View source for UKCA Chemistry and Aerosol UMvn13.0 Tutorial 12

[[UKCA Chemistry and Aerosol Tutorials at UMvn13.0]]

{| class="wikitable" border = "1px"         
|- 
| Difficulty ||  '''<span style="color:red">HARD</span>'''
|- 
| Time to Complete ||  '''2 or more hours'''
|-
| Video instructions ||  
|}

'''Remember to run <tt>mosrs-cache-password</tt>.'''

==What you will learn in this Tutorial==

In this tutorial you will learn how to output and process aerosol diagnostics from UKCA.

===Python===

In this Tutorial you will make extensive use of Python to process the UM output. Instructions as to how to use this are in [[UKCA_Chemistry_and_Aerosol_vn11.8_Tutorial_5#Using_python_to_regrid_your_emissions|Tutorial 5]].

Example python scripts are provided for each Task, and you should take the time to read through these and understand what they are doing. None of these scripts plot any of the output, so as an extension to these tasks you could try extending the scripts to plot the output from python directly, rather than visualising via Xconv. Further information (and examples) on how Iris plots can be found here:

* https://scitools-iris.readthedocs.io/en/latest/userguide/plotting_a_cube.html
* https://scitools-iris.readthedocs.io/en/latest/generated/gallery/general/plot_global_map.html

==Task 12.1: Output aerosol diagnostics==

<span style="color:green">'''TASK 12.1:''' Output the following aerosol and radiation diagnostics to the '''UPA''' output stream. You should make a new ''time profile'' (called TRAD) to only output these on '''radiation timesteps'''. You will also need to make a new ''domain profile'' (called D3DAR) for s02i530 and s02i540, to '''output these on both model levels and pseudo levels'''. You should also remove the existing entry for s02i301 "ACCUM MODE (SOLUBLE) OPTICAL DEPTH" that is output as T3HMN.</span>

{| class="collapsible collapsed wikitable"
|-
! Hint 
|-
| Remember to output your aerosol diagnostics on the AOT pseudo levels using the DIAGAOT profile.
|}

{| class="wikitable" border = "1px"
!style="text-align:top;"|STASH Section
!style="text-align:top;"|STASH Item
!style="text-align:top;"|STASH Name
|-  style="background:lightgrey;"
|    1 ||  207 || INCOMING SW RAD FLUX (TOA): ALL TSS 
|-  style="background:lightgrey;"
|    1 ||  208 || OUTGOING SW RAD FLUX (TOA)          
|-  style="background:lightgrey;"
|    2 ||  205 || OUTGOING LW RAD FLUX (TOA)          
|- 
|    2 ||  285 || MINERAL DUST OPTICAL DEPTH IN RADN. 
|- 
|    2 ||  300 || AITKEN MODE (SOLUBLE) OPTICAL DEPTH 
|- 
|    2 ||  301 || ACCUM MODE (SOLUBLE) OPTICAL DEPTH  
|- 
|    2 ||  302 || COARSE MODE (SOLUBLE) OPTICAL DEPTH 
|- 
|    2 ||  303 || AITKEN MODE (INSOL) OPTICAL DEPTH   
|- 
|    2 ||  304 || ACCUM MODE (INSOL) OPTICAL DEPTH    
|- 
|    2 ||  305 || COARSE MODE (INSOL) OPTICAL DEPTH   
|-  style="background:lightgrey;"
|    2 ||  585 || MINERAL DUST ABS. OPICAL DEPTH   
|- style="background:lightgrey;"
|    2 ||  240 || AITKEN (SOLUBLE) ABS OPTICAL DEPTH  
|- style="background:lightgrey;" 
|    2 ||  241 || ACCUM (SOLUBLE) ABS OPTICAL DEPTH   
|- style="background:lightgrey;"
|    2 ||  242 || COARSE (SOLUBLE) ABS OPTICAL DEPTH  
|- style="background:lightgrey;"
|    2 ||  243 || AITKEN (INSOL) ABS OPTICAL DEPTH    
|- style="background:lightgrey;" 
|    2 ||  244 || ACCUM (INSOL) ABS OPTICAL DEPTH     
|- style="background:lightgrey;" 
|    2 ||  245 || COARSE (INSOL) ABS OPTICAL DEPTH               
|- 
|    2 ||  530 || UKCA 3D AEROSOL EXTINCTION 
|- 
|    2 ||  540 || CLASSIC 3D AEROSOL EXTINCTION  
|}

==Radiation Timesteps==

The number of shortwave radiation timesteps per day is given by '''<tt>i_sw_radstep_perday_prog</tt>''', found in um <math>\rightarrow</math> namelist <math>\rightarrow</math> UM Science Settings <math>\rightarrow</math> Section 01 - 02 Radiation  <math>\rightarrow</math> Shortwave. The equivalent for longwave is '''<tt>i_lw_radstep_perday_prog</tt>''', found in um <math>\rightarrow</math> namelist <math>\rightarrow</math> UM Science Settings <math>\rightarrow</math> Section 01 - 02 Radiation  <math>\rightarrow</math> Longwave.

In the UKCA training suite, both of these are set to '''16''', i.e. a call every 90 minutes. This value is very configuration dependent - sometimes radiation is called every hour (24), sometimes every 3 hours (8) etc. You should check the settings in your suite if you need to consider any of the radiation diagnostics.

