Output: Difference between revisions

From icon-art guide
Jump to navigation Jump to search
(used the pandoc -> mediawiki markdown converted text instead of pandoc -> html and added some formatting to the tables)
(Syntaxhighlighting)
 
(19 intermediate revisions by one other user not shown)
Line 1: Line 1:
__TOC__
= Output =



''Last Update: 2014/06/24 Daniel Rieger''
== General Remarks ==


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:
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:
Line 11: Line 12:
* The type of horizontal 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:
For the best results it is recommended to use NETCDF output on the icosahedral grid which ICON-ART is using. However in some applications remapping the grid to a latitude-longitude grid may be required, which can be set via the <code>remap</code> option. A corresponding output namelist for sea salt on model levels can be seen here:


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



<pre>ml_varlist = 'group:ART_AERO_SEAS'</pre>
There is an option to obtain all diagnostic Variables of a certain Group without having to specifying all of them. For example, you may use the group ART_DIAGNOSTICS.
The output variables that are associated to this group will be written. You can check the groups of output variables in the tables in .

To include a group of Variables in the output file change the namelist variable ml_varlist from the example above to the following:

<pre>ml_varlist = 'group:ART_AEROSOL'</pre>
The output variables that are associated to this group will be written to the output file. You can check the groups of output variables in this [[#OutputTable | Table]] .

== Aerosol Naming Conventions ==
The following table contains an overview of the possible output variables.

There are several ways to choose the Naming of the output variables, depending on your application

* '''Externally mixed Aerosols:''' : The Tracers for Dust, Seasalt, Ash and Soot are combined with the three Possible modes a, b and c, which correspond to the different size bins of the particles <div id="OutputTable"></div>

::{| class="wikitable" style="text-align:left;"
|+ Externally mixed Tracer modes
!|| dust||seasalt ||ash ||soot
|-
!a
| dusta ||seasa ||asha ||soota
|-
!b
| dustb ||seasb ||ashb ||-
|-
!c
| dustc||seasc ||ashc ||-
|-
|}



* '''Internally mixed Aerosols ([[AERODYN]]):''' Here a tracer is defined in a different way, with the goal being to have a more flexible framework for various applications. In this framework modes are created in a different way, as illustrated int the table below:

<div id="OutputTable"></div>
::{| class="wikitable" style="text-align:left;"
|+ AERODYN mode configurations
! || aitken || accumulation || coarse || giant
|-
! soluble
| sol_aitken || sol_acc || sol_coarse || sol_giant
|-
! insoluble
|insol_aitken || insol_acc || insol_coarse || insol_giant
|-
! mixed
| mixed_aitken ||mixed_acc || mixed_coarse || mixed_giant
|-
|}

The modes are then combined with The Tracername to obtain the name of the Variable using <code>varname = 'Tracer' + '_' + 'mode from Table'</code>.
Example : <code> dust_insol_acc </code>

* '''Monodisperse Aerosols'''


== Available Output Variables ==
== Available Output Variables ==
The following Table contains an overview over the diagnostic Icon-ART Variables. Expressions in Brackets are Placeholders which can be used to construct the name of the actual variables:


[aeronet wavelength] => [340, 380, 440, 500, 550, 675, 870, 1020, 1064]
''Last Update: 2015/03/13 Daniel Rieger''


[ceilo_wavelength] => [355,532,1064]
The possible prognostic output fields are shown in , the diagnostic fields in and .


[pollen] => [ALNU,BETU,...] to be defined in diagnostics.xml
<div id="tab:output_prog">



{| class="wikitable" style="margin:auto"

|+ Available prognostic output fields.

