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[[UKCA Chemistry and Aerosol Tutorials | Back to UKCA Chemistry and Aerosol Tutorials]]
  
[[UKCA Chemistry and Aerosol Tutorials | Back to UKCA Chemistry and Aerosol Tutorials]]
   
  +
==What you will learn in this Tutorial==
−
==Adding new Chemical Reactions==
  
   
  +
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.
−
UKCA currently uses two different methods of defining the chemical reactions solved in the model. The first is a backward Euler solver, and is used for the ''RAQ'' and ''StdTrop'' chemistry schemes where the solver itself is created by a code-writer. The second makes use of the [http://www.atm.ch.cam.ac.uk/acmsu/asad/ ASAD chemical integration software package], and is used for the ''CheT/TropIsop'', ''CheS/Strat'', and ''CheST/StratTrop'' chemistry schemes. ASAD can use many different solvers, although currently it uses symbolic Newton-Raphson solver. In this tutorial we will only consider the ASAD framework, as this is easily extended by a user.
  
   
  +
==Task 9.1: adding new dry deposition values==
−
ASAD considers four different types of chemical reactions: bimolecular reactions, termolecular reactions, heterogeneous reactions, and photolysis reactions. To make changes and add reactions you will need to make changes to the UKCA source code which can be found in
 
   
  +
<span style="color:green">'''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_strattrop''' are:</span>
−
vn8.2_<span style="color:blue">your_branch_name</span>/src/atmosphere/UKCA
  
   
  +
{| border="1"
−
During this tutorial you will be tasked with adding a new reaction into your branch.
  
  +
! 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
  +
|}
   
  +
<span style="color:green">i.e. the same as for CO.</span>
−
==Biomolecular Reactions==
  
   
  +
{| class="collapsible collapsed wikitable"
−
For most bimolecular reactions, it is sufficient to provide the <math>k_{0}</math>, <math>\alpha</math>, and <math>\beta</math> coefficients that are used to compute the rate coefficient <math>k</math> from the Arrhenius expression
  
  +
|-
  +
! 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 <tt>CASE</tt> statement.
  +
|}
   
  +
'''Note:''' If you were unable to successfully complete [[UKCA Chemistry and Aerosol Tutorial 8#Task 8.1: Add a bimolecular reaction|Task 8.1]], then please take a copy of the '''h''' job from the Tutorial experiment (''Tutorial: solution to Task 8.1 - add a new bimolecular reaction'') and work from there, as this will allow you to only make the changes required for this task.
−
<math>
  
−
k = k_{0} \left(\frac{T}{300}\right)^{\alpha} \textrm{exp} \left(\frac{-\beta}{T}\right)
  
−
</math>
  
   
  +
==Adding Dry Deposition==
−
===Bimolecular Reaction Definition===
  
   
  +
UKCA uses two different dry-deposition schemes:
−
The bimolecular reactions are defined in the '''ukca_chem_<span style="color:blue">scheme</span>.F90''' routines using the '''ratb_t''' Fortran type specification, and are held in arrays. At the end of this routine the '''ratb_defs_<span style="color:blue">scheme</span>''' array is created from these, and if that scheme is selected in UKCA these reactions are copied across into the master '''ratb_defs''' array.
  
   
  +
* A simple 2D parameterisation described by Giannakopoulos (1999)[1], Ganzeveld and Lelieveld (1995)[2], and Sander and Crutzen (1996)[3].
−
The format of this '''ratb_t''' type is
  
  +
* A more detailed interactive parameterisation, based on the Wesely scheme (Wesely, 1989; Sanderson 2007)[4,5]
   
  +
The default scheme is the 2D scheme. To choose the interactive dry deposition scheme in the UMUI, go to '''Model Selection &rarr; Atmosphere &rarr; Model Configuration &rarr; UKCA Chemistry and Aerosols &rarr; COUPL''' and select '''UKCA interactive dry deposition scheme'''.
−
ratb_t('Reactant 1','Reactant 2','<span style="color:blue">Product 1 </span>','<span style="color:red">Product 2 </span>','<span style="color:green">Product 3 </span>',&
  
−
'<span style="color:purple">Product 4 </span>', <math>k_{0}</math>, <math>\alpha</math>, <math>\beta</math>, <span style="color:blue">Fraction of Product 1 produced</span>, <span style="color:red">Fraction of Product 2 produced</span>, &
  
−
<span style="color:green">Fraction of Product 3 produced</span>, <span style="color:purple">Fraction of Product 4 produced</span>), &
 
   
  +
'''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. As the 2D scheme is the default, it must always have values set.
−
If fractional products are not required for a reaction, then the ''fraction of each product'' formed should be set to 0.000. If fractional products are required for any one of the products then the fraction of each product formed should be set to its correct value.
  
