UKCA Chemistry and Aerosol vn10.4 Tutorial 8

UKCA Chemistry and Aerosol Tutorials at vn10.4

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_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 $H_{eff}$ are held in the henry_defs_scheme array, and has format

\ 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

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.

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:

$\ 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 u-ai084@26593

The specific Rose changes made are (this is just to update the branch revision number):

Index: trunk/app/fcm_make_um/rose-app.conf
===================================================================
--- trunk/app/fcm_make_um/rose-app.conf	(revision 26562)
+++ trunk/app/fcm_make_um/rose-app.conf	(revision 26593)
@@ -45,4 +45,4 @@
 stash_version=1A
 timer_version=3A
 um_rev=vn10.4
-um_sources=branches/dev/mohitdalvi/vn10.4_scale_lightning_nox@19623 branches/dev/stevenhardiman/vn10.4_ukca_tropopause_amendment@19627 branches/dev/alistairsellar/vn10.4_no_expvolc_so2@19808 branches/dev/marcuskoehler/vn10.4_ukca_fix_glomap_climatol_surfarea@24038 branches/dev/lukeabraham/vn10.4_UKCA_Tutorial_Solns@31374
+um_sources=branches/dev/mohitdalvi/vn10.4_scale_lightning_nox@19623 branches/dev/stevenhardiman/vn10.4_ukca_tropopause_amendment@19627 branches/dev/alistairsellar/vn10.4_no_expvolc_so2@19808 branches/dev/marcuskoehler/vn10.4_ukca_fix_glomap_climatol_surfarea@24038 branches/dev/lukeabraham/vn10.4_UKCA_Tutorial_Solns@31398

These differences can be found in the file /home/ukca/Tutorial/worked_solutions/Task8.1/task8.1.rose.diff on PUMA.

For a working UM branch that has completed this task, please see fcm:um.x_br/dev/lukeabraham/vn10.4_UKCA_Tutorial_Solns@31398

The specific UM changes made are:

Index: src/atmosphere/UKCA/ukca_chem_strattrop.F90
===================================================================
--- src/atmosphere/UKCA/ukca_chem_strattrop.F90	(revision 31374)
+++ src/atmosphere/UKCA/ukca_chem_strattrop.F90	(revision 31398)
@@ -58,8 +58,8 @@
 INTEGER, PARAMETER, PUBLIC :: ndry_st_aer    = 5         ! Aerosol chemistry
 
 ! No of wet deposited species
-INTEGER, PARAMETER, PUBLIC :: nwet_strattrop = 29        ! Stratos chemistry
-INTEGER, PARAMETER, PUBLIC :: nwet_st_aer    = 34        ! Aerosol chemistry
+INTEGER, PARAMETER, PUBLIC :: nwet_strattrop = 30        ! Stratos chemistry
+INTEGER, PARAMETER, PUBLIC :: nwet_st_aer    = 35        ! Aerosol chemistry
 
 
 ! ATA NLA CheST Chemistry v1.2
@@ -216,8 +216,8 @@
 chch_t( 75,'N2        ',  1,'CT        ','          ',  0,  0,  0),  &
 !  76 DD:37
 chch_t( 76,'ALICE     ',  1,'TR        ','          ',  1,  0,  1),  &
-!  77 
-chch_t( 77,'BOB       ',  1,'TR        ','          ',  0,  0,  0)   &
+!  77       WD:30
+chch_t( 77,'BOB       ',  1,'TR        ','          ',  0,  1,  0)   &
   /)
 