==Making new STASH profiles==

While we have covered outputting and creating new diagnostics in [[UKCA_Chemistry_and_Aerosol_vn11.8_Tutorial_3|Tutorial 3]], [[UKCA_Chemistry_and_Aerosol_vn11.8_Tutorial_4|Tutorial 4]], [[UKCA_Chemistry_and_Aerosol_vn11.8_Tutorial_5|Tutorial 5]], and [[UKCA_Chemistry_and_Aerosol_vn11.8_Tutorial_9|Tutorial 9]], you were only making use of existing profiles. Here you will learn how to make new '''time''', '''domain''', and '''usage''' profiles. 

===Time profiles===

[[Image:UM11.8_newtime.png|thumb|300px|right|The new time panel in Rose.]]
To make a new time profile, go to: '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> STASH Requests and Profiles <math>\rightarrow</math> Time Profiles'''. This contains a list of existing time profiles, with names like ''<tt>t3hmn_039ecafe</tt>'' etc.

To make a new time profile, you should:

# Right-click anywhere on the list and click the green plus symbol ('''<span style="color:green">+</span>''') named '''Add new section'''
#: This will make a new blank line (usually labelled '''1''', the next '''2''' etc.) with a red '''<span style="color: red">X</span>''' next to it.
# Right-click this new line and click '''View namelist'''.
# Fill-in the values as required for what you want to do. 
# When you have finished, you will need to run the When you have finished, you will need to run the '''stashindices.TidyStashTransform''' macro by going to the '''Metadata <math>\rightarrow</math> um''' drop-down menu. This will rename the new profile into the correct format.

====Example: Output on Radiation Timesteps====

You will have discovered that there are 16 radiation timesteps per day, but to work out how to output diagnostics you need to know many model timesteps per day there are. This can be found at: um <math>\rightarrow</math> namelist <math>\rightarrow</math> Top Level Model Control <math>\rightarrow</math> Model Domain and Timestep. The number is given by the variable '''<tt>steps_per_periodim</tt>''', which is defined as the number of steps per period given (in seconds) by '''<tt>secs_per_periodim</tt>'''. For one day, this value is 86400.

In the UKCA training suite, <tt>secs_per_periodim</tt>=86400, and <tt>steps_per_periodim</tt>=48. This means that there are 48 timesteps per day, i.e. each timestep is '''30 minutes'''. 

We can combine this with the number of radiation timesteps per day (16), to calculate that '''radiation is called every third model timestep''' (48/16 = 3) in this configuration. We can now fill-in the values in the new time profile accordingly, e.g.

* '''<tt>ityp</tt>:''' No time processing
* '''<tt>tim_name</tt>:''' e.g. TRAD
* '''<tt>unt3</tt>:''' Timesteps (1)
* '''<tt>iopt</tt>:''' Regular intervals
* '''<tt>istr</tt>:''' 1 (i.e. start on first timestep)
* '''<tt>iend</tt>:''' -1 (i.e. never stop outputting)
* '''<tt>ifre</tt>:''' 3 (i.e. output every third timestep)

We need to start at timestep 1, as radiation is called on the first timestep, and then called every third model timestep after that. In contrast, the UKCA Newton-Raphson chemical solver is first called on the first hour, and then every hour after that. For the UKCA training suite this would mean that <tt>istr</tt>=2 and <tt>ifre</tt>=2, but for standard UKCA runs at N96eL85 with a 20-minute timestep this would have <tt>istr</tt>=3 and <tt>ifre</tt>=3.

===Domain profiles===

[[Image:Vn10.9_newdom.png|thumb|300px|right|The new domain panel in Rose.]]
To make a new time profile, go to: '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> STASH Requests and Profiles <math>\rightarrow</math> Domain Profiles'''. This contains a list of existing domain profiles, with names like ''<tt>dallth_1e2e730d</tt>'' etc.

To make a new domain profile, you should:

# Right-click anywhere on the list and click the green plus symbol ('''<span style="color:green">+</span>''') named '''Add new section'''
#: This will make a new blank line (usually labelled '''1''', the next '''2''' etc.) with a red '''<span style="color: red">X</span>''' next to it.
# Right-click this new line and click '''View namelist'''.
# Fill-in the values as required for what you want to do. 
# When you have finished, you will need to run the When you have finished, you will need to run the '''stashindices.TidyStashTransform''' macro by going to the '''Metadata <math>\rightarrow</math> um''' drop-down menu. This will rename the new profile into the correct format.

====Example: Output AOT pseudo levels on all model theta levels====

Aerosol diagnostics are defined on a series of 6 '''pseudo levels''', corresponding to 0.38, 0.44, 0.55, 0.67, 0.87, and 1.02 microns. You will therefore need to output on your data on all of these. For some diagnostics, such as AOD, these are defined on a single level, but others, such as extinction, are a 3D field over the whole atmosphere. Therefore, to output the 3D aerosol extinction we need to make a new profile over all model (theta grid) levels, ''and'' all 6 pseudo levels.

We can now fill-in the values in the new domain profile accordingly, e.g.

