Output

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

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:

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

path_list=$SCRIPTPATH/list 

Change the name of the list to:

path_list=$SCRIPTPATH/samoa_list_icon-art 

Now you may use SAMOA with the ICON-ART output file out.nc with the following command:

./samoa.sh out.nc

For all options see:

./samoa.sh --help

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

"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." (http://meteora.ucsd.edu/~pierce/ncview_home_page.html)

NCL

"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." (https://www.ncl.ucar.edu/)

ParaView

"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." (http://www.paraview.org/)

Python

On the official Website Python describes itself as

Python is powerful... and fast;
plays well with others;
runs everywhere;
is friendly & easy to learn;
is Open.

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 1.4

Helpful Python Packages and their primary usage for Visualisation

numpy	predefined Mathematical functions
matplotlib	Plotting framework
xarray	reading in and processing netcdf datasets
...