Formatting of GenChem files

Three types of simple text file are needed to describe chemical mechanisms in the GenChem system: Reactions, Species and Shorthands. The formatting of these is described briefly here, and further information and background can be found in Simpson et al 2020.

Reactions files


* Some simple lines
1.4e-12*EXP(-1310.*TINV)          : O3 + NO    = NO2 + <O2>  ; acp2004
5.681e-34*EXP(-2.6*LogTdiv300)    : OP + <O2> + <M>  = O3 ; acp2004
2.15e-11*EXP(110.*TINV)           : OD + <N2>  = OP       ; Updated (IUPAC 2009)

rcemis(NO,KDIM)                        : = NO  ;
  • END-OF-LINE is “;”. Text after this (e.g. references, or unused “products”) will be ignored.
  • Separator between rate coefficient and reaction is “:”.
  • lines beginning with “*” are comments (no “;” needed here)
  • lines beginning with “rcemis” are emission terms
  • lines beginning with “emisfiles” give name of emission files, e.g. nox
  • Some coefficients are defined in GenIn.shorthand, e.g. TINV, LogTdiv300
  • Anything else is simply used as the rate coefficient. (Do not add spaces!)

Four types of tracers/catalysts/yields are allowed, denoted by different types of parentheses:

  1. e.g. [OH] + VOC -> SOA will put xnew(OH) into the loss rate of VOC, but will not change the loss rate of OH.
  2. e.g. {O2} + OD -> OP will ignore the O2 term. Make sure it is in the reaction rate though if needed!
  3. e.g. OP + <O2> + <M> -> O3 will ignore the O2 and M term AND add their concentrations to the reaction rate (multiply it). This system is only used for these “special” species (O2, N2, M) as they must be pre-defined, e.g. O2(k), in boxChem and/or EMEP codes.
  4. e.g. 1.36e-11 : [OXYL] + [OH] = |YCOXY(0)| ASOC_ug1 + … will replace the contents of the || term with yield coefficients which will be updated each time-step in the EMEP model. These variables (here YCOXY(0)) must be predefined in order for and the emep model to compile.

Species files

The input to the script is GenIn_Species.csv, but this is assembled by do.GenChem from all needed _Species.csv files from the base_mechanisms and extra_mechanisms sub-directories. For example, for a typical emep run with base EmChem19a, do.GenChem appends EmChem19a_Species.csv, SeaSalt_Species.csv, and many more into one GenIn_Species.csv. The file contains columns with species name, type, formula, and various settings related to dry and wet deposition

The GenIn_Species.csv file is a spreadsheet-friendly comma-separated file where the characteristics of the chemical compounds are given:

BSOC_ng1e2,2,C,12.,ALD,ROOH,Cstar:0.1;DeltaH:30.0;OM25;PCM;BSOA,"! semi-volatile OC from BVOC "

The meaning of the columns is:

Spec - Species name as used in model.

adv - Type of compound. CTMs usually distinguish between advected and non-advected (or short-lived) species, in order to minimise CPU needs (concentrations of short-lived compounds only need chemical reaction terms, not advection). In addition, the EMEP model handles semivolatile SOA species through special handling (see below), and some species are so long-lived (e.g. CH4) that they can be accurately calculated without multiple iterations. Allowed values of type are:

0 - for short lived compounds (e.g. OH), which are not advected in the EMEP model.

1 - for advected compounds (e.g. O3, HCHO)

2 - for semivolatile SOA compounds (e.g. BSOC_ng100). The EMEP model (and boxChem) tracks such species by compound rather than phase, and calculates the partitioning between the phases dynamically, based upon the compound’s volatilty. Species labelled with type 2 are accounted within the list of advected species, but the start and end of the semivolatile list is calculated by, to produce integer variables which demarcate these semivolatile compounds, e.g. FIRST_SEMIVOL=136 and LAST_SEMIVOL=176.

3 - for compounds which react very slowly (e.g. CH4).

formula - If a true chemical formula is provided (e.g. CH3CHO, or O=CHC(O2)(CH3)CH2OH) then GenChem will calculate the number of atoms (C, H, O, S or N) and the molecular weight. Such formula must use capital letters; lower case letters are ignored as far as processing is concerned, but may be used to help document the intention, e.g. nC4H10 is identical to C4H10, or pm25 is particulate matter but whose formula we do not know. For example, an entry for an organic nitrate might have formula ‘someNO3’ which mixes lower and upper case. In this case the molecular weight must be given if this is needed for the chemical modelling. (Typically we do need the mass of emitted species, but not always the mass of other species since we usually use mixing ratios for advection and output in ppb units. Occassionally examples occur where mass is not strictly required, but where one wants to know the nitrogen content, typically where outputs are given in terms of e.g. ug(N)/m3. In this case, the ‘someNO3’ formula would be enough to allow GenChem to figure out that this compound contains one nitrogen atom.)

MW - can be dummy (xx) or a real number giving the molecular weight of the compound. When given, this value is used in place of any MW calculated from the formula. As noted above, the MW value is sometimes but not always needed. For some emitted compounds, usually connected with particulate matter where we do not know the composition, we have to give a dummy molecular weight. This information is used internally in the model to get associated mixing ratios, but outputs for such compounds should always be in mass-units so that consistency is preserved.

DRY - dry-deposition surrogate. The EMEP and ESX models calculate dry-deposition explicitly for a limited number of compounds, and here we can choose which of these compounds can be used as a surrogate for the desired species. For example, for O3 we simply use O3; for C2H5OOH we use the ROOH surrogate. If not dry-deposited, simply use xx. For the semivolatile SOA species EMEP/ESX CTMs will use this rate for the gas-phase fraction of the SOA.

WET - wet-deposition surrogate - similar to the dry deposition system. For example, for HCHO we simply use HCHO; for the semivolatile SOA species such as BSOC_ng100 we specify the same wet-deposition as for fine-particulate matter (denoted PMf), and the EMEP/ESX CTMs will use this rate for the condensed fraction of the SOA.

Groups - specifies groups which species belong to (e.g. OXN for oxidised nitrogen, RO2 for peroxy radicals) and allows surrogate species or factors to be assigned to these groups, e.g. Cstar:10.0;Extinc:0.4 assigns a vapour pressure Cstar (used in SOA modelling) to be 10 (ug/m3) and an Extinc coefficient to be 0.4. It is important that these groups are separated by semi-colons, not commas. This rather powerful feature is discussed further in Simpson et al. (Submitted, 2020).

Shorthands file

Shorthands are text-strings used in the Reactions.txt file, usually to represent commonly used rate-coefficients. The meaning of the text-string is given in _Shorthand.txt file, e.g.

XT           temp
FH2O         (1.0+1.4e-21*h2o*exp(2200.0*TINV))
KHO2RO2      2.91e-13*exp(1300.*TINV) ! MCM2001 ...
KMT12        IUPAC_troe(2.8e-31*exp(2.6*Log300divT),2.0e-12,exp(-TEMP/472.),M,0.75-1.27*(-TEMP/472.)/LOG(10.))

In these examples, XT is just a character-saving replacement for temp, FH2O gives a more complex expression, which also uses the pre-defined variable TINV = 1/temp. KHO2RO2 is a common rate-coefficient, but here we see that comments are allowed - anything afer the 2nd term. FInally, the KMT12 term shows that complex fuction calls are also allowed. IMPORTANT - avoid white space in any terms!