Difference between revisions of "UKCA Chemistry and Aerosol UMvn13.0 Tutorial 10"
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| Time to Complete || '''Under 1 hour''' |
| Time to Complete || '''Under 1 hour''' |
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− | | Video instructions || |
+ | | Video instructions || [https://www.youtube.com/watch?v=n3yE-oYy-gU&t=12959s Walkthrough (YouTube)] |
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− | '''Remember to run <tt>mosrs-cache-password</tt> |
+ | '''Remember to run <tt>mosrs-cache-password</tt>.''' |
==What you will learn in this Tutorial== |
==What you will learn in this Tutorial== |
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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. |
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. |
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− | ==Task |
+ | ==Task 10.1: Add wet deposition of a species== |
− | <span style="color:green">'''Task |
+ | <span style="color:green">'''Task 10.1:''' Add in wet deposition for '''BOB''', using the following values:</span> |
{| class="wikitable" border = "1px" |
{| class="wikitable" border = "1px" |
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where <math>k\left(298\right)</math> is the rate constant at 298K. |
where <math>k\left(298\right)</math> is the rate constant at 298K. |
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− | During this tutorial you will be tasked with adding the wet deposition of one of your new tracers. |
+ | During this tutorial you will be tasked with adding the wet deposition of one of your new tracers. '''You will only need to make changes to your UKCA branch.''' |
'''References''' |
'''References''' |
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==Turning on Wet Deposition for a Species== |
==Turning on Wet Deposition for a Species== |
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+ | === <tt>src/science/core/chemistry/ukca_chem_master.F90</tt> === |
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− | ===Chemistry Scheme Specification=== |
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− | Within the UKCA code, whether a species is wet deposited or not is controlled in the '''< |
+ | Within the UKCA code, whether a species is wet deposited or not is controlled in the '''<tt>ukca_chem_master.F90</tt>''' module. In the '''<tt>chch_defs_master</tt>''' array there are lines like |
! 9 DD: 6,WD: 4, |
! 9 DD: 6,WD: 4, |
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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. |
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. |
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⚫ | |||
− | ===Setting Henry's Law values=== |
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− | |||
⚫ | |||
{| class="wikitable" border = "1px" |
{| class="wikitable" border = "1px" |
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− | | '''< |
+ | | '''<tt>N</tt>''' || '''<tt><span style="color:red">'SPECIES '</span></tt>''' |
|- |
|- |
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| <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>\ 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 |
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|- |
|- |
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− | | '''< |
+ | | '''<tt><span style="color:red">SCHEME</span></tt>''' || '''<tt><span style="color:green">QUALIFIER</span></tt>''' || '''<tt><span style="color:blue">DISQUALIFIER</span></tt>''' || '''<tt>VN</tt>''' |
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(/0.21e+06,0.87e+04,0.157e+02,0.00e+00,0.00e+00,0.00e+00/),s,0,0,107), & |
(/0.21e+06,0.87e+04,0.157e+02,0.00e+00,0.00e+00,0.00e+00/),s,0,0,107), & |
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− | ==Solution to Task |
+ | ==Worked Solution to Task 10.1: Add wet deposition of a species== |
You were given the task |
You were given the task |
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− | For a working Rose suite that has completed this task, please see |
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⚫ | |||
− | * '''vm:''' <code>u-ca024@182959</code> |
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− | The specific Rose changes made are: |
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− | * '''vm:''' https://code.metoffice.gov.uk/trac/roses-u/changeset/182959/c/a/0/2/4/trunk |
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⚫ | |||
− | '''vm:''' |
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− | Index: app/fcm_make/rose-app.conf |
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=================================================================== |
=================================================================== |
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− | --- |
+ | --- src/science/core/chemistry/ukca_chem_master.F90 (revision 567) |
− | +++ |
+ | +++ src/science/core/chemistry/ukca_chem_master.F90 (revision 568) |
− | @@ - |
+ | @@ -106,7 +106,7 @@ |
⚫ | |||
− | thread_utils=false |
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− | timer_version=3A |
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− | um_rev=$BASE_UM_REV |
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− | -um_sources=branches/dev/lukeabraham/vn11.8_UKCA_Tutorial_Solns@94072 |
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− | +um_sources=branches/dev/lukeabraham/vn11.8_UKCA_Tutorial_Solns@94120 |
