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 after 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’>

useRAMonly: (optional): 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

Warning

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.

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	True	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:

model:
  plugin:
    name: CHIMERE
    version: std
    type: model

  # Mandatory arguments
  direxec: XXXXX
  nphour_ref: XXXXX
  ichemstep: XXXXX
  ideepconv: XXXXX
  nivout: XXXXX
  nlevemis: XXXXX

  # Optional arguments
  autoflush: XXXXX
  dir_sources: XXXXX
  periods: XXXXX
  ihoursu: XXXXX
  useemisb: XXXXX
  dumpnctype: XXXXX
  dumpncoutput: XXXXX
  dumpncpar: XXXXX
  usechemistry: XXXXX
  useemissions: XXXXX
  usetransmix: XXXXX
  usewetdepos: XXXXX
  usedepos: XXXXX
  nsavedepos: XXXXX
  nitgs: XXXXX
  nitgssu: XXXXX
  useabsclipconc: XXXXX
  clipconc: XXXXX
  ntyperate: XXXXX
  nvegtype: XXXXX
  nlduse: XXXXX
  nparammax: XXXXX
  hpulse: XXXXX
  auto-recompile: XXXXX
  force-recompile: XXXXX
  compile-mode: XXXXX
  compile-clean: XXXXX
  compile-only: XXXXX
  force-compile-stderr: XXXXX
  nlevemis_bio: XXXXX
  nmdoms: XXXXX
  nzdoms: XXXXX
  mpirun: XXXXX
  ignore_input_dates: XXXXX
  useRAMonly: XXXXX
  force_clean_run: XXXXX
  stopORmore: XXXXX