Arts2 {

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

AgendaSet(propmat_clearsky_agenda)
{
Ignore(rtp_mag)
Ignore(rtp_los)
propmat_clearskyInit
propmat_clearskyAddOnTheFly
}

AgendaSet(abs_xsec_agenda)
{
abs_xsec_per_speciesInit
abs_xsec_per_speciesAddLines
}

Copy( iy_main_agenda, iy_main_agenda__Emission )
Copy( iy_surface_agenda, iy_surface_agenda__UseSurfaceRtprop )
Copy( iy_space_agenda, iy_space_agenda__CosmicBackground )
Copy( ppath_agenda, ppath_agenda__FollowSensorLosPath )
Copy( ppath_step_agenda, ppath_step_agenda__GeometricPath )
Copy( surface_rtprop_agenda, surface_rtprop_agenda__Blackbody_SurfTFromt_field)

IndexSet( stokes_dim, 1 )

VectorNLogSpace( p_grid, 41, 1000e2, 1 )
VectorNLinSpace( lat_grid, 2, -60, 60)
VectorNLinSpace( lon_grid, 2, -30, 30)
MatrixSet(sensor_los, [1.126885514276187e2,0;   1.122589281936843e2,0;   1.118213323268050e2,0])
MatrixSet(sensor_pos, [600e3, 0, 0;600e3,0,0;600e3,0,0])

refellipsoidEarth( refellipsoid, "Sphere" )
AtmosphereSet3D

abs_speciesSet( species=["CO2-626"] )
 
VectorCreate(tmp_kayser)
VectorLinSpace( tmp_kayser, 600, 650, 1 )
FrequencyFromCGSKayserWavenumber( f_grid, tmp_kayser )

#WriteXML("ascii",tmp_kayser,"cm.xml")
#WriteXML("ascii",f_grid,"f.xml")

ReadXML(abs_lines_per_species,"testdata/NLTE_CO2_testlines.xml")
abs_lines_per_speciesSetNormalizationForAll(option="VVH")
abs_lines_per_speciesCutOffForAll(option=750e9)
isotopologue_ratiosInitFromBuiltin
sensorOff
jacobianOff
cloudboxOff
StringSet( iy_unit, "W/(m^2 m-1 sr)" )

# Note that this data is not at all reliable and does not represent a real world scenario...
AtmWithNLTERawRead(  basename = "testdata/tropical" )
AtmFieldsCalcExpand1D
Extract( z_surface, z_field, 0 )

VectorCreate(ev)
ReadXML(ev,"testdata/tropical.ev.xml")
nlteSetByQuantumIdentifiers(vibrational_energies = ev)

#NumericSet(ppath_lmax,5e3)

abs_xsec_agenda_checkedCalc
propmat_clearsky_agenda_checkedCalc
atmfields_checkedCalc
atmgeom_checkedCalc
cloudbox_checkedCalc
sensor_checkedCalc
yCalc

VectorCreate(y_nlte_ref)
# WriteXML("ascii",y,"TestNLTE_NLTE_old_method.xml")
ReadXML(y_nlte_ref,"TestNLTE_NLTE_old_method.xml")
CompareRelative(y,y_nlte_ref,1e-5, "NLTE old method")

Tensor4Create(tmp_t4)
ArrayOfQuantumIdentifierCreate(tmp_aoqi)
Copy(tmp_t4, nlte_field)
Copy(tmp_aoqi, nlte_level_identifiers)
nlteOff

abs_xsec_agenda_checkedCalc
propmat_clearsky_agenda_checkedCalc
atmfields_checkedCalc
atmgeom_checkedCalc
cloudbox_checkedCalc
sensor_checkedCalc
yCalc

VectorCreate(y_lte_ref)
# WriteXML("ascii",y,"TestNLTE_LTE_old_method.xml")
ReadXML(y_lte_ref, "TestNLTE_LTE_old_method.xml")
CompareRelative(y,y_lte_ref,1e-5, "LTE old method")

# NOTE:  There is potentially a bug in AddLines2 for vib-NLTE.
#        For some reason, the source function is almost exactly
#        twice as large.  It is not known whether AddLines2 or
#        AddLines have the correct results... neither is as well
#        validated as the pure population distribution computations,
#        which only works in AddLines2.
AgendaSet(abs_xsec_agenda) { abs_xsec_per_speciesInit abs_xsec_per_speciesAddLines2 }
Copy(nlte_field, tmp_t4)
Copy(nlte_level_identifiers, tmp_aoqi)
IndexSet(nlte_do, 1)

abs_xsec_agenda_checkedCalc
propmat_clearsky_agenda_checkedCalc
atmfields_checkedCalc
atmgeom_checkedCalc
cloudbox_checkedCalc
sensor_checkedCalc
yCalc

# WriteXML("ascii",y,"TestNLTE_NLTE_new_method.xml")
ReadXML(y_nlte_ref,"TestNLTE_NLTE_new_method.xml")
CompareRelative(y,y_nlte_ref,1e-5, "NLTE new method")

nlteOff
abs_lines_per_speciesSetNlteOffForAll

abs_xsec_agenda_checkedCalc
propmat_clearsky_agenda_checkedCalc
atmfields_checkedCalc
atmgeom_checkedCalc
cloudbox_checkedCalc
sensor_checkedCalc
yCalc

# WriteXML("ascii",y,"TestNLTE_LTE_new_method.xml")
ReadXML(y_lte_ref, "TestNLTE_LTE_new_method.xml")
CompareRelative(y,y_lte_ref,1e-5, "LTE new method")

}