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--- user_area:fluorescence_explorer_flex [2013/10/15 11:34]
arve
+++ user_area:fluorescence_explorer_flex [2013/10/15 19:20]
arve
@@ Line 32: / Line 32: @@
 resolution((Fontenla, J., White, O. R., Fox, P. A., Avrett, E. H., and
 Kurucz, R. L.: Calculation of solar irradiances. I. Synthesis of the
-solar spectrum, The Astrophysical Journal, 518, 480–499, 1999.))
+solar spectrum, The Astrophysical Journal, 518, 480-499, 1999.))
 The solar spectrum must have the same units as the fluorescence
 spectrum. We use units of photons/nm/s/m<sup>2</sup> in order to be
@@ Line 40: / Line 40: @@
   source solar ./UVSPEC_FLUORESCENCE_kurucz_640.0_810.0.dat_vac_0.01_0.01
-The wavelengths to be covered are set as follows:
+Also note that inclusion of fluorescence requires that internally the
+transmittance is calculated at the same grid as the solar_file. The
+first wavelength in the ''wavelength_grid_file'' must be the same as
+that specified by ''wavelength''. The wavelengths to be covered are
+set as follows:
   wavelength 750 770 #  O2-A band
+  wavelength_grid_file  kurucz_750_801_trans_0.01
 Change this to
   wavelength 677 697 #  O2-B band
+  wavelength_grid_file  kurucz_677_801_trans_0.01
-for the  O<sub>2</sub>-B band.
+for the  O<sub>2</sub>-B band. Note that ''wavelength_grid_file'' does
+not have to be included if ''raman'' is specified.
 ===== O2-A and B band absorption =====
@@ Line 103: / Line 111: @@
 abs_lines_per_speciesCreateFromLines
-# Atmospheric profiles (there is several data in the
+# Atmospheric profiles
-# arts-xml-data/atmosphere directory, fascod includes the standard
-# atmospheres which we also have in libRadtran (altitude only up to
-# 95 km !!). When you want to use the molecular_tau_file from arts,
-# the atmosphere_file for uvspec must correspond to the ARTS
-# atmosphere files which are defined here!!)
 AtmRawRead( t_field_raw, z_field_raw, vmr_field_raw, abs_species,
   "/home/arve/arts/arts-xml-data-1.1.31/atmosphere/fascod/midlatitude-summer" )
@@ Line 143: / Line 146: @@
   mol_tau_file abs ./UVSPEC_FLUORESCENCE_arts-640-810.nc
 ===== Atmosphere =====
@@ Line 153: / Line 155: @@
   atmosphere_file ./afglms_95.dat
+===== Surface input =====
+For the surface the surface albedo and the flourescence must be
+specified. We use spectral data from the ESA-FLUSS project((see  also Miller,
+J. R., Berger, M., Goulas, Y., Jacquemond, S., Lous, J., Moise, N.,
+Mohammed, G., Moreno, J., Moya, I., Pedrós, R., Verhoef, W., and
+Zarco-Tejada, P. J.: Development of a Vegetation Fluorescence Canopy
+Model, Final Report, Tech. rep., ESTEC Contract No. 16365/NL/FF,
+.)) The following parameters were used: Chlorophyll a and
+b 40; Stoichiometry 1; Fluorescence 0.02; Relative azimuth angle 40;
+Viewing zenith angle 41.4; Leaf are index 3; Soil-type code 2; Solar
+zenith angle 30.
+  fluorescence_file ./UVSPEC_FLUORESCENCE.FLU_ph
+  albedo_file ./UVSPEC_FLUORESCENCE.TOC
+===== Geometry =====
+The solar zenith angle must be specified. This should equal the solar
+zenith angle used to calculate the fluorescence and surface albedo
+spectra.
+  sza 30.0
+Furthermore we assume the instrument is nadir viewing and of course is
+at TOA.
+  umu 1     # Looking down
+  zout toa  # top of atmosphere
+===== Rotational Raman scattering =====
+Rotational Raman scattering may be included by adding the following
+line. Note that this will increase the computing time by about a
+factor of 480.
+  #raman # Uncomment to include rotational Raman scattering.
