UKCA & UMUI Tutorial 8: Difference between revisions

Latest revision as of 15:37, 15 July 2013

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

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle 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 Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle 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 Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle H_{eff}} are held in the henry_defs_scheme array, and has format

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)\ }

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)\ }

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)} for the 1st dissociation

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)} for the 1st dissociation

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)} for the 2nd dissociation

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\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, Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle H_{eff}} is further multiplied by a factor of

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle 1+\frac{k(aq)}{H^{+}} }

where

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle 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 Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle k(298)} and column 4 contains the value of Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle -{\Delta H}/R} . Similarly, if the species dissociates a second time then a further factor of Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle 1+k(aq)/H^{+}} is applied, where this value of Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle k(aq)} is calculated from the values of Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle k(298)} and Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle -{\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.

Task 8.1: Add wet deposition of a species

Task 8.1: Add in wet deposition for BOB, using the following values:

Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)} for the 1st dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)} for the 1st dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ k(298)} for the 2nd dissociation	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ -\left({\Delta H}/R\right)} for the 2nd dissociation
Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.21 \times 10^{+06}\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.87 \times 10^{+04}\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.2 \times 10^{+02}\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.0\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 0.0\ }	Failed to parse (SVG (MathML can be enabled via browser plugin): Invalid response ("Math extension cannot connect to Restbase.") from server "https://en.wikipedia.org/api/rest_v1/":): {\displaystyle \ 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.

Remember: If you are using MONSooN you will need to delete/move any existing output files in your archive directory.

Solution

Written by Luke Abraham 2013

@@ Line 3: / Line 3: @@
 ==Adding Wet Deposition==
-The formulationn used in UKCA is described in Giannakopoulos (1999)[1]. This scheme uses the following formula to calculate the effective Henry's Law coefficient
+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>
-H_{eff} = k(298) \textrm{exp} \left(-\frac{\deltaH{/R}\left[\left(\frac{1}{T} - \frac{1}{298}\right]\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.
+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_<span style="color:blue">scheme</span>.F90''' file. In the '''chch_defs_<span style="color:blue">scheme</span>''' array there are lines like
+ chch_t( 10,'HONO2     ',  1,'TR        ','          ',  1,  <span style="color:red">'''1'''</span>,  0),  & !  10 DD: 7,WD: 4,
+ chch_t( 11,'H2O2      ',  1,'TR        ','          ',  1,  <span style="color:red">'''1'''</span>,  0),  & !  11 DD: 8,WD: 5,
+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.
+===Setting Henry's Law values===
+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
+{| border="1"
+|  <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
+<math>
++\frac{k(aq)}{H^{+}}
+</math>
+where
+<math>
+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.
+'''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.
+Examples for this array are
+.2100E+06, 0.8700E+04, 0.2000E+02, 0.0000E+00, 0.0000E+00, 0.0000E+00,&   !    4  HONO2
+.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 <tt>$HOME/umui_jobs/<span style="color:blue">jobid</span></tt> directory.
+==Task 8.1: Add wet deposition of a species==
+<span style="color:green">'''Task 8.1:''' Add in wet deposition for '''BOB''', using the following values:</span>
+{| border="1"
+!  <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 & UMUI 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.
+'''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 8 Task 8.1 | Solution]]
- ! The following formula is used to calculate the effective Henry's Law coef,
- ! which takes the affects of dissociation and complex formation on a species'
- ! solubility (see Giannakopoulos, 1998)
- !
- !       H(eff) = K(298)exp{[-deltaH/R]x[(1/T)-(1/298)]}
- !
- ! The data in columns 1 and 2 above give the data for this gas-aqueous transfer,
- !       Column 1 = K(298) [M/atm]
- !       Column 2 = -deltaH/R [K-1]
- !
- ! If the species dissociates in the aqueous phase the above term is multiplied by
- ! another factor of 1+{K(aq)/[H+]}, where
- !       K(aq) = K(298)exp{[-deltaH/R]x[(1/T)-(1/298)]}
- ! The data in columns 3 and 4 give the data for this aqueous-phase dissociation,
- !       Column 3 = K(298) [M]
- !       Column 4 = -deltaH/R [K-1]
- ! The data in columns 5 and 6 give the data for a second dissociation,
- ! e.g for SO2, HSO3^{-}, and SO3^{2-}
- !       Column 5 = K(298) [M]
- !       Column 6 = -deltaH/R [K-1]
 ----