{| class="wikitable"
|+ Output Overview
|-
!
!
! varname
!
! groups
! '''Description'''
! unit
! '''Groups'''
! descripition
! namelist switch
! required xml
|-
|-
!rowspan="19" style="vertical-align:top;" | Aerosols
| seasa
| diam_[mode]
| iart_seasalt = 1
| ART_DIAGNOSTICS
| Sea salt mode A mass concentration
| m
| ART_AERO _SEAS
| with AERODYN : aerosol diameter
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| diam_[aerosol][mode]
| seasb
| ART_DIAGNOSTICS
| iart_seasalt = 1
| m
| Sea salt mode B mass concentration
| WITHOUT AERODYN: aerosol diameter
| ART_AERO _SEAS
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| aod_[aerosol]_[aeronet wavelength]nm
| seasc
| ART_DIAGNOSTICS , ART_ROUTINE_DIAG
| iart_seasalt = 1
| Layer-1
| Sea salt mode C mass concentration
| [AEROSOL] optical depth
| ART_AERO _SEAS
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| bsc_[arosol]_[ceilo_wavelength]nm
| seasa0
| ART_DIAGNOSTICS
| iart_seasalt = 1
| m-1 sr-1
| Sea salt mode A number concentration
| [AEROSOL] backscatter
| ART_AERO _SEAS
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| ceil_[arosol]_[ceilo_wavelength]nm
| seasb0
| ART_DIAGNOSTICS , ART_ROUTINE_DIAG
| iart_seasalt = 1
| m-1 sr-1
| Sea salt mode B number concentration
| [AEROSOL] Attenuated Backscatter Ceilometer
| ART_AERO _SEAS
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| sat_[arosol]_[ceilo_wavelength]nm
| seasc0
| ART_DIAGNOSTICS
| iart_seasalt = 1
| m-1 sr-1
| Sea salt mode C number concentration
| [AEROSOL] Attenuated Backscatter Satellite
| ART_AERO _SEAS
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| AOD_550_so4_sol
| dusta
| ART_DIAGNOSTICS
| iart_dust = 1,2
| layer-1
| Mineral dust mode A mass concentration
| SO4 sol Optical Depth
| ART_AERO _DUST
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| AOD_550_ash_insol
| dustb
| ART_DIAGNOSTICS
| iart_dust = 1,2
| layer-1
| Mineral dust mode B mass concentration
| Ash insol Optical Depth
| ART_AERO _DUST
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| AOD_550_ash_mixed
| dustc
| ART_DIAGNOSTICS
| iart_dust = 1,2
| layer-1
| Mineral dust mode C mass concentration
| Ash mixed Optical Depth
| ART_AERO _DUST
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| AOD_550_ash_giant
| dusta0
| ART_DIAGNOSTICS
| iart_dust = 1,2
| layer-1
| Mineral dust mode A number concentration
| Ash giant Optical Depth
| ART_AERO _DUST
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| ustar_thres
| dustb0
| ART_ROUTINE_DIAG
| iart_dust = 1,2
| m s-1
| Mineral dust mode B number concentration
| threshold friction velocity for dust emission'
| ART_AERO _DUST
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| dustc0
| ustar
| ART_ROUTINE_DIAG
| iart_dust = 1,2
| m s-1
| Mineral dust mode C number concentration
| Friction velocity
| ART_AERO _DUST
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| acc_drydepo_[tracer]
| asha
| ART_DIAGNOSTICS , ART_ROUTINE_DIAG
| iart_volcano = 2
| tracer-unit m-2
| Mineral dust mode A mass concentration
| accumulated dry deposition of tracer
| ART_AERO _VOLC
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| acc_sedim_[tracer]
| ashb
| ART_DIAGNOSTICS , ART_ROUTINE_DIAG
| iart_volcano = 2
| tracer-unit m-2
| Mineral dust mode B mass concentration
| accumulated sedimentation of tracer
| ART_AERO _VOLC
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| acc_wetdepo_gscp_[tracer]
| ashc
| ART_DIAGNOSTICS , ART_ROUTINE_DIAG
| iart_volcano = 2
| tracer-unit m-2
| Mineral dust mode C mass concentration
| accumulated wet deposition by grid scale precipitation of tracer
| ART_AERO _VOLC
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| acc_wetdepo_con_[tracer]
| asha0
| ART_DIAGNOSTICS , ART_ROUTINE_DIAG
| iart_volcano = 2
| tracer-unit m-2
| Mineral dust mode A number concentration
| accumulated wet deposition by convective precipitation of tracer
| ART_AERO _VOLC
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| acc_wetdepo_rrsfc_[tracer]
| ashb0
| ART_DIAGNOSTICS , ART_ROUTINE_DIAG
| iart_volcano = 2