* '''<tt>dom_name</tt>:''' e.g. D3DAR
* '''<tt>iopl</tt>:''' Variable derived on model theta levels (Charney-Phillips Grid) (2)
* '''<tt>ilevs</tt>:''' provide range <nowiki>[</nowiki>bottom and top level numbers<nowiki>]</nowiki>
* '''<tt>ilevb</tt>:''' 1 (i.e. 20m level)
* '''<tt>ilevt</tt>:''' 38 (i.e. highest level)
* '''<tt>plt</tt>:''' Radiation bands for calculating aerosol optical depth (4)
: This will then insert a new option below (<tt>pslist</tt>) to allow you to specify the bands you require.
* '''<tt>pslist</tt>:''' press the green plus symbol ('''<span style="color:green">+</span>''') 5 times, and enter the numbers 1 to 6 in each of the boxes to output all AOT pseudo levels.
* '''<tt>iopa</tt>:''' Full model area (1) 
* '''<tt>imsk</tt>:''' Land and sea points
* '''<tt>imn</tt>:''' None (0)
* '''<tt>iwt</tt>:''' None
* '''<tt>ts</tt>:''' false

===Usage profiles===

[[Image:Vn10.9_newuse.png|thumb|300px|right|The new usage panel in Rose.]]
Making new usage profiles is not as straight-forward as for time and domain profiles, as these are used to output diagnostics to different output files (and possibly to climate mean files). To see what output streams are available, go to: '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> Model Output Streams'''. In the UKCA training suite, only '''pp0''' is active. 

To look at climate meaning, go to: '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> Dumping and Meaning'''. This is controlled by the logical '''<tt>l_meaning_sequence</tt>''', which in the UKCA training suite is set to '''false''' (i.e. no climate meaning). If this is set to ''true'' then various settings will need to be chosen, such as the reference time, the frequency of files, and which files to output. 

To view the usage profiles, go to: '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> STASH Requests and Profiles <math>\rightarrow</math> Usage Profiles'''. This contains a list of existing domain profiles, with names like ''<tt>upa_ffb3f00b</tt>'' etc. If you look at the '''upa''' namelist (by right-clicking on it and clicking '''view namelist''') you can see that this corresponds with the ''pp0'' output stream.

It is also possible to write diagnostics to a '''tag''', which can then be read by other parts of the code. This is how UKCA couples to the UM, via tag=98. This can be seen in the '''upukca''' usage profile.

When you take a copy of an existing configuration it is unlikely that you will need to make any changes to any (or make new) usage profiles. However, if you do want to make a new usage profile, you should:

# Right-click anywhere on the list and click the green plus symbol ('''<span style="color:green">+</span>''') named '''Add new section'''
#: This will make a new blank line (usually labelled '''1''', the next '''2''' etc.) with a red '''<span style="color: red">X</span>''' next to it.
# Right-click this new line and click '''View namelist'''.
# Fill-in the values as required for what you want to do.
# When you have finished, you will need to run the When you have finished, you will need to run the '''stashindices.TidyStashTransform''' macro by going to the '''Metadata <math>\rightarrow</math> um''' drop-down menu. This will rename the new profile into the correct format.

'''Note''' that if you are making a new usage profile that is not associated with a ''tag'', you may also need to make changes to the output streams. This could be quite involved.

===Using your new profiles===

Once you have made your new profiles you should then use them in the usual way when outputting diagnostics, as covered in [[UKCA_Chemistry_and_Aerosol_vn11.8_Tutorial_3#STASH_Panel|Tutorial 3]].

When all your new STASH is set-up, you can use the Validator Macros to check if the names are correct, or if there are any unused STASH items etc. To run this, go to '''Metadata <math>\rightarrow</math> Check all Validator Macros''' from the drop-down menu. You can also check for ''fail-if'' or ''warn-if'' issues. However, these won't warn of incorrect domain requests (i.e. requesting pressure-levels for diagnostics only defined on a single level), so some care should still be taken.

==Solution to Task 12.1==

You were given the task

* ''Output the following aerosol and radiation diagnostics to the '''UPA''' output stream. You should make a new ''time profile'' (called TRAD) to only output these on '''radiation timesteps'''. You will also need to make a new ''domain profile'' (called D3DAR) for s02i530 and s02i540, to '''output these on both model levels and pseudo levels'''. You should also remove the existing entry for s02i301 "ACCUM MODE (SOLUBLE) OPTICAL DEPTH" that is output as T3HMN.''

{| class="wikitable" border = "1px"
!style="text-align:top;"|STASH Section
!style="text-align:top;"|STASH Item
!style="text-align:top;"|STASH Name
|-  style="background:lightgrey;"
|    1 ||  207 || INCOMING SW RAD FLUX (TOA): ALL TSS 
|-  style="background:lightgrey;"
|    1 ||  208 || OUTGOING SW RAD FLUX (TOA)          
|-  style="background:lightgrey;"
|    2 ||  205 || OUTGOING LW RAD FLUX (TOA)          
|- 
|    2 ||  285 || MINERAL DUST OPTICAL DEPTH IN RADN. 
|- 
|    2 ||  300 || AITKEN MODE (SOLUBLE) OPTICAL DEPTH 
|- 
|    2 ||  301 || ACCUM MODE (SOLUBLE) OPTICAL DEPTH  
|- 
|    2 ||  302 || COARSE MODE (SOLUBLE) OPTICAL DEPTH 
|- 
|    2 ||  303 || AITKEN MODE (INSOL) OPTICAL DEPTH   
|- 
|    2 ||  304 || ACCUM MODE (INSOL) OPTICAL DEPTH    
|- 
|    2 ||  305 || COARSE MODE (INSOL) OPTICAL DEPTH   
|-  style="background:lightgrey;"
|    2 ||  585 || MINERAL DUST ABS. OPICAL DEPTH   
|- style="background:lightgrey;"
|    2 ||  240 || AITKEN (SOLUBLE) ABS OPTICAL DEPTH  
|- style="background:lightgrey;" 
|    2 ||  241 || ACCUM (SOLUBLE) ABS OPTICAL DEPTH   
|- style="background:lightgrey;"
|    2 ||  242 || COARSE (SOLUBLE) ABS OPTICAL DEPTH  
|- style="background:lightgrey;"
|    2 ||  243 || AITKEN (INSOL) ABS OPTICAL DEPTH    
|- style="background:lightgrey;" 
|    2 ||  244 || ACCUM (INSOL) ABS OPTICAL DEPTH     
|- style="background:lightgrey;" 
|    2 ||  245 || COARSE (INSOL) ABS OPTICAL DEPTH               
|- 
|    2 ||  530 || UKCA 3D AEROSOL EXTINCTION 
|- 
|    2 ||  540 || CLASSIC 3D AEROSOL EXTINCTION  
|}