   
  +
During this tutorial you will be tasked with adding the dry deposition of one of your new tracers.
−
The specifications of the individual reactions are done as, e.g.
  
   
  +
'''References'''
−
ratb_t('O3 ','C5H8 ','HO2 ','OH ',' ',& ! B133
 
  +
# 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.
−
' ', 3.33E-15, 0.00, 1995.00, 0.750, 0.750, 0.000, 0.000), & ! B133 IUPAC2007*
 
  +
# 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.
−
...
  
  +
# 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.
−
ratb_t('OH ','C5H8 ','ISO2 ',' ',' ',& ! B144
 
  +
# 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.
−
' ', 2.70E-11, 0.00, -390.00, 0.000, 0.000, 0.000, 0.000), & ! B144 IUPAC2009
 
  +
# 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
−
...
  
−
ratb_t('OH ','HCl ','H2O ','Cl ',' ',& ! B159
 
−
' ', 1.80E-12, 0.00, 250.00, 0.000, 0.000, 0.000, 0.000), & ! B159 JPL2011
 
   
  +
==Chemistry Scheme Specification==
−
The first reaction in these examples takes its kinetic data from [http://www.iupac-kinetic.ch.cam.ac.uk/ IUPAC]. Going to this website, this reaction is defined [http://www.iupac-kinetic.ch.cam.ac.uk/datasheets/xhtml/HOx_VOC8_HO_CH2C%28CH3%29CHCH2%28isoprene%29.xhtml_mathml.xml here]. The second reaction above takes its kinetic data from [http://jpldataeval.jpl.nasa.gov/ NASA's Jet Propulsion Laboratory]. The rate for this can be found on page 1-19 of the [http://jpldataeval.jpl.nasa.gov/pdf/JPL%2010-6%20Final%2015June2011.pdf JPL2011 document]. When adding new reactions you will need to increment the size of the array holding the <tt>ratb_t</tt> type.
  
   
  +
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_<span style="color:blue">scheme</span>.F90''' file. In the '''chch_defs_<span style="color:blue">scheme</span>''' array there are lines like
−
To add new bimolecular reactions you will need to append equivalent lines for the new reactions to the end of the '''ratb_defs_<span style="color:blue">scheme</span>''' array (increasing the array sizes accordingly). If there is a reaction that is an exception to the general Arrhenius equation then special code needs to be placed in the '''asad_bimol.F90''' routine, which is held in the <tt>UKCA/</tt> source-code directory.
  
   
  +
chch_t( 10,'HONO2 ', 1,'TR ',' ', <span style="color:red">'''1'''</span>, 1, 0), & ! 10 DD: 7,WD: 4,
−
===Increase the size of JPBK (and JPNR)===
  
  +
chch_t( 11,'H2O2 ', 1,'TR ',' ', <span style="color:red">'''1'''</span>, 1, 0), & ! 11 DD: 8,WD: 5,
   
−
As well as adding these reactions to the ''ukca_chem_<span style="color:blue">scheme</span>.F90'' routine (and incrementing the size of the arrays in that routine accordingly, you will also need to increase the values of two parameters that UKCA needs. These are
 +
Where the <span style="color:red">'''1'''</span> 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==
−
* '''JPBK''' is the number of bimolecular reactions
  
−
* '''JPNR''' is the total number of reactions
  
   
  +
The deposition velocities for the 2D scheme are defined in the '''depvel_defs_<span style="color:blue">scheme</span>''' array, which is held in the '''ukca_chem_<span style="color:blue">scheme</span>.F90''' module. This is a large array made up of size (6,5) blocks. These blocks mean
−
These are set automatically in the UMUI (depending on what scheme is chosen), and are placed in the <code>&RUN_UKCA</code> namelist in '''CNTLATM'''. You will need to make a hand-edit to change these accordingly. The current values can be found by saving and processing the job, and then viewing the ''CNTLATM'' file in your <tt>$HOME/umui_jobs/<span style="color:blue">jobid</span></tt> directory.
  