 TYPE(chch_t), PUBLIC :: chch_defs_strattrop_aer(1:89)=(/             &
@@ -373,19 +373,19 @@
 chch_t( 75,'N2        ',  1,'CT        ','          ',  0,  0,  0),  &
 !  76 DD:37
 chch_t( 76,'ALICE     ',  1,'TR        ','          ',  1,  0,  1),  &
-!  77 
-chch_t( 77,'BOB       ',  1,'TR        ','          ',  0,  0,  0),  &
+!  77       WD:31
+chch_t( 77,'BOB       ',  1,'TR        ','          ',  0,  1,  0),  &
 !  78
 chch_t( 78,'DMS       ',  1,'TR        ','          ',  0,  0,  0),  &
-!  79 DD:37,WD:31,EM:10
+!  79 DD:37,WD:32,EM:10
 chch_t( 79,'SO2       ',  1,'TR        ','          ',  1,  1,  1),  &
 !  80
 chch_t( 80,'H2SO4     ',  1,'TR        ','          ',  0,  0,  0),  &
 !  81
 chch_t( 81,'MSA       ',  1,'TR        ','          ',  0,  0,  0),  &
-!  82 DD:38,WD:32
+!  82 DD:38,WD:33
 chch_t( 82,'DMSO      ',  1,'TR        ','          ',  1,  1,  0),  &
-!  83 DD:39,WD:33,EM:11
+!  83 DD:39,WD:34,EM:11
 chch_t( 83,'NH3       ',  1,'TR        ','          ',  1,  1,  1),  &
 !  84
 chch_t( 84,'CS2       ',  1,'TR        ','          ',  0,  0,  0),  &
@@ -397,7 +397,7 @@
 chch_t( 87,'SO3       ',  1,'TR        ','          ',  0,  0,  0),  &
 !  88 DD:40,      EM: 12
 chch_t( 88,'Monoterp  ',  1,'TR        ','          ',  1,  0,  1),  &
-!  89 DD:41,WD:34
+!  89 DD:41,WD:35
 chch_t( 89,'Sec_Org   ',  1,'TR        ','          ',  1,  1,  0)   &
   /)
 
@@ -914,7 +914,9 @@
 !   28  MeCO2H
  0.4700e+04, 0.6000e+04, 0.1800e-04, 0.0000e+00, 0.0000e+00, 0.0000e+00,&
 !   29  MeOH
- 0.2300e+03, 0.4900e+04, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00 &
+ 0.2300e+03, 0.4900e+04, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,&
+!   30  BOB
+ 0.2100E+06, 0.8700E+04, 0.2000E+02, 0.0000E+00, 0.0000E+00, 0.0000E+00 &
   /),(/  6, nwet_strattrop/) )
 
 
@@ -979,13 +981,15 @@
  0.4700e+04, 0.6000e+04, 0.1800e-04, 0.0000e+00, 0.0000e+00, 0.0000e+00,&
 !   30  MeOH
  0.2300e+03, 0.4900e+04, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,&
-!   31  SO2
+!   31  BOB
+ 0.2100E+06, 0.8700E+04, 0.2000E+02, 0.0000E+00, 0.0000E+00, 0.0000E+00,&
+!   32  SO2
  0.1230e+01, 0.3020e+04, 0.1230e-01, 0.2010e+04, 0.6000e-07, 0.1120e+04,&
-!   32  DMSO
+!   33  DMSO
  0.5000e+05, 0.6425e+04, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,&
-!   33  NH3 (H*)
+!   34  NH3 (H*)
  0.1000e+07, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00, 0.0000e+00,&
-!   34  SEC_ORG
+!   35  SEC_ORG
  0.1000e+06, 0.1200e+02, 0.0000e-00, 0.0000e+00, 0.0000e+00, 0.0000e+00 &
   /),(/  6,  nwet_st_aer/) )
 
Index: src/atmosphere/UKCA/ukca_setup_chem_mod.F90
===================================================================
--- src/atmosphere/UKCA/ukca_setup_chem_mod.F90	(revision 31374)
+++ src/atmosphere/UKCA/ukca_setup_chem_mod.F90	(revision 31398)
@@ -255,7 +255,7 @@
   jppj            = 56
   jphk            = 0
   jpdd            = 37
-  jpdw            = 29
+  jpdw            = 30
   ! If aerosol chemistry on, add additional reactions
   IF (l_ukca_chem_aero) THEN
     l_ukca_achem     =.TRUE.

These differences can be found in the file /home/ukca/Tutorial/worked_solutions/Task8.1/task8.1.um.diff on PUMA.

If you open the .pk file in Xconv, you should still see the following fields:

 0    : 192   144   36    1     O3 MASS MIXING RATIO
 1    : 192   144   36    1     Molar flux density
 2    : 192   144   85    1     O3 MASS MIXING RATIO
 3    : 192   144   85    1     Field code =  2164
 4    : 192   144   85    1     Field code =  2165

Sample output from this task can be found at /work/n02/n02/ukca/Tutorial/vn10.4/sample_output/Task8.1/ai084a.pk19880901 on ARCHER.

Tutorial 9

Written by Luke Abraham 2016