UKCA Chemistry and Aerosol vn11.8 Tutorial 8: Difference between revisions
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| Time to Complete || '''Under 1 hour''' |
| Time to Complete || '''Under 1 hour''' |
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| Video instructions || '''https://youtu.be/6XqYfW2qHKY?t=641''' |
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Sample output from this task can be found at '''<code>Tutorials/vn11.8/sample_output/Task08.1/atmosa.pa19810901_00</code>'''. |
Sample output from this task can be found at '''<code>Tutorials/vn11.8/sample_output/Task08.1/atmosa.pa19810901_00</code>'''. |
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''Note that there is a typo in the above solution - all entries should be added with the same version number (i.e. 111), however in this case a version number of 107 would still work as it is lower than 111. If the version number were set higher than the version number being used then the changes would not initially be included.'' |
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==Checklist== |
==Checklist== |
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Latest revision as of 17:11, 28 February 2022
UKCA Chemistry and Aerosol Tutorials at vn11.8
| Difficulty | EASY |
| Time to Complete | Under 1 hour |
| Video instructions | https://youtu.be/6XqYfW2qHKY?t=641 |
Remember to run mosrs-cache-password in your Rose suite and UM branch terminals.
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:
| 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\ } |
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_master.F90 module. In the chch_defs_master array there are lines like
! 9 DD: 6,WD: 4, ! No dry deposition for HO2NO2 in R and T schemes chch_t1( 9,'HO2NO2 ',1,'TR ',' ',0,1,r+t,0,0,107), & chch_t1( 9,'HO2NO2 ',1,'TR ',' ',1,1,ti+s+st+cs,0,0,107), & ! 10 DD: 7,WD: 5, (20) chch_t1(10,'HONO2 ',1,'TR ',' ',1,1,ti+s+t+st+r+cs, & 0,0,107), &
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_master.F90 module 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_master array (of defined size n_wet_master), and has format
N |
'SPECIES '
| ||||
| 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 |
SCHEME |
QUALIFIER |
DISQUALIFIER |
VN
|
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.
Examples for this array are
! WD: 4 wetdep(4,'HO2NO2 ', & (/0.13e+05,0.69e+04,0.10e-04,0.00e+00,0.00e+00,0.0e+00/),ti+t+st+r+cs,0,0,107),& wetdep(4,'HO2NO2 ', & (/0.20e+05,0.00e+00,0.10e-04,0.00e+00,0.00e+00,0.00e+00/),s,0,0,107), & ! WD: 5 wetdep(5,'HONO2 ', & (/0.21e+06,0.87e+04,0.20e+02,0.00e+00,0.00e+00,0.0e+00/),ti+t+st+r+cs,0,0,107),& wetdep(5,'HONO2 ', & (/0.21e+06,0.87e+04,0.157e+02,0.00e+00,0.00e+00,0.00e+00/),s,0,0,107), &
Solution to Task 8.1: Add wet deposition of a species
You were given the task
- 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\ } |
For a working Rose suite that has completed this task, please see
- vm:
u-ca024@182959
The specific Rose changes made are:
vm:
Index: app/fcm_make/rose-app.conf =================================================================== --- app/fcm_make/rose-app.conf (revision 182833) +++ app/fcm_make/rose-app.conf (revision 182959) @@ -43,4 +43,4 @@ thread_utils=false timer_version=3A um_rev=$BASE_UM_REV -um_sources=branches/dev/lukeabraham/vn11.8_UKCA_Tutorial_Solns@94072 +um_sources=branches/dev/lukeabraham/vn11.8_UKCA_Tutorial_Solns@94120
These differences can be found in the file Tutorials/vn11.8/worked_solutions/Task08.1/Task08.1_rose.patch.
The specific UM changes made are:
Index: src/atmosphere/UKCA/ukca_chem_master.F90 =================================================================== --- src/atmosphere/UKCA/ukca_chem_master.F90 (revision 94072) +++ src/atmosphere/UKCA/ukca_chem_master.F90 (revision 94120) @@ -97,7 +97,7 @@ INTEGER, PARAMETER :: n_chch_master = 329 ! number of known species INTEGER, PARAMETER :: n_het_master = 18 ! number of heterogeneous reactions INTEGER, PARAMETER :: n_dry_master = 150 ! number of dry deposition reactions -INTEGER, PARAMETER :: n_wet_master = 106 ! number of wet deposition reactions +INTEGER, PARAMETER :: n_wet_master = 107 ! number of wet deposition reactions INTEGER, PARAMETER :: n_bimol_master= 855 ! number of bimolecular reactions INTEGER, PARAMETER :: n_ratj_master = 158 ! number of photolysis reactions INTEGER, PARAMETER :: n_ratt_master = 76 ! number of termolecular reactions @@ -847,7 +847,7 @@ ! 272 chch_t1(272,'ALICE ',1,'TR ',' ',1,0,st,0,0,111), & ! 273 -chch_t1(273,'BOB ',1,'TR ',' ',0,0,st,0,0,111) & +chch_t1(273,'BOB ',1,'TR ',' ',0,1,st,0,0,111) & /) ! ---------------------------------------------------------------------- @@ -2058,7 +2058,10 @@ (/2.30e+02,4.90e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00/),cs,0,0,107), & ! WD: 96. Using MeOH Henry's Law Coeffs wetdep( 96, 'ARNOH17 ', & -(/2.30e+02,4.90e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00/),cs,0,0,107) & +(/2.30e+02,4.90e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00/),cs,0,0,107), & +! UKCA Tutorial: wet deposition of BOB +wetdep(97,'BOB ', & +(/0.21e+06,0.87e+04,0.20e+02,0.00e+00,0.00e+00,0.00e+00/),st,0,0,107) & /) ! ---------------------------------------------------------------------
These differences can be found in the file Tutorials/vn11.8/worked_solutions/Task08.1/Task08.1_code.patch.
Sample output from this task can be found at Tutorials/vn11.8/sample_output/Task08.1/atmosa.pa19810901_00.
Note that there is a typo in the above solution - all entries should be added with the same version number (i.e. 111), however in this case a version number of 107 would still work as it is lower than 111. If the version number were set higher than the version number being used then the changes would not initially be included.
Checklist
- ☐ Put a 1 in the W column of the
chch_defs_masterinukca_chem_master.F90. - ☐ Append the Henry's Law parameter values in the
depvel_defs_masterarray, and incrementn_wet_master.
Written by Luke Abraham 2021