   
  +
{| border="1"
−
==Termolecular Reactions==
  
  +
| 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
  +
|}
   
  +
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
−
As well as defining reactions involving a third body, the termolecular rate definition can also be used to define unimolecular reactions.
 
   
  +
! 1 O3 (Ganzeveld & Lelieveld (1995) note 1 (modified to same as Guang)
−
The pressure and temperature dependent rate, <math>k</math>, of a termolecular reaction is given by
  
  +
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
  +
! 2 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
   
  +
'''Note:''' When adding new deposition values you should be careful. UKCA assumes that the order of this array is the same as the order of the species in the '''chch_defs_<span style="color:blue">scheme</span>''' array. If you are adding values for a species in the middle of the list then you will need to make sure that you slot it in to the appropriate place in the existing '''depvel_defs_<span style="color:blue">scheme</span>''' array (and change the size of this array accordingly).
−
<math>
  
−
k = \left(\frac{k_{0}\left[M\right]}{1+k_{0}\left[M\right]/k_{\infty}}\right)F_{c}^{\left(1+\left[\textrm{log}_{10}\left(\frac{k_{0}\left[M\right]}{k_{\infty}}\right)\right]^{2}\right)^{-1}}
  
−
</math>
  
   
  +
This scheme is controlled in '''ukca_ddeprt.F90'''. The deposition only occurs in the bottom (i.e. 'surface') layer.
−
where the low pressure rate constant <math>k_{0}</math> is given by
  
   
  +
==Interactive Dry Deposition Scheme==
−
<math>
  
−
k_{0} = k_{1} \left(\frac{T}{300}\right)^{{\alpha}_{1}} \textrm{exp} \left(\frac{-{\beta}_{1}}{T}\right)
  
−
</math>
  
   
  +
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''.
−
and the high pressure rate constant <math>k_{\infty}</math> is given by
  
  +
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 {{pdf|Umdp84_vn82.pdf|UKCA documentation paper for UM version 8.2}}.
   
  +
When using this scheme, dry deposition occurs throughout the boundary layer, rather than just in the lowest model (i.e. surface) layer.
−
<math>
  
−
k_{\infty} = k_{2} \left(\frac{T}{300}\right)^{{\alpha}_{2}} \textrm{exp} \left(\frac{-{\beta}_{2}}{T}\right)
  
−
</math>
  
   
  +
===Changes to ukca_aerod.F90===
−
===Termolecular Reaction Definition===
  
   
  +
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 <math>m^{2}s^{-1}</math>). 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 <math>d_{0,\textrm{species}}</math> is calculated as
−
The termolecular reactions are defined in the '''ukca_chem_<span style="color:blue">scheme</span>.F90''' routines using the '''ratt_t''' Fortran type specification, and are usually held in one single array (there are not usually enough reactions to require splitting the reactions over several arrays).
 
   
  +
<math>
−
To format of this '''ratt_t''' type is
  
  +
d_{0,\textrm{species}} = d_{0,H_{2}O} \ \sqrt[]{M_{H_{2}O}/M_{\textrm{species}}}
  +
</math>
   
  +
Where <math>M_{H_{2}O}</math> is the relative molecular mass of H2O, and <math>M_{\textrm{species}}</math> is the relative molecular mass of the species being deposited, and <math>d_{0,H_{2}O}</math> is the diffusion coefficient for H2O (2.08E-5 <math>m^{2}s^{-1}</math>).
−
ratt_t('Reactant 1','Reactant 2','<span style="color:blue">Product 1 </span>','<span style="color:red">Product 2 </span>', <math>f</math>, &
  
−
<math>k_{1}</math>, <math>{\alpha}_{1}</math>, <math>{\beta}_{1}</math>, <math>k_{1}</math>, <math>{\alpha}_{1}</math>, <math>{\beta}_{1}</math>, <span style="color:blue">Fraction of Product 1 produced</span>, <span style="color:red">Fraction of Product 2 produced</span>), &
 
   
  +
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
−
and as in <tt>ratb_t</tt>, where the fraction of a product should be set to 0.000 if this functionality does not need to be used.
  