and were given the hint

:* ''Remember to output your aerosol diagnostics on the AOT pseudo levels using the DIAGAOT profile.''

The specific Rose changes made are:
* https://code.metoffice.gov.uk/trac/roses-u/changeset/238683/c/q/9/8/8/trunk


The specific Rose changes made are:

 Index: app/um/rose-app.conf
 ===================================================================
 --- app/um/rose-app.conf	(revision 237899)
 +++ app/um/rose-app.conf	(revision 238683)
 @@ -3252,6 +3252,40 @@
  ukca_mode_seg_size=4
  ussp_seg_size=32
  
 +[namelist:umstash_domain(d3dar_17f7e88a)]
 +dom_name='D3DAR'
 +!!iest=0
 +ilevs=1
 +imn=0
 +imsk=1
 +!!inth=0
 +iopa=1
 +iopl=2
 +!!isth=0
 +!!iwst=0
 +iwt=0
 +!!l_spml_ts=.false.
 +levb=1
 +!!levlst=0
 +levt=38
 +plt=4
 +pslist=1,2,3,4,5,6
 +!!rlevlst=0
 +!!spml_bot=0
 +!!spml_ew=0
 +!!spml_ns=0
 +!!spml_top=0
 +!!tblim=0
 +!!tblimr=0
 +!!telim=0
 +!!tnlim=0
 +ts=.false.
 +!!tslim=0
 +!!tsnum=0
 +!!ttlim=0
 +!!ttlimr=0
 +!!twlim=0
 +
  [namelist:umstash_domain(dallrh_0496a967)]
  dom_name='DALLRH'
  !!iest=0
 @@ -3533,6 +3567,22 @@
  tim_name='TALLTS'
  use_name='UPUKCA'
  
 +[namelist:umstash_streq(01207_ed72c304)]
 +dom_name='DIAG'
 +isec=1
 +item=207
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(01208_83140cd8)]
 +dom_name='DIAG'
 +isec=1
 +item=208
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
  [namelist:umstash_streq(01235_3511dd9f)]
  dom_name='DIAG'
  isec=1
 @@ -3541,14 +3591,142 @@
  tim_name='TALLTS'
  use_name='UPUKCA'
  
 -[namelist:umstash_streq(02301_0f7c5f4a)]
 +[namelist:umstash_streq(02205_357bf644)]
 +dom_name='DIAG'
 +isec=2
 +item=205
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02240_aa529a3b)]
  dom_name='DIAGAOT'
  isec=2
 +item=240
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02241_23ef484a)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=241
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02242_a20a365a)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=242
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02243_982f92ad)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=243
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02244_e3af9288)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=244
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02245_49aef66c)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=245
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02285_7a37d547)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=285
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02300_9a80ef10)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=300
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02301_2c782a37)]
 +dom_name='DIAGAOT'
 +isec=2
  item=301
 -package='UKCA Testing'
 -tim_name='T3HMN'
 +package=''
 +tim_name='TRAD'
  use_name='UPA'
  
 +[namelist:umstash_streq(02302_2f4799de)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=302
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02303_f5122b3b)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=303
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02304_e52b9b1e)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=304
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02305_17b2f987)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=305
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02530_3cd868ec)]
 +dom_name='D3DAR'
 +isec=2
 +item=530
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02540_8e66e6b5)]
 +dom_name='D3DAR'
 +isec=2
 +item=540
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
 +[namelist:umstash_streq(02585_a1d86f30)]
 +dom_name='DIAGAOT'
 +isec=2
 +item=585
 +package=''
 +tim_name='TRAD'
 +use_name='UPA'
 +
  [namelist:umstash_streq(03025_c8768f77)]
  dom_name='DIAG'
  isec=3
 @@ -4099,6 +4277,25 @@
  !!unt2=2
  unt3=1
  
 +[namelist:umstash_time(trad_acd872d3)]
 +!!iedt=0
 +iend=-1
 +ifre=3
 +!!intv=0
 +!!ioff=0
 +iopt=1
 +!!isam=0
 +!!isdt=0
 +!!iser=0
 +istr=1
 +!!itimes=0
 +ityp=1
 +!!lts0=.false.
 +tim_name='TRAD'
 +!!unt1=1
 +!!unt2=1
 +unt3=1
 +
  [namelist:umstash_use(upa_ffb3f00b)]
  file_id='pp0'
  locn=3


These differences can be found here:

