This is the plugin to run the CTM CHIMERE. Please see further details on the CTM itself here.

YAML arguments#

The following arguments are used to configure the plugin. pyCIF will return an exception at the initialization if mandatory arguments are not specified, or if any argument does not fit accepted values or type:

Mandatory arguments#

direxec : str, mandatory

Path to CHIMERE sources and/or executables. For executables, fwdchimere.e, tlchimere.e and achimere.e should be in ${path}/src, ${path}/src_tl and ${path}/src_ad respective sub-folders.

nphour_ref : int, mandatory

Number of physical steps per hour. 6 is well tested for regional cases.

ichemstep : int, mandatory

Number of chemical refined iterations, i.e., refined time steps relative to physical time steps. Down to 1/4 degree resolution, phys=6 and step=1 is fine; For finer grids (5-10 kms), take at least step=4; For grids of 2-5 kms, try step=6 or more.

ideepconv : 0 or 1 or 2, mandatory

Computation of the deep convection.

  • 0: No deep convection

  • 1: Select deep convection automatically according to resolution, deep conv fluxes from Tiedtke

  • 2: Select deep convection automatically according to resolution, deep conv fluxes from meteorological data

nivout : int, mandatory

Number of vertical layers in output files.

nlevemis : int, mandatory

Number of levels for emissions. Applies to AEMISSION files.

Optional arguments#

autoflush : bool, optional, default False

Cleans big temporary files when the simulation is done. Triggers the function flushrun of the model if available

dir_sources : str, optional, default “”

Path to CHIMERE sources. Overwrites direxec if specified.

periods : str, optional, default “1D”

Length of sub-simulations periods. Use Pandas frequency strings

ihoursu : int, optional, default 0

Number of spin-up hours.

useemisb : bool, optional, default False

Include biogenic emissions, i.e. the file

dumpnctype : “double” or “float”, optional, default “float”

Precision for the output NetCDF files. Do not impact the values in mod.txt

  • “double”: double precision: needed if precise post-processing of output files

  • “float”: float precision: save some disk space

dumpncoutput : bool, optional, default True

Dump outputs into a NetCDF file.

dumpncpar : bool, optional, default False

Dump parameters into a NetCDF file.

usechemistry : 0 or 1, optional, default 0

Use chemistry.

useemissions : 0 or 1, optional, default 1

Use emisions.

usetransmix : 0 or 1, optional, default 1

Use transport and mixing.

usewetdepos : 0 or 1, optional, default 0

Use wet deposition.

usedepos : 0 or 1, optional, default 0

Use dry deposition.

nsavedepos : int, optional, default 4

Save deposition in NetCDF file every … hours.

nitgs : 1 or 2, optional, default 1

Number of Gauss-Seidel iterations in the TWOSTEP solver.

  • 1: for model testing, and when using the adjoint

  • 2: for better accuracy

nitgssu : 1 or 2, optional, default 1

Same during spin-up

  • 1: for model testing, and when using the adjoint

  • 2: for better accuracy

useabsclipconc : 0 or 1, optional, default 0

Clip small (in absolute value) concentrations when = 1; clip small (including all negative) concentrations when = 0. Warning: the clipping is done in twostep, not only when writing the output writing; thus, clipping must be used with care as it can alter the mass conservationsee CHIMERE doc for more information on the use of clipconc

clipconc : float, optional, default 1

Clipping concentration (in molecule/cm3)

ntyperate : int, optional, default 50

Max number of reaction types

nvegtype : int, optional, default 16

Number of vegetation types

nlduse : int, optional, default 9

Max number of landuse classes

nparammax : int, optional, default 30

Max number of output parameters

hpulse : int, optional, default 0

Hour of emission pulse. All emissions before this hour from the beginning of the simulations are ignored, and all transport/chemistry computations are skipped.To be used when computing response functions from a given hour

auto-recompile : bool, optional, default False

Auto-compile executables before running if executables not available

force-recompile : bool, optional, default False

Force compilation even if executables available

compile-mode : “PROD” or “DEBUG”, optional, default “PROD”

