UKCA Chemistry and Aerosol UMvn13.0 Tutorial 10

UKCA Chemistry and Aerosol Tutorials at UMvn13.0

Difficulty	EASY
Time to Complete	Under 1 hour
Video instructions	Walkthrough (YouTube)

Remember to run mosrs-cache-password.

What you will learn in this Tutorial

In this tutorial you will learn how the wet deposition of chemical species is handelled in UKCA. You will then add-in the wet deposition of one of your new tracers.

Task 10.1: Add wet deposition of a species

Task 10.1: Add in wet deposition for BOB, using the following values:

$\ k(298)\$	$\ -\left({\Delta H}/R\right)\$	$\ k(298)$ for the 1st dissociation	$\ -\left({\Delta H}/R\right)$ for the 1st dissociation	$\ k(298)$ for the 2nd dissociation	$\ -\left({\Delta H}/R\right)$ for the 2nd dissociation
$\ 0.21\times 10^{+06}\$	$\ 0.87\times 10^{+04}\$	$\ 0.2\times 10^{+02}\$	$\ 0.0\$	$\ 0.0\$	$\ 0.0\$

Adding Wet Deposition

The formulation used in UKCA is described in Giannakopoulos (1999)[1]. This scheme uses the following formula to calculate the effective Henry's Law coefficient

$H_{eff}=k\left(298\right)\exp \left(-{\frac {\Delta H}{R}}\left[\left({\frac {1}{T}}\right)-\left({\frac {1}{298}}\right)\right]\right)$

where $k\left(298\right)$ is the rate constant at 298K.

During this tutorial you will be tasked with adding the wet deposition of one of your new tracers. You will only need to make changes to your UKCA branch.

References

1. Giannakopoulos, C., M. P. Chipperfield, K. S. Law, and J. A. Pyle (1999), Validation and intercomparison of wet and dry deposition schemes using 210Pb in a global three-dimensional off-line chemical transport model, J. Geophys. Res., 104(D19), 23761–23784, doi:10.1029/1999JD900392.

Turning on Wet Deposition for a Species

src/science/core/chemistry/ukca_chem_master.F90

Within the UKCA code, whether a species is wet deposited or not is controlled in the ukca_chem_master.F90 module. In the chch_defs_master array there are lines like

!   9 DD:  6,WD:  4,
! No dry deposition for HO2NO2 in R and T schemes
chch_t1( 9,'HO2NO2    ',1,'TR        ','          ',0,1,r+t,0,0,107),          &
chch_t1( 9,'HO2NO2    ',1,'TR        ','          ',1,1,ti+s+st+cs,0,0,107),   &
!  10 DD:  7,WD:  5,   (20)
chch_t1(10,'HONO2     ',1,'TR        ','          ',1,1,ti+s+t+st+r+cs,        &
                                                                0,0,107),      &

Where the 1 in the 7th column turns on wet deposition of that species (being 0 otherwise). You will need to change the 0 to a 1 for the species that you wish to now wet deposit.

The parameters required to calculate $H_{eff}$ are held in the henry_defs_master array (of defined size n_wet_master), and has format

N	'SPECIES   '
$\ k(298)\$	$\ -\left({\Delta H}/R\right)\$	$\ k(298)$ for the 1st dissociation	$\ -\left({\Delta H}/R\right)$ for the 1st dissociation	$\ k(298)$ for the 2nd dissociation	$\ -\left({\Delta H}/R\right)$ for the 2nd dissociation
SCHEME	QUALIFIER	DISQUALIFIER	VN

Columns 3 and 4 are used if the species dissociates in the aqueous phase. In this case, $H_{eff}$ is further multiplied by a factor of

$1+{\frac {k(aq)}{H^{+}}}$

where

$k(aq)=k\left(298\right)\exp \left(-{\frac {\Delta H}{R}}\left[\left({\frac {1}{T}}\right)-\left({\frac {1}{298}}\right)\right]\right)$

and column 3 contains the values of $k(298)$ and column 4 contains the value of $-{\Delta H}/R$. Similarly, if the species dissociates a second time then a further factor of $1+k(aq)/H^{+}$ is applied, where this value of $k(aq)$ is calculated from the values of $k(298)$ and $-{\Delta H}/R$ in columns 5 and 6.

