UKCA Chemistry and Aerosol UMvn13.0 Tutorial 9

UKCA Chemistry and Aerosol Tutorials at UMvn13.0

Difficulty	MEDIUM
Time to Complete	1-2 hours
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 two UKCA dry deposition schemes are implemented. You will then make changes to allow one of your new tracers to be dry-deposited.

Task 9.1: adding new dry deposition values

TASK 9.1: You should now add in the dry deposition of ALICE. This species deposits in a similar way to CO. The values for depvel_defs_master are:

Surface Type	Summer (day)	Summer (night)	Summer (24h ave)	Winter (day)	Winter (night)	Winter (24h ave)
Water	0.00	0.00	0.00	0.00	0.00	0.00
Forest	0.03	0.03	0.03	0.03	0.03	0.03
Grass	0.03	0.03	0.03	0.03	0.03	0.03
Desert	0.03	0.03	0.03	0.03	0.03	0.03
Ice	0.00	0.00	0.00	0.00	0.00	0.00

i.e. the same as for CO.

Hint
You will need to make changes for both dry deposition schemes. The changes to ukca_surfddr.F90 can be made very easily by adding equivalent options for ALICE where CO is found.

Adding Dry Deposition

UKCA uses two different dry-deposition schemes:

• A simple 2D parameterisation described by Giannakopoulos (1999)[1], Ganzeveld and Lelieveld (1995)[2], and Sander and Crutzen (1996)[3].
• A more detailed interactive parameterisation, based on the Wesely scheme (Wesely, 1989; Sanderson 2007)[4,5]

The default scheme is the interactive scheme, which is chosen by setting l_ukca_intdd to true in the UKCA panel.

Note: If you are using the interactive scheme and wish to add new values to it, you will also need to add values to the 2D scheme as well, otherwise you will get an error.

During this tutorial you will be tasked with adding the dry 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.
2. Ganzeveld, L., and J. Lelieveld (1995), Dry deposition parameterization in a chemistry general circulation model and its influence on the distribution of reactive trace gases, J. Geophys. Res., 100(D10), 20999–21012, doi:10.1029/95JD02266.
3. Sander, R., and P. J. Crutzen (1996), Model study indicating halogen activation and ozone destruction in polluted air masses transported to the sea, J. Geophys. Res., 101(D4), 9121–9138, doi:10.1029/95JD03793.
4. M.L. Wesely, Parameterization of surface resistances to gaseous dry deposition in regional-scale numerical models, Atmospheric Environment (1967), Volume 23, Issue 6, 1989, Pages 1293-1304, ISSN 0004-6981, http://dx.doi.org/10.1016/0004-6981(89)90153-4.
5. Sanderson, M. G., Collins, W. J., Hemming, D. L. and Betts, R. A. (2007), Stomatal conductance changes due to increasing carbon dioxide levels: Projected impact on surface ozone levels. Tellus B, 59: 404–411. doi: 10.1111/j.1600-0889.2007.00277.x

2D Dry Deposition Scheme

While the 2D scheme still exists within the code, all science configuration use the interactive scheme. However, it is still necessary to set the 2D scheme values.

src/science/core/chemistry/ukca_chem_master.F90

Within the UKCA code, whether a species is dry deposited or not is controlled in the ukca_chem_master.F90 file.

In the chch_defs_master array there are lines like

!   6 DD:  3,WD:  2,
! No dry deposition for NO3 in RAQ/S/T schemes.
chch_t1( 6,'NO3       ',1,'TR        ','NOx       ',0,1,r+s+t,0,0,107),        &
chch_t1( 6,'NO3       ',1,'TR        ','NOx       ',1,1,ti+st+cs,0,0,107),     &
chch_t1( 6,'NO3       ',1,'CF        ','NOx       ',0,0,ol,0,0,107),           &

Where the 1 in the 6th column turns on dry 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 dry deposit.

