Output: Difference between revisions

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== Output Checks with SAMOA ==



SAMOA performs a sanity check on all model outputs that can be read by CDO. It checks if a variable lies in-between a predefined range and if the minimum and maximum value of each variable are the same. For this purpose CDO version 1.6.2rc3 is required currently (see https://code.zmaw.de/projects/cdo).

For more information about the usage please refer to the README-file within the SAMOA package. You can get a copy of the SAMOA script by writing an e-mail to the contact person of the ART code (see http://icon-art.imk-tro.kit.edu). SAMOA is licensed under the GNU GENERAL PUBLIC LICENSE Version 3.

As SAMOA is primarily developed for the usage with COSMO-ART and COSMO-CLM, you have to do a minor change before using it. The latest version of SAMOA has a list for the usage of SAMOA with ICON-ART output included but not loaded automatically. This list is called samoa_list_icon-art. You have to replace the default (COSMO) list that is used by SAMOA by editing samoa.sh:

Search for the following lines:

<pre># Path to the list with variables (is overwritten when -l specified)
# Assumed to be on the same path as script

path_list=$SCRIPTPATH/list </pre>
Change the name of the list to:

<pre>path_list=$SCRIPTPATH/samoa_list_icon-art </pre>
Now you may use SAMOA with the ICON-ART output file out.nc with the following command:

<pre>./samoa.sh out.nc</pre>
For all options see:

<pre>./samoa.sh --help</pre>
== Visualisation ==

The horizontal grid structure of the output is essential for the visualization. In general, there are two possibilities. The output may exist on the ICON grid and it may exist on an interpolated longitude/latitude grid. This can be chosen by adaptions of the output namelist (see ). Although it comes along with a loss in information, it is recommended to use interpolated output. By this, the visualization is much easier to handle.

In the following sections, three tools are introduced which can be used to visualize ICON output. Note, that '''only NETCDF''' is supported by ICON-ART so far. With the tool Ncview (see ) it is very easy to have a quick look into the interpolated model output. NCL (see ) is a very comprehensive tool for all kind of data formats and visualization. With ParaView (see ), a nice-looking three-dimensional visualization can be created.

=== Ncview ===

&quot;Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.&quot; (http://meteora.ucsd.edu/~pierce/ncview_home_page.html)

=== NCL ===

&quot;NCL is an interpreted language designed specifically for scientific data analysis and visualization. Portable, robust and free, NCL is available as binaries or open source.&quot; (https://www.ncl.ucar.edu/)

=== ParaView ===

&quot;ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.

ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of exascale size as well as on laptops for smaller data.&quot; (http://www.paraview.org/)

=== Python ===

On the [https://www.python.org/about/ official Website] Python describes itself as

<pre>Python is powerful... and fast;
plays well with others;
runs everywhere;
is friendly &amp; easy to learn;
is Open.</pre>
Using Python is a simple but effective way to display ICON-ART model output data. There is a large number of Packages available to help with Visualisation, the most useful Packages for visualising ICON-ART data are given in Table [[#tab:pythonpackages|1.4]]

<div id="tab:pythonpackages">

{| class="wikitable" style="text-align:left;"
|+ Helpful Python Packages and their primary usage for Visualisation
|align="center"| numpy
|align="center"| predefined Mathematical functions
|-
|align="center"| matplotlib
|align="center"| Plotting framework
|-
|align="center"| xarray
|align="center"| reading in and processing netcdf datasets
|-
|align="center"| ...
|align="center"|
|}


</div>

Revision as of 13:04, 21 December 2022

Output

In principle, output of ICON-ART variables works the same way as for ICON variables. As described in , the following five quantities of the output have to be specified:

  • The time interval between two model outputs.
  • The name of the output file.
  • The name of the variable(s) and/or variable group(s).
  • The type of vertical output grid.
  • The type of horizontal output grid.