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− | |||
− | These differences can be found in the file '''<code>Tutorials/vn11.8/worked_solutions/Task08.1/Task08.1_rose.patch</code>'''. |
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− | |||
⚫ | |||
⚫ | |||
− | |||
⚫ | |||
− | =================================================================== |
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− | --- src/atmosphere/UKCA/ukca_chem_master.F90 (revision 94072) |
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− | +++ src/atmosphere/UKCA/ukca_chem_master.F90 (revision 94120) |
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− | @@ -97,7 +97,7 @@ |
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⚫ | |||
INTEGER, PARAMETER :: n_het_master = 18 ! number of heterogeneous reactions |
INTEGER, PARAMETER :: n_het_master = 18 ! number of heterogeneous reactions |
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− | INTEGER, PARAMETER :: n_dry_master = |
+ | INTEGER, PARAMETER :: n_dry_master = 162 ! number of dry deposition reactions |
− | -INTEGER, PARAMETER :: n_wet_master = |
+ | -INTEGER, PARAMETER :: n_wet_master = 159 ! number of wet deposition reactions |
− | +INTEGER, PARAMETER :: n_wet_master = |
+ | +INTEGER, PARAMETER :: n_wet_master = 160 ! number of wet deposition reactions |
− | INTEGER, PARAMETER :: n_bimol_master= |
+ | INTEGER, PARAMETER :: n_bimol_master = 1211 ! number of bimolecular reactions |
− | INTEGER, PARAMETER :: n_ratj_master = |
+ | INTEGER, PARAMETER :: n_ratj_master = 183 ! number of photolysis reactions |
− | INTEGER, PARAMETER :: n_ratt_master = |
+ | INTEGER, PARAMETER :: n_ratt_master = 116 ! number of termolecular reactions |
− | @@ - |
+ | @@ -921,7 +921,7 @@ |
− | ! |
+ | ! 284 |
− | chch_t1( |
+ | chch_t1(284,'ALICE ',1,'TR ',' ',1,0,st+cs,0,0,131), & |
− | ! |
+ | ! 285 |
− | -chch_t1( |
+ | -chch_t1(285,'BOB ',1,'TR ',' ',0,0,st+cs,0,0,131) & |
− | +chch_t1( |
+ | +chch_t1(285,'BOB ',1,'TR ',' ',0,1,st+cs,0,0,131) & |
− | + | ] |
|
+ | |||
− | ! ---------------------------------------------------------------------- |
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− | @@ - |
+ | @@ -2498,7 +2498,10 @@ |
− | + | [1.84e+05,6.00e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00],cs,0,0,119), & |
|
− | ! WD: |
+ | ! WD: 120 (Schwantes (2020) MVKN) |
− | wetdep( |
+ | wetdep(120, 'RU10NO3 ', & |
− | - |
+ | -[1.84e+05,6.00e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00],cs,0,0,119) & |
− | + |
+ | +[1.84e+05,6.00e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00],cs,0,0,119), & |
− | +! |
+ | +! UKCA Tutorial: wet deposition of BOB |
− | +wetdep( |
+ | +wetdep(121,'BOB ', & |
− | + |
+ | +[0.21e+06,0.87e+04,0.20e+02,0.00e+00,0.00e+00,0.00e+00],st+cs,0,0,131) & |
− | + | ] |
|
! --------------------------------------------------------------------- |
! --------------------------------------------------------------------- |
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− | These differences can be found |
+ | These differences can be found here: |
+ | |||
+ | Tutorials/UMvn13.0/worked_solutions/Task10.1/Task10.1_ukca.patch |
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+ | |||
+ | Sample output from this task can be found at |
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+ | |||
+ | Tutorials/UMvn13.0/sample_output/Task10.1/ |
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+ | |||
+ | '''Note''' that while the concentrations of ALICE and BOB will have changed slightly, it will be hard to see any differences when plotting the species. If you look in the |
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+ | |||
+ | cylc-run/'''[SUITE-ID]'''/work/1/atmos/pe_output/atmos.fort6.pe0 |
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+ | |||
+ | file and search for <tt>BOB</tt> you will be able to see the following lines |
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+ | |||
+ | 285 BOB TR 0 1 131 |
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+ | |||
+ | and |
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+ | BOB |
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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>'''. |
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+ | 0.210000E+06 0.870000E+04 0.200000E+02 0.000000E+00 0.000000E+00 0.000000E+00 |
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+ | These are showing that the dry deposition switch is now on (the '''1''' after the <tt>TR 0</tt>) and provides the list of Henry's Law values. |
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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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− | : <span style="font-size:20px">☐</span> Put a 1 in the W column of the < |
+ | : <span style="font-size:20px">☐</span> Put a 1 in the W column of the <tt>chch_defs_master</tt> in <tt>ukca_chem_master.F90</tt>. |
− | : <span style="font-size:20px">☐</span> Append the Henry's Law parameter values in the < |
+ | : <span style="font-size:20px">☐</span> Append the Henry's Law parameter values in the <tt>depvel_defs_master</tt> array, and increment <tt>n_wet_master</tt>. |
[[UKCA Chemistry and Aerosol UMvn13.0 Tutorial 11|Tutorial 11]] |
[[UKCA Chemistry and Aerosol UMvn13.0 Tutorial 11|Tutorial 11]] |
Latest revision as of 13:49, 13 May 2023
UKCA Chemistry and Aerosol Tutorials at UMvn13.0
Difficulty | EASY |
Time to Complete | Under 1 hour |
Video instructions | Walkthrough (YouTube) |
Remember to run mosrs-cache-password.