| tracer-unit m-2
| Mineral dust mode B number concentration
| accumulated wet deposition of tracer if precipitation reaches surface
| ART_AERO _VOLC
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| emiss_[tracer]
| ashc0
| ART_DIAGNOSTICS , ART_ROUTINE_DIAG
| iart_volcano = 2
| tracer-unit m-2 s-1
| Mineral dust mode C number concentration
| emission of tracer
| ART_AERO _VOLC
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
| acc_emiss_[tracer]
| CS137
| ART_DIAGNOSTICS , ART_ROUTINE_DIAG
| iart_radioact = 1
| Radioactive tracer:Caesium 137
| tracer-unit m-2
| accumulated emission of tracer
| ''future release''
| lart_aerosol=True and lart_diag_out=True
| requires cart_diagnostics_xml file
|-
|-
!rowspan="9" style="vertical-align:top;"| Pollen
| I131
| [pollen]rprec
| iart_radioact = 1
| ART_ROUTINE_DIAG
| Radioactive tracer:Iodine 131
| m-2
| ''future release''
| precipitation reservoir of [pollen]
| iart_pollen&gt;0
| REQUIRES diagnostics.xml
|-
|-
| [pollen]reso
| TE132
| ART_ROUTINE_DIAG
| iart_radioact = 1
| m-2
| Radioactive tracer:Tellurium 132
| Pollen reservoir (previous timestep) of [pollen]
| ''future release''
| iart_pollen&gt;0
| REQUIRES diagnostics.xml
|-
|-
| [pollen]ress
| ZR95
| ART_ROUTINE_DIAG
| iart_radioact = 1
| m-2
| Radioactive tracer:Zirconium 95
| Pollen reservoir (daily sum) of [pollen]
| ''future release''
| iart_pollen&gt;0
| REQUIRES diagnostics.xml
|-
|-
| [pollen]sdes
| XE133
| ART_ROUTINE_DIAG
| iart_radioact = 1
| -
| Radioactive tracer:Xenon 133
| State of pollen season of [pollen]
| ''future release''
| iart_pollen&gt;0
| REQUIRES diagnostics.xml
|-
|-
| [pollen]ctsum
| I131g
| ART_ROUTINE_DIAG
| iart_radioact = 1
| K
| Radioactive tracer:Iodine (gaseous) 131
| Cumulated weighted 2m temperature sum of [pollen]
| ''future release''
| iart_pollen&gt;0
| REQUIRES diagnostics.xml
|-
|-
| [pollen]saisn
| I131o
| ART_ROUTINE_DIAG
| iart_radioact = 1
| days
| Radioactive tracer:Iodine 131
| Number of days since start of pollen season of [pollen]
| ''future release''
| iart_pollen&gt;0
| REQUIRES diagnostics.xml
|-
|-
| [pollen]saisl
| BA140
| ART_ROUTINE_DIAG
| iart_radioact = 1
| days
| Radioactive tracer:Barium 140
| length of pollen season of [pollen]
| ''future release''
| iart_pollen&gt;0
| REQUIRES diagnostics.xml
|-
|-
| [pollen]saisa
| RU103
| ART_ROUTINE_DIAG
| iart_radioact = 1
| days
| Radioactive tracer:Ruthenium 103
| Number of days since the start of pollen season of [pollen]. if present day is out of the season: length of current season
| ''future release''
| REQUIRES diagnostics.xml
|
|-
|-
| [pollen]fe
| ash1
| ART_ROUTINE_DIAG
| iart_volcano = 1
| m-2 s-1
| Volcanic ash size bin 1
| Emission flux of [pollen]
| ''future release''
| iart_pollen&gt;0
| REQUIRES diagnostics.xml
|-
|-
!rowspan="18" style="vertical-align:top;" | Chemistry
| ash2
| reac_rates
| iart_volcano = 1
| ART_DIAGNOSTICS
| Volcanic ash size bin 2
| s-1
| ''future release''
| MECCA reaction rates
| lart_mecca=True, lart_diag_out=True
|
|-
|-
| ash3
| art_o3
| kg/kg
| iart_volcano = 1
| Ozone mass mixing ratio
| Volcanic ash size bin 3
| lart_chem =True, lart_diag_out=True
| ''future release''
|
|
|-
|-
| OH_Nconc
| ash4
| # / cm3
| iart_volcano = 1
| OH number concentration
| Volcanic ash size bin 4
| lart_chem =TRUE
| ''future release''
|
|
|-
|-
| ash5
| photo
| -
| iart_volcano = 1
| s-1
| Volcanic ash size bin 5
| photolysis rates
| ''future release''
| lart_chem=TRUE, lart_mecca=TRUE
|
|-
|-
| art_full_chemistry_o3_col
| ash6
| -
| iart_volcano = 1
| DU
| Volcanic ash size bin 6
| Ozone column
| ''future release''
| lart_chem=TRUE, lart_mecca=TRUE
|
|-
|-
| sts_liqsur
| TRCHBr3
| ART_DIAGNOSTICS
| iart_chem_mechanism = 0
| cm2 cm-3
| Stratospheric tracer:CHBr3
| liquid area density of STS
| ''future release''
| lart_chem=TRUE , lart_psc=TRUE
|
|-
|-
| cgaml
| TRCH2Br2
| ART_DIAGNOSTICS
| iart_chem_mechanism = 0
| -
| Stratospheric tracer:CH2Br2
| STS uptake coefficient of the reaction
| ''future release''
| lart_chem=TRUE , lart_psc=TRUE
|}
|