   
  +
CASE ('O3 ','NO2 ','O3S ','NO3 ')
−
The <math>f</math> value is used to define the <math>F_{c}</math> value by
  
  +
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_<span style="color:blue">species</span>''' value for your new species, you will need to do this in '''ukca_constants.F90'''.
−
<blockquote>
  
−
If <math>f < 1.0</math> then <math>F_{c} = f</math><br/>
  
−
else <math>F_{c} = \textrm{exp}\left(-T/f\right)</math>
  
−
</blockquote>
  
   
  +
===Changes to ukca_surfddr.F90===
−
as <math>F_{c}</math> may or may not be highly temperature dependent.
  
   
  +
The Wesely scheme considers 9 different surface types:
−
Examples of these reactions are
  
   
  +
# Broadleaved trees
−
ratt_t('N2O5 ','m ','NO2 ','NO3 ', 0.3, & ! T023
 
  +
# Needleleaf trees
−
1.30E-03, -3.50, 11000.00, 9.70E+14, 0.10, 11080.00, 0.000, 0.000), & ! T023 IUPAC 2002
 
  +
# C3 Grass
−
ratt_t('NO ','NO ','NO2 ','NO2 ', 0.0, & ! T024
 
  +
# C4 Grass
−
3.30E-39, 0.00, -530.00, 0.00E+00, 0.00, 0.00, 0.000, 0.000) & ! T024 IUPAC 2001
 
  +
# Shrub
  +
# Urban
  +
# Water
  +
# Bare Soil
  +
# Ice
   
  +
'''ukca_surfddr.F90''' sets the surface resistance (in <math>sm^{-1}</math>) 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.
−
To add new termolecular reactions you will need to append equivalent lines for the new reactions to the end of the '''ratt_defs_<span style="color:blue">scheme</span>''' array (increasing the array sizes accordingly).
  
   
  +
Examples of how this is already done are
−
===Increase the size of JPTK (and JPNR)===
  
   
  +
CASE ('NO2 ','NO3 ')
−
As with the bimolecular reactions, you will also need to increase the values of two parameters that UKCA needs. These are
  
  +
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==
−
* '''JPTK''' is the number of termolecular reactions
  
−
* '''JPNR''' is the total number of reactions
  
−  
−
These are set automatically in the UMUI (depending on what scheme is chosen), and are placed in the <code>&RUN_UKCA</code> namelist in '''CNTLATM'''. You will need to make a hand-edit to change these accordingly. The current values can be found by saving and processing the job, and then viewing the ''CNTLATM'' file in your <tt>$HOME/umui_jobs/<span style="color:blue">jobid</span></tt> directory.
  
−  
−
==Heterogeneous Reactions==
  
−  
−
Heterogeneous reactions are those that occur on aerosol surfaces. There is no functional form defined for these reactions, with special code needed to be added for each case.
  
−  
−
===Heterogeneous Reaction Definition===
  
−  
−
The heterogeneous reactions are defined in the '''ukca_chem_<span style="color:blue">scheme</span>.F90''' routines using the '''rath_t''' Fortran type specification, usually in one array.
  
−
To format of this '''rath_t''' type is
  
−  
−
rath_t('Reactant 1','Reactant 2','<span style="color:blue">Product 1 </span>','<span style="color:red">Product 2 </span>','<span style="color:green">Product 3 </span>',&
  
−
'<span style="color:purple">Product 4 </span>', <span style="color:blue">Fraction of Product 1 produced</span>, <span style="color:red">Fraction of Product 2 produced</span>, &
  
−
<span style="color:green">Fraction of Product 3 produced</span>, <span style="color:purple">Fraction of Product 4 produced</span>), &
 
−  
−
i.e. there is no rate information provided. For reactions on PSCs special code has been added to the routines in '''ukca_hetero_mod.F90''', and for other reactions there is code in '''asad_hetero.F90'''. Examples of this type are
  
−  
−
rath_t('ClONO2 ','H2O ','HOCl ','HONO2 ',' ', &
  
−
' ', 0.000, 0.000, 0.000, 0.000), &
  
−
...
  
−
rath_t('SO2 ','H2O2 ','NULL0 ',' ',' ', & !HSO3+H2O2(aq)
  
−
' ', 0.000, 0.000, 0.000, 0.000), &
  
−  
−
To add new heterogeneous reactions you will need to append equivalent lines for the new reactions to the end of the '''ratt_defs_<span style="color:blue">scheme</span>''' array (increasing the array sizes accordingly), before adding code to either '''ukca_hetero_mod.F90''' or '''asad_hetero.F90'''.
  