 Tutorials/UMvn13.0/worked_solutions/Task12.1/Task12.1_ukca.patch

Sample output from this task can be found at 

 Tutorials/UMvn13.0/sample_output/Task12.1/

If you open the '''.pa''' file in Xconv, you should see the following additional fields:

 0    : 96    72    1     2     field200: INCOMING SW RAD FLUX (TOA): ALL TSS 
 1    : 96    72    1     2     field201: OUTGOING SW RAD FLUX (TOA)          
 2    : 96    72    1     2     olr: OUTGOING LW RAD FLUX (TOA)
 3    : 96    72    6     2     unspecified: AITKEN (SOLUBLE) ABS OPTICAL DEPTH      
 4    : 96    72    6     2     unspecified: ACCUM (SOLUBLE) ABS OPTICAL DEPTH      
 5    : 96    72    6     2     unspecified: COARSE (SOLUBLE) ABS OPTICAL DEPTH
 6    : 96    72    6     2     unspecified: AITKEN (INSOL) ABS OPTICAL DEPTH 
 7    : 96    72    6     2     unspecified: ACCUM (INSOL) ABS OPTICAL DEPTH 
 8    : 96    72    6     2     unspecified: COARSE (INSOL) ABS OPTICAL DEPTH      
 9    : 96    72    6     2     unspecified: MINERAL DUST OPTICAL DEPTH IN RADN. 
 10   : 96    72    6     2     unspecified: AITKEN MODE (SOLUBLE) OPTICAL DEPTH 
 11   : 96    72    6     2     unspecified: ACCUM MODE (SOLUBLE) OPTICAL DEPTH  
 12   : 96    72    6     2     unspecified: COARSE MODE (SOLUBLE) OPTICAL DEPTH 
 13   : 96    72    6     2     unspecified: AITKEN MODE (INSOL) OPTICAL DEPTH   
 14   : 96    72    6     2     unspecified: ACCUM MODE (INSOL) OPTICAL DEPTH    
 15   : 96    72    6     2     unspecified: COARSE MODE (INSOL) OPTICAL DEPTH   
 16   : 96    72    38    2     unspecified: UKCA 3D AEROSOL EXTINCTION
 17   : 96    72    38    2     unspecified: UKCA 3D AEROSOL EXTINCTION
 18   : 96    72    38    2     unspecified: UKCA 3D AEROSOL EXTINCTION
 19   : 96    72    38    2     unspecified: UKCA 3D AEROSOL EXTINCTION
 20   : 96    72    38    2     unspecified: UKCA 3D AEROSOL EXTINCTION
 21   : 96    72    38    2     unspecified: UKCA 3D AEROSOL EXTINCTION
 22   : 96    72    38    2     unspecified: CLASSIC 3D AEROSOL EXTINCTION
 23   : 96    72    38    2     unspecified: CLASSIC 3D AEROSOL EXTINCTION
 24   : 96    72    38    2     unspecified: CLASSIC 3D AEROSOL EXTINCTION
 25   : 96    72    38    2     unspecified: CLASSIC 3D AEROSOL EXTINCTION
 26   : 96    72    38    2     unspecified: CLASSIC 3D AEROSOL EXTINCTION
 27   : 96    72    38    2     unspecified: CLASSIC 3D AEROSOL EXTINCTION
 28   : 96    72    6     2     unspecified: MINERAL DUST ABS. OPICAL DEPTH

==Task 12.2: Calculate aerosol optical depth==

<span style="color:green">'''TASK 12.2:''' Calculate the aerosol optical depth at 0.55 microns on the second radiation timestep.</span>

{| class="collapsible collapsed wikitable"
|-
! Hint 
|-
| The UM calculates optical depth diagnostics on 6 pseudo levels corresponding to 0.38, 0.44, 0.55, 0.67, 0.87, and 1.02 microns, therefore 0.55 microns is pseudo level 3.
|}

'''Note:''' You will need to use the CLASSIC mineral dust optical depth diagnostic, as the configuration used in these tutorials does not use modal dust. Likewise, the insoluble accumulation and coarse mode diagnostics will be zero as these modes are not used in the configuration used here.

===Python notebook===

To calculate the total aerosol optical depth at 0.55 microns, you should sum up the contribution from the different aerosol components. 

An example python notebook to do this has been provided at '''<tt>Tutorials/UMvn13.0/notebooks/UM-UKCA_T122.ipynb</tt>'''.

==Solution to Task 12.2 ==

<gallery widths=300px heights=200px>
Image:T12_aod_002.png|0.55 micron AOD calculated from the component aerosol AOD diagnostics.
</gallery>

You were asked to

* ''Calculate the aerosol optical depth at 0.55 microns on the second radiation timestep.''

and were given the hint

:* ''The UM calculates optical depth diagnostics on 6 pseudo levels corresponding to 0.38, 0.44, 0.55, 0.67, 0.87, and 1.02 microns, therefore 0.55 microns is pseudo level 3.''

You should make use of the python notebook provided to do this.

Sample output from this task can be found in the '''<tt>Tutorials/vn11.8/sample_output/Task10.2</tt>''' directory.

