CHIMERE model training course

International Research Network ChimSur

Characterizing spatial-temporal evolution of atmospheric composition in the south cone with CHIMERE

Sept. 4, 2024, CIMA-IFAECI (Buenos Aires)

Guillaume Siour (LISA), Sylvain Mailler (LMD).

Get CHIMERE and emiSURF

cd salidas

tar xvf /salidas3/guillaume.siour/ARCHIVES/chimere_v2023r2.tar

tar xvf /salidas3/ guillaume.siour/ARCHIVES/emiSURF_v2023r1.tar

Horizontal domain definition: edit domains/domainlist.nml

# Each domain definition:

# Domain e_we e_sn dx dy geores dt ref_lat ref_lon Proj

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PAPILA 263 340 27000 27000 modis_landuse_20class_30s_with_lakes 100 -26.7 -61. mercator

BUENOSA 58 58 9000 9000 modis_landuse_20class_30s_with_lakes 100 -35. -58.1 mercator

BUENOSAn 58 58 9000 9000 modis_landuse_20class_30s_with_lakes 100 -26.7 -61. mercator

• e_we: Number of cells in the west-east direction
• e_sn: Number of cells in the south-north direction

• dx: grid spacing in the west-east direction
• dy: grid spacing in the south-north direction

• ref_lon (degrees): The longitude of the center of the domain
• ref_lat (degrees): The latitude of the center of the domain

• Proj = lambert: Well suited for mid latiudes. Cannot contain poles.
• Proj = Mercator: well suited for low latitudes.
• Proj = polar: well suited for high latitudes especially if the domain contains a pole
• Proj = lat-lon: classic yet chic

• For more flexibility you will need to also modify the namelists_wrf/namelist.wps.sed

Horizontal domain definition: domains/domainlist.nml nesting case

# Nested domains (parent i,j are given by DomainWizard or manually chosen)

# format should be in the following order:

# NEST Nested_domain Coarse_domain grid_ratio iparst jparst

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NEST BUENOSAn PAPILA 3 133 125

• Nested_domain: Name of the nest
• Coarse_domain: Name of the parent domain
• grid_ratio: Grid rafinement ratio (3 or 5 are recommended)
• iparst : id of the parent grid cell in the wes-east direction including the lower-left point of the nest
• jparst: id of the parent grid cell in the south-north direction including the lower-left point of the nest

iparst

jparst

Coarse_domain

Nested_domain

Create your domain

[$istopchemprep] Make chemical input data and exit (0/1) : 1

chimere.par : User defined parameters

[$parameter_name] Parameter description : value1, value2, …valueN

chimere.par : User defined parameters

[$parameter_name] Parameter description : value1, value2, …valueN

ON THE LEFT:

​

• All different CHIMERE options
• Parameters organized by sections
• The key words can be used in chimere.par

chimere.par : User defined parameters

[$parameter_name] Parameter description : value1, value2, …valueN

ON THE LEFT:

​

• All different CHIMERE options
• Parameters organized by sections
• The key words can be used in chimere.par

SEPARATOR

:

chimere.par : User defined parameters

[$parameter_name] Parameter description : value1, value2, …valueN

ON THE RIGHT:

​

• Comma separated values
• Each column corresponds to a different configuration

​

ON THE LEFT:

​

• All different CHIMERE options
• Parameters organized by sections
• The key words can be used in chimere.par

SEPARATOR

:

Define your simulation domain in chimere.buenosa.par

# run list is separated by blank spaces. 1 to take the first column, 2 for the second, and so on.

# 1 2 to run the first and then the second right after

runs : 1

Which column to treat ?

Define your simulation domain in chimere.buenosa.par

# CHIMERE simulation domain

[$nested] Nested run? (yes/no) : no, yes

[$dom] CHIMERE domain : BUENOSA, dom2

[$nlevels] Number of vertical layers : 15

[$pres_topdom] Top layer pressure : 200

[$pres_top1lev] First layer pressure : 998

BUENOSA is the domain we have defined above in domainlist.nml

# run list is separated by blank spaces. 1 to take the first column, 2 for the second, and so on.

# 1 2 to run the first and then the second right after

runs : 1

Which column to treat ?

Define your simulation domain in chimere.buenosa.par

# CHIMERE simulation domain

[$nested] Nested run? (yes/no) : no, yes

[$dom] CHIMERE domain : BUENOSA, dom2

[$nlevels] Number of vertical layers : 15

[$pres_topdom] Top layer pressure : 200

[$pres_top1lev] First layer pressure : 998

# Processors

[$nproc_chimere] Number of CHIMERE processors : 20

[$nproc_wrf] Number of WRF processors : 10

[$nproc_xios] Number of xios processors : 2

BUENOSA is the domain we have defined above in domainlist.nml

Most of the time :

nproc_chimere>>nproc_wrf

nproc_xios : 2 (for I/O)

# run list is separated by blank spaces. 1 to take the first column, 2 for the second, and so on.

# 1 2 to run the first and then the second right after

runs : 1

Which column to treat ?

