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

Latest revision as of 14:28, 15 December 2015

Back to UKCA Chemistry and Aerosol Tutorials

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\$

Note: If you were unable to successfully complete Task 7.1, then please take a copy of the h job from the Tutorial experiment (Tutorial: solution to Task 7.1 - add new dry deposition) and work from there, as this will allow you to only make the changes required for this task. Please also make a new branch and merge-in branch fcm:um_br/dev/luke/vn8.4_UKCA_Tutorial_Solns/src at revision number 14711 to allow you to proceed.

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 with a hand-edit, the value of JPDW being set in the CNTLATM file in your $HOME/umui_jobs/jobid directory.

Solution to Task 8.1: Add wet deposition of a species

Please see this page for a solution of Task 8.1.

Written by Luke Abraham 2014

@@ Line 1: / Line 1: @@
 [[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 wet deposition of chemical species is handelled in UKCA. You will then add-in the wet deposition of one of your new tracers.
-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 8.1: Add wet deposition of a species==
-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 8.1:''' Add in wet deposition for '''BOB''', using the following values:</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.
+!  <math>\ k(298)\ </math>  ||  <math>\ -\left({\Delta H}/R\right)\ </math>  ||  <math>\ k(298)</math> for the 1st dissociation  ||  <math>\ -\left({\Delta H}/R\right)</math> for the 1st dissociation  ||  <math>\ k(298)</math> for the 2nd dissociation  ||  <math>\ -\left({\Delta H}/R\right)</math> for the 2nd dissociation
+|-
+|  <math>\ 0.21 \times 10^{+06}\ </math> || <math>\ 0.87 \times 10^{+04}\ </math> || <math>\ 0.2 \times 10^{+02}\ </math> || <math>\ 0.0\ </math> || <math>\ 0.0\ </math> || <math>\ 0.0\ </math>
+|}
+'''Note:''' If you were unable to successfully complete [[UKCA Chemistry and Aerosol Tutorial 7#Task 7.1: adding new dry deposition values|Task 7.1]], then please take a copy of the '''h''' job from the Tutorial experiment (''Tutorial: solution to Task 7.1 - add new dry deposition'') and work from there, as this will allow you to only make the changes required for this task. Please also make a new branch and merge-in branch '''fcm:um_br/dev/luke/vn8.4_UKCA_Tutorial_Solns/src''' at revision number '''14711''' to allow you to proceed.
-==Biomolecular Reactions==
+==Adding Wet Deposition==
-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
+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
 <math>
-k = k_{0} \left(\frac{T}{300}\right)^{\alpha} \textrm{exp} \left(\frac{-\beta}{T}\right)
+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)
 </math>
+where <math>k\left(298\right)</math> is the rate constant at 298K.
-===Bimolecular Reaction Definition===
+During this tutorial you will be tasked with adding the wet deposition of one of your new tracers.
-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.
+'''References'''
-The format of this '''ratb_t''' type is
+# 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==
- 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>), &
+===Chemistry Scheme Specification===
-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.
+Within the UKCA code, whether a species is wet 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
-The specifications of the individual reactions are done as, e.g.
- ratb_t('O3        ','C5H8      ','HO2       ','OH        ','          ',& ! B133
+ chch_t( 10,'HONO2     ',  1,'TR        ','          ',  1,  <span style="color:red">'''1'''</span>,  0),  & !  10 DD: 7,WD: 4,
- '          ',  3.33E-15,  0.00,   1995.00, 0.750, 0.750, 0.000, 0.000), & ! B133 IUPAC2007*
+ chch_t( 11,'H2O2      ',  1,'TR        ','          ',  1,  <span style="color:red">'''1'''</span>,  0),  & !  11 DD: 8,WD: 5,
- ...
- ratb_t('OH        ','C5H8      ','ISO2      ','          ','          ',& ! B144
- '          ',  2.70E-11,  0.00,   -390.00, 0.000, 0.000, 0.000, 0.000), & ! B144 IUPAC2009
- ...
- ratb_t('OH        ','HCl       ','H2O       ','Cl        ','          ',& ! B159
- '          ',  1.80E-12,  0.00,    250.00, 0.000, 0.000, 0.000, 0.000), & ! B159 JPL2011
+Where the <span style="color:red">'''1'''</span> 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.
-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.
+===Setting Henry's Law values===
-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.