−  
−
===Increase the size of JPHK (and JPNR)===
  
−  
−
As with the bimolecular and termolecular reactions, you will also need to increase the values of two parameters that UKCA needs. These are
  
−  
−
* '''JPHK''' is the number of heterogeneous reactions
  
−
* '''JPNR''' is the total number of reactions
  
−  
−
These are set automatically in the UMUI (depending on what scheme is chosen), and are placed in the <code>&RUN_UKCA</code> namelist in '''CNTLATM'''. You will need to make a hand-edit to change these accordingly. The current values can be found by saving and processing the job, and then viewing the ''CNTLATM'' file in your <tt>$HOME/umui_jobs/<span style="color:blue">jobid</span></tt> directory.
  
−  
−
==Photolysis Reactions==
  
−  
−
These define a reaction where a chemical compound is broken down by photons. There is no functional form defined for this type of reaction. Instead, either (in the troposphere) input files are used to define the reaction rates for each species, while (in the stratosphere) on-line look-up tables are generated for the rates for each species, or separate photolysis codes, '''Fast-J''' or '''Fast-JX''', are used to interactively calculate the rate of reaction throughout the troposphere (for Fast-J) or the whole atmosphere (for Fast-JX). These interactive schemes are preferred as they take the effect of aerosols or clouds into account at each timestep, allowing for more feedbacks to be investigated. In the upper stratosphere there are some wavelength regions that Fast-JX does not consider, and so the 3D on-line look-up tables are also used for these regions.
  
−  
−
===Tropospheric Off-Line Photolysis===
 
−  
−
If Fast-JX is not being used, then the off-line two-dimensional (zonally average) tropospheric photolysis is used (for all schemes). It is based on the work of Hough (1988)[1] and Law ''et al'' (1998)[2].
  
−  
−
This scheme makes use of datafiles which define the reaction rate for a particular species (e.g. H2O2), or if no rate is known, a '''nil''' rate can be used. For UM 8.2 these files (in ASCII format) can be found in
  
−
 
−
/work/n02/n02/hum/vn8.2/ctldata/UKCA/tropdata/photol
  
−  
−
on HECToR, and in
  
−  
−
/projects/um1/vn8.2/ctldata/UKCA/tropdata/photol
  
−  
−
on MONSooN. To use this scheme, in the UMUI go to '''Model Selection &rarr; Atmosphere &rarr; Model Configuration &rarr; UKCA Chemistry and Aerosols &rarr; PHOTO''' and click '''2D Photolysis Scheme'''. You will then need to give the location of the files (above). The code controlling this scheme is held in '''ukca_phot2d.F90'''.
  
−  
−
It is advised that this scheme is no longer used, and interactive photolysis should be used instead. For the ''CheS/Strat'' or ''CheST/StratTrop'' schemes, Fast-JX should be used as this covers the stratosphere as well as the troposphere.
  
−  
−
'''References'''
  
−
# Hough, A. M.: The calculation of photolysis rates for use in global modelling studies, Tech. rep., UK Atomic Energy Authority, Harwell, Oxon., UK, 1988
  
−
# Law, K., Plantevin, P., Shallcross, D., Rogers, H., Pyle, J., Grouhel, C., Thouret, V., and Marenco, A.: Evaluation of modeled O3 using Measurement of Ozone by Airbus In-Service Aircraft (MOZAIC) data, J. Geophys. Res., 103, 25721–25737, 1998
  
−  
−
===Stratospheric Look-Up Table Photolysis===
  
−  
−
In a chemistry scheme which has stratospheric chemistry, such as ''CheS/Strat'' and ''CheST/StratTrop'', if interactive photolysis is not used, then above 300hPa the look-up table approach of Lary and Pyle (1991)[1] is used (below 300hPa the tropospheric scheme described above is used). To use this scheme, in the UMUI go to '''Model Selection &rarr; Atmosphere &rarr; Model Configuration &rarr; UKCA Chemistry and Aerosols &rarr; PHOTO''' and click '''2D Photolysis Scheme'''. The code for this scheme is held in '''ukca_photolib.F90'''.
  
−  
−
'''References'''
  
−
# Lary, D. and Pyle, J.: Diffuse-radiation, twilight, and photochemistry, J. Atmos. Chem., 13, 393–406, 1991.
  