Define your simulation domain in chimere.buenosa.par

# CHIMERE simulation domain

[$nested] Nested run? (yes/no) : no, yes

[$dom] CHIMERE domain : BUENOSA, dom2

[$nlevels] Number of vertical layers : 15

[$pres_topdom] Top layer pressure : 200

[$pres_top1lev] First layer pressure : 998

# Processors

[$nproc_chimere] Number of CHIMERE processors : 20

[$nproc_wrf] Number of WRF processors : 10

[$nproc_xios] Number of xios processors : 2

BUENOSA is the domain we have defined above in domainlist.nml

Most of the time :

nproc_chimere>>nproc_wrf

nproc_xios : 2 (for I/O)

# run list is separated by blank spaces. 1 to take the first column, 2 for the second, and so on.

# 1 2 to run the first and then the second right after

runs : 1

Which column to treat ?

# Simulation output labels and directories

[$lab] Simulation label : BUENOSA

[$clab] Coarse domain label : dom1

[$sim] Current run label : ${idatestart}_${nhours}_${lab}

[$simuldir] Simulation output directory : /salidas3/`whoami`/CHIMOUT/${lab}

[$coarsedir] Simulation output directory : /salidas3/`whoami`/CHIMOUT/${clab}

$lab can be used to define path

it also defines output file names

# Simulation output labels and directories

[$istopdom] Make domains and exit(0/1) : 1

We need to construct the domain first

Launch chimere - geogrid

#take interactive node

qsub -I -X -l nodes=1:ppn=12 -l walltime=1:00:00

#launch chimere (after returning into the chimere_v2023r2 directory)

./chimere.sh -par chimere.buenosa.par -todo s -startdate 2022010100 -hours 24 -restart optional

Launch chimere - geogrid

#take interactive node

qsub -I -X -l nodes=1:ppn=12 -l walltime=1:00:00

#launch chimere (after returning into the chimere_v2023r2 directory)

./chimere.sh -par chimere.buenosa.par -todo s -startdate 2022010100 -hours 24 -restart optional

Launch chimere - geogrid

ncview ~/salidas/chimere_v2023r2/domains/BUENOSA/geog_BUENOSA.nc

#take interactive node

qsub -I -X -l nodes=1:ppn=12 -l walltime=1:00:00

#launch chimere (after returning into the chimere_v2023r2 directory)

./chimere.sh -par chimere.buenosa.par -todo s -startdate 2022010100 -hours 24 -restart optional

Build emissions: emisurf

1. Reads gridded surface emission fluxes from some input database (monthly or annual)
2. Interpolates data on the CHIMERE horizontal grid
3. Applies spatial proxies (mainy landuse)
4. Applies temporal profiles
5. Applies Vertical profils
6. Maps inventory pollutants on real chemical species
7. Lumps real species to model species

​

emisurf.buenosa.par

# Number of processors to use in 'domain' parallel mode

[$npx] : 1

[$npy] : 1

[$first_month] : 01

[$last_month] : 01

​

# Years to simulate or scenario

[$scenlist] : 2022

# Apply summer/winter time in netcdf files for emissions

# sumwintime=0 no (prefer this option for southern hemisphere cases or cclimatic cases to minimize errors)

# sumwintime=1 yes (adopt a 1 hour win/sum time from april to October files for the whole donain)

# All necessary information is stored in the output emission file to manage the winter/summer shift at the grid level,

# This will be done in the next CHIMERE version

[$sumwintime] : 0

emisurf.buenosa.par

# CHIMERE and local parameters

# where is the chimere model? (we need its makefiles)

[$chimeredir] : /salidas3/`whoami`/chimere_v2020r2

​

# what is your chimere domain for these emissions?

[$dom] : BUENOSA

[$exp] : CAMS

​

# where do you want the results

[$outdir] : /salidas3/`whoami`/EMISURFOUT/${dom}_${exp}

[$domainsdir] : ${chimeredir}/domains

​

# possible sources: EMEP01x01, CAMS, HTAP01, RCP85

[$emisdatabase] : CAMS

​

# link to geog file used only if use_geog=True

[$geogfile] : ${chimeredir}/domains/${dom}/geog_${dom}.nc

[$use_geog] : True

emisurf: launch it

#take interactive node

qsub -I -X -l nodes=1:ppn=12 -l walltime=1:00:00

#launch emisurf

./emisurf.sh emisurf.buenosa.par

emisurf: launch it

#take interactive node

qsub -I -X -l nodes=1:ppn=12 -l walltime=1:00:00

#launch emisurf

./emisurf.sh emisurf.buenosa.par

emisurf: launch it

#take interactive node

qsub -I -X -l nodes=1:ppn=12 -l walltime=1:00:00

#launch emisurf

./emisurf.sh emisurf.buenosa.par

Launch chimere

#take interactive node

qsub -I -X -l nodes=1:ppn=32 -l walltime=1:00:00

#launch chimere

./chimere.sh -par ${chimparams} -todo s -startdate 2022010100 -hours 24 -restart optional

Launch chimere

#take interactive node

qsub -I -X -l nodes=1:ppn=32 -l walltime=1:00:00

#launch chimere

./chimere.sh -par ${chimparams} -todo s -startdate 2022010100 -hours 24 -restart optional

Launch chimere

#take interactive node

qsub -I -X -l nodes=1:ppn=32 -l walltime=1:00:00

#launch chimere

./chimere.sh -par ${chimparams} -todo s -startdate 2022010100 -hours 24 -restart optional