Difference between revisions of "UKCA Chemistry and Aerosol vn11.8 Tutorial 8"

Revision as of 11:57, 11 January 2021

UKCA Chemistry and Aerosol Tutorials at vn11.8

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:

$\ 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.

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_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.

Setting Henry's Law values

In the ukca_chem_master.F90 module 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),         &

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:

$\ 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\$

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.

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 9

Written by Luke Abraham 2021

@@ Line 76: / Line 76: @@
 and column 3 contains the values of <math>k(298)</math> and column 4 contains the value of <math>-{\Delta H}/R</math>. Similarly, if the species dissociates a second time then a further factor of <math>1+k(aq)/H^{+}</math> is applied, where this value of <math>k(aq)</math> is calculated from the values of <math>k(298)</math> and <math>-{\Delta H}/R</math> in columns 5 and 6.
-'''Note:''' As with the 2D dry deposition values in '''<code>depvel_defs_master</code>''', the order of '''<code>henry_defs_master</code>''' also assumes that the values are in the same order as the species (that wet deposit) in the '''<code>chch_defs_master</code>''' array.
 Examples for this array are