Compilation mode

  • “PROD”: production mode; all optimizations are activated

  • “DEBUG”: check-all and traceback are activated, hence slowing down the execution

compile-clean : bool, optional, default True

Cleaning repositories before compiling; slows the compilation but prevent side-effects from re-compiling.Can be switched of for minor modifications in the code

compile-only : list, optional, default [‘A’, ‘L’, ‘D’]

Compile only part of the available CHIMERE modes (tangent-linear, forward and adjoint)

force-compile-stderr : bool, optional, default False

Force printing stderr from compiling (even when executable correctly generated after compiling)

nlevemis_bio : int, optional, default 1

Number of vertical levels in biogenic emissions (

nmdoms : int, optional, default 1

Number of parallel domains in meridional direction

nzdoms : int, optional, default 1

Number of parallel domains in zonal direction

mpirun : str, optional, default “mpirun”

path to mpirun

ignore_input_dates : bool, optional, default False

Forces CHIMERE to by-pass the checks on the consistency of dates in AEMISSIONS, BEMISSIONS, BOUN_CONCS, INI_COCNS and METEO; useful to use input files from another periodwithout duplicating them only for the dates.

useRAMonly : bool, optional, default False

Force relying on the RAM only, instead of TMP files, to save forward simulations necessary for the adjoint. This trades I/O burden with TMP files with RAM burden


This option can use a LOT of RAM. Please test the option on a simple case and compare with a case using TMP files. Depending on your cluster and your test case, choose the fastest one.

force_clean_run : bool, optional, default False

Clean run subdirectory just after running to limit disk space usage

stopORmore : list, optional, default []

To avoid running simulations for which the simulated concentrations are smaller than a given thresholdfor a set of species; please provide a list of tuples (species,threshold) (species is from ACTIVE_SPECIES and treshold in XXUNITXX

pre-computed-meteo : bool, optional, default True

Simplified METEO mapper when the meteo is already computed. Set to False if using diagmet transform


The current plugin requires the present plugins to run properly:

Requirement name

Requirement type

Explicit definition

Any valid

Default name

Default version

















































YAML template#

Please find below a template for a YAML configuration:

 2  plugin:
 3    name: CHIMERE
 4    version: std
 5    type: model
 7    # Mandatory arguments
 8    direxec: XXXXX  # str
 9    nphour_ref: XXXXX  # int
10    ichemstep: XXXXX  # int
11    ideepconv: XXXXX  # 0|1|2
12    nivout: XXXXX  # int
13    nlevemis: XXXXX  # int
15    # Optional arguments
16    autoflush: XXXXX  # bool
17    dir_sources: XXXXX  # str
18    periods: XXXXX  # str
19    ihoursu: XXXXX  # int
20    useemisb: XXXXX  # bool
21    dumpnctype: XXXXX  # double|float
22    dumpncoutput: XXXXX  # bool
23    dumpncpar: XXXXX  # bool
24    usechemistry: XXXXX  # 0|1
25    useemissions: XXXXX  # 0|1
26    usetransmix: XXXXX  # 0|1
27    usewetdepos: XXXXX  # 0|1
28    usedepos: XXXXX  # 0|1
29    nsavedepos: XXXXX  # int
30    nitgs: XXXXX  # 1|2
31    nitgssu: XXXXX  # 1|2
32    useabsclipconc: XXXXX  # 0|1
33    clipconc: XXXXX  # float
34    ntyperate: XXXXX  # int
35    nvegtype: XXXXX  # int
36    nlduse: XXXXX  # int
37    nparammax: XXXXX  # int
38    hpulse: XXXXX  # int
39    auto-recompile: XXXXX  # bool
40    force-recompile: XXXXX  # bool
41    compile-mode: XXXXX  # PROD|DEBUG
42    compile-clean: XXXXX  # bool
43    compile-only: XXXXX  # list
44    force-compile-stderr: XXXXX  # bool
45    nlevemis_bio: XXXXX  # int
46    nmdoms: XXXXX  # int
47    nzdoms: XXXXX  # int
48    mpirun: XXXXX  # str
49    ignore_input_dates: XXXXX  # bool
50    useRAMonly: XXXXX  # bool
51    force_clean_run: XXXXX  # bool
52    stopORmore: XXXXX  # list
53    pre-computed-meteo: XXXXX  # bool