It is recommended to use NETCDF output on an interpolated grid. A corresponding output namelist for sea salt on model levels can be seen here:

NAMELIST EXAMPLE
&output_nml
 filetype            =  4     ! output format: 2=GRIB2, 4=NETCDFv2
 dom                 =  1     ! write output for domain 1
 output_start        =  "JJJJ-MM-DDTHH:MM:SSZ" !put date in
 output_end          =  "JJJJ-MM-DDTHH:MM:SSZ" !put date in
 output_interval     =   "PT1H"  ! \href{ISO8601}{https://en.wikipedia.org/wiki/ISO_8601}  
 steps_per_file      =  1     ! max. num. of time steps within one file
 mode                =  1     ! 1: forecast mode (relative t-axis)
 include_last        = .TRUE. ! include the last time step
 output_filename     = '<INSERTFILENAME>' ! file name base
 ml_varlist          = 'seasa','seasb','seasc',
 'seasa0','seasb0','seasc0'
 remap               = 1      ! output is transferred to lat long grid
 reg_lon_def         = -180.,0.5,179.5   !start, incr., end, in deg.
 reg_lat_def         = 90.,-0.5, -90. !start, incr., end, in deg.

There is an option to obtain all sea salt variables without having to specifying all of them. Therefore, you may use the group ART_AERO_SEAS.

This changes the namelist variable ml_varlist from the example above to the following:

ml_varlist          = 'group:ART_AERO_SEAS'

The output variables that are associated to this group will be written. You can check the groups of output variables in the tables in .

Available Output Variables

The following table contains an overview of the possible output variables.

