Input

Requirements for a Simulation

To run a Simulation with ICON-ART there are three main points to consider: Setting the namelist parameters, preparing the xmls, and optionally prepare additional Input data.

Namelist Inputs

To run a simulation with ICON-ART installed the first thing to prepare is the runfile. It is usually best to start with an existing and working runfile and adapt parts as needed. The runfile contains the majority of parameters to run a simulation, like the length, timesteps and grids used, as well as a variety of options for methods and parametrisations used in the model. The runfile contents are then split up in several namelists that the model reads at the beginning of a simulation. An overview of the Namelist Parameters can be found in Namelist.

To enable ART in an ICON simulation, the switch lart = .TRUE. has to be set in the section &run_nml. This is the global on/off switch for ICON-ART. This is how this could look like in the context of a runfile:

! run_nml: general switches ----------
&run_nml
 ltestcase = .FALSE.
 num_lev = 50
 ltransport = .TRUE.
.............
 lart = .TRUE.

Generally the first letters of a namelist switch refer to its type, the "l" in "lart" stands for logical, meaning it has to be either True or False. Here are some examples.

Some namelist switches and their data types.

namelist switch	type
lart	logical
cart_aerosol_xml	character
iart_init_aero	integer

The namelist &art_nml is used for general options of the ART simulation. To run a certain kind of simulation the according switch has to be set to .TRUE.. For Example to include a point source the switch cart_aerosol_xml has to be set to .TRUE..

XML Inputs

This enables the inclusion of a .xml file containing additional information like location and strength of the point source. The table below contains the most important &art_nml namelist parameters and additional namelist parameters required if they are set to .TRUE..

XML files and their namelist dependencies

XML File	Description	Namelist parameter dependency	Default	Further Information
cart_chemtracer_xml	Switch for simple OH chemistry	lart_chemtracer	.FALSE.	Chemistry Tracers
cart_mecca_xml	Switch for kpp chemistry	lart_mecca	.FALSE.	Atmospheric Chemistry
cart_pntSrc_xml	Enables creation of point sources emitting given Aerosols at a given rate	lart_pntSrc	.FALSE.	Point Source
cart_aerosol_xml	Main switch for the treatment of atmospheric aerosols	lart_aerosol	.FALSE.	Aerosol Tracers
cart_modes_xml	Main switch for the treatment of atmospheric aerosols	lart_aerosol	.FALSE.	Aerosol Modes
cart_diagnostics_xml	Enables diagnostic output fields	lart_diag_out	.FALSE.	-
cart_emiss_xml_file	XML File for emission metadata	-	-	Aerosol Emission
cart_ext_data_xml	XML File for metadata of datasets prescribing tracers	-	-	-
cart_coag_xml	XML File containing additional information about coagulation	-	-	-

Aerosol Tracers

tag	type	options	description
htop_proc	real	in m	top height for processes
initc	character	file	initialize from Input file
inucl	integer	0 (off), 1 (on)	H2SO4 nucleation for so4 tracer (default=1); 1 for so4_sol_ait, 0 for other so4 tracer)
label	character	e.g., dusta	allows to name tracers individually
latbc	character	file	read data for LBC
lfeedback	integer	0 (off), 1 (on)	child -> parent feedback in nested simulations (default=0)
mode	character	insol_acc, mixed_acc,..	indicates in which modes the tracer occurs
mol_weight	real	in kg/mol	value for molar weight
moment	integer	0, 3	zeroth (number) or third (mass) moment
rho	real	in g/m3	density of tracer, not needed for zeroth moment
sol	integer	0 (no), 1 (yes)	indicates whether the tracer is soluble or not
transport	character	stdaero, stdchem, ..., off	choice of transport template
unit	character	e.g., mug kg-1, kg-1	unit of tracer
bold letters indicate which tags are always required.

