e9, 0.90e9, 1000e6 ;
      	     183.31e9, 1.00e9,  500e6 ;
      	     183.31e9, 3.00e9, 1000e6 ;
      	     183.31e9, 7.00e9, 2000e6 ] )
#sensor_responseSimpleAMSU
sensorOff
#Jacobian calculation
# ---
jacobianInit
VectorCreate(g1)
VectorCreate(g2)
VectorCreate(g3)

jacobianAddAbsSpecies( 	jacobian_quantities, jacobian_agenda, atmosphere_dim,
	p_grid, lat_grid, lon_grid, p_grid, lat_grid, lon_grid, "H2O")
# jacobianAddAbsSpecies( 	jacobian_quantities, jacobian_agenda, atmosphere_dim,
# 	p_grid, lat_grid, lon_grid, p_grid, lat_grid, lon_grid, "O2")
jacobianClose
#jacobianCalcAbsSpeciesAnalytical

# Perform RT calculations
# ---
 abs_xsec_agenda_checkedCalc
 propmat_clearsky_agenda_checkedCalc
 atmfields_checkedCalc
 atmgeom_checkedCalc
 cloudbox_checkedCalc
 sensor_checkedCalc
 iyCalc
 WriteXML( "ascii", iy_aux, "results/iy_aux.xml" )
ArrayOfStringSet( iy_aux_vars, [ "Optical depth"] ) 
 yCalc




# Write output
# ---
 #Extract( odepth, y_aux, 0 )
 #Extract( abs, y_aux, 1 )
 WriteXML( "ascii", iy, "results/bt.xml" )
 WriteXML( "ascii", f_grid, "results/f_grid.xml" )
 WriteXML( "ascii", abs_species, "results/species.xml" )
 WriteXML( "ascii", y_aux, "results/y_aux.xml" )
 WriteXML( "ascii", jacobian, "results/jacobian.xml" )
 WriteXML( "ascii", z_field, "results/z_field.xml" )

} # End of Main