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 .. admonition:: All parameters in ``parameters.nml`` :class: dropdown * ``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/m\ :sup:`2`/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) .. admonition:: All variables in ``chemical_scheme.nml`` :class: dropdown * ``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/cm\ :sup:`3` - ``[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