==Task 12.3: Calculate the single-scattering albedo==

<span style="color:green">'''TASK 12.3:''' Calculate the single-scattering albedo at 0.55 microns on the second radiation timestep, defined as: </span>

<math>
1 - \left(\frac{\textrm{Absorption}\ \textrm{Aerosol}\ \textrm{Optical}\ \textrm{Depth}}{\textrm{Aerosol}\ \textrm{Optical}\ \textrm{Depth}}\right)
</math>

===Python notebook===

To calculate the single-scattering albedo at 0.55 microns, you should sum up the contribution to AAOD and AOD from the different aerosol components. 

An example python notebook to do this has been provided at '''<tt>Tutorials/UMvn13.0/notebooks/UM-UKCA_T123.ipynb</tt>'''.

==Solution to Task 12.3 ==

<gallery widths=300px heights=200px>
Image:T12_ssa_003.png|0.55 micron single-scattering albedo.
</gallery>

You were asked to

* ''Calculate the single-scattering albedo at 0.55 microns on the second radiation timestep, defined as:''

<math>
1 - \left(\frac{\textrm{Absorption}\ \textrm{Aerosol}\ \textrm{Optical}\ \textrm{Depth}}{\textrm{Aerosol}\ \textrm{Optical}\ \textrm{Depth}}\right)
</math>

You should use the python notebook provided to do this.

Sample output from this task can be found in the '''<tt>Tutorials/UMvn13.0/sample_output/Task12.3</tt>''' directory.

==Task 12.4: Calculate the top of the atmosphere net downward radiative flux==

<span style="color:green">'''TASK 12.4:''' Calculate the net downward top of the atmosphere radiative flux on the second radiation timestep.</span>

===Python notebook===

To calculate the net TOA downward radiative flux, you should sum up the outgoing contributions from shortwave and longwave radiation, and take this away from the incoming shortwave radiative flux. 

An example python notebook to do this has been provided at '''<tt>Tutorials/UMvn13.0/notebooks/UM-UKCA_T124.ipynb</tt>'''.

==Solution to Task 12.4 ==

<gallery widths=300px heights=200px>
Image:T12_toa_004.png|Net downward TOA radiative flux.
</gallery>

You were asked to

* ''Calculate the net downward top of the atmosphere radiative flux on the second radiation timestep.''

You should use the python notebook provided to do this.

Sample output from this task can be found in the '''<tt>Tutorials/UMvn13.0/sample_output/Task12.4</tt>''' directory.

==Task 12.5: Calculate aerosol optical depth from the 3D aerosol extinction==

<span style="color:green">'''TASK 12.5:''' Using the 3D aerosol extinction, calculate the 0.55 micron aerosol optical depth on the second radiation timestep, and compare this to your AOD from Task 12.2.</span>

{| class="collapsible collapsed wikitable"
|-
! Hint 
|-
| You will need to include contributions from both UKCA and CLASSIC (due to the dust scheme).
|-
| Remember to correctly calculate the grid-cell heights.
|}

===Python notebook===

To calculate the AOD from the aerosol extinction, you will need to integrate this in the column. To do this you should first multiply by the height of each grid-cell before summing-up. 

An example python notebook to do this has been provided at '''<tt>Tutorials/UMvn13.0/notebooks/UM-UKCA_T125.ipynb</tt>'''. This script will also difference the two different methods.

==Solution to Task 12.5 ==

<gallery widths=300px heights=200px>
Image:T12_aod_005.png|0.55 micron AOD calculated from the 3D extinction diagnostics.
Image:T12_aoddiff_005.png|Difference in AODs calculated by the two methods.
</gallery>

You were asked to

* ''Using the 3D aerosol extinction, calculate the 0.55 micron aerosol optical depth on the second radiation timestep, and compare this to your AOD from Task 12.2.''

and were given the hints

:* ''You will need to include contributions from both UKCA and CLASSIC (due to the dust scheme).''
:* ''Remember to correctly calculate the grid-cell heights.''

You should use the python notebook provided to do this.

Sample output from this task can be found in the '''<tt>Tutorials/UMvn13.0/sample_output/Task12.5</tt>''' directory.

==Task 12.6: Calculate the difference in aerosol impacts when <tt>Sec_Org</tt> is no longer formed from ALICE==

<span style="color:green">'''TASK 12.6:''' You should now remove the formation of '''<tt>Sec_Org</tt>''' from the chemical reaction added in Task 6.1, giving</span>

<math>
\textrm{ALICE} + \textrm{OH} \longrightarrow \textrm{BOB}
</math>

<span style="color:green">and assess the impact this has on the aerosol diagnostics calculated in the previous tasks, 10.2, 10.3, and 10.4.</span>

{| class="collapsible collapsed wikitable"
|-
! Hint 
|-
| Remember to remove <tt>Sec_Org</tt> from the diagnostics as well as the reaction.
|-
| As <tt>Sec_Org</tt> is now no longer included, it should no longer have the '''<tt>a</tt>''' qualifier.
|}

'''Note:''' as this a very short run (that is still spinning-up) and you will only be considering a single timestep, the results will be incredibly noisy.

The following python scripts have been provided that can be used to difference the AOD, SSA, and TOA fields. These are provided in the '''<tt>Tutorials/vn11.8/Task10/</tt>''' directory.
 Task106_diff_AOD_rxn.py
 Task106_diff_SSA_rxn.py
 Task106_diff_TOA_rxn.py
You should edit your scripts for the previous Tasks in this Tutorial to calculate the AOD, SSA, & TOA from your sensitivity run.