+===== Miscellanoues =====
+In addition to the above input we need to specify where uvspec may
+find additional data files, what radiative transfer solver to use
+(only disort can handle fluorescence and rotational Raman scattering
+at the moment)
+  data_files_path /home/arve/develop/libRadtran/data/
+  number_of_streams 16
+  rte_solver disort
+As output we want solar irradiance (''edir''), upward irradiance (''eup'') and
+nadir radiance (''uu'' as specified by ''umu'' above)  as a function
+of wavelength
+  output_user lambda edir eup uu
+And we turn of any warning messages.
+  quiet     # Turn of messages.
+===== Complete uvspec input file =====
+With all this in place the complete uvspec input file is (with some
+comments included)
+<code>
+atmosphere_file ./afglms_95.dat
+# Note that solar_file and fluorescence_file must have the same units.
+source solar ./UVSPEC_FLUORESCENCE_kurucz_640.0_810.0.dat_vac_0.01_0.01
+# Fluorescence and top of canopy reflectance spectra
+fluorescence_file ./UVSPEC_FLUORESCENCE.FLU_ph
+albedo_file ./UVSPEC_FLUORESCENCE.TOC
+#  Use gas absorption calculated by arts.
+mol_tau_file abs ./UVSPEC_FLUORESCENCE_arts-640-810.nc
+# Specify wavelength region
+wavelength 750 770 #  O2-A band
+wavelength_grid_file  kurucz_750_810_trans_0.01
+#wavelength 677 697 #  O2-B band
+#wavelength_grid_file  kurucz_677_810_trans_0.01
+#wavelength 650 800 #  Both, very memory consuming if raman is on.
+#wavelength_grid_file  kurucz_650_801_trans_0.01
+sza 30.0
+umu 1 # Simulate nadir viewing satellite.
+zout toa
+data_files_path /home/arve/develop/libRadtran/data/
+number_of_streams 16
+rte_solver disort
+output_user lambda eglo eup uu
+quiet
+#raman # Uncomment to include rotational Raman scattering.
+</code>
+===== Clouds and aerosols =====
+No aerosol nor liquid water and ice clouds are included in this
+examples. These may be included as described in the
+[[http://www.libradtran.org/doc/libradtran.pdf|libRadtran User's
+Guide]].
+===== Note on input directory and file names =====
+Note that the input file contains references to other files with input
+data. The file path to these files must be correctly set in order to
+run this example. As the paths are set they reflect my setup.
+===== Results =====
+uvspec is run with the following command (assuming the input is stored
+in the file ''UVSPEC_FLUORESCENCE.INP'')
+  uvspec < UVSPEC_FLUORESCENCE.INP > UVSPEC_FLUORESCENCE_650_880_noraman.OUT
+The output from uvspec is at 0.01 nm resolution. We want it at FLORIS
+resolution. This is achieved by convolution by a spectral response
+function with FWHM of 0.3 nm. We assume it to be triangular and
+generate it with the command:
+  make_slitfunction -f 0.3 -r0.001 > SLIT_0.3.dat
+The convolution is carried out with the libradtran ''conv'' tool.
+  conv UVSPEC_FLUORESCENCE_650_880_noraman.OUT SLIT_0.3.dat  > UVSPEC_FLUORESCENCE_650_880_noraman.OUTc_0.3
+The TOA radiance for the full wavelength region covered by the
+O<sub>2</sub>-A and B bands,is shown in the Figure below at high, 0.01
+nm (blue line), and FLORIS, 0.3 nm (magenta line), spectral resolution. The
+fluorescence spectrum, multiplied by a factor of 100, is shown in red
+while the surface albedo used for the simulation is shown by the green
+line.
+{{:user_area:fluorescence_explorer_flex:toa_spectra.png?600|}}
+The radiance for the O<sub>2</sub>-B band with and without
+fluorescence is shown in the Figure below.
+{{:user_area:fluorescence_explorer_flex:toa_fluor_02b.png?600|}}
+Rotational Raman scattering was included in the spectra above. The
+filling-in with and without fluorescence is given below:
+{{:user_area:fluorescence_explorer_flex:toa_fi_02b.png?600|}}
+===== Input files =====
+The various input and output files discussed above are available as a
+gzipped tar ball
+{{:user_area:fluorescence_explorer_flex:flex_example.tgz|}}.