Aerosol Modes

tag	type	options	description
condensation	integer	0 (off), 1 (on)	condensation of H2SO4 on this mode?
d_gn	real	in m	value for the initial median diameter of the number distribution
dissfac_mean	real		dissociation factor (needed with ikoehler=1)
icoag	integer	0 (off), 1 (on)	mode involved in coagulation? If 1 for any mode, then provide coagulate.xml
ikoehler	integer	0 (off), 1 (on)	Activation via Köhler theory (warm clouds), needs dissfac_mean tag
kind	character	1mom or 2mom	1-moment or 2-moment description of distribution
sigma_g	real		standard deviation of the distribution
shift2larger	character	e.g., sol_acc	Name of larger mode to be shifted to, when diameter threshold (shift_diam) exceeded
shift2mixed	character	e.g., mixed_acc	Name of mixed mode to be shifted to, when soluble mass threshold of 5% exceeded
shift_diam	real	in m	diameter threshold for shift2larger

Aerosol Emission

tag	type	options	description
nmodes	integer		number of emission modes
d_g0_*	real		median diameter of number distribution of mode * (e.g., d_g0_1, d_g0_2, d_g0_3)
d_g3_*	real		median diameter of mass distribution of mode * (e.g., d_g3_1, d_g3_2, d_g3_3)
rho	real	in kg/m3	particle density (same for all modes)
sigma_g_*	real		standard deviation of mode *
substance	character	ash, dust, na, cl, soot	emitted substance
bold letters indicate which tags are always required. routine options: volc, volc fplume, dust, biomass burn, seas smith, seas monahan, seas martensson, seas mode1, seas mode2, seas mode3

Point Source

tag	type	options	description
dg3_emiss	real	in m	median diameter of aerosol mass distribution
emiss_profile	character		anti-derivative of emission profile
endTime	character		end time of emission (default=9999-12-31T00:00:00)
height	real	in m	emission height
height_bot	real	in m	bottom height
lat	real	in degree	latitude
lon	real	in degree	longitude
sigma_emiss	real		standard deviation of aerosol distribution
startTime	character		start time of emission (default=1582-10-15T00:00:00)
source_strength	real		emission source strength
substance	character	e.g., TRSO2	substance nme from tracer xml
unit	character	e.g., kg s-1	unit of source strength
bold letters indicate which tags are always required.

Chemistry Tracers

tag	type	options	description
c_solve	character	param, lt, cold, OH, linoz, simnoy, passive	solving mechanism/strategy
emissions		anthropogenic, biogenic, biomassBurning	usage see in tracers_chemtracer_amip.xml (*)
htop_proc	real	in m	top height for processes
iconv	integer	0 (off), 1 (on)	transport by convection (default=1)
initc	character	file	initialize from Input file
init_mode	integer	0 (off), 1 (on)	initialize tracer
init_name	character		name of tracer in initialization file
iturb	integer	0 (off), 1 (on)	transport by turbulence (default=1)
latbc	character	file	read data for LBC
lfeedback	integer	0 (off), 1 (on)	child -> parent feedback in nested simulations (default=0)
lifetime	real	in s	value for lifetime
mol_weight	real	in kg/mol	value for molar weight
products	character	name of tracer	name of resulting tracer after depletion
tag001,...	character		name of tag to be added to tracer name
transport	character	stdaero, stdchem, ..., off	choice of transport template
unit	character	e.g., mol mol-1	unit of tracer
bold letters indicate which tags are always required. <br\> (*) in icon-kit/externals/art/runctrl_examples/xml_ctrl/

The reason for the use of those additional .xml files is that the ART variables they contain (sea salt, mineral dust etc.) might be different for every run which differs from the Icon Variables (Temperature, Pressure, etc.) which usually don’t change between runs. .xml files are readable for both humans and machines, which makes them easy to tweak and integrate. An Example for the contents of an .xml file adding ash particles can be seen below.

<modes>
  <aerosol id="asha">
    <kind type="char">2mom</kind>
    <d_gn type="real">1.190E-6</d_gn>
    <sigma_g type="real">1.410E+0</sigma_g>
    <rho type="real">2.600E+3</rho>
  </aerosol>
</modes>

Here is an example for a more complex .xml using AERODYN: This is an example for the number and mass concentration of dust in a tracer .xml.

<tracers>  
    <aerosol id="nmb">    
      <moment type="int">0</moment>    
      <mode type="char">insol_acc,insol_coa</mode>    
      <unit type="char">kg-1</unit>    
      <transport type="char">hadv52aero</transport>  
    </aerosol>  
    <aerosol id="dust">    
      <moment type="int">3</moment>    
      <mode type="char">insol_acc,insol_coa</mode>    
      <sol type="real">1.0</sol>    
      <mol_weight type="real">50.00E-3</mol_weight>    
      <rho type="real">2.650E3</rho>    
      <unit type="char">mug kg-1</unit>    
      <transport type="char">hadv52aero</transport>  
    </aerosol>
</tracers>

Further .xml examples can be fount in /your_ART_Directory/runctrl_examples/xml_ctrl.