ICON-ART Output Variables
varname groups unit descripition namelist switch required xml
Aerosols
aerosol=[dust,seas,ash,soot] soot requires iart_fire>1 , seasalt requires iart_seasalt>1 , dust and ash are already included
modes=[a, b, c]
diam_[modes] ART_DIAGNOSTICS m lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
aeronet wavelength=[340, 380, 440, 500, 550, 675, 870, 1020, 1064]
aod_[aerosol]_[aeronet wavelength]nm ART_DIAGNOSTICS , ART_ROUTINE_DIAG Layer-1 [AEROSOL] optical depth lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
ceilo_wavelength = [355,532,1064]
bsc_[arosol]_[ceilo_wavelength]nm ART_DIAGNOSTICS m-1 sr-1 [AEROSOL] backscatter lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
ceil_[arosol]_[ceilo_wavelength]nm ART_DIAGNOSTICS , ART_ROUTINE_DIAG m-1 sr-1 [AEROSOL] Attenuated Backscatter Ceilometer lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
sat_[arosol]_[ceilo_wavelength]nm ART_DIAGNOSTICS m-1 sr-1 [AEROSOL] Attenuated Backscatter Satellite lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
AOD_550_so4_sol ART_DIAGNOSTICS layer-1 SO4 sol Optical Depth lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
AOD_550_ash_insol ART_DIAGNOSTICS layer-1 Ash insol Optical Depth lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
AOD_550_ash_mixed ART_DIAGNOSTICS layer-1 Ash mixed Optical Depth lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
AOD_550_ash_giant ART_DIAGNOSTICS layer-1 Ash giant Optical Depth lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
ustar_thres ART_ROUTINE_DIAG m s-1 threshold friction velocity for dust emission' lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
ustar ART_ROUTINE_DIAG m s-1 Friction velocity lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
acc_drydepo_[xml defined] ART_DIAGNOSTICS , ART_ROUTINE_DIAG tracer-unit m-2 accumulated dry deposition of tracer lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
acc_sedim_[xml defined] ART_DIAGNOSTICS , ART_ROUTINE_DIAG tracer-unit m-2 accumulated sedimentation of tracer lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
acc_wetdepo_gscp_[xml defined] ART_DIAGNOSTICS , ART_ROUTINE_DIAG tracer-unit m-2 accumulated wet deposition by grid scale precipitation of tracer lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
acc_wetdepo_con_[xml defined] ART_DIAGNOSTICS , ART_ROUTINE_DIAG tracer-unit m-2 accumulated wet deposition by convective precipitation of tracer lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
acc_wetdepo_rrsfc_[xml defined] ART_DIAGNOSTICS , ART_ROUTINE_DIAG tracer-unit m-2 accumulated wet deposition of tracer if precipitation reaches surface lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
emiss_[xml defined] ART_DIAGNOSTICS , ART_ROUTINE_DIAG tracer-unit m-2 s-1 emission of tracer lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
acc_emiss_[xml defined] ART_DIAGNOSTICS , ART_ROUTINE_DIAG tracer-unit m-2 accumulated emission of tracer lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
pollen variables from art_ext%pollen_prop%pollen_type(jt) iart_pollen>0 REQUIRES diagnostics.xml
Chemistry
reac_rates ART_DIAGNOSTICS s-1 MECCA reaction rates lart_mecca=True, lart_diag_out=True
art_o3 kg/kg Ozone mass mixing ratio lart_chem =True, lart_diag_out=True
OH_Nconc # / cm3 OH number concentration lart_chem =TRUE
photo - s-1 photolysis rates lart_chem=TRUE, lart_mecca=TRUE
art_full_chemistry_o3_col - DU Ozone column lart_chem=TRUE, lart_mecca=TRUE
sts_liqsur ART_DIAGNOSTICS cm2 cm-3 liquid area density of STS lart_chem=TRUE , lart_psc=TRUE
cgaml ART_DIAGNOSTICS - STS uptake coefficient of the reaction lart_chem=TRUE , lart_psc=TRUE
dens_ice ART_DIAGNOSTICS m-3 number density of ice particles lart_chem=TRUE , lart_psc=TRUE
radius_ice ART_DIAGNOSTICS m radius of ice particles lart_chem=TRUE , lart_psc=TRUE
radius_STS ART_DIAGNOSTICS m radius of STS particles lart_chem=TRUE , lart_psc=TRUE
dens_NAT ART_DIAGNOSTICS m-3 number density of NAT particles lart_chem=TRUE , lart_psc=TRUE
radius_NAT ART_DIAGNOSTICS m radius of NAT particles lart_chem=TRUE , lart_psc=TRUE
HNO3_Nconc_s ART_DIAGNOSTICS cm-3 number concentration of HNO3 in NAT lart_chem=TRUE , lart_psc=TRUE
HNO3_Nconc_l ART_DIAGNOSTICS cm-3 number concentration of HNO3 in STS lart_chem=TRUE , lart_psc=TRUE
ice_vmr_Marti ART_DIAGNOSTICS mol mol-1 volume mixing ratio of solid water by Marti and Mauersberger lart_chem=TRUE , lart_psc=TRUE
NAT_sedi_rel_difference ART_DIAGNOSTICS - relative difference of NAT mass bef and aft sedi (aft - bef) * 2 / (aft + bef) lart_chem=TRUE , lart_psc=TRUE
NAT_sedi_vel ART_DIAGNOSTICS m s-1 sedimentation velocity of NAT particles lart_chem=TRUE , lart_psc=TRUE
art_so2_col ART_DIAGNOSTICS DU SO2 column lat_chem=TRUE , lart_chemtracer=TRUE
Radioactive Tracers Diagnostics
wet deposition of xml defined tracer ART_DIAGNOSTICS, ART_ROUTINE_DIAG Bq m-2 wet deposition of xml defined tracer lart_aerosol=True and iart_radioact=1
dry deposition of xml defined tracer ART_DIAGNOSTICS, ART_ROUTINE_DIAG Bq m-2 dry deposition of xml defined tracer lart_aerosol=True and iart_radioact=1
Averaged air concentration of xml defined traer ART_DIAGNOSTICS, ART_ROUTINE_DIAG Bq m-3 Averaged air concentration of xml defined traer lart_aerosol=True and iart_radioact=1
FPLUME Output
plume_height ART_FPLUME m plume height iart_fplume/=0
plume_MFR ART_FPLUME kg s-1 plume MFR iart_fplume/=0
MER_transport ART_FPLUME kg s-1 Amount of very fine ash for transport iart_fplume/=0
solution_with ART_FPLUME - FPlume off, Mastin, or FPlume iart_fplume/=0