−  
−
===Interactive Photolysis===
  
−  
−
The Fast-J scheme (Wild ''et al'', 2000)[1] uses 7 different wavelength bins appropriate for the troposphere, and the Fast-JX scheme (Neu et al, 2007)[2] adds up to an extra 11 bins allowing use in the stratosphere.
  
−  
−
To use these schemes, in the UMUI go to '''Model Selection &rarr; Atmosphere &rarr; Model Configuration &rarr; UKCA Chemistry and Aerosols &rarr; PHOTO''' and click either '''FASTJ Photolysis Scheme''' or '''FASTJX Photolysis Scheme'''. You will then need to give the location of several input data files used by these schemes. The code for Fast-J is in the <tt>UKCA/</tt> directory in the '''fastj_*.F90''' files (controlled by '''ukca_fastj.F90'''), and the code for Fast-JX is in the '''fastjx_*.F90''' files (controlled by '''ukca_fastjx.F90''').
  
−  
−
Further details on the Fast-JX scheme, and how it is used in UKCA, can be found in [http://www.geosci-model-dev.net/6/161/2013/gmd-6-161-2013.html Telford ''et al'' (2013)][3].
  
−  
−
The Fast-J/Fast-JX data files are held in
 
−  
−
/work/n02/n02/hum/vn8.2/ctldata/UKCA/fastj
  
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−
on HECToR, and
 
−  
−
/projects/um1/vn8.2/ctldata/UKCA/fastj
  
−  
−
on MONSooN.
  
−  
−
'''References'''
  
−
# Wild, O., Zhu, X., and Prather, M.: Fast-J: accurate simulation of in- and below-cloud photolysis in tropospheric chemical models, J. Atmos. Chem., 37, 245–282, doi:10.1023/A:1006415919030, 2000
  
−
# Neu, J., Prather, M., and Penner, J.: Global atmospheric chemistry: integrating over fractional cloud cover, J. Geophys. Res., 112, D11306, 12 pp., doi:10.1029/2006JD008007, 2007
  
−
# Telford, P. J., Abraham, N. L., Archibald, A. T., Braesicke, P., Dalvi, M., Morgenstern, O., O'Connor, F. M., Richards, N. A. D., and Pyle, J. A.: Implementation of the Fast-JX Photolysis scheme (v6.4) into the UKCA component of the MetUM chemistry-climate model (v7.3), Geosci. Model Dev., 6, 161-177, doi:10.5194/gmd-6-161-2013, 2013.
  
−  
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===Photolysis Reaction Definition===
  
−  
−
The photolysis reactions are defined in the '''ukca_chem_<span style="color:blue">scheme</span>.F90''' routines using the '''ratj_t''' Fortran type specification, usually in several arrays.
  
−
To format of this '''ratj_t''' type is
  
−  
−
ratj_t('Reactant 1','Reactant 2','<span style="color:blue">Product 1 </span>','<span style="color:red">Product 2 </span>','<span style="color:green">Product 3 </span>',&
  
−
'<span style="color:purple">Product 4 </span>', <span style="color:blue">Fraction of Product 1 produced</span>, <span style="color:red">Fraction of Product 2 produced</span>, &
  
−
<span style="color:green">Fraction of Product 3 produced</span>, <span style="color:purple">Fraction of Product 4 produced</span>, Quantum Yield, Look-up Label), &
 
−  
−
The '''Look-Up Label''' is used to define the file used for the 2D photolysis, and is used by Fast-J/Fast-JX to find the correct values for each species in the input data files. This is a 10-character string, although only the first '''7''' characters are read by Fast-JX.
  
−  
−
Examples of this type are
  
−  
−
ratj_t('H2O2 ','PHOTON ','OH ','OH ',' ', &
  
−
' ', 0.0, 0.0, 0.0, 0.0, 100.000,'jh2o2 ') , &
  
−
ratj_t('HCHO ','PHOTON ','HO2 ','HO2 ','CO ', &
  
−
' ', 0.0, 0.0, 0.0, 0.0, 100.000,'jhchoa ') , &
  
−  
−
===Increase the size of JPPJ (and JPNR)===
  
−  
−
As with the bimolecular, termolecular, and heterogeneous reactions, you will also need to increase the values of two parameters that UKCA needs. These are
  
−  
−
* '''JPPJ''' is the number of photolysis reactions
  
−
* '''JPNR''' is the total number of reactions
  
−  
−
These are set automatically in the UMUI (depending on what scheme is chosen), and are placed in the <code>&RUN_UKCA</code> namelist in '''CNTLATM'''. You will need to make a hand-edit to change these accordingly. The current values can be found by saving and processing the job, and then viewing the ''CNTLATM'' file in your <tt>$HOME/umui_jobs/<span style="color:blue">jobid</span></tt> directory.
  
