# An example ARTS controlfile that calculates absorption
# coefficients. 


# --------------------< A specific method >--------------------
#                      -------------------
# Read the spectroscopic line data from the MYTRAN catalogue and
# create the workspace variable `lines':
# NOTE: MYTRAN IS LIMITED TO DEDICATED BANDS!!!!
linesReadFromMytran2 {
   filename = "../../../data/spectroscopy/mytran/mytran98.my2"
   fmin     = 200e9
   fmax     = 400e9
}

# Read the spectroscopic line data from the JPL catalogue and
# create the workspace variable `lines':
# Note: Catalogue contains only species known to arts!
#linesReadFromJpl {
#   filename = "../../../data/spectroscopy/jpl00/jpl00.cat"
#   fmin     = 200e9
#   fmax     = 400e9
#}

# Read the spectroscopic line data from the HITRAN catalogue and
# create the workspace variable `lines':
#linesReadFromHitran {
#   filename = "../../../data/spectroscopy/hitran96/hitran96_lowfreq.par"
#   fmin     = 200e9
#   fmax     = 400e9
#}

# Optionally write the line list to a file:
linesWriteToFile{""} 

 
# This defines the list of tag groups (`tag_groups'). Absorption
# coefficients will be calculated separately for each tag group. This
# is necessary in order to calculate weighting functions later on.
# The lines are assigned to the tag groups in the order as the groups
# are specified here. That means the last group H2O gets assigned all
# the H2O lines that do not fit in any other group.
tgsDefine{
      ["H2O",
       "HCN",
       "CO",
       "H2CO",
       "NO",
       "O2",
       "H2O2",
       "HCl",
       "N2O",
       "NO2",
       "O3",
       "CH3Cl",
       "ClO",
       "HOCl",
       "OCS",
       "HNO3",
       "SO2",
       "COF2"]
}

# This separates the lines into the different tag groups and creates
# the workspace variable `lines_per_tg':
lines_per_tgCreateFromLines{}

#lines_per_tgWriteToFile{""} 


# --------------------< A generic method >--------------------
#                      ------------------
# Read the pressure, temperature, and altitude profiles and create 
# the workspace variable `raw_ptz_1d':
MatrixReadAscii (raw_ptz_1d) 
        {"../../../data/atmosphere/fascod/midlatitude-summer.tz.am"}

# The same for the input VMR profiles:
raw_vmrs_1dReadFromScenario
        {"../../../data/atmosphere/fascod/midlatitude-summer"}

# Optionally write this to a file:
#ArrayOfMatrixWriteAscii (raw_vmrs_1d) {""}

# Create the pressure grid `p_abs':
# VectorNLogSpace(p_abs){
#         start = 100000
#         stop  = 10
#         n     = 140
#}

# read the pressure grid used in the iup forward program
VectorReadAscii(p_abs){"master_b.iup_old.p_abs"}


VectorWriteAscii(p_abs){""}


# Now interpolate all the raw atmospheric input onto the pressure 
# grid and create the atmospheric variables `t_abs', `z_abs', `vmrs'
AtmFromRaw1D{}

# Optionally write these to files:
#VectorWriteAscii (t_abs) {""}
VectorWriteAscii (z_abs) {""}
#ArrayOfVectorWriteAscii (vmrs)  {""}

# define the h2o_abs vector, containing the total wv vmr
VectorCopyFromArrayOfVector (h2o_abs, vmrs) {index=0}


# Create the frequency grid `f_mono':
VectorNLinSpace(f_mono){
        start = 295e9
        stop  = 305e9
        n     = 1000    
}

# Write frequency grid to file:
VectorWriteAscii (f_mono) {""}

# define the lineshape to use
lineshapeDefine {shape="Voigt_Kuntz6"
                 normalizationfactor="quadratic"
		 cutoff=-1
                }

# define the water vapor vmr
VectorCopyFromArrayOfVector ( h2o_abs, vmrs ) { 0 } 

# Calculate absorption coefficients, both total (`abs') and 
# separately for each tag group (`abs_per_tg'):
absCalc{}

# These we definitely want to write to files!
MatrixWriteAscii (abs) {""}
ArrayOfMatrixWriteAscii (abs_per_tg) {""}