The deposition velocities for the 2D scheme are defined in the depvel_defs_master array. This is a large derived type containing a length 30 array, usually formatted to be made up of size (6,5) blocks (for ease of reading), of the format

N	'SPECIES   '
Summer (day) velocity over water	Summer (night) velocity over water	Summer (24h ave.) velocity over water	Winter (day) velocity over water	Winter (night) velocity over water	Winter (24h ave.) velocity over water
Summer (day) velocity over forest	Summer (night) velocity over forest	Summer (24h ave.) velocity over forest	Winter (day) velocity over forest	Winter (night) velocity over forest	Winter (24h ave.) velocity over forest
Summer (day) velocity over grass	Summer (night) velocity over grass	Summer (24h ave.) velocity over grass	Winter (day) velocity over grass	Winter (night) velocity over grass	Winter (24h ave.) velocity over grass
Summer (day) velocity over desert	Summer (night) velocity over desert	Summer (24h ave.) velocity over desert	Winter (day) velocity over desert	Winter (night) velocity over desert	Winter (24h ave.) velocity over desert
Summer (day) velocity over ice	Summer (night) velocity over ice	Summer (24h ave.) velocity over ice	Winter (day) velocity over ice	Winter (night) velocity over ice	Winter (24h ave.) velocity over ice
SCHEME	QUALIFIER	DISQUALIFIER	VN

and are in cm/s. The desert category is not used, and only the day and night values are considered in the calculation of the dry-deposition velocities. Examples of these values are

depvel_t(1,'O3        ',& ! (Ganzeveld & Lelieveld (1995) note 1)
                          ! (modified to be the same as Guang version)
(/0.05,  0.05,  0.05,  0.05,  0.05,  0.05,&   ! DD:  1.1
  0.85,  0.30,  0.65,  0.65,  0.25,  0.45,&   ! DD:  1.2
  0.65,  0.25,  0.45,  0.65,  0.25,  0.45,&   ! DD:  1.3
  0.18,  0.18,  0.18,  0.18,  0.18,  0.18,&   ! DD:  1.4
  0.05,  0.05,  0.05,  0.05,  0.05,  0.05/),& ! DD:  1.5
  ti+st+cs,0,0,107),                                                           &
! 2*
depvel_t(1,'O3        ',                                                       &
(/0.05,  0.05,  0.05,  0.05,  0.05,  0.05,                                     &
  1.00,  0.11,  0.56,  0.26,  0.11,  0.19,                                     &
  1.00,  0.37,  0.69,  0.59,  0.46,  0.53,                                     &
  0.26,  0.26,  0.26,  0.26,  0.26,  0.26,                                     &
  0.05,  0.05,  0.05,  0.05,  0.05,  0.05/),                                   &
  t+r,0,0,107),                                                                &
! 3**
! O3 (Ganzeveld& Lelieveld (1995) - note 1)
depvel_t(1,'O3        ',                                                       &
(/0.07,  0.07,  0.07,  0.07,  0.07,  0.07,                                     &
  1.00,  0.11,  0.56,  0.26,  0.11,  0.19,                                     &
  1.00,  0.37,  0.69,  0.59,  0.46,  0.53,                                     &
  0.26,  0.26,  0.26,  0.26,  0.26,  0.26,                                     &
  0.07,  0.07,  0.07,  0.07,  0.07,  0.07/),                                   &
  s,0,0,107),                                                                  &

Note: as you can see above, this definition makes use of the N, SCHEME, QUALIFIER, DISQUALIFIER, and VN format, and the settings for these are the same as in the adding new tracers tutorial, although here N should be incremented for each new deposition, where there might be the same species specified several times with changes to deposition velocities.

This scheme is controlled in src/science/core/chemistry/deposition/ukca_ddeprt.F90. The deposition only occurs in the bottom (i.e. 'surface') layer.

Interactive Dry Deposition Scheme

Adding in new species to the interactive scheme is slightly more involved than for the 2D scheme. This scheme is controlled from the src/science/core/chemistry/deposition/ukca_ddepctl.F90 routine which is called from whichever ukca_chemistry_ctl routine is used (held within src/science/core/chemistry/). You will likely not need to edit this routine directly.

The two routines src/science/core/chemistry/deposition/ukca_aerod.F90 and src/science/core/chemistry/deposition/ukca_surfddr.F90 contain species specific information, and it is these routines that need to be altered to add in values for a new species. Further details on this scheme can be found in the The UKCA UM documentation paper.