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 10.1: Add wet deposition of a species
Task 10.1: Add in wet deposition for BOB, using the following values:
for the 1st dissociation | for the 1st dissociation | for the 2nd dissociation | for the 2nd dissociation | ||
---|---|---|---|---|---|
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
where is the rate constant at 298K.
During this tutorial you will be tasked with adding the wet deposition of one of your new tracers. You will only need to make changes to your UKCA branch.
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
src/science/core/chemistry/ukca_chem_master.F90
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.
The parameters required to calculate are held in the henry_defs_master array (of defined size n_wet_master), and has format
N | 'SPECIES ' | ||||
for the 1st dissociation | for the 1st dissociation | for the 2nd dissociation | 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, is further multiplied by a factor of
where
and column 3 contains the values of and column 4 contains the value of . Similarly, if the species dissociates a second time then a further factor of is applied, where this value of is calculated from the values of and 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), &
Worked Solution to Task 10.1: Add wet deposition of a species
You were given the task
- Add in wet deposition for BOB, using the following values:
for the 1st dissociation | for the 1st dissociation | for the 2nd dissociation | for the 2nd dissociation | ||
---|---|---|---|---|---|
The specific UKCA changes made are:
Index: src/science/core/chemistry/ukca_chem_master.F90 =================================================================== --- src/science/core/chemistry/ukca_chem_master.F90 (revision 567) +++ src/science/core/chemistry/ukca_chem_master.F90 (revision 568) @@ -106,7 +106,7 @@ INTEGER, PARAMETER :: n_chch_master = 358 ! number of known species INTEGER, PARAMETER :: n_het_master = 18 ! number of heterogeneous reactions INTEGER, PARAMETER :: n_dry_master = 162 ! number of dry deposition reactions -INTEGER, PARAMETER :: n_wet_master = 159 ! number of wet deposition reactions +INTEGER, PARAMETER :: n_wet_master = 160 ! number of wet deposition reactions INTEGER, PARAMETER :: n_bimol_master = 1211 ! number of bimolecular reactions INTEGER, PARAMETER :: n_ratj_master = 183 ! number of photolysis reactions INTEGER, PARAMETER :: n_ratt_master = 116 ! number of termolecular reactions @@ -921,7 +921,7 @@ ! 284 chch_t1(284,'ALICE ',1,'TR ',' ',1,0,st+cs,0,0,131), & ! 285 -chch_t1(285,'BOB ',1,'TR ',' ',0,0,st+cs,0,0,131) & +chch_t1(285,'BOB ',1,'TR ',' ',0,1,st+cs,0,0,131) & ] @@ -2498,7 +2498,10 @@ [1.84e+05,6.00e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00],cs,0,0,119), & ! WD: 120 (Schwantes (2020) MVKN) wetdep(120, 'RU10NO3 ', & -[1.84e+05,6.00e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00],cs,0,0,119) & +[1.84e+05,6.00e+03,0.00e+00,0.00e+00,0.00e+00,0.00e+00],cs,0,0,119), & +! UKCA Tutorial: wet deposition of BOB +wetdep(121,'BOB ', & +[0.21e+06,0.87e+04,0.20e+02,0.00e+00,0.00e+00,0.00e+00],st+cs,0,0,131) & ] ! ---------------------------------------------------------------------
These differences can be found here:
Tutorials/UMvn13.0/worked_solutions/Task10.1/Task10.1_ukca.patch
Sample output from this task can be found at
Tutorials/UMvn13.0/sample_output/Task10.1/
Note that while the concentrations of ALICE and BOB will have changed slightly, it will be hard to see any differences when plotting the species. If you look in the
cylc-run/[SUITE-ID]/work/1/atmos/pe_output/atmos.fort6.pe0
file and search for BOB you will be able to see the following lines
285 BOB TR 0 1 131
and
BOB 0.210000E+06 0.870000E+04 0.200000E+02 0.000000E+00 0.000000E+00 0.000000E+00
These are showing that the dry deposition switch is now on (the 1 after the TR 0) and provides the list of Henry's Law values.
Checklist
- ☐ Put a 1 in the W column of the chch_defs_master in ukca_chem_master.F90.
- ☐ Append the Henry's Law parameter values in the depvel_defs_master array, and increment n_wet_master.
UKCA Chemistry and Aerosol Tutorials at UMvn13.0
Written by Luke Abraham 2022