Input
Contents
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:
1 ! run_nml: general switches ----------
2 &run_nml
3 ltestcase = .FALSE.
4 num_lev = 50
5 ltransport = .TRUE.
6 .............
7 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.
| 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 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 | - | - | - |
| 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. | |||
| 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 |
| 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 | |||
| 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. | |||
| 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.
1 <modes>
2 <aerosol id="asha">
3 <kind type="char">2mom</kind>
4 <d_gn type="real">1.190E-6</d_gn>
5 <sigma_g type="real">1.410E+0</sigma_g>
6 <rho type="real">2.600E+3</rho>
7 </aerosol>
8 </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.
1 <tracers>
2 <aerosol id="nmb">
3 <moment type="int">0</moment>
4 <mode type="char">insol_acc,insol_coa</mode>
5 <unit type="char">kg-1</unit>
6 <transport type="char">hadv52aero</transport>
7 </aerosol>
8 <aerosol id="dust">
9 <moment type="int">3</moment>
10 <mode type="char">insol_acc,insol_coa</mode>
11 <sol type="real">1.0</sol>
12 <mol_weight type="real">50.00E-3</mol_weight>
13 <rho type="real">2.650E3</rho>
14 <unit type="char">mug kg-1</unit>
15 <transport type="char">hadv52aero</transport>
16 </aerosol>
17 </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.
| 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.
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.
| 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.
| 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.
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:
1 cat > NAMELIST_GRAPH << EOF
2 &graph_ini
3 nroot = ${R}
4 grid_levels = ${B}
5 /
6 EOF
7
8 echo global_graph_generator null > $commandFile
9 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:
1 cat > NAMELIST_GRID << EOF
2 &grid_ini
3 nroot = ${R}
4 grid_levels = ${B}
5 /
6 &grid_options
7 itype_optimize = 4
8 /
9 EOF
10
11 echo global_grid_generator null > $commandFile
12 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):
1 level=1;
2 while [[ $level -le $maxlev_optim ]] ; do
3 cp iconR${R}B0${level}-grid_spr0.90.nc iconR${R}B0${level}-grid.nc
4 ((level=$level+1))
5 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!
1 cat > NAMELIST_GRIDREF << EOF
2 &gridref_ini
3 grid_root = 2
4 start_lev = 6
5 n_dom = 4
6 parent_id = 1,2,3
7 l_circ = .true.
8 l_plot = .true.
9 radius = 20.,12.,12.
10 center_lon = 10.,5.,5.
11 center_lat = 40.,47.5,47.5
12 bdy_indexing_depth = 14
13 lsep_gridref_info = .false.
14 /
15 EOF
16
17 echo global_grid_refine null > $commandFile
18 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).