Input Data

Depending on the type of simulation there might be additional input files required. These are essential files that are not contained in classical ICON initialisation data. For example for the emission of mineral dust there has to be information about the soil types supplied to the model. The additional input files should be renamed to a netcdf file and follow the naming convention shown in fig 1.1. Please note that the XXX has to be replaced by one of the indices mentionend in Table input-init and input-emissions.

Additional input files for the initialisation

Species	Namelist switch	Options	XXX
Gas	iart_init_gas	0 (cold start), 5 (from file)	ICE
Aerosol	iart_init_aero	0 (cold start), 5 (from file)	IAE

Obtaining Input Data

The 2 ways of obtaining input data are to generate it yourself or download it.

How to generate input data

How to download input data

Emission Data

In every ICON-ART, there is the possibility to add additional input data like emission data that correspond with different sources. A quick overview about them can be found below.

Additional input files for the emissions

Type	Data	XXX
Point souces	XML-file	-
Sea salt	no extra data necessary	-
Mineral Dust	Soil Type Data	ART_STY
Biogenic VOCs	Emissions or Vegetatiom	ART_STY
Athropogenic emissions	Emission data sets	ART_BIO ART_ANT
Biomass burning	Satellite data	ART_BCF

Chemical Tracer

Emission data can be obtained from several sources. The following table should give an overview about which emission data are available for a corresponding tracer. To find out when to use which emission data type we recommend respective further reading.

Emission Data Sources

Tracer	Emission Type	Emission	Resolution
C2H6	ANT	EDGA	R2B04_ECHAM
		EDGAR+	R2B05_0014
		EDGAR-monthly	R2B05_0014
			R2B06_0024
			B2B06_EU_nest
			R2B07_nest
			R2B07_NSR_D_nest
			R3B07_0026
		MACCity	R2B04_0012
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R2B07_polstrNest
			R3B07_0022
	BBE	GFED	R2B04_ECHAM
		GFED3	R2B06_0024
			R2B06_EU_nest
			R2B07_nest
			R2B07_NSR_D_nest
	BIO	MEGA	R2B04_ECHAM
		MEGAN-MACC	R2B04_0012
			R2B05_0014
			R2B06_0016
			R2B06_0024
			R2B06_EU_nest
			R2B07_nest
			R2B07_NSR_D_nest
			R2B07_0018
			R2B07_polstrNest
			R3B07_0022
C3H8	ANT	EDGA	R2B04_ECHAM
		EDGAR+	R2B05_0014
		EDGAR432-monthly	R2B05_0014
			R2B06_0024
			B2B06_EU_nest
			R2B07_nest
			R2B07_NSR_D_nest
			R3B07_0026
		MACCity	R2B04_0012
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
	BBE	GFED	R2B04_ECHAM
		GFED3	R2B06_0024
			R2B06_EU_nest
			R2B07_nest
			R2B07_NSR_D_nest
	BIO	MEGA	R2B04_ECHAM
		MEGAN-MACC	R2B04_0012
			R2B05_0014
			R2B06_0016
			R2B06_0024
			R2B07_nest
			R2B07_0018
			R3B07_0022
C5H8	BBE	MACCity	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
	BIO	MEGAN-MACC	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
CFCl3	ANT	GEIA	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
CH3CN	BBE	GFED.1s_Akagi_daily	R2B04_0012
			R2B04_ECHAM
		GFED.1s_Akagi_monthly	R2B04_0012
			R2B04_ECHAM
		GFED.1s_Stockwell_daily	R2B04_0012
			R2B04_ECHAM
		GFED.1s_Stockwell_monthly	R2B04_0012
			R2B04_ECHAM
		MACCity	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
CH3COCH3	ANT	MACCity	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
			R3B07_0026
		POET	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
	BBE	GFED3	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		GICC	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		GUESS-ES	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		POET	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		RETRO	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
	BIO	MEGAN-MACC	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		MEGANv2	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
CH3I	BIO	Bell	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		Ziska	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
CH4	ANT	EDGA	R2B04_ECHAM
		EDGAR+	R2B05_0014
		EDGAR432-monthly	R2B05_0014
			R2B06_0024
			B2B06_EU_nest
			R2B07_nest
			R2B07_NSR_D_nest
			R3B07_0026
			R3B08_0049
		EDGARv4.2	R2B04_0012
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R2B07_polstrNest
			R3B07_0022
		EDGARv4.3.1	R2B04_0012
			R2B05_0014
CHBr3	BIO	Liang	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		Ordonez	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		Ziska	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
CO	ANT	EDGAR	R2B04_ECHAM
		EDGAR+	R2B05_0014
		EDGAR432-monthly	R2B05_0014
			R2B06_0024
			B2B06_EU_nest
			R2B07_nest
			R2B07_NSR_D_nest
			R3B07_0026
		EDGARv4.2	R2B04_0012
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R2B07_polstrNest
			R3B07_0022
		MACCity	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		POET	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
	BBE	GFED3	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		GICC	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		GUESS-ES	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		RETRO	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
	BIO	MEGAN	R2B04_ECHAM
		MEGAN-MACC	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		MEGANv2	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
CO2	ANT	EDGARv4.2	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B06_0024
			R2B06_0031_nest
			R2B07_0018
			R2B07_nest
			R3B07_0022
			B3B07_0026
	BBE	GFED3	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
DMS	BBE	GFED3	R2B04_0012
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		MACCity	R2B04_0012
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
N2O	ANT	EDGARv4.2	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R2B07_polstrNest
			R3B07_0022
	BBE	GFED3	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R2B07_polstrNest
			R3B07_0022
NH3	ANT	MACCity	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
		MACCity_agriculture	R2B06_0016
		MACCity_agric_waste	R2B06_0016
		MACCity_energy	R2B06_0016
		MACCity_industrial	R2B06_0016
		MACCity_residential	R2B06_0016
		MACCity_transport	R2B06_0016
SF6	ANT	EDGARLevin	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022
SO2	ANT	MACCity	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B06_0016
			R2B07_0018
			R2B07_nest
			R3B07_0022
		GFED3	R2B04_0012
			R2B04_ECHAM
			R2B05_0014
			R2B06_0016
			R2B07_0018
			R3B07_0022

