Input files

LMDZ-SACS input files are all in NetCDF format for binary files and namelist format for text files (execpt trajectory files which are save in raw binary format for I/O speed).

Note

NetCDF files containing species related fields can be named and formated in two ways:

• [fieldtype].nc: can contain data for several species

• [fieldtype]_[spec].nc: can contain data for only one species [spec] (this naming scheme has priority when LMDZ search for a NetCDF file)

Variables for a species "spec" are be named spec for forward or adjoint variables and spec_tl for tangent linear variables

Parameters file

• parameters.nml: namelist containing the parameters of the model

All parameters in parameters.nml

• dims namelist

  • ntrac: number of tracer species

• tracers namelist

  • tracer_species: array of tracer species name

  • tracer_flux: array of boolean indicating whether tracer have emissions

  • tracer_molar_mass: array of tracer species molar mass in g/mol

• time namelist

  • year: year of the simulation

  • month: month of the simulation

  • days_in_month: number of days in the month

  • nday: number of days in the simulation

  • period_flux: time frequency of the input fluxes in hours

  • nsplit_dyn: dynamics time step split (depend on grid resolution)

  • nsplit_phy: physics time step split (depend on grid resolution)

• flags namelist

  • forward: Execute the forward model (otherwise execute the adjoint model)

  • tangent: Execute the tangent linear model (forward must be true if tangent is true)

  • do_physics: Compute the physics

  • do_chemistry: Compute the chemistry

  • read_start_ad: Read the adjoint initial state (used when chaining multiple adjoint simulation)

  • save_trajq: Save trajectory files (necessary for forward chen also running adjoint simulation)

  • use_float: Use float precision instead of double precision for trajectory files

Domain files

• domain.nc: 3D domain coordinates (latitude, longitude, hybrid sigma pressure levels)

• mesh.nc: domain grid geometry (only used for dynamico grid)

Mass fluxes files

• fluxstoke.nc: 3 hourly mean of dynamics variables

• fluxstokev.nc: 3 hourly mean of dynamics variables (only used for regular grid)

• phystoke.nc: 3 hourly mean of physics variables, most variable are sparse and thus are compressed

Observation file

• obs.nc: observation information

  • time variable: observation time in seconds since first day of the month

  • icell variable: observation cell index (only used for dynamico grid)

  • ilon variable: observation longitude index (only used for regular grid)

  • ilat variable: observation latitude index (only used for regular grid)

  • ilon variable: observation longitude index

  • itrac variable: observation tracer index

  • obs_ad variable: mixing ratio sensitivity, required for adjoint

Tracers related fields files

Initial conditions files

• start.nc, start_[species].nc: initial mass mixing ratio for all tracers, in kg of species per kg of dry air.

  • [species] (lev, lat, lon) or (lev, cell) variable: initial mass mixing ratio, required for forward and tangent linear

  • [species]_tl (lev, lat, lon) or (lev, cell) variable: initial mass mixing ratio increments in kg/m²/s, required for tangent linear

  • [species] (lev, lat, lon) or (lev, cell) variable: initial mass mixing ratio sensitivity, required for adjoint when read_start_ad is true

Emissions files

• flux.nc, flux_[species].nc: tracers surface emissions in kg/m²/s

  • [species] (time, lat, lon) or (time, cell) variable: emissions, required for forward, tangent linear and adjoint

  • [species]_tl (time, lat, lon) or (time, cell) variable: emissions increments, required for tangent linear

Trajectory files

• trajq_[species].bin: 3 hourly tracers trajectory saved by the forward model, in kg of species per kg of dry air, required for adjoint only

Chemistry files

Chemical scheme file

• chemical_scheme.nml: namelist containing the parameters of the chemistry scheme (species names, reactions)

All variables in chemical_scheme.nml

• dims namelist

  • nprescr: number of prescribed species

  • nprodloss: number of tracer species with production and loss

  • ndepvel: number of tracer species with deposition velocity

  • njrates: number of J rates variables for photolysis reactions

  • nreac: number of reactions

• species namelist

  • prescribed_species: prescribed species names

  • prodloss_species: tracer species with production and loss names

  • deposition_species: tracer species with deposition velocity names

  • jrates_varname: J rates variables names

• reactions namelist

  • reactants: array (nreac, 2) of reactant species names in reactions

  • products: array (nreac, 2) of product species names in reactions

  • products_stoi: array (nreac, 2) of product species stoichiometric numbers in reactions

  • rate_type: array (nreac) of reaction types

  • rate_terms: array (nreac, 4) of reaction rate formula terms

  • jrates: array (nreac) of J rates variables names

Kinetic file

• kinetic.nc: daily 3D fields used to compute chemical reaction rates

  • pmid (time, lev, lat, lon) variable: pressure at mid-level in Pa

  • temp (time, lev, lat, lon) variable: temperature in K

Prescribed concentrations files

• prescrconcs.nc, prescrconcs_[species].nc: daily 3D fields of prescribed concentrations in mol/mol

  • [species] (time, lev, lat, lon) or (time, lev, cell) variable: prescribed concentrations, required for forward, tangent linear and adjoint

  • [species]_tl (time, lev, lat, lon) or (time, lev, cell) variable: prescribed concentrations increments, required for tangent linear

Note

Prescribed concentrations files are typically linked and not written by CIF, thus tangent linear and forward variables are always in separated files

Production and loss files

• prodloss3d.nc, prodloss3d_[species].nc: daily 3D fields of production (and loss if negative) in molec/cm³

  • [species] (time, lev, lat, lon) or (time, lev, cell) variable: production/loss concentrations, required for forward, tangent linear and adjoint

  • [species]_tl (time, lev, lat, lon) or (time, lev, cell) variable: production/loss concentrations increments, required for tangent linear

Note

Production concentrations files are typically linked and not written by CIF, thus tangent linear and forward variables are always in separated files

Deposition velocity files

• depositon.nc, depositon_[species].nc: daily 2D fields of deposition velocity in cm/s

  • [species], Dep_[species] (time, lat, lon) or (time, cell) deposition velocity

Photochemistry rates file

• photorates.nc: daily 3D fields of rates for photolysis reactions