When using this scheme, dry deposition can either occur throughout the boundary layer or from just the lowest model (i.e. surface) layer. This is controlled by the namelist variable l_ukca_ddep_lev1 in the UKCA panel.

src/science/core/chemistry/deposition/ukca_aerod.F90

This routine calculates the aerodynamic and quasi-laminar surface resistances. The species dependant information that is needed is the diffusion coefficient, d0 (in units of $m^{2}s^{-1}$). By default this is set to -1 if the species is not deposited. If it is deposited, and there are no values for this coefficient in the literature, it is suggested that $d_{0,{\textrm {species}}}$ is calculated as

$d_{0,{\textrm {species}}}=d_{0,H_{2}O}\ {\sqrt[{}]{M_{H_{2}O}/M_{\textrm {species}}}}$

Where $M_{H_{2}O}$ is the relative molecular mass of H2O, and $M_{\textrm {species}}$ is the relative molecular mass of the species being deposited, and $d_{0,H_{2}O}$ is the diffusion coefficient for H2O (2.08E-5 $m^{2}s^{-1}$).

You should add in an appropriate value for the new species that you are depositing in the CASE statement in this routine. Examples of how this is already done are

           CASE ('O3        ','NO2       ','O3S       ','NO3       ')
             d0(j) = 1.4e-5
           CASE ('HONO      ')
             d0(j) = d_h2o * SQRT(m_h2o / m_hono)

Note: If you have not yet defined a M_species value for your new species, you will need to do this in ukca_constants.F90.

src/science/core/chemistry/deposition/ukca_surfddr.F90

The Wesely scheme considers 9, 13, 17, or 27 different surface types:

9 Surface Types	13 Surface Types	17 Surface Types	27 Surface Types
5 Plant Functional Types	9 Plant Functional Types	13 Plant Functional Types	13 Plant Functional Types
Broadleaved trees Needleleaf trees C3 Grass C4 Grass Shrub Urban Water Bare Soil Ice	Broadleaved deciduous trees Broadleaved evergreen tropical trees Broadleaved evergreen temperate trees Needleleaf deciduous trees Needleleaf evergreen trees C3 Grass C4 Grass Shrub deciduous Shrub evergreen Urban Water Bare Soil Ice	Broadleaved deciduous trees Broadleaved evergreen tropical trees Broadleaved evergreen temperate trees Needleleaf deciduous trees Needleleaf evergreen trees C3 Grass C3 Crop C3 Pasture C4 Grass C4 Crop C4 Pasture Shrub deciduous Shrub evergreen Urban Water Bare Soil Ice	Broadleaved deciduous trees Broadleaved evergreen tropical trees Broadleaved evergreen temperate trees Needleleaf deciduous trees Needleleaf evergreen trees C3 Grass C3 Crop C3 Pasture C4 Grass C4 Crop C4 Pasture Shrub deciduous Shrub evergreen Urban Water Bare Soil Ice Elevated ice level 1 Elevated ice level 2 Elevated ice level 3 Elevated ice level 4 Elevated ice level 5 Elevated ice level 6 Elevated ice level 7 Elevated ice level 8 Elevated ice level 9 Elevated ice level 10

The examples below are given for 9 surface types, but you will need to make changes for all options.

ukca_surfddr.F90 sets the surface resistance (in $sm^{-1}$) for each of the species dry-deposited (rsurf)). If a species is not deposited onto a particular type of surface (but is deposited onto other types) then its resistance on this type can be set to a very large value (r_null). Often many species are assigned the same values. You will need to add in appropriate values for your species into the CASE statement within this routine.

Examples of how this is already done are

           CASE ('NO2       ','NO3       ')
       rsurf(:,n)=(/225.,225.,400.,400.,600.,1200.,2600.,1200.,       &
         3500. /)
           CASE ('CO        ')
       rsurf(:,n)=(/3700.,7300.,4550.,1960.,4550.0,r_null,r_null,     &
         4550.0,r_null /)  ! Shrub+bare soil set to C3 grass (guess)

Remember to make the changes for ALL the case statements associated with the different numbers of surface types.

Notice above that NO2 and NO3 are treated the same way with the same rsurf values, whereas CO is treated separately. When species deposit in the same way it is possible to simplify the routine and group them together in this way. Whether this is done or not will be down to your judgement when setting the values - if species deposit in a similar way then it's possible to group them like this. If they deposit differently then you will need a new block of code.

Towards the end of the ukca_surfddr.F90 routine there is a large IF block where modifications are made to certain species. You may also need to make modifications here or add-in new code depending on how the resistance needs to be calculated.

Note that ukca_surfddr.F90 is a complex routine that has many different options for the different surface types that could be available. Care should be taken when editing this routine to ensure that changes are made correctly.