==Code changes required to modify a reaction==

Modifying a reaction is very similar to [[UKCA_Chemistry_and_Aerosol_vn11.8_Tutorial_6#Adding_new_Chemical_Reactions|adding a new one]], although simpler as you are only changing what is already there. The exact routines that will need to be altered will depend on the reaction, but likely include:

===<tt>ukca_chem_master.F90</tt>===

You must edit the master list of reactions, given by '''<tt>ratb_defs_master</tt>''' for bimolecular reactions, '''<tt>ratt_defs_master</tt>''' for termolecular reactions, '''<tt>rath_defs_master</tt>''' for heterogeneous reactions, or '''<tt>ratj_defs_master</tt>''' for photolysis reactions.

===<tt>ukca_config_defs_mod.F90</tt>===

You may need to adjust the values of <tt>nr_therm</tt> or <tt>nr_phot</tt> if you adjust the qualifier or disqualifier options. This may mean changing the values for the aerosol chemistry and/or non-aerosol chemistry definitions as appropriate.

===<tt>asad_bimol.F90</tt>, <tt>asad_trimol.F90</tt>, <tt>ukca_hetero_mod.F90</tt>, <tt>asad_hetero.F90</tt>, <tt>ukca_phot2d.F90</tt>, and <tt>ukca_strat_update.F90</tt>===

If you added any special code for the reaction(s) to <tt>asad_bimol.F90</tt>, <tt>asad_trimol.F90</tt>, <tt>ukca_hetero_mod.F90</tt>, <tt>asad_hetero.F90</tt>, <tt>ukca_phot2d.F90</tt>, or <tt>ukca_strat_update.F90</tt> it will need to be altered accordingly. The location of the reaction in the complete list is usually found by searching on the reactants and products, and if these change then the lookup will fail unless it is altered here too.

===<tt>asad_flux_dat.F90</tt>===

If there are any diagnostics to output the reactions you are modifying, you may need to alter this specification as well if you have changed the reactants and/or products.

==Solution to Task 12.6 ==

<gallery widths=300px heights=300px>
Image:UM11.8_Task106_AOD_diff.png|Difference in AOD.
Image:UM11.8_Task106_SSA_diff.png|Difference in single-scattering albedo.
Image:UM11.8_Task106_TOA_diff.png|Difference in net downward TOA fluxes.
</gallery>

You were asked to

* ''You should now remove the formation of '''<tt>Sec_Org</tt>''' from the chemical reaction added in Task 6.1, giving''

<math>
\textrm{ALICE} + \textrm{OH} \longrightarrow \textrm{BOB}
</math>

: ''and assess the impact this has on the aerosol diagnostics calculated in the previous tasks, 10.2, 10.3, and 10.4.''

and were given the hints

:* ''Remember to remove <tt>Sec_Org</tt> from the diagnostics as well as the reaction.''
:* ''As <tt>Sec_Org</tt> is now no longer included, it should no longer have the '''<tt>a</tt>''' qualifier.''

You should use the above python scripts provided to do this.

For a working Rose suite that has completed this task, please see
* '''vm:''' <tt>u-ca024@183506</tt>

The specific Rose changes made are:

* '''vm:''' https://code.metoffice.gov.uk/trac/roses-u/changeset/183506/c/a/0/2/4/trunk

'''vm:'''
 Index: app/fcm_make/rose-app.conf
 ===================================================================
 --- app/fcm_make/rose-app.conf	(revision 183486)
 +++ app/fcm_make/rose-app.conf	(revision 183506)
 @@ -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@94303
 +um_sources=branches/dev/lukeabraham/vn11.8_UKCA_Tutorial_Solns@94453

These differences can be found in the file '''<tt>Tutorials/vn11.8/worked_solutions/Task10.6/Task10.6_rose.patch</tt>'''.

The specific UM changes made are:
* https://code.metoffice.gov.uk/trac/um/changeset/94453/main/branches/dev/lukeabraham/vn11.8_UKCA_Tutorial_Solns

 Index: src/atmosphere/UKCA/asad_flux_dat.F90
 ===================================================================
 --- src/atmosphere/UKCA/asad_flux_dat.F90	(revision 94303)
 +++ src/atmosphere/UKCA/asad_flux_dat.F90	(revision 94453)
 @@ -4179,9 +4179,9 @@
  
  ! Additional diagnostics for UKCA tutorials
  TYPE(asad_flux_defn), PARAMETER, PUBLIC :: ukca_tutorial_fluxes(3) = (/        &
 -asad_flux_defn('RXN',50996,'B',.FALSE.,0,4,                                    &
 +asad_flux_defn('RXN',50996,'B',.FALSE.,0,3,                                    &
  (/'ALICE     ','OH        '/),                                                 &
 -(/'BOB       ','Sec_Org   ','          ','          '/)),                      &
 +(/'BOB       ','          ','          ','          '/)),                      &
  asad_flux_defn('DEP',50997,'D',.FALSE.,0,1,                                    &
  (/'ALICE     ','          '/),                                                 &
  (/'          ','          ','          ','          '/)),                      &
 Index: src/atmosphere/UKCA/ukca_chem_master.F90
 ===================================================================
 --- src/atmosphere/UKCA/ukca_chem_master.F90	(revision 94303)
 +++ src/atmosphere/UKCA/ukca_chem_master.F90	(revision 94453)
 @@ -4716,8 +4716,8 @@
  ! B697
  ratb_t1(697,'MSIA      ','NO3       ','MeSO2     ','HONO2     ','          ',  &
  '          ',1.00e-13,  0.00,    0.00, 0.00, 0.00, 0.00, 0.00,cs,a,0,107),     &
 -ratb_t1(698,'ALICE     ','OH        ','BOB       ','Sec_Org   ','          ',  & 
 -'          ',2.70E-11,  0.00, -390.00, 0.00, 0.00, 0.00, 0.00,st,a,0,111)      &
 +ratb_t1(698,'ALICE     ','OH        ','BOB       ','          ','          ',  & 
 +'          ',2.70E-11,  0.00, -390.00, 0.00, 0.00, 0.00, 0.00,st,0,0,111)      &
  /)
  
