UKCA Chemistry and Aerosol vn10.9 Tutorial 7

UKCA Chemistry and Aerosol Tutorials at vn10.9+

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 7.1: adding new dry deposition values

TASK 7.1: You should now add in the dry deposition of ALICE. This species deposits in a similar way to CO. The values for depvel_defs_strattrop 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 ALICE to the CO block in the CASE statement.

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.

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

Chemistry Scheme Specification

The default is to use the 2D scheme, although it is advisable to use the interactive scheme. 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

!  10 DD: 7,WD: 4,
chch_t1(10,'HONO2     ',1,'TR        ','          ',1,1,0,TI+S+T+ST+R,0,0,107),&
!  11 DD: 8,WD: 5,
chch_t1(11,'H2O2      ',1,'TR        ','          ',1,1,0,TI+S+T+ST+OL+R,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.

2D Dry Deposition Scheme

The deposition velocities for the 2D scheme are defined in the depvel_defs_master array, which is held in the ukca_chem_master.F90 module. This is a large derived type containing an array made up of size (6,5) blocks, 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

! 7  
! R and T are at older revision than S and ST. Make consistent
depvel_t(7,'O3        ',& ! (Ganzeveld& Lelieveld (1995) note 1 
                          ! (modified to be the same as Guang's version)
(/0.05,  0.05,  0.05,  0.05,  0.05,  0.05,& !      1.1
  0.85,  0.30,  0.65,  0.65,  0.25,  0.45,& !      1.2
  0.65,  0.25,  0.45,  0.65,  0.25,  0.45,& !      1.3
  0.18,  0.18,  0.18,  0.18,  0.18,  0.18,& !      1.4
  0.05,  0.05,  0.05,  0.05,  0.05,  0.05/),& !      1.5
  TI+ST,0,0,107),&
depvel_t(7,'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),&
depvel_t(7,'O3        ',&
! O3 (Ganzeveld& Lelieveld (1995) - note 1)
(/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),&
! 9  
! No DD of NO in R scheme
depvel_t(8,'NO        ',& ! (inferred from NO2 - see Giannakopoulos (1998))
(/0.00,  0.00,  0.00,  0.00,  0.00,  0.00,& !      2.1
  0.14,  0.01,  0.07,  0.01,  0.01,  0.01,& !      2.2
  0.10,  0.01,  0.06,  0.01,  0.01,  0.01,& !      2.3
  0.01,  0.01,  0.01,  0.01,  0.01,  0.01,& !      2.4
  0.00,  0.00,  0.00,  0.00,  0.00,  0.00/),& !      2.5
  TI+T+S+ST,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 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 ukca_ddepctl.F90 routine which is called from ukca_chemistry_ctl.F90. The two routines ukca_aerod.F90 and 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 occurs throughout the boundary layer, rather than just in the lowest model (i.e. surface) layer.

Changes to 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.

Changes to 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 both 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)

Increase the value of JPDD

When you added a new chemical reaction you needed to increment a counter which gave the number of reactions, when adding new dry deposition of a species you will need to increase the size of the JPDD counter. This is done in the ukca_setup_chem_mod.F90 module.

Solution to Task 7.1: 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_strattrop 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 ALICE to the CO block in the CASE statement.

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

• ARCHER: u-as292@60203
• vm: u-as297@60160

The specific Rose changes made are:

• ARCHER: https://code.metoffice.gov.uk/trac/roses-u/changeset/60203/a/s/2/9/2/trunk
• vm: https://code.metoffice.gov.uk/trac/roses-u/changeset/60160/a/s/2/9/7/trunk

The specific Rose changes made are:

ARCHER:

Index: app/fcm_make/rose-app.conf
===================================================================
--- app/fcm_make/rose-app.conf	(revision 60067)
+++ app/fcm_make/rose-app.conf	(revision 60203)
@@ -42,4 +42,4 @@
 stash_version=1A
 timer_version=3A
 um_rev=vn10.9
-um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46619
+um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46683