Worked Solution to Task 9.1: adding new dry deposition values

You were given the task

• You should now add in the dry deposition of ALICE. This species deposits in a similar way to CO. The values for depvel_defs_master are:

Surface Type	Summer (day)	Summer (night)	Summer (24h ave)	Winter (day)	Winter (night)	Winter (24h ave)
Water	0.00	0.00	0.00	0.00	0.00	0.00
Forest	0.03	0.03	0.03	0.03	0.03	0.03
Grass	0.03	0.03	0.03	0.03	0.03	0.03
Desert	0.03	0.03	0.03	0.03	0.03	0.03
Ice	0.00	0.00	0.00	0.00	0.00	0.00

i.e. the same as for CO.

You were given the hint:

• You will need to make changes for both dry deposition schemes. The changes to ukca_surfddr.F90 can be made very easily by adding equivalent options for ALICE where CO is found.

The specific UKCA changes made are:

• https://code.metoffice.gov.uk/trac/ukca/changeset/567/main/branches/dev/lukeabraham/um13.0_ukca_tutorial_solutions

Index: src/science/core/chemistry/deposition/ukca_aerod.F90
===================================================================
--- src/science/core/chemistry/deposition/ukca_aerod.F90	(revision 556)
+++ src/science/core/chemistry/deposition/ukca_aerod.F90	(revision 567)
@@ -170,7 +170,8 @@
     m_dhpr12ooh,                                                               &
     m_dhcarb9,                                                                 &
     m_ru12no3,                                                                 &
-    m_ru10no3
+    m_ru10no3,                                                                 &
+    m_alice
 
 USE ukca_um_legacy_mod,      ONLY: rmol, vkman, gg => g
 USE parkind1,                ONLY: jprb, jpim
@@ -571,6 +572,9 @@
     CASE ('RU12OOH   ')
          ! m_cri = 150 (same as sec_org) => d0(j) = 0.72e-5
       d0(j) = d_h2o * SQRT(m_h2o / m_cri)
+    CASE ('ALICE     ')
+      ! UKCA Tutorial - dry deposition of ALICE
+      d0(j) = d_h2o * SQRT(m_h2o / m_alice)
     END SELECT
   END DO
   !
Index: src/science/core/chemistry/deposition/ukca_surfddr.F90
===================================================================
--- src/science/core/chemistry/deposition/ukca_surfddr.F90	(revision 556)
+++ src/science/core/chemistry/deposition/ukca_surfddr.F90	(revision 567)
@@ -739,7 +739,7 @@
         ELSE
           rsurf(:,n)=tenpointzero
         END IF
-      CASE ('CO        ')
+      CASE ('CO        ','ALICE     ')
         IF (l_fix_improve_drydep) THEN
           rsurf(:,n)=[ 3700.0, 7300.0, 4550.0, 1960.0, 4550.0,                 &
                         r_null, r_null, 4550.0, r_null ]
@@ -927,7 +927,7 @@
         rsurf(:,n)=rooh
       CASE ('NH3       ')
         rsurf(1:6,n)=[ 137.0,111.1,111.9,131.3,130.4,209.8 ]
-      CASE ('CO        ')
+      CASE ('CO        ','ALICE     ')
         rsurf(1:6,n)=[ 3700.0,3700.0,3700.0,7300.0,7300.0,4550.0 ]
         ! Shrub+bare soil set to C3 grass (guess)
       CASE ('CH4       ')
@@ -1065,7 +1065,7 @@
         rsurf(7:13,n)=[ 618.6,648.6,784.3,888.9,4000.0,1290.3,4000.0 ]
       CASE ('NH3       ')
         rsurf(7:13,n)=[ 196.1,185.8,196.1,180.7,148.9,213.5,215.1 ]
-      CASE ('CO        ')
+      CASE ('CO        ','ALICE     ')
         rsurf(7:13,n)=[ 1960.0,4550.0,4550.0,r_null,r_null,4550.0,r_null ]
           ! Shrub+bare soil set to C3 grass (guess)
       CASE ('HCHO      ')
@@ -1178,7 +1178,7 @@
       CASE ('NH3       ')
         rsurf(7:17,n)=[ 209.8,209.8,196.1,196.1,196.1,                         &
                          185.8,196.1,180.7,148.9,213.5,215.1 ]
-      CASE ('CO        ')
+      CASE ('CO        ','ALICE     ')
         rsurf(7:17,n)=[ 4550.0,4550.0,1960.0,1960.0,1960.0,                    &
                          4550.0,4550.0,r_null,r_null,4550.0,r_null ]
           ! Shrub+bare soil set to C3 grass (guess)
@@ -1277,7 +1277,7 @@
       CASE ('NH3       ')
         rsurf(18:27,n)=[ 215.1,215.1,215.1,215.1,215.1,                        &
                           215.1,215.1,215.1,215.1,215.1 ]
-      CASE ('CO        ')
+      CASE ('CO        ','ALICE     ')
         rsurf(18:27,n)=[ r_null,r_null,r_null,r_null,r_null,                   &
                           r_null,r_null,r_null,r_null,r_null ]
           ! Shrub+bare soil set to C3 grass (guess)
@@ -2513,7 +2513,8 @@
 
