5.6 Chemistry Input

The number densities of the chemical species must be provided as cell-centred quantities quc in cm$^{-3}$ (see Sect. 3.6). The array (UIO) headers must be named following this example: "Number density of H2".

The chemistry input file contains all data for the reaction network. It is a text file with a strict format following the UMIST 99 ratefile standard:

FORMAT(I4,5(A8,1X),2(1X,A4),1X,1PE8.2,3X,0PF5.2,2X,0PF8.1,A16)                                                

It consists of 12 columns with the following meaning:

col.	meaning	format
1	reaction ID	I4
2-4	reactants (max. 3 symbols with 8 characters)	3(A8,1X)
5-8	products (max. 4 symbols, first two with	2(A8,1X),2(1X,A4)
	8 characters, last 2 with 4 characters	2(A8,1X),2(1X,A4)
9	reaction coefficient $\alpha$	1PE8.2
10	reaction coefficient $\beta$	0PF5.2
11	reaction coefficient $\gamma$	0PF8.1
12	reference	A16

The symbols are usually the chemical symbols of the involved species, e.g. C for carbon. The present species are recognised automatically. Molecules consisting of more than one atom of the same chemical element, e.g. H$_2$, are also possible (H2). A special case is the representative metal M which is a catalytic element only, i.e. it must appear as reactant and product. The special symbol PHOTON represents a photon as reaction product. Currently no photon can be used as reactant ionising or exciting another species.

The reaction coefficients are needed to calculate the chemical rates at runtime. The basic rate is then given by

$$k = \alpha {T_{300}}^{\beta} e^{-\gamma/T}\enspace,$$ (93)

where $T_{300} = T/300$ K with $T$ the gas temperature. For catalytic reactions which involve a representative metal also the number density $n_\mathrm{M}$ of the metal enters:

$$k = n_\mathrm{M} \alpha {T_{300}}^{\beta} e^{-\gamma/T} \enspace.$$ (94)

An input file could look like this:

5001 H        H        H2       H2       H2                 9.00E-33   -0.6        0.0  -  AK
5002 H        H        H        H2       H                  4.43e-28   -4.0        0.0  DBDDG72
4069 H2       H2                H2       H        H         1.00e-08    0.00   84100.0L 28034
4071 H2       OH                O        H2       H         6.00e-09    0.00   50900.0L 16964
  66 C        OH                O        CH                 2.25e-11    0.50   14800.0L  4934
  67 C        OH                CO       H                  1.81e-11    0.50       0.0  -  W80
3707 C        O                 CO       PHOTON             1.58e-17    0.34    1297.4C BDD90
7001 C        O        H        CO       H                  2.14e-29   -3.08   -2114.0D DBDDG76
4076 CO       M                 O        C        M         2.79e-03   -3.52  128700.0D CBDDG76

Refer to [Wedemeyer-Böhm et al. (2005)] for more details.