These differences can be found in the file /home/ukca/Tutorial/vn10.9/worked_solutions/Task7.1/Task7.1_rose.patch on PUMA.

vm:

Index: app/fcm_make/rose-app.conf
===================================================================
--- app/fcm_make/rose-app.conf	(revision 59986)
+++ app/fcm_make/rose-app.conf	(revision 60160)
@@ -42,4 +42,4 @@
 stash_version=1A
 timer_version=3A
 um_rev=vn10.9
-um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46619
+um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46683

The specific UM changes made are:

Index: src/atmosphere/UKCA/ukca_chem_master.F90
===================================================================
--- src/atmosphere/UKCA/ukca_chem_master.F90	(revision 46619)
+++ src/atmosphere/UKCA/ukca_chem_master.F90	(revision 46683)
@@ -81,7 +81,7 @@
 ! define size of master chemistry
 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  =  57 ! number of dry deposition 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_bimol_master= 401 ! number of bimolecular reactions
 INTEGER, PARAMETER :: n_ratj_master =  76 ! number of photolysis reactions
@@ -377,7 +377,7 @@
 chch_t1(113,'MEMALD    ',1,'TR        ','          ',0,0,0,R,0,0,107),&
 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        ','          ',0,0,1,ST,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)/)
 
 ! Heterogeneous chemistry
@@ -3329,7 +3329,15 @@
   0.50,  0.50,  0.50,  0.50,  0.50,  0.50,&
   0.50,  0.50,  0.50,  0.50,  0.50,  0.50,&
   0.50,  0.50,  0.50,  0.50,  0.50,  0.50/),&
-  TI,A,0,107) /)
+  TI,A,0,107),&
+! UKCA Tutorial Task7.1
+depvel_t(53,'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,0,0,107) /)
 
 ! determine which chemistry is to be used. Test here that only one scheme is 
 ! selected.
Index: src/atmosphere/UKCA/ukca_surfddr.F90
===================================================================
--- src/atmosphere/UKCA/ukca_surfddr.F90	(revision 46619)
+++ src/atmosphere/UKCA/ukca_surfddr.F90	(revision 46683)
@@ -433,7 +433,7 @@
                      r_null,12500.0, 500.0,12500.0 /)
       CASE ('NH3       ')
         rsurf(:,n)=tenpointzero
-      CASE ('CO        ')
+      CASE ('CO        ','ALICE     ')
         rsurf(:,n)=(/ 3700.0, 7300.0, 4550.0, 1960.0, 4550.0,                 &
                       r_null, r_null, 4550.0, r_null /)  
         ! Shrub+bare soil set to C3 grass (guess)
@@ -517,7 +517,7 @@
         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       ')
@@ -594,7 +594,7 @@
         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      ')
@@ -648,7 +648,7 @@
       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)
@@ -706,7 +706,7 @@
       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)
Index: src/atmosphere/UKCA/ukca_aerod.F90
===================================================================
--- src/atmosphere/UKCA/ukca_aerod.F90	(revision 46619)
+++ src/atmosphere/UKCA/ukca_aerod.F90	(revision 46683)
@@ -231,6 +231,8 @@
       d0(j) = d_h2o * SQRT(m_h2o / m_meoh)
     CASE ('Monoterp  ')
       d0(j) = d_h2o * SQRT(m_h2o / m_monoterp)
+    CASE ('ALICE     ')
+      d0(j) = d_h2o * SQRT(m_h2o / m_ALICE)
     END SELECT
   END DO
   !

These differences can be found in the file /home/ukca/Tutorial/vn10.9/worked_solutions/Task7.1/Task7.1_code.patch on PUMA.

Sample output from this task can be found at /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task7.1/atmosa.pa19810901_00 on ARCHER.

Tutorial 8

---

Written by Luke Abraham 2017