Remapping Emissions

A comprehensible manual can be found here. The document was provided by M. Weimer (June 2019). This document provides an overview of the workflow to be done in order to remap a set of emission data onto your own ICON grid. The raw emission data can be taken from emission inventories such as Edgar, MACCity, etc. (see above). The desired files can be copied to an own directory where they serve as input for the remap procedure described in the manual. Additional remarks:

• The mentioned workflow was initially designed for FH2. Should be tested on other machines as well
• The automatic addition of emission tags to the tracer.xml (add_emissions_to_tracer_xml.py) is very sensitive to tracer names and emission species. In doubt, add emission tags manually.
• In any case, double check if all emission tags have been assigned to the correct tracer

Running a Limited Area Meteorology (LAM) Simulation

General

Here are some notes on setting up an ICON-ART LAM simulation. Theses settings are important if you use initial data and boundary data from different sources. It is preferable to use data from the same source to be consistent. However, in certain situations this is not possible due to limitations of the model (e.g. initialization routines).

Required data for LAM domain

Grid of LAM domain external parameters of LAM domain external parameters containing soil parameters (only necessary for dust simulations) initial data (ICON-ART or IFS)

Required data for LAM boundaries

Auxiliary grid (grid containing boundary area of the LAM domain, generated during remapping process with ICONtools) forcing data for the boundaries

Initialization

There are two different possible methods to read in the dust during initialization. You can either pass a file containing meteorological variables and a second file containing dust data. The vertical levels may differ between these two files and the dust must be delivered as ART_IAE file. The corresponding namelist setting in &art_nml is iart_init_aero=5

The other possibility is to pass all variables required for the initialization in a single file. The vertical levels must all be consistent and the corresponding namelist setting in &art_nml is iart_init_aero=0 . Furthermore you have to add file in the tracer xml file.

