UKCA Chemistry and Aerosol vn10.9 Tutorial 8

UKCA Chemistry and Aerosol Tutorials at vn10.9+

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 8.1: Add wet deposition of a species

Task 8.1: Add in wet deposition for BOB, using the following values:

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)} for the 1st dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)} for the 1st dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)} for the 2nd dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)} for the 2nd dissociation
Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.21 \times 10^{+06}\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.87 \times 10^{+04}\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.2 \times 10^{+02}\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.0\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.0\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 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

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle 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 Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle 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.

References

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

Chemistry Scheme Specification

Within the UKCA code, whether a species is wet deposited or not is controlled in the ukca_chem_scheme.F90 file. In the chch_defs_scheme array there are lines like

chch_t( 10,'HONO2     ',  1,'TR        ','          ',  1,  1,  0),  & !  10 DD: 7,WD: 4,       
chch_t( 11,'H2O2      ',  1,'TR        ','          ',  1,  1,  0),  & !  11 DD: 8,WD: 5,

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.

Setting Henry's Law values

In the ukca_chem_scheme.F90 the parameters required to calculate Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle H_{eff}} are held in the henry_defs_scheme array, and has format

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)} for the 1st dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)} for the 1st dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)} for the 2nd dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)} for the 2nd dissociation

Columns 3 and 4 are used if the species dissociates in the aqueous phase. In this case, Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle H_{eff}} is further multiplied by a factor of

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle 1+\frac{k(aq)}{H^{+}} }

where

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle 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 Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle k(298)} and column 4 contains the value of Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle -{\Delta H}/R} . Similarly, if the species dissociates a second time then a further factor of Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle 1+k(aq)/H^{+}} is applied, where this value of Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle k(aq)} is calculated from the values of Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle k(298)} and Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle -{\Delta H}/R} in columns 5 and 6.

Note: As with the 2D dry deposition values in depvel_defs_scheme, the order of henry_defs_scheme also assumes that the values are in the same order as the species (that wet deposit) in the chch_defs_scheme array.

Examples for this array are

0.2100E+06, 0.8700E+04, 0.2000E+02, 0.0000E+00, 0.0000E+00, 0.0000E+00,&   !    4  HONO2
0.8300E+05, 0.7400E+04, 0.2400E-11,-0.3730E+04, 0.0000E+00, 0.0000E+00,&   !    5  H2O2

Increase the value of JPDW

Similar to when adding dry deposition of a species you will need to increase the size of the JPDW counter. This is done in the ukca_setup_chem_mod.F90 module.

Solution to Task 8.1: Add wet deposition of a species

You were given the task

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

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)} for the 1st dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)} for the 1st dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)} for the 2nd dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)} for the 2nd dissociation
Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.21 \times 10^{+06}\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.87 \times 10^{+04}\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.2 \times 10^{+02}\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.0\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.0\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.0\ }

For a working Rose suite that has completed this task, please see

ARCHER: u-as292@60205
vm: u-as297@60206

The specific Rose changes made are:

ARCHER:

Index: app/fcm_make/rose-app.conf
===================================================================
--- app/fcm_make/rose-app.conf	(revision 60203)
+++ app/fcm_make/rose-app.conf	(revision 60205)
@@ -42,4 +42,4 @@
 stash_version=1A
 timer_version=3A
 um_rev=vn10.9
-um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46683
+um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46696

These differences can be found in the file /home/ukca/Tutorial/vn10.9/worked_solutions/Task8.1/Task8.1_rose.patch on PUMA.

vm:

 Index: app/fcm_make/rose-app.conf
===================================================================
--- app/fcm_make/rose-app.conf	(revision 60160)
+++ app/fcm_make/rose-app.conf	(revision 60206)
@@ -42,4 +42,4 @@
 stash_version=1A
 timer_version=3A
 um_rev=vn10.9
-um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46683
+um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46696

The specific UM changes made are:

Index: src/atmosphere/UKCA/ukca_chem_master.F90
===================================================================
--- src/atmosphere/UKCA/ukca_chem_master.F90	(revision 46683)
+++ src/atmosphere/UKCA/ukca_chem_master.F90	(revision 46696)
@@ -82,7 +82,7 @@
 INTEGER, PARAMETER :: n_chch_master = 150 ! number of known species
 INTEGER, PARAMETER :: n_het_master  =  10 ! number of heterogeneous reactions
 INTEGER, PARAMETER :: n_dry_master  =  58 ! number of dry deposition reactions
-INTEGER, PARAMETER :: n_wet_master  =  49 ! number of wet deposition reactions
+INTEGER, PARAMETER :: n_wet_master  =  50 ! number of wet deposition reactions
 INTEGER, PARAMETER :: n_bimol_master= 401 ! number of bimolecular reactions
 INTEGER, PARAMETER :: n_ratj_master =  76 ! number of photolysis reactions
 INTEGER, PARAMETER :: n_ratt_master =  49 ! number of termolecular reactions
@@ -378,7 +378,7 @@
 chch_t1(114,'GLY       ',1,'TR        ','          ',0,1,0,R,0,0,107),&
 chch_t1(115,'oXYLENE   ',1,'TR        ','          ',0,0,1,R,0,0,107),&
 chch_t1(116,'ALICE     ',1,'TR        ','          ',1,0,1,ST,0,0,107),&
-chch_t1(117,'BOB       ',1,'TR        ','          ',0,0,0,ST,0,0,107)/)
+chch_t1(117,'BOB       ',1,'TR        ','          ',0,1,0,ST,0,0,107)/)
 
 ! Heterogeneous chemistry
 ! Columns take the following meanings:
@@ -1039,7 +1039,10 @@
 wetdep(38,'s-BuOOH   ',&
 (/0.34e+03,0.57e+04,0.00e+00,0.00e+00,0.00e+00,0.00e+00/),R,0,0,107), & 
 wetdep(39,'GLY       ',&
-(/0.36e+06,0.00e+00,0.00e+00,0.00e+00,0.00e+00,0.00e+00/),R,0,0,107) /)
+(/0.36e+06,0.00e+00,0.00e+00,0.00e+00,0.00e+00,0.00e+00/),R,0,0,107),&
+!    UKCA Tutorial: wet deposition of BOB
+wetdep(40,'BOB       ',&
+(/0.21e+06,0.87e+04,0.20e+02,0.00e+00,0.00e+00,0.00e+00/),ST,0,0,107) /)
 
 ! Bimolecular reactions are too many to define here in one statement.
 TYPE(ratb_t1) :: ratb_defs_master(1:n_bimol_master)

These differences can be found in the file /home/ukca/Tutorial/vn10.9/worked_solutions/Task8.1/Task8.1_code.patch on PUMA.

Sample output from this task can be found at /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task8.1/atmosa.pa19810901_00 on ARCHER.

Tutorial 9

Written by Luke Abraham 2017