−  
−
==Task 6.1: Add a bimolecular reaction==
  
−  
−
<span style="color:green">'''TASK 6.1:''' You should now add in the bimolecular reaction of '''ALICE''' with '''OH''' to form '''BOB'''. This reaction is given by:</span>
  
−  
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<math>
  
−
\textrm{ALICE} + \textrm{OH} \longrightarrow \textrm{BOB}
  
−
</math>
  
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{| border="1"
  
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! Parameter || Value
  
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|-
  
−
| <math>k_{0}</math> || 2.70E-11
  
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|-
  
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| <math>\alpha</math> || 0.00
  
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|-
  
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| <math>\beta</math> || -390.00
  
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|}
  
   
  +
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 with a hand-edit, the value of '''JPDD''' being set in the '''CNTLATM''' file in your <tt>$HOME/umui_jobs/<span style="color:blue">jobid</span></tt> directory.
−
'''Note:''' If you were unable to successfully complete [[UKCA & UMUI Tutorial 5#Task 5.2: make the required code changes to add your emission into UKCA| Task 5.2]], then please take a copy of the '''f''' job from the Tutorial experiment (''Tutorial: solution to Task 5.2 - adding new chemical emissions in UKCA'') and work from there, as this will allow you to only make the required changes.
  
   
  +
==Solution to Task 9.1: adding new dry deposition values==
−
'''Remember:''' If you are using MONSooN you will need to delete/move any existing output files in your '''[[UKCA & UMUI Tutorials: Things to know before you start#Archiving|archive]]''' directory.
  
   
−
[[Solution to UKCA & UMUI Tutorial 6 Task 6.1 | Solution]]
 +
Please see [[Solution to UKCA & UMUI Tutorial 7 Task 7.1 |this page]] for a solution to [[#Task 9.1: adding new dry deposition values|Task 9.1]].
   
 
----
  
----

Revision as of 12:32, 18 February 2014

Back to UKCA Chemistry and Aerosol Tutorials

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_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.

Note: If you were unable to successfully complete Task 8.1, then please take a copy of the h job from the Tutorial experiment (Tutorial: solution to Task 8.1 - add a new bimolecular reaction) and work from there, as this will allow you to only make the changes required for this task.

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 2D scheme. To choose the interactive dry deposition scheme in the UMUI, go to Model Selection → Atmosphere → Model Configuration → UKCA Chemistry and Aerosols → COUPL and select UKCA interactive dry deposition scheme.

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. As the 2D scheme is the default, it must always have values set.

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_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 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_scheme array, which is held in the ukca_chem_scheme.F90 module. This is a large array made up of size (6,5) blocks. These blocks mean

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

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 

!  1  O3 (Ganzeveld & Lelieveld (1995) note 1 (modified to same as Guang)           
  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
!  2  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

Note: When adding new deposition values you should be careful. UKCA assumes that the order of this array is the same as the order of the species in the chch_defs_scheme array. If you are adding values for a species in the middle of the list then you will need to make sure that you slot it in to the appropriate place in the existing depvel_defs_scheme array (and change the size of this array accordingly).

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 Pdficon small.png UKCA documentation paper for UM version 8.2 Info circle.png.

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 ). 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 is calculated as

Where is the relative molecular mass of H2O, and is the relative molecular mass of the species being deposited, and is the diffusion coefficient for H2O (2.08E-5 ).

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 different surface types:

  1. Broadleaved trees
  2. Needleleaf trees
  3. C3 Grass
  4. C4 Grass
  5. Shrub
  6. Urban
  7. Water
  8. Bare Soil
  9. Ice

ukca_surfddr.F90 sets the surface resistance (in ) 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 with a hand-edit, the value of JPDD being set in the CNTLATM file in your $HOME/umui_jobs/jobid directory.

Solution to Task 9.1: adding new dry deposition values

Please see this page for a solution to Task 9.1.

Written by Luke Abraham 2014

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