Boundary Data

The boundary data can only be passed to the model as one single file per time step. The vertical levels for all time steps must be the same. Otherwise an error occurs. If you use data from a different source than the one used for initialization, it is crucial to decouple the reading of the boundary data from the reading of initial data. During the start of the simulation it is possible to read the first boundary data from the initial data when using ICON-ART data. To prevent this and to read the boundary data from a separate file during initialization, set init_latbc_from_fg = .FALSE. in &limarea_nml . Additionally you have to add file in the tracer xml file.

---

#Aerosol Tracers

Creating A Nested ICON-Grid

There are four steps to create a grid. The steps have to be run separately as they are dependent on each other.

Graph Generation

The first step is creating the graph. Ensure that you specify R and B for the finest nest! I.e. if you plan a global R2B6 grid with a R2B7 Nest, you have to set R=2 and B=7. An example namelist in a runscript looks like this:

cat > NAMELIST_GRAPH << EOF
&graph_ini
  nroot       = ${R}
  grid_levels = ${B}
/
EOF

echo global_graph_generator null > $commandFile
job_submit -c p -p 1 -t 60 -m 32000 ${run_commmand}

You might have to increase the allocated memory (-m 64000) if the process crashes (-p 1 is maximum because of lacking parallelization)

Grid generation

The second step is the generation of all (global) grids. I.e., if you choose R=2 and B=7, you get global grids for R2B1, R2B2, R2B3, R2B4, R2B5, R2B6 and R2B7. Even if you want R2B7 to be your nest, you have to do this step down to R2B7! This means, that the values of R and B for step 1 and 2 must not differ. As far as I could figure out, the spring dynamics optimization is the one to choose. Therefore, you should choose @itype_optimize = 4@. An example namelist looks like this:

cat > NAMELIST_GRID << EOF
&grid_ini
 nroot       = ${R}
 grid_levels = ${B}
/
&grid_options
 itype_optimize = 4
/
EOF

echo global_grid_generator null > $commandFile
job_submit -c p -p 1 -t 600 -m 32000 ${run_commmand}

If you want to generate a finer grid (e.g. R2B10) you might have to increase the allocated memory (-m 256000).

Modify the filenames

The spring-dynamics-optimized files carry this information within their filename. In order to continue, the names have to be changed to the standard names of grids. This can be done within a script as shown in the following. (@maxlev_optim@ is a parameter, that specifies the maximum level to which optimizations are applied. This is set in the previous step within the grid_options namelist. As the default is 100, there is usually no need to change this. You just have to set the variable @maxlev_optim@ within the script for the copying):

level=1;
while [[ $level -le $maxlev_optim ]] ; do
    cp iconR${R}B0${level}-grid_spr0.90.nc iconR${R}B0${level}-grid.nc
    ((level=$level+1))
done

Nested grid creation

As a last step, you have to specify the nests. In the following example, three nests are added to a global R2B6 grid. Therefore, @start_lev = 6@ and @n_dom = 4@. As these nests are subsequent, the @parent_id@ of each nest is the one of the domain with one rank higher. I.e. R2B6 has the ID 1, therefore the @parent_id@ of R2B7 is 1. R2B8 has the ID of the R2B7 as @parent_id@ and therefore 2. The different domains are seperated by commas in the namelist. The global domain does of course not show up (you produced the global grid files in step 2). In this example, the further namelist variables mean the following: @l_circ@ gives the nests a circular instead of an rectangular shape. @l_plot@ provides output which can be used to plot the grids with GMT scripts. @radius, center_lon, center_lat@ define the location of the nests. With @lsep_gridref_info = .true.@ the grid information is stored within an additional grid description file. This needs then to be specified within ICON!

cat > NAMELIST_GRIDREF << EOF
&gridref_ini
  grid_root  = 2
  start_lev  = 6
  n_dom      = 4
  parent_id  = 1,2,3
  l_circ     = .true.
  l_plot     = .true.
  radius     =  20.,12.,12.
  center_lon =  10.,5.,5.
  center_lat =  40.,47.5,47.5
  bdy_indexing_depth = 14
  lsep_gridref_info = .false.
/
EOF

echo global_grid_refine null > $commandFile
job_submit -c p -p 64 -t 60 -m 16000 ${run_commmand}

If you want to generate a finer grid (e.g. R2B10) you might have to increase the allocated memory (-m 64000).

All input data required for standard configurations

https://bwsyncandshare.kit.edu/s/YdaqfMDgJPfo8QF