Use LMDS-SACS with CIF

Use LMDS-SACS with CIF#

This section explains how to setup a YAML configuration file to CIF to run LMDZ-SACS. For exaustive list of options, please refer to the plugins documentation pages

Model configuration#

LMDZ-SACS needs the LMDZ/reg-ico model plugin

Note

If pycif was installed in editable mode, there is no need to provide the path to the executable or the sources directory. The plugin will automatically find source directory that was cloned with CIF along side the pycif sources.

Minimal configuration#

Input arguments#

  • grid:

    the grid type, “regular” or “dynamico”, will change the required domain plugin

  • auto-recompile:

    allow CIF to automatically compile LMDZ-SACS executables

  • compile-acc-target:

    the device on which LMDZ-SACS will run, “gpu” or “multicore”

  • do_chemistry:

    all the chemistry computation will be skipped if set to false

  • autoflush:

    automatically flush the input files after each sub-period run

YAML example#

model:
  plugin:
    name: LMDZ
    version: reg-ico

  grid: dynamico

  auto-recompile: true
  compile-acc-target: gpu

  do_chemistry: false
  autoflush: true

Chemical scheme#

LMDZ-SACS needs a chemical scheme (even if chemistry is not enabled), provided by LMDZ/SACS chemistry plugin

Input arguments#

  • active_species:

    list of tracers to be transported in the model with their molar mass in g/mol. A parameter in the inicond component of the datavect plugin will be required for each emitted species

  • emitted_species:

    list of tracers with emissions, by default all active species have emissions. A parameter in the flux component of the datavect plugin will be required for each emitted species

  • prescribed_species:

    list of prescribed species. A parameter in the precrconcs component of the datavect plugin will be required for each emitted species

  • prodloss_species:

    list of production/loss species. A parameter in the prodloss3d component of the datavect plugin will be required for each emitted species

  • deposition_species:

    list of deposition species. A parameter in the deposition component of the datavect plugin will be required for each emitted species

  • reactions:

    list of tracers to be transported in the model with their molar mass in g/mol

Reactions syntax#

Reactions are defined by a string of the form "[reactants] -> [products] [rate_formula], [rate_terms]", where [reactants] is composed of the reactives species names separated by "+", [products] is composed of the reactives species names separated by "+" with optional stoichiometric coefficients (for example "2*H2O"), [rate_formula] is one of the supported rate formula (see below), and [rate_terms] is a comma separated list of terms.

Reactants must be either in active_species or prescribed_species. Products that are not in active_species will be ignored.

Accepted rate formula#

  • Constant rate \(k = \mathrm{cste}\): k = [value]

  • Simplified arrhenius \(k(T) = A\exp\left( \frac{-B}{T} \right)\): k(T) = A*exp(-B/T)

  • Complete arrhenius \(k(T) = A\exp\left( \frac{-B}{T} \right) \left( \frac{300}{T} \right)^N\): k(T) = A*exp(-B/T)*(300/T)^N

  • Relative pressure \(k(P) = A\left( B + C \frac{P}{P_\mathrm{ref}} \right)\): k(P) = A(B+C*P/Pref)

Photolysis rate formula#

A photolysis reaction is defined by a string of the form "[reactant] + hv -> [products] J = [variable_name]", where [reactant] is the reactive species, and [variable_name] the corresponding J rate variable name.

YAML example#

chemistry:
  plugin:
    name: LMDZ
    version: SACS

  active_species:
    CH4:
      molar_mass: 16.0425
    C2H6:
      molar_mass: 30.069

  emitted_species:
    - CH4
    - C2H6

  prescribed_species:
    - OH
    - O1D
    - Cl

  reactions:
    - CH4 + O1D -> PRODUCTS    k = 1.75e-10
    - CH4 + OH -> CH3 + H2O    k(T) = Aexp(-B/T), A=2.45e-12, B=1775
    - CH4 + Cl -> HCl + CH3    k(T) = Aexp(-B/T), A=7.1e-12, B=1270
    - C2H6 + OH -> H2O + C2H5  k(T) = Aexp(-B/T), A = 7.66e-12, B = 1020
    - C2H6 + Cl -> HCl + C2H5  k(T) = Aexp(-B/T), A = 7.2e-11, B = 70

Domain definition#

LMDZ-SACS domain is defined by the LMDZ/regular domain plugin for the regular lat-lon grid or by the LMDZ/dynamico domain plugin for the icosahedral grid.

YAML example for the regular grid#

domain:
  plugin:
    name: LMDZ
    version: regular
  dir: /path/to/LMDZ/grid/directory
  file: LMDZ_grid_144x143x79.nc

YAML example for the icosahedral grid#

The LMDZ/dynamico domain plugin requires an additional input file to be provided.

domain:
  plugin:
    name: LMDZ
    version: dynamico
  dir: /path/to/LMDZ/grid/directory
  file: dynamico_grid_nbp80.nc
  file_vcoord: dynamico_vcoord_L79.nc
  file_mesh: dynamico_mesh_nbp80.nc
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