Difference between revisions of "Solution to UKCA Chemistry and Aerosol Tutorial 5 Task 5.1"
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| − | [[UKCA Chemistry and Aerosol Tutorials | Back to UKCA Chemistry and Aerosol Tutorials]] |
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| − | [[UKCA Chemistry and Aerosol Tutorial 5#Solution to Task_5.1: Make slots for two new tracers | Back to the adding new chemical tracers tutorial]] |
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| − | ==Task== |
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| − | You were asked to |
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| − | <blockquote> |
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| − | Add in two new tracers in to slots 64 and 65. The tracer in slot 64 will be called '''ALICE''' and the tracer in slot 65 will be called '''BOB'''. You should also output these two tracers through the '''pb/UPB''' stream in STASH as daily means. |
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| − | </blockquote> |
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| − | ==Solution== |
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| − | ===1. The user STASHmaster file=== |
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| − | Go to '''Model Selection → Atmosphere → STASH → User-STASHmaster files. Diags, Progs & Ancills.'''. In this panel you will see that a number of user STASHmaster files listed. The one containing the tracers is ''UKCA_Tr_StratTrop.prestash''. |
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| − | Take a copy of the '''UKCA_Tr_StratTrop.prestash''' user STASHmaster file, which can be found at |
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| − | /home/ukca/userprestash/VN8.2/UKCA_Tr_StratTrop.prestash |
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| − | on PUMA, and copy it to your own directory. Edit this file to add the lines |
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| − | # |
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| − | 1| 1 | 34 | 64 |UKCA TUTORIAL TRACER: ALICE | |
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| − | 2| 2 | 0 | 1 | 1 | 2 | 10 | 11 | 0 | 0 | 0 | 0 | |
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| − | 3| 000000000000000000000000000064 | 00000000000000000001 | 1 | |
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| − | 4| 1 | 0 | -99 -99 -99 -99 -99 -99 -99 -99 -99 -99 | |
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| − | 5| 0 | 1861 | 0 | 65 | 0 | 0 | 0 | 0 | 0 | |
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| − | # |
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| − | 1| 1 | 34 | 65 |UKCA TUTORIAL TRACER: BOB | |
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| − | 2| 2 | 0 | 1 | 1 | 2 | 10 | 11 | 0 | 0 | 0 | 0 | |
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| − | 3| 000000000000000000000000000065 | 00000000000000000001 | 1 | |
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| − | 4| 1 | 0 | -99 -99 -99 -99 -99 -99 -99 -99 -99 -99 | |
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| − | 5| 0 | 1861 | 0 | 65 | 0 | 0 | 0 | 0 | 0 | |
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| − | # |
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| − | An example file can be found at |
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| − | /home/ukca/userprestash/VN8.2/Tutorial/Task4.1_UKCA_Tr_StratTrop.prestash |
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| − | |||
| − | ===2. Initialise the new tracers=== |
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| − | Go to '''Model Selection → Atmosphere → STASH → Initialisation of User Prognostics''', scroll down the list of variables until you find your new tracers and set these to option '''3''' (i.e. zero). |
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| − | ===3. Add the hand-edit=== |
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| − | Run the '''/home/ukca/bin/make_tracer_list''' script on your user STASHmaster file to produce the following output |
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| − | TC_UKCA=1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1, |
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| − | 1,0,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0,1,1,1,0,1,1,1,1,1,1,1,1,1,1,0,0,0, |
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| − | 1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,1,1,1,0,0, |
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| − | 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, |
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| − | 0,0,0,0,0,0,0,1,1, |
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| − | TR_UKCA=74, |
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| − | You can make a hand-edit file like this |
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| − | # Hand edit to add tracers for UKCA tutorial |
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| − | # vn8.2 64:ALICE, 65:BOB |
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| − | ed SIZES<<\EOF |
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| − | /TC_UKCA=/ |
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| − | d |
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| − | d |
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| − | d |
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| − | d |
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| − | d |
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| − | i |
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| − | TC_UKCA=1,1,1,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1, |
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| − | 1,0,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0,1,1,1,0,1,1,1,1,1,1,1,1,1,1,0,0,0, |
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| − | 1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,1,1,1,0,0, |
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| − | 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, |
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| − | 0,0,0,0,0,0,0,1,1, |
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| − | . |
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| − | w |
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| − | q |
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| − | EOF |
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| − | ed SIZES<<\EOF |
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| − | /TR_UKCA=/ |
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| − | d |
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| − | i |
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| − | TR_UKCA=74, |
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| − | . |
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| − | w |
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| − | q |
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| − | EOF |
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| − | and make this script executable (<tt>chmod a+rx <span style="color:blue">script.ed</span></tt>). |
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| − | An example of this hand-edit can be found at |
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| − | /home/ukca/hand_edits/VN8.2/Tutorial/Task4.1_add_UKCA_Tr_StratTrop.ed |
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| − | Add your hand-edit to the UMUI at '''Model Selection → Input/Output Control and Resource → User hand edit files''' by placing it in the table and putting a '''Y''' in the ''Include Y/N'' column. |
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| − | ===Changes to STASH=== |
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| − | Go to the STASH panel at '''Model Selection → Atmosphere → STASH → STASH. Specification of Diagnostic requirements''' and go to '''Diagnostics → Load New Diagnostics''' and scroll down the list until you come to section '''34''' and double-click where it says '''UKCA Chemistry'''. Scroll down the list until you get to the ALICE and BOB tracers, and add them to STASH like so |
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| − | 34 64 UKCA TUTORIAL TRACER: ALICE TDAYM DALLTH UPB Y + N X |
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| − | 34 65 UKCA TUTORIAL TRACER: BOB TDAYM DALLTH UPB Y + N X |
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| − | You will see that the final two columns say ''N'' (''Avail'') and ''X'' (''I+P+A''). This is because STASH thinks that these tracers are not available as they are not turned on until the ''Process'' stage when the hand-edit defined above is applied. Also, if you verify diagnostics you get the following warning |
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| − | Diag: "UKCA TUTORIAL TRACER: ALICE " (34,64) (TDAYM,DALLTH,UPB) |
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| − | DIAGNOSTIC ERROR: Diagnostic is not available for this model configuration. |
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| − | Diag: "UKCA TUTORIAL TRACER: BOB " (34,65) (TDAYM,DALLTH,UPB) |
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| − | DIAGNOSTIC ERROR: Diagnostic is not available for this model configuration. |
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| − | However, you should not worry about this, as the tracers are available and will be output. However, they will contain zeros as nothing has been placed into them (yet). |
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| − | '''Note:''' If you find that you get this error message, but with different names (although the section and item numbers are the same) then you should '''save''' your job and '''close''' it. Now when you re-open it and open the STASH panel again you will find that the names have been updated. This occurs because STASH only reads the user STASHmaster files the first time the panel is opened (in that job instance) so you must re-load the job for the changes to properly take effect. |
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| − | ==Output== |
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| − | If you open the '''pb''' file in your '''[[UKCA & UMUI Tutorials: Things to know before you start#Archiving|archive]]''' directory you will find that it now contains the fields |
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| − | 0 : 192 145 85 1 Stash code = 34001 |
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| − | 1 : 192 145 85 1 Stash code = 34064 |
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| − | 2 : 192 145 85 1 Stash code = 34065 |
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| − | If you open 34064 and 34065 you will find that they only contain zeros. |
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| − | '''Sample output''' from this job can be found in |
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| − | /work/n02/n02/ukca/Tutorial/sample_output/Task4.1/ |
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| − | on HECToR, and in |
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| − | /projects/ukca/Tutorial/sample_ouput/Task4.1/ |
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| − | on MONSooN. |
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| − | ==Worked Solution== |
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| − | There is a worked solution to this problem in the UMUI Tutorial experiment. This is job '''d''': ''Tutorial: solution to Task 5.1 - adding new chemical tracers to the UMUI''. |
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| − | ---- |
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| − | ''Written by [[User:Nla27 | Luke Abraham]] 2014'' |
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