  
 Index: src/atmosphere/UKCA/ukca_config_defs_mod.F90
 ===================================================================
 --- src/atmosphere/UKCA/ukca_config_defs_mod.F90	(revision 94303)
 +++ src/atmosphere/UKCA/ukca_config_defs_mod.F90	(revision 94453)
 @@ -316,7 +316,7 @@
              'C2H6      ','C3H8      ','Me2CO     ','MeCHO     ',               &
              'C5H8      ', nm_meoh_em ,'ALICE     ','NO_aircrft'/)
        n_chem_tracers = 73         ! No chem tracers
 -      nr_therm       = 220        ! thermal reactions
 +      nr_therm       = 221        ! thermal reactions
        nr_phot        = 55         ! photolytic (ATA)
  
      ELSE  ! If using aerosol chemistry
 Index: rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf
 ===================================================================
 --- rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf	(revision 94303)
 +++ rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf	(revision 94453)
 @@ -26285,8 +26285,8 @@
      =Available only if NetCDF emission system of UKCA is used
  
  [stashmaster:code(50996)]
 -description=RXN FLX: ALICE+OH->BOB+Sec_Org
 -help=Flux through the ALICE+OH->BOB+Sec_Org reaction
 +description=RXN FLX: ALICE+OH->BOB
 +help=Flux through the ALICE+OH->BOB reaction
  
  [stashmaster:code(50997)]
  description=DRY DEP FLUX: ALICE (3D)
 @@ -29805,8 +29805,8 @@
      =Available for Strat and StratTrop chemistry only
  
  [stashmaster:code(52996)]
 -description=RXN FLX: ALICE+OH->BOB+Sec_Org PLEV
 -help=Flux through the ALICE+OH->BOB+Sec_Org reaction
 +description=RXN FLX: ALICE+OH->BOB         PLEV
 +help=Flux through the ALICE+OH->BOB reaction
      = on Pressure Levels
  
  [stashmaster:code(52997)]
 Index: rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A
 ===================================================================
 --- rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A	(revision 94303)
 +++ rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A	(revision 94453)
 @@ -27521,7 +27521,7 @@
  4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |
  5|    0 |    0 |    0 |  129 |    0 |    0 |    0 |    0 |    0 |
  #
 -1|    1 |   50 |  996 |RXN FLUX: ALICE+OH->BOB+Sec_Org     |
 +1|    1 |   50 |  996 |RXN FLUX: ALICE+OH->BOB             |
  2|    0 |    0 |   17 |    1 |    2 |   10 |   11 |    0 |    0 |    0 |    0 |
  3| 000000000000000000000000010000 | 00000000000000000001 |    3 |
  4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |
 @@ -30643,7 +30643,7 @@
  # pressure levels not meaningful. Do not use these slots for other diagnostics.
  #===============================================================================
  #
 -1|    1 |   52 |  996 |RXN FLUX: ALICE+OH->BOB+Sec_Org PLEV|
 +1|    1 |   52 |  996 |RXN FLUX: ALICE+OH->BOB         PLEV|
  2|    0 |    0 |   17 |    1 |    3 |    1 |    2 |    0 |    0 |    0 |    1 |
  3| 000000000000000000000000010000 | 00000000000000000001 |    3 |
  4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |

These differences can be found in the file '''<tt>Tutorials/vn11.8/worked_solutions/Task10.6/Task10.6_code.patch</tt>'''.

Sample output from this task can be found in the '''<tt>Tutorials/vn11.8/sample_output/Task10.6</tt>''' directory.

==Checklist==

: <span style="font-size:20px">☐</span> Make new time and domain profiles as needed.
: <span style="font-size:20px">☐</span> Run the TidyStashTransform transform macro.
: <span style="font-size:20px">☐</span> Output your diagnostics in STASH at: um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> STASH Requests and Profiles <math>\rightarrow</math> STASH Requests.
: <span style="font-size:20px">☐</span> When adding new aerosol diagnostics, remember to output on pseudo levels if appropriate.
: <span style="font-size:20px">☐</span> Run the TidyStashTransform transform macro again for the diagnostic requests.
: <span style="font-size:20px">☐</span> Save your suite.
: <span style="font-size:20px">☐</span> In the <tt>roses/[SUITE-ID]</tt> directory, run <tt>fcm commit</tt> to commit your changes to the repository.
: <span style="font-size:20px">☐</span> When modifying chemical reactions, remember to make changes for diagnostics and special cases, as well as altering <tt>ukca_chem_master.F90</tt>.
: <span style="font-size:20px">☐</span> The Iris python library can be used to process and visualise Unified Model output.


[[UKCA Chemistry and Aerosol Tutorials at UMvn13.0]]
----
''Written by [[User:Nla27 | Luke Abraham]] 2021.''