</div>
<div id="tab:output_diag_aero">

{| class="wikitable" style="margin:auto"
|+ Available diagnostic output fields for aerosol.
!
!
! '''Description'''
! '''Groups'''
|-
|-
| dens_ice
| seasa_diam
| ART_DIAGNOSTICS
| iart_seasalt = 1 lart_diag_out = .true.
| m-3
| Median diameter of sea salt mode A
| number density of ice particles
| ART_AERO _SEAS
| lart_chem=TRUE , lart_psc=TRUE
|
|-
|-
| radius_ice
| seasb_diam
| ART_DIAGNOSTICS
| iart_seasalt = 1 lart_diag_out = .true.
| m
| Median diameter of sea salt mode B
| radius of ice particles
| ART_AERO _SEAS
| lart_chem=TRUE , lart_psc=TRUE
|
|-
|-
| radius_STS
| seasc_diam
| ART_DIAGNOSTICS
| iart_seasalt = 1 lart_diag_out = .true.
| m
| Median diameter of sea salt mode C
| radius of STS particles
| ART_AERO _SEAS
| lart_chem=TRUE , lart_psc=TRUE
|
|-
|-
| dens_NAT
| dusta_diam
| ART_DIAGNOSTICS
| iart_dust = 1,2 lart_diag_out = .true.
| m-3
| Median diameter of mineral dust mode A
| number density of NAT particles
| ART_AERO _DUST
| lart_chem=TRUE , lart_psc=TRUE
|
|-
|-
| radius_NAT
| dustb_diam
| ART_DIAGNOSTICS
| iart_dust = 1,2 lart_diag_out = .true.
| m
| Median diameter of mineral dust mode B
| radius of NAT particles
| ART_AERO _DUST
| lart_chem=TRUE , lart_psc=TRUE
|
|-
|-
| HNO3_Nconc_s
| dustc_diam
| ART_DIAGNOSTICS
| iart_dust = 1,2 lart_diag_out = .true.
| cm-3
| Median diameter of mineral dust mode C
| number concentration of HNO3 in NAT
| ART_AERO _DUST
| lart_chem=TRUE , lart_psc=TRUE
|
|-
|-
| HNO3_Nconc_l
| tau_seas_550nm
| ART_DIAGNOSTICS
| iart_seasalt = 1 lart_diag_out = .true.
| cm-3
| Sea salt aerosol optical depth (AOD) at <math display="inline">550\,\mathrm{nm}</math>.
| number concentration of HNO3 in STS
| ART_AERO _SEAS
| lart_chem=TRUE , lart_psc=TRUE
|
|-
|-
| ice_vmr_Marti
| tau_dust_550nm
| ART_DIAGNOSTICS
| iart_dust = 1,2 lart_diag_out = .true.
| mol mol-1
| Mineral dust aerosol optical depth (AOD) at <math display="inline">550\,\mathrm{nm}</math>.
| volume mixing ratio of solid water by Marti and Mauersberger
| ART_AERO _DUST
| lart_chem=TRUE , lart_psc=TRUE
|}
|