     END IF
 
-  ELSE IF (speci(nldepd(j)) == 'CO        ') THEN
+  ELSE IF ((speci(nldepd(j)) == 'CO        ') .OR.                             &
+           (speci(nldepd(j)) == 'ALICE     ')) THEN
 
     !         Only assign values for CO if microbes are active.
     ! Shrub and bare soil are assumed to be tundra if latitude > 60N;
Index: src/science/core/chemistry/ukca_chem_master.F90
===================================================================
--- src/science/core/chemistry/ukca_chem_master.F90	(revision 556)
+++ src/science/core/chemistry/ukca_chem_master.F90	(revision 567)
@@ -105,7 +105,7 @@
 ! Define size of master chemistry
 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  = 161 ! number of dry deposition 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_bimol_master = 1211 ! number of bimolecular reactions
 INTEGER, PARAMETER :: n_ratj_master = 183 ! number of photolysis reactions
@@ -919,7 +919,7 @@
 ! 283
 chch_t1(283,'MACO3     ',1,'OO        ','          ',0,0,cs,rp,0,119),         &
 ! 284
-chch_t1(284,'ALICE     ',1,'TR        ','          ',0,0,st+cs,0,0,131),       &
+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)        &
 ]
@@ -8332,7 +8332,15 @@
   0.63,  0.06,  0.35,  0.08,  0.06,  0.07,                                     &
   0.03,  0.03,  0.03,  0.03,  0.03,  0.03,                                     &
   0.01,  0.01,  0.01,  0.01,  0.01,  0.01],                                    &
-  cs,0,0,119)                                                                  &
+  cs,0,0,119),                                                                 &
+! UKCA Tutorial - ALICE dry deposition
+depvel_t(162,'ALICE     ',                                                     &
+[0.00,  0.00,  0.00,  0.00,  0.00,  0.00,                                      &
+  0.03,  0.03,  0.03,  0.03,  0.03,  0.03,                                     &
+  0.03,  0.03,  0.03,  0.03,  0.03,  0.03,                                     &
+  0.03,  0.03,  0.03,  0.03,  0.03,  0.03,                                     &
+  0.00,  0.00,  0.00,  0.00,  0.00,  0.00],                                    &
+  st+cs,0,0,131)                                                               &
 ]
 
 ! ----------------------------------------------------------------------

These differences can be found here:

Tutorials/UMvn13.0/worked_solutions/Task09.1/Task09.1_ukca.patch

Sample output from this task can be found at

Tutorials/UMvn13.0/sample_output/Task09.1/

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 ALICE you will be able to see the following lines

284 ALICE      TR 1 0 131

and

ALICE
0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
0.030000  0.030000  0.030000  0.030000  0.030000  0.030000
0.030000  0.030000  0.030000  0.030000  0.030000  0.030000
0.030000  0.030000  0.030000  0.030000  0.030000  0.030000
0.000000  0.000000  0.000000  0.000000  0.000000  0.000000

These are showing that the dry deposition switch is now on (the 1 after the TR) and provides the list of 2D dry deposition values.

Checklist

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

☐ Append deposition velocity values to the depvel_defs_master array, and increment n_dry_master.

☐ Put the correct M_species value in ukca_constants.F90.

☐ In ukca_aerod.F90, append the CASE statement with your new species to set a value for d0.

☐ In ukca_surfddr.F90, append all the CASE statements (for the various different numbers of surface types) with the values for your new species.

Tutorial 10

UKCA Chemistry and Aerosol Tutorials at UMvn13.0

---

Written by Luke Abraham 2022