#
# Run this control file and type in AMI:
#    f=read_artsvar('full','f_mono');   
#    za=read_artsvar('full','za_pencil'); 
#    y=read_artsvar('full','y');   
#    plot(f/1e9,reshape(y2,length(f),length(za))) 
#
# You should then get something similar to Figure 4 in Paper A of my thesis.
# By typing 
#    Y=read_artsvar('full','ybatch');  
# you get the result of the batch calculations.
#

### Spectroscopy: ############################################################
tag_groupsDefine    { ["O3-666","ClO","H2O-161","N2O-446"] }
#tag_groupsDefine    { ["ClO"] }
lineshapeDefine     { shape               = "Voigt_Kuntz1"
                      normalizationfactor = "quadratic" } 
#
linesReadFromHitran { filename = "/u/patrick/arts/data/spectroscopy/hitran96/hitran96_lowfreq.par"
		      fmin     = 498e9
                      fmax     = 505e9 }
lines_per_tgCreateFromLines {}  


### Load an atmosphere ########################################################
MatrixReadAscii (raw_ptz_1d) { "/u/patrick/arts/data/atmosphere/fascod/midlatitude-winter.tz.am" }
raw_vmrs_1dReadFromScenario  { "/u/patrick/arts/data/atmosphere/fascod/midlatitude-winter" }


### Monochromatic frequency grid ##############################################
VectorLinSpace (f_mono)    { start = 501.18e+9
                             stop  = 501.58e+9
		             step  = 0.5e6       }
VectorWriteAscii (f_mono) {""}


### The ground ################################################################
# Set r_geoid to EARTH_RADIUS
r_geoidStd{}
# Set r_geoid to the WGS84 geoid 
#r_geoidWGS84{ latitude     = 0
#              obsdirection = 0 }
NumericSet (z_ground) { 0.0 }
NumericSet (t_ground) { 290.0 }
VectorSetLengthFromVector(e_ground,f_mono){value=0.75}



### Vertical profiles #########################################################
VectorNLogSpace (p_abs)    { start = 1.013300e+05
                             stop  = 0.0914023919463313
                             n     = 201 }
AtmFromRaw1D               {}
VectorSetLengthFromVector ( h2o_abs, p_abs ) { 0 } 
z_absHydrostatic{
   g0    = 9.81
   pref  = 101330
   zref  = 0
   niter = 2 }
VectorWriteAscii (p_abs)  {""}
VectorWriteAscii (t_abs)  {""}
VectorWriteAscii (z_abs)  {""}
#ArrayOfVectorWriteAscii (vmrs) {""}


### Calculate absorption ######################################################
absCalc                    {}
#MatrixWriteBinary (abs) {""}
#ArrayOfMatrixWriteBinary (abs_per_tg) {""}


### Observation geometry ######################################################
NumericSet (z_plat) { 620e3 }
VectorNLinSpace (za_pencil) { start = 113
                              stop  = 114.1
                              n     = 11 }
#VectorSet  (za_pencil) { length = 1
#                         value  = 0 }
VectorWriteAscii( za_pencil ){""}
NumericSet (l_step) { 10e3 }


### Cosmic radiation ##########################################################
y_spaceStd{ "cbgr" }
#y_spacePlanck{300}


### Refraction ################################################################
IntSet(refr) {0}
NumericSet (l_step_refr) { 1e3 }
refr_indexBoudourisDryAir{}


### Line of sight (LOS) #######################################################
losCalc{}
# A function assuming no refraction
#losNoRefraction{}
# A function assuming no refraction and no ground intersection
#losUpward{}
#LosWriteBinary(los){""}
#LosReadBinary(los){""}
sourceCalc{}
transCalc{}


### Calculate spectra #########################################################
yRte{}
#yRteNoGround{}
#yBl{}
#yBlNoGround{}



