Chemical mechanism

Chemical mechanism#

A chemical scheme is defined in 12 text files: ACTIVE_SPECIES, ANTHROPIC, BIOGENIC, CHEMISTRY, DEPO_PARS, DEPO_SPEC, FAMILIES, OUTPUT_SPECIES, PHOTO_PARAMETERS, REACTION_RATES, STOICHIOMETRY, WETD_SPEC. They must be named NAME.name_of_the_chemical_scheme (with NAME one of the 12) and stored in a directory named chemical_scheme/name_of_the_chemical_scheme.

See also the chemistry plugin for CHIMERE for documentation on the chemical mechanism.

ACTIVE_SPECIES#

Each line contains columns for the number of the species (the number of the line), its name, the number of the transport scheme on the horizontal (1 = PPM, 2 = Van Leer, other = up-wind), the number of the transport scheme on the vertical (1 = up-wind, 2 = Van Leer), the indicator for dry or humid boundary conditions (1 for dry BCs, which will then be converted into humid values for use by CHIMERE)

Each line thus reads as follows:

${LINE_NB} ${SPEC_NAME} ${HORIZ_SCHEME} ${VERT_SCHEME} ${DRY_HUMID_BC}

ANTHROPIC#

Each line contains columns for the number of the species (the number of the line) and its name (chosen among the ACTIVE_SPECIES).

BIOGENIC#

If not empty, each line contains columns for the number of the species (the number of the line) and its name (chosen among the ACTIVE_SPECIES).

CHEMISTRY#

Each line contains information on a chemical reaction, with columns for the number of reactants, the list of the names of these reactants, the number of products, the list of the names of these products. All names of species are taken from ACTIVE_SPECIES and the list of prescribed species: M, O2, N2, H2O. XXX see how to change them with TT version?XXX

DEPO_PARS#

A table of various deposition parameters, built from various references. The columns correspond to vegetation types, the lines to characteristics linked to deposition. Example for MELCHIOR2

DEPO_SPEC#

Each line contains columns for the name of the deposited species (among ACTIVE_SPECIES) and four related parameters: the molar mass of the model species (“rMx”), the effective Henry’s law constant (M. atm−1 ) for the gas (“rHx”), a normalized (0 to 1) reactivity factor for the dissolved gas (“rf0”) and a parameter that is not used so far (“rRwat”).

FAMILIES#

If not empty, contains the list of families. Each family is a sum of given ACTIVE_SPECIES, the sum is done for writing the output files, not used for any process in the model. Each line contains the name of the family (which must be different from any aCTIVE_SPECIES) = SPEC1 + SPEC2 + etc with SPECX among the ACTIVE_SPECIES.

OUTPUT_SPECIES#

Each line contains columns for the name of the species to print in the output file and its conversion factor: < 0 = ppb as computed by CHIMERE, 0 = dry ppb (e.g., for comparison to surface in-situ measurements), > 0 = converting factor to use as such.

PHOTO_PARAMETERS#

If not used, must contain “0 0 0 0”. Otherwise, contains the tabulated photolyis rates. The first line gives the number of tabulated zenithal angles, the number of photlysis reactions, a number of wavelenghts not used so far, the number of tabulated photolysis levels and the list of the altitudes of these levels. After three lines not used so far, each line contain the name of the photolysed species, t he zenithal angle, three values not used so far and the clear-sky photolysis rates for this angle and each of the altitude level.

REACTION_RATES#

Each line contains information on a chemical reaction, in the same order as CHEMISTRY, with columns for the number of the reaction (the number of the line), the type of kinetics rate and the various tabulated values required for this type of rate.

STOICHIOMETRY#

If not empty, each line gives the name of a species, a list of stoichiometric coefficients for a given number of temperatures (4 by default) and the number of the reaction (as in CHEMISTRY) in which the stoichiometry of the species applies.

WETD_SPEC#

Each line contains the name of the species to be wet-deposited (among ACTIVE_SPECIES), the type of wet deposition and three related parameters.

Parameters for advanced users:#

To make the reading of files easier, some maximal numbers are set:

  • ntyperate: maximal number of reaction types. Increase if the number of types of kinetics rates dealt with in rates increases.

  • nvegtype: maximal number of vegetation types. Increase if the number of vegetation types provided in DEPO_PARS increases.

  • nlduse: maximal number of land-use classes. Increase it the number of land-uses provided in LANDUSE_DOM increases.

    Warning

    must be kept consistent with the hard-coded definition of fveg in inidepo