UKCA & UMUI Tutorial 6

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Adding new Chemical Reactions

UKCA currently uses two different methods of defining the chemical reactions solved in the model. The first is a backward Euler solver, and is used for the RAQ and StdTrop chemistry schemes where the solver itself is created by a code-writer. The second makes use of the ASAD chemical integration software package, and is used for the CheT/TropIsop, CheS/Strat, and CheST/StratTrop chemistry schemes. ASAD can use many different solvers, although currently it uses symbolic Newton-Raphson solver. In this tutorial we will only consider the ASAD framework, as this is easily extended by a user.

ASAD considers four different types of chemical reactions: bimolecular reactions, termolecular reactions, heterogeneous reactions, and photolysis reactions.

Biomolecular Reactions

For most bimolecular reactions, it is sufficient to provide the $k_{0}$, $\alpha$, and $\beta$ coefficients that are used to compute the rate coefficient $k$ from the Arrhenius expression

$k=k_{0}\left({\frac {T}{300}}\right)^{\alpha }{\textrm {exp}}\left({\frac {-\beta }{T}}\right)$

Chemistry Defition Routines

The bimolecular reactions are defined in the ukca_chem_scheme.F90 routines using the ratb_t Fortran type specification, and are held in arrays. At the end of this routine the ratb_defs_scheme array is created from these, and if that scheme is selected in UKCA these reactions are copied across into the master ratb_defs array.

To format of this ratb_t type is

ratb_t('Reactant 1','Reactant 2','Product 1 ','Product 2 ','Product 3 ',&
'Product 4 ',  $k_{0}$,  $\alpha$,  $\beta$, Fraction of Product 1 produced, Fraction of Product 2 produced, Fraction of Product 3 produced, Fraction of Product 4 produced), & 

Where the fraction of a product can be set to 0.000 if this functionality does not need to be used, i.e. the fraction is 1.0.

The specifications of the induvidual reactions are done as, e.g.

ratb_t('OH        ','C5H8      ','ISO2      ','          ','          ',& ! B144 
'          ',  2.70E-11,  0.00,   -390.00, 0.000, 0.000, 0.000, 0.000), & ! B144 IUPAC2009   
...
ratb_t('OH        ','HCl       ','H2O       ','Cl        ','          ',& ! B159 
'          ',  1.80E-12,  0.00,    250.00, 0.000, 0.000, 0.000, 0.000), & ! B159 JPL2011   

The first reaction in these examples takes its kinetic data from IUPAC. Going to this website, this reaction is defined here. The second reaction above takes its kinetic data from NASA's Jet Propulsion Laboritory. The rate for this can be found on page 1-19 of the JPL2011 document.

If there is a reaction that is an exception to the general Arrhenius equation then special code needs to be placed in the asad_bimol.F90 routine, which is held in the UKCA/ directory.

Increase the size of JPBK (and JPNR)

As well as adding these reactions to the ukca_chem_scheme.F90 routine (and incrementing the size of the arrays in that routine accordingly, you will also need to increase the values of two parameters that UKCA needs. These are

• JPBK is the number of bimolecular reactions
• JPNR is the total number of reactions

These are set automatically in the UMUI (depending on what scheme is chosen), and are placed in the &RUN_UKCA namelist in CNTLATM. You will need to make a hand-edit to change these accordingly. The current value can be found by saving and processing the job, and then viewing the CNTLATM file in the $HOME/umui_jobs/jobid directory.

Task 6.1: Add a bimolecular reaction

TASK 6.1: You should now add in the bimolecular reaction of ALICE with OH to form BOB. This reaction is given by:

${\textrm {ALICE}}+{\textrm {OH}}\longrightarrow {\textrm {BOB}}$

Parameter	Value
$k_{0}$	2.70E-11
$\alpha$	0.00
$\beta$	-390.00

Note: If you were unable to successfully complete Task 5.2, then please take a copy of the f job from the Tutorial experiment (Tutorial: solution to Task 5.2 - adding new chemical emissions into a UKCA tracer) and work from there, as this will allow you to make only the required UKCA changes.

Solution

Termolecular Reactions

As well as defining reactions involving a third body, the termolecular rate definition can also be used to define unimolecular reactions.

The pressure and temperature dependent rate, $k$, of a termolecular reaction is given by

$k=\left({\frac {k_{0}\left[M\right]}{1+k_{0}\left[M\right]/k_{\infty }}}\right)F_{c}^{\left(1+\left[{\textrm {log}}_{10}\left({\frac {k_{0}\left[M\right]}{k_{\infty }}}\right)\right]^{2}\right)^{-1}}$

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Written by Luke Abraham 2013