+In the '''ukca_chem_<span style="color:blue">scheme</span>.F90''' the parameters required to calculate <math>H_{eff}</math> are held in the '''henry_defs_<span style="color:blue">scheme</span>''' array, and has format
-===Increase the size of JPBK (and JPNR)===
+{| border="1"
-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
+|  <math>\ k(298)\ </math>  ||  <math>\ -\left({\Delta H}/R\right)\ </math>  ||  <math>\ k(298)</math> for the 1st dissociation  ||  <math>\ -\left({\Delta H}/R\right)</math> for the 1st dissociation  ||  <math>\ k(298)</math> for the 2nd dissociation  ||  <math>\ -\left({\Delta H}/R\right)</math> for the 2nd dissociation
+|}
+Columns 3 and 4 are used if the species dissociates in the aqueous phase. In this case, <math>H_{eff}</math> is further multiplied by a factor of
-* '''JPBK''' is the number of bimolecular 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.
-==Termolecular Reactions==
-As well as defining reactions involving a third body, the termolecular rate definition can also be used to define unimolecular reactions.
-The pressure and temperature dependent rate, <math>k</math>, of a termolecular reaction is given by
 <math>
++\frac{k(aq)}{H^{+}}
-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>
+where
-where the low pressure rate constant <math>k_{0}</math> is given by
 <math>
-k_{0} = k_{1} \left(\frac{T}{300}\right)^{{\alpha}_{1}} \textrm{exp} \left(\frac{-{\beta}_{1}}{T}\right)
+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)
 </math>
+and column 3 contains the values of <math>k(298)</math> and column 4 contains the value of <math>-{\Delta H}/R</math>. Similarly, if the species dissociates a second time then a further factor of <math>1+k(aq)/H^{+}</math> is applied, where this value of <math>k(aq)</math> is calculated from the values of <math>k(298)</math> and <math>-{\Delta H}/R</math> in columns 5 and 6.
-and the high pressure rate constant <math>k_{\infty}</math> is given by
+'''Note:''' As with the 2D dry deposition values in '''depvel_defs_<span style="color:blue">scheme</span>''', the order of '''henry_defs_<span style="color:blue">scheme</span>''' also assumes that the values are in the same order as the species (that wet deposit) in the '''chch_defs_<span style="color:blue">scheme</span>''' array.
-<math>
-k_{\infty} = k_{2} \left(\frac{T}{300}\right)^{{\alpha}_{2}} \textrm{exp} \left(\frac{-{\beta}_{2}}{T}\right)
-</math>
+Examples for this array are
-===Termolecular Reaction Definition===
+.2100E+06, 0.8700E+04, 0.2000E+02, 0.0000E+00, 0.0000E+00, 0.0000E+00,&   !    4  HONO2
-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).
+.8300E+05, 0.7400E+04, 0.2400E-11,-0.3730E+04, 0.0000E+00, 0.0000E+00,&   !    5  H2O2
+===Increase the value of JPDW===
-To format of this '''ratt_t''' type is
- 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>), &
-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.
-The <math>f</math> value is used to define the <math>F_{c}</math> value by
-<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>
-as <math>F_{c}</math> may or may not be highly temperature dependent.
-Examples of these reactions are
- ratt_t('N2O5      ','m         ','NO2       ','NO3       ',     0.3,    & ! T023
-.30E-03, -3.50, 11000.00,  9.70E+14,  0.10, 11080.00, 0.000, 0.000), & ! T023 IUPAC 2002
- ratt_t('NO        ','NO        ','NO2       ','NO2       ',     0.0,    & ! T024
-.30E-39,  0.00,  -530.00,  0.00E+00,  0.00,     0.00, 0.000, 0.000)  & ! T024 IUPAC 2001
-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).
-===Increase the size of JPTK (and JPNR)===
-As with the bimolecular reactions, you will also need to increase the values of two parameters that UKCA needs. These are
-* '''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
-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.
-===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>
-<math>
-\textrm{ALICE} + \textrm{OH} \longrightarrow \textrm{BOB}
-</math>
-{| border="1"
-! Parameter || Value
-|-
-| <math>k_{0}</math>  || 2.70E-11
-|-
-| <math>\alpha</math>  || 0.00
-|-
-| <math>\beta</math>  || -390.00
-|}
+Similar to when adding dry deposition of a species you will need to increase the size of the '''JPDW''' counter. This is done with a hand-edit, the value of '''JPDW''' 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 8.1: Add wet deposition of a species==
-'''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 Chemistry and Aerosol Tutorial 8 Task 8.1 |this page]] for a solution of [[#Task 8.1: Add wet deposition of a species|Task 8.1]].
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