CHIMERE / std

Description

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: (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.

accepted type: <class ‘str’>

nphour_ref: (mandatory)

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

accepted type: <class ‘int’>

ichemstep: (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.

accepted type: <class ‘int’>

ideepconv: (mandatory)

Computation of the deep convection.

accepted values:

  • 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: (mandatory)

Number of vertical layers in output files.

accepted type: <class ‘int’>

nlevemis: (mandatory)

Number of levels for emissions. Applies to AEMISSION files.

accepted type: <class ‘int’>

Optional arguments

autoflush: (optional): False

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

accepted type: <class ‘bool’>

dir_sources: (optional):

Path to CHIMERE sources. Overwrites direxec if specified.

accepted type: <class ‘str’>

periods: (optional): 1D

Length of sub-simulations periods. Use Pandas frequency strings

accepted type: <class ‘str’>

ihoursu: (optional): 0

Number of spin-up hours.

accepted type: <class ‘int’>

useemisb: (optional): False

Include biogenic emissions, i.e. the file BEMISSIONS.nc

accepted type: <class ‘bool’>

dumpnctype: (optional): float

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

accepted values:

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

  • float: float precision: save some disk space

dumpncoutput: (optional): True

Dump outputs into a NetCDF file.

accepted type: <class ‘bool’>

dumpncpar: (optional): False

Dump parameters into a NetCDF file.

accepted type: <class ‘bool’>

usechemistry: (optional): 0

Use chemistry.

accepted values: [0, 1]

useemissions: (optional): 1

Use emisions.

accepted values: [0, 1]

usetransmix: (optional): 1

Use transport and mixing.

accepted values: [0, 1]

usewetdepos: (optional): 0

Use wet deposition.

accepted values: [0, 1]

usedepos: (optional): 0

Use dry deposition.

accepted values: [0, 1]

nsavedepos: (optional): 4

Save deposition in NetCDF file every … hours.

accepted type: <class ‘int’>

nitgs: (optional): 1

Number of Gauss-Seidel iterations in the TWOSTEP solver.

accepted values:

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

  • 2: for better accuracy

nitgssu: (optional): 1

Same during spin-up

accepted values:

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

  • 2: for better accuracy

useabsclipconc: (optional): 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

accepted values: [0, 1]

clipconc: (optional): 1

Clipping concentration (in molecule/cm3)

accepted type: <class ‘float’>

ntyperate: (optional): 50

Max number of reaction types

accepted type: <class ‘int’>

nvegtype: (optional): 16

Number of vegetation types

accepted type: <class ‘int’>

nlduse: (optional): 9

Max number of landuse classes

accepted type: <class ‘int’>

nparammax: (optional): 30

Max number of output parameters

accepted type: <class ‘int’>

hpulse: (optional): 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

accepted type: <class ‘int’>

auto-recompile: (optional): False

Auto-compile executables before running if executables not available

accepted type: <class ‘bool’>

force-recompile: (optional): False

Force compilation even if executables available

accepted type: <class ‘bool’>

compile-mode: (optional): PROD

Compilation mode

accepted values:

  • PROD: production mode; all optimizations are activated

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

compile-clean: (optional): 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

accepted type: <class ‘bool’>

compile-only: (optional): [‘A’, ‘L’, ‘D’]

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

accepted type: <class ‘list’>

force-compile-stderr: (optional): False

Force printing stderr from compiling (even when executable correctly generated at compiling

accepted type: <class ‘bool’>

nlevemis_bio: (optional): 1

Number of vertical levels in biogenic emissions (BEMISSIONS.nc)

accepted type: <class ‘int’>

nmdoms: (optional): 1

Number of parallel domains in meridional direction

accepted type: <class ‘int’>

nzdoms: (optional): 1

Number of parallel domains in zonal direction

accepted type: <class ‘int’>

mpirun: (optional): mpirun

path to mpirun

accepted type: <class ‘str’>

ignore_input_dates: (optional): 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.

accepted type: <class ‘bool’>

force_clean_run: (optional): False

Clean run subdirectory just after running to limit disk space usage

accepted type: <class ‘bool’>

stopORmore: (optional): []

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

accepted type: <class ‘list’>

Requirements

The current plugin requires the present plugins to run properly:

Requirement name

Requirement type

Explicit definition

Any valid

Default name

Default version

domain

Domain

False

False

CHIMERE

std

chemistry

Chemistry

False

False

CHIMERE

gasJtab

flux

DataStream

True

False

CHIMERE

AEMISSIONS

bioflux

DataStream

True

False

CHIMERE

AEMISSIONS

meteo

DataStream

False

False

CHIMERE

std

latcond

DataStream

True

False

CHIMERE

icbc

topcond

DataStream

True

False

CHIMERE

icbc

inicond

DataStream

True

False

CHIMERE

icbc

Yaml template

Please find below a template for a Yaml configuration:

 1model:
 2  plugin:
 3    name: CHIMERE
 4    version: std
 5    type: model
 6
 7  # Mandatory arguments
 8  direxec: XXXXX
 9  nphour_ref: XXXXX
10  ichemstep: XXXXX
11  ideepconv: XXXXX
12  nivout: XXXXX
13  nlevemis: XXXXX
14
15  # Optional arguments
16  autoflush: XXXXX
17  dir_sources: XXXXX
18  periods: XXXXX
19  ihoursu: XXXXX
20  useemisb: XXXXX
21  dumpnctype: XXXXX
22  dumpncoutput: XXXXX
23  dumpncpar: XXXXX
24  usechemistry: XXXXX
25  useemissions: XXXXX
26  usetransmix: XXXXX
27  usewetdepos: XXXXX
28  usedepos: XXXXX
29  nsavedepos: XXXXX
30  nitgs: XXXXX
31  nitgssu: XXXXX
32  useabsclipconc: XXXXX
33  clipconc: XXXXX
34  ntyperate: XXXXX
35  nvegtype: XXXXX
36  nlduse: XXXXX
37  nparammax: XXXXX
38  hpulse: XXXXX
39  auto-recompile: XXXXX
40  force-recompile: XXXXX
41  compile-mode: XXXXX
42  compile-clean: XXXXX
43  compile-only: XXXXX
44  force-compile-stderr: XXXXX
45  nlevemis_bio: XXXXX
46  nmdoms: XXXXX
47  nzdoms: XXXXX
48  mpirun: XXXXX
49  ignore_input_dates: XXXXX
50  force_clean_run: XXXXX
51  stopORmore: XXXXX