</div>
<div id="tab:output_diag_aci">

{| class="wikitable" style="margin:auto"|+ Available diagnostic output fields for aerosol-cloud-interactions.
!
!
! '''Description'''
! '''Groups'''
|-
|-
| NAT_sedi_rel_difference
| ncalls_warm
| ART_DIAGNOSTICS
| iart_aci_warm = 1 lart_diag_out = .true.
| -
| Number of calls of activation routine (accumulated)
| relative difference of NAT mass bef and aft sedi (aft - bef) * 2 / (aft + bef)
| ''future release''
| lart_chem=TRUE , lart_psc=TRUE
|
|-
|-
| NAT_sedi_vel
| aci_nnuctot_warm
| ART_DIAGNOSTICS
| iart_aci_warm = 1 lart_diag_out = .true.
| m s-1
| Number of activated particles (accumulated, warm-phase)
| sedimentation velocity of NAT particles
| ''future release''
| lart_chem=TRUE , lart_psc=TRUE
|
|-
|-
| art_so2_col
| aci_nnucfhh_warm
| ART_DIAGNOSTICS
| iart_aci_warm = 1 lart_diag_out = .true.
| DU
| Number of activated particles according to FHH theory (accumulated, warm-phase)
| SO2 column
| ''future release''
| lat_chem=TRUE , lart_chemtracer=TRUE
|
|-
|-
!rowspan="3" style="vertical-align:top;"| Radioactive Tracer Diagnostics
| smax_water
| wet deposition of xml defined tracer
| iart_aci_warm = 1 lart_diag_out = .true.
| ART_DIAGNOSTICS, ART_ROUTINE_DIAG
| Maximum supersaturation over liquid water
| Bq m-2
| ''future release''
| wet deposition of xml defined tracer
| lart_aerosol=True and iart_radioact=1
|
|-
|-
| dry deposition of xml defined tracer
| ncalls_cold
| ART_DIAGNOSTICS, ART_ROUTINE_DIAG
| iart_aci_cold = 1,2,3,4,5,6 lart_diag_out = .true.
| Bq m-2
| Number of calls of ice nucleation routine (accumulated)
| dry deposition of xml defined tracer
| ''future release''
| lart_aerosol=True and iart_radioact=1
|
|-
|-
| Averaged air concentration of xml defined traer
| aci_nnuctot_cold
| ART_DIAGNOSTICS, ART_ROUTINE_DIAG
| iart_aci_cold = 1,2,3,4,5,6 lart_diag_out = .true.
| Bq m-3
| Number of total nucleated (homogeneous freezing + heterogeneous nucleation) particles (accumulated, cold-phase)
| Averaged air concentration of xml defined traer
| ''future release''
| lart_aerosol=True and iart_radioact=1
|
|-
|-
!rowspan="4" style="vertical-align:top;"| FPLUME Output
| aci_nnuchet_cold
| plume_height
| iart_aci_cold = 1,2,3,4,5,6 lart_diag_out = .true.
| ART_FPLUME
| Number of heterogeneously nucleated particles (accumulated, cold-phase)
| m
| ''future release''
| plume height
| iart_fplume/=0
|
|-
|-
| plume_MFR
| smax_ice
| ART_FPLUME
| iart_aci_cold = 1,2,3,4,5,6 lart_diag_out = .true.
| kg s-1
| Maximum supersaturation over ice
| plume MFR
| ''future release''
| iart_fplume/=0
|}
|


</div>
== Output Checks with SAMOA ==

''Last Update: 2015/01/13 Daniel Rieger''

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="margin:auto"
|+ Helpful Python Packages and their primary usage for Visualisation
|align="center"| numpy
|align="center"| predefined Mathematical functions
|-
|-
| MER_transport
|align="center"| matplotlib
| ART_FPLUME
|align="center"| Plotting framework
| kg s-1
| Amount of very fine ash for transport
| iart_fplume/=0
|
|-
|-
| solution_with
|align="center"| xarray
| ART_FPLUME
|align="center"| reading in and processing netcdf datasets
|-
| -
| FPlume off, Mastin, or FPlume
|align="center"| ...
| iart_fplume/=0
|align="center"|
|
|}
|}


</div>
<span id="tab:pythonpackages" label="tab:pythonpackages">[tab:pythonpackages]</span>

Latest revision as of 09:15, 7 September 2023


General Remarks

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.