Examples for this array are

! WD: 4
wetdep(4,'HO2NO2    ',                                                         &
(/0.13e+05,0.69e+04,0.10e-04,0.00e+00,0.00e+00,0.0e+00/),ti+t+st+r+cs,0,0,107),&
wetdep(4,'HO2NO2    ',                                                         &
(/0.20e+05,0.00e+00,0.10e-04,0.00e+00,0.00e+00,0.00e+00/),s,0,0,107),          &
! WD: 5
wetdep(5,'HONO2     ',                                                         &
(/0.21e+06,0.87e+04,0.20e+02,0.00e+00,0.00e+00,0.0e+00/),ti+t+st+r+cs,0,0,107),&
wetdep(5,'HONO2     ',                                                         &
(/0.21e+06,0.87e+04,0.157e+02,0.00e+00,0.00e+00,0.00e+00/),s,0,0,107),         &

Worked Solution to Task 10.1: Add wet deposition of a species

You were given the task

• Add in wet deposition for BOB, using the following values:

$\ k(298)\$	$\ -\left({\Delta H}/R\right)\$	$\ k(298)$ for the 1st dissociation	$\ -\left({\Delta H}/R\right)$ for the 1st dissociation	$\ k(298)$ for the 2nd dissociation	$\ -\left({\Delta H}/R\right)$ for the 2nd dissociation
$\ 0.21\times 10^{+06}\$	$\ 0.87\times 10^{+04}\$	$\ 0.2\times 10^{+02}\$	$\ 0.0\$	$\ 0.0\$	$\ 0.0\$

The specific UKCA changes made are:

• https://code.metoffice.gov.uk/trac/ukca/changeset/568/main/branches/dev/lukeabraham/um13.0_ukca_tutorial_solutions

Index: src/science/core/chemistry/ukca_chem_master.F90
===================================================================
--- src/science/core/chemistry/ukca_chem_master.F90	(revision 567)
+++ src/science/core/chemistry/ukca_chem_master.F90	(revision 568)
@@ -106,7 +106,7 @@
 INTEGER, PARAMETER :: n_chch_master = 358 ! number of known species
 INTEGER, PARAMETER :: n_het_master  =  18 ! number of heterogeneous reactions
 INTEGER, PARAMETER :: n_dry_master  = 162 ! number of dry deposition reactions
-INTEGER, PARAMETER :: n_wet_master  = 159 ! number of wet deposition reactions
+INTEGER, PARAMETER :: n_wet_master  = 160 ! number of wet deposition reactions
 INTEGER, PARAMETER :: n_bimol_master = 1211 ! number of bimolecular reactions
 INTEGER, PARAMETER :: n_ratj_master = 183 ! number of photolysis reactions
 INTEGER, PARAMETER :: n_ratt_master = 116 ! number of termolecular reactions
@@ -921,7 +921,7 @@
 ! 284
 chch_t1(284,'ALICE     ',1,'TR        ','          ',1,0,st+cs,0,0,131),       &
 ! 285
-chch_t1(285,'BOB       ',1,'TR        ','          ',0,0,st+cs,0,0,131)        &
+chch_t1(285,'BOB       ',1,'TR        ','          ',0,1,st+cs,0,0,131)        &
 ]
 
 
@@ -2498,7 +2498,10 @@
 [1.84e+05,6.00e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00],cs,0,0,119),           &
 ! WD: 120  (Schwantes (2020) MVKN)
 wetdep(120, 'RU10NO3   ',                                                      &
-[1.84e+05,6.00e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00],cs,0,0,119)            &
+[1.84e+05,6.00e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00],cs,0,0,119),           &
+! UKCA Tutorial: wet deposition of BOB
+wetdep(121,'BOB       ',                                                       &
+[0.21e+06,0.87e+04,0.20e+02,0.00e+00,0.00e+00,0.00e+00],st+cs,0,0,131)         &
 ]
 
 ! ---------------------------------------------------------------------

These differences can be found here:

Tutorials/UMvn13.0/worked_solutions/Task10.1/Task10.1_ukca.patch

Sample output from this task can be found at

Tutorials/UMvn13.0/sample_output/Task10.1/

Note that while the concentrations of ALICE and BOB will have changed slightly, it will be hard to see any differences when plotting the species. If you look in the

cylc-run/[SUITE-ID]/work/1/atmos/pe_output/atmos.fort6.pe0

file and search for BOB you will be able to see the following lines

285 BOB        TR 0 1 131

and

BOB
0.210000E+06   0.870000E+04   0.200000E+02   0.000000E+00   0.000000E+00   0.000000E+00

These are showing that the dry deposition switch is now on (the 1 after the TR 0) and provides the list of Henry's Law values.

Checklist

☐ Put a 1 in the W column of the chch_defs_master in ukca_chem_master.F90.

☐ Append the Henry's Law parameter values in the depvel_defs_master array, and increment n_wet_master.

Tutorial 11

UKCA Chemistry and Aerosol Tutorials at UMvn13.0

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Written by Luke Abraham 2022