### Calculate species weighting function matrix and save ######################
absloswfsCalc{}
kxInit{}
#kbInit{}
VectorCopy( k_grid, p_abs ){}
VectorWriteAscii (k_grid)  {""}
kSpecies{    nr   = 1
             unit = "frac" }
#kSpeciesAll{ unit = "frac" }
kxAppend{}
#kxAppendUsingH(h1){}
kContAbs{ order = 1 }
kxAppend{}
#kxAppendUsingH(h1){}
kTempNoHydro{}
kxAppend{}
#MatrixApplyH(kx,h1,kx){}
#
# To test kDiffH
#kDiffHFast{ name    = "Proportional"
#             delta   = 0.01
#             grid    = 0
#             apriori = 0}
#kxAppend{}
#
# To test kManual
#VectorCopy(y0,y){}
#y_spaceStd{1}
#yRte{}
#kManual{ name    = "CBGR"
#         delta   = 2.73
#         grid    = 0
#         apriori = 2.73}
#kxAppendUsingH(h1){}
#
MatrixWriteBinary(kx){""}  
MatrixWriteBinary(kx_index){""}  
MatrixWriteBinary(kx_aux){""}  
ArrayOfStringWriteBinary(kx_names){""}
#MatrixWriteAscii(kb){""}  
#MatrixWriteAscii(kb_index){""}  
#MatrixWriteAscii(kb_aux){""}  
#ArrayOfStringWriteBinary(kb_names){""}


### Conversion to different temperature scales ################################
VectorCopy(f_sensor,f_mono){}
VectorCopy(za_sensor,za_pencil){}
yTRJ{}
#yTB{}
#VectorPlanck(y_cal1,f_sensor){temp=78}
#VectorPlanck(y_cal2,f_sensor){temp=300}
#VectorSetLengthFromVector(i_cal1,y_cal1){value=78}
#VectorSetLengthFromVector(i_cal2,y_cal2){value=300}          
#yLoadCalibration{}


### Save spectra #############################################################
VectorWriteBinary( y ) {""}



### Produce batch data for varoius variables ##################################

StringSet( batchname ) { "/u/patrick/ARTS/Batch/full" }

sDiagonalLengthFromVector ( p_abs )
{ 
  stddev     = 3
}

BatchdataGaussianTemperatureProfiles{
   n     = 20
   g0    = 9.81
   pref  = 101330
   zref  = 0
   niter = 2 
}

sDiagonalLengthFromVector ( p_abs )
{ 
  stddev     = 0.3
}

BatchdataGaussianSpeciesProfiles{
   n       = 20
   do_tags = ["O3-666"]
   unit    = "frac"
}


BatchdataUniformOffSets ( za_sensor ) {
   n    = 20
   low  = -0.01
   high = 0.01
}

# These lines produce thermal noise, but the covariance cannot be 
# created for the selected f_sensor and za_sensor without 
# diagonal/banded covariance matrices.
#
#sDiagonalLengthFromVectors ( f_sensor, za_sensor )
#{ 
#  stddev     = 0.2
#}
#
#BatchdataGaussianZeroMean {
#   n       = 20
#   varname = "noise"
#}

BatchdataSinusoidalRippleNoCorrelations( f_sensor, za_sensor )
{
  n         = 20
  period    = 20e6
  amplitude = 0.2
  pdf       = "gaussian"
  varname   = "ripple"
}


### Calculate spectra for the batch data,  ####################################
### convert to RJ and add noise and ripple

ybatchAbsAndRte{
   ncalc     = 10
   do_t      = 1
   t_file    = ""
   do_z      = 1
   z_file    = ""
   do_tags   = ["O3-666"]
   tag_files = [""]
   do_f      = 0
   f_file    = ""
   do_za     = 1
   za_file   = ""
}

ybatchTRJ{}
#MatrixFillWithVector( ybatch, y ){ 10 }

ybatchAdd{ "ripple" }
#ybatchAdd{ "noise" }

MatrixWriteBinary( ybatch ) {""}