For the best results it is recommended to use NETCDF output on the icosahedral grid which ICON-ART is using. However in some applications remapping the grid to a latitude-longitude grid may be required, which can be set via the remap option. A corresponding output namelist for sea salt on model levels can be seen here: 

NAMELIST EXAMPLE
&amp;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'  ! see 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 diagnostic Variables of a certain Group without having to specifying all of them. For example, you may use the group ART_DIAGNOSTICS.

To include a group of Variables in the output file change the namelist variable ml_varlist from the example above to the following: 

ml_varlist          = 'group:ART_AEROSOL'

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

Aerosol Naming Conventions

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

There are several ways to choose the Naming of the output variables, depending on your application

  • Externally mixed Aerosols: : The Tracers for Dust, Seasalt, Ash and Soot are combined with the three Possible modes a, b and c, which correspond to the different size bins of the particles
Externally mixed Tracer modes
dust seasalt ash soot
a dusta seasa asha soota
b dustb seasb ashb -
c dustc seasc ashc -


  • Internally mixed Aerosols (AERODYN): Here a tracer is defined in a different way, with the goal being to have a more flexible framework for various applications. In this framework modes are created in a different way, as illustrated int the table below:
AERODYN mode configurations
aitken accumulation coarse giant
soluble sol_aitken sol_acc sol_coarse sol_giant
insoluble insol_aitken insol_acc insol_coarse insol_giant
mixed mixed_aitken mixed_acc mixed_coarse mixed_giant

The modes are then combined with The Tracername to obtain the name of the Variable using varname = 'Tracer' + '_' + 'mode from Table'. Example : dust_insol_acc

  • Monodisperse Aerosols

Available Output Variables

The following Table contains an overview over the diagnostic Icon-ART Variables. Expressions in Brackets are Placeholders which can be used to construct the name of the actual variables:

[aeronet wavelength] => [340, 380, 440, 500, 550, 675, 870, 1020, 1064]

[ceilo_wavelength] => [355,532,1064]

[pollen] => [ALNU,BETU,...] to be defined in diagnostics.xml



Output Overview
varname groups unit descripition namelist switch required xml
Aerosols diam_[mode] ART_DIAGNOSTICS m with AERODYN : aerosol diameter lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
diam_[aerosol][mode] ART_DIAGNOSTICS m WITHOUT AERODYN: aerosol diameter lart_aerosol=True and lart_diag_out=True requires cart_diagnostics_xml file
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
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_[tracer] 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_[tracer] 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_[tracer] 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_[tracer] 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_[tracer] 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_[tracer] 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_[tracer] 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 [pollen]rprec ART_ROUTINE_DIAG m-2 precipitation reservoir of [pollen] iart_pollen>0 REQUIRES diagnostics.xml
[pollen]reso ART_ROUTINE_DIAG m-2 Pollen reservoir (previous timestep) of [pollen] iart_pollen>0 REQUIRES diagnostics.xml
[pollen]ress ART_ROUTINE_DIAG m-2 Pollen reservoir (daily sum) of [pollen] iart_pollen>0 REQUIRES diagnostics.xml
[pollen]sdes ART_ROUTINE_DIAG - State of pollen season of [pollen] iart_pollen>0 REQUIRES diagnostics.xml
[pollen]ctsum ART_ROUTINE_DIAG K Cumulated weighted 2m temperature sum of [pollen] iart_pollen>0 REQUIRES diagnostics.xml
[pollen]saisn ART_ROUTINE_DIAG days Number of days since start of pollen season of [pollen] iart_pollen>0 REQUIRES diagnostics.xml
[pollen]saisl ART_ROUTINE_DIAG days length of pollen season of [pollen] iart_pollen>0 REQUIRES diagnostics.xml
[pollen]saisa ART_ROUTINE_DIAG days Number of days since the start of pollen season of [pollen]. if present day is out of the season: length of current season REQUIRES diagnostics.xml
[pollen]fe ART_ROUTINE_DIAG m-2 s-1 Emission flux of [pollen] 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 Tracer 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
Retrieved from "https://www.icon-art.kit.edu/userguide/index.php?title=Output&oldid=301"