View source for Advanced UKCA Chemistry and Aerosol UMvn13.9 Tutorial 1

[[Advanced UKCA Chemistry and Aerosol Tutorials at UMvn13.9]]

{| class="wikitable" border = "1px"         
|- 
| Difficulty ||  '''<span style="color:green">EASY</span>'''
|- 
| Time to Complete ||  '''Under 1 hour'''
|-
| Video instructions ||  [https://www.youtube.com/watch?v=n3yE-oYy-gU&t=89s Walkthrough (YouTube)]
|}

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

==What you will learn in this tutorial==

In this tutorial you will learn how to copy a UKCA Box Model suite, run it, and plot the output.

==Copying and Running an Existing Rose Suite==

{| class="wikitable" border = "1px"
!style="text-align:top;|Machine 
!style="text-align:top;|UM Version/Configuration
!style="text-align:top;|Suite ID
|-
| vm || UMvn13.0 UKCA Box Model || '''[https://code.metoffice.gov.uk/trac/roses-u/browser/d/r/4/0/7/trunk u-dr407]''' 
|-
|}

You will need to login to the VM using SSH via a Terminal

 ssh -X ukca

When you first login to your virtual machine you should then be asked for your Met Office Science Repository Service (MOSRS) password. Once you enter this, if this is the first time you are logging in, you will also be asked for your MOSRS username. This will likely be your name in lower case, and is '''not''' your username on the VM.

Then copy the rose suite by:

 rosie copy u-dr407

[[Image:T01_rosegcylc.png|thumb|300px|right|UKCA Box Model opened with Rose and GCylc running on the VM via X2Go.]]
This will open an editor containing text similar to this:

 description=Copy of u-dr407/trunk@328566
 owner=lukeabraham
 project=ukca
 title=Cylc 8 UMvn13.9 UKCA Box Model
 
 # Make changes ABOVE these lines.
 # The "owner", "project" and "title" fields are compulsory.
 # Any KEY=VALUE pairs can be added. Known fields include:
 # "access-list", "description" and "sub-project".

You can edit the title to make it more descriptive if you like. Then save (e.g. Ctrl-s) and close the file (e.g. Ctrl-q). The press '''y''' on the keyboard when prompted and press return.

The suite will now copy and checkout to your <tt>/home/'''$USER'''/roses</tt> directory, into a sub-directory that is the same as the SUITE-ID. You should change into this directory now using '''cd''', e.g.

 cd roses/u-ab123

then open the suite by typing

 rose edit &

and pressing return. You run the suite by typing

 cylc vip

in the terminal when you are in its top-level directory (i.e. <tt>u-ab123</tt>). This is a [https://cylc.github.io/ Cylc] command that means '''validate''', '''install''', and '''play'''. You will then get similar output to following in the terminal:

 vagrant@vagrant:~/roses/u-ds042$ cylc vip
 $ cylc validate /home/vagrant/roses/u-ds042
 Valid for cylc-8.4.3
 $ cylc install /home/vagrant/roses/u-ds042
 INSTALLED u-ds042/run1 from /home/vagrant/roses/u-ds042
 $ cylc play u-ds042/run1
 
  ▪ ■  Cylc Workflow Engine 8.4.3
  ██   Copyright (C) 2008-2025 NIWA
 ▝▘    & British Crown (Met Office) & Contributors
 
 INFO - Extracting job.sh to /home/vagrant/cylc-run/u-ds042/run1/.service/etc/job.sh
 u-ds042/run1: vagrant PID=347531

To view the progress of this suite you can either use the Cylc TUI ("terminal user interface") or Cylc GUI ("graphical user interface"). The TUI can be opened using the command

 cylc tui

which will then open a terminal-based view similar to that seen in the figure below. This lists all your suites, some of which will have been run previously when setting-up your virtual machine. To navigate through the TUI you should use the arrow keys to move up and down, and the right and left arrow keys to open and collapse sections that are availble, indicated by the "<tt>+</tt>" symbol.

A linux alias has been made for you to run the GUI. In the terminal type

 cylc-gui 

(note the <tt>-</tt>). This is equivalent to opening an <tt>lxterminal</tt> and then running the following command:

 cylc gui --ServerApp.open_browser=False --ServerApp.port=PORT --ServerApp.ip=0.0.0.0 

This starts the graphical Cylc server, and you then need to CONNECT TO IT AS DESCRIBED IN DOCUMENTATION.

A screenshot of the GUI, equivalent to the TUI output, can be seen in the figure below. Information about what the symbols and colours mean can be found in the [https://cylc.github.io/cylc-doc/stable/html/user-guide/running-workflows/tasks-jobs-ui.html Cylc documenation].

<gallery widths=400px heights=350px>
Image:Cylc8_tui.png|Cylc terminal user interface
Image:Cylc8_gui.png|Cylc graphical user interface
</gallery>

For this suite to run you need the UKCA branch

 fcm:ukca.x_br/dev/lukeabraham/um13.9_ukca_box

checked-out into your <tt>home/</tt> directory. This has been done for you.

If you are using your own VM, times will vary depending on the specifications of the host. It may take 2 or 3 minutes to compile the code (''fcm_make'') for the first time (and a few seconds when recompiling), followed by another few seconds to run UKCA itself (''ukca''). Any unsuccessful jobs will be highlighted in red and have a status of "failed".

When the suite has finished successfully it will then become blank with the message '''stopped''''.

==Version Control==

Rose suites are all held under version control, using [https://www.metoffice.gov.uk/research/weather/weather-science-it/fcm fcm]. When making changes to a suite, you will need to '''save''' it before you can '''run''' the suite. Once you are happy with the settings, you can also '''commit''' these changes back to the repository - to do this change directory to the 

 /home/'''$USER'''/roses/'''[SUITE-ID]'''

and then type

 '''fcm commit'''

a text editor will then open, and you should type a short message describing what the changes you have made do. You should then close the editor and type '''y''' in the terminal. It is recommended that you commit frequently (even on configurations that aren't working) as this protects you against mistakes and accidental deletions etc.

These suites can be viewed on the SRS here: [https://code.metoffice.gov.uk/trac/roses-u https://code.metoffice.gov.uk/trac/roses-u (password required)]

'''It is recommended that you commit your suites regularly.'''

==Output Directory Structure==

<gallery widths=400px heights=250px>
Image:UKCA_BoxModel_DirStruct_139.png|Simplified cylc-run directory structure. '''[SUITE-ID]''' will be e.g. '''''u-ds042''''', and '''[CYCLE]''' is the cycle-point, e.g. '''''1'''''
</gallery>

The output directory structure of rose suites are rather complex. The schematic gives a broad overview of the general structure. Everything can be found within the '''<tt>[SUITE-ID]</tt>''' (e.g. ''u-ds042'' etc.) directory, which can be found within your '''<tt>$HOME/cylc-run</tt>''' directory.

Within this directory there are several directories, including:

* '''<tt>run1</tt>''', '''<tt>run2</tt>''', ..., '''<tt>runN</tt>''': these directories contain all the other directories used when the job actually runs. Each new <tt>cylc vip</tt> command will make a new <tt>runX</tt> directory, with <tt>runN</tt> symbolicially linked to the latest one. 
* '''<tt>log</tt>''': this contains all the job.out (containing output from UM <tt>WRITE</tt> statements from the <tt>umPrint</tt> subroutine) and job.err files etc., as well as the script used to run the job. 
* '''<tt>work</tt>''': this contains the directories used when the job actually runs. Real-time output will be sent to files here (held in a <tt>pe_output</tt> directory). Model output will also be here in the form of <tt>.csv</tt> text files that can be read by a spreadsheet program (such as gnumeric), gnuplot, or python.


Within these directories there will be many sub-directories. Some of these will be named from the '''cycle-point''' (labelled '''<tt>[CYCLE]</tt>''' in the graphic. For the UKCA Training Suite this will be '''1'''. The sub-directories will (eventually) be named after the '''app''' (labelled by '''<tt>[JOB NAME]</tt>''' in the table below) that the output is from, e.g. <tt>fcm_make</tt>, <tt>ukca</tt> etc.

{| class="wikitable" border = "1px"
!style="text-align:top;|Files
!style="text-align:top;|General Path
!style="text-align:top;|Example
|-
| Most recent ''job.out'' files || <tt>/home/vagrant/cylc-run/'''[SUITE-ID]'''/runN/log/job/1/'''[JOB NAME]'''/NN</tt> ||  <tt>/home/vagrant/cylc-run/u-ds042/runN/log/job/1/ukca/NN</tt> 
|-
| Processor output (while running) || <tt>/home/vagrant/cylc-run/'''[SUITE-ID]'''/runN/work/1/'''[JOB NAME]'''/pe_output</tt> || <tt>/home/vagrant/cylc-run/u-ds042/runN/work/1/ukca/pe_output</tt> 
|-
| UKCA Box Model output text files in ASCII format<br/><tt>tracer_out.csv</tt><br/><tt>flux_out.csv</tt> || <tt>/home/vagrant/cylc-run/'''[SUITE-ID]'''/runN/work/1/ukca</tt>  || <tt>/home/vagrant/cylc-run/u-ds042/runN/work/1/ukca</tt>
|}

===Notes===

* The <tt>job.out</tt> files can also be viewed through the Cylc TUI or GUI.
* UKCA Box Model output file will be <tt>tracer_out.csv</tt> for tracers and <tt>flux_out.csv</tt> for chemical reaction fluxes. These can be renamed in Rose in the '''ukca <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output''' panel.

==Exploring Rose==

Take a look at your suite, and click through the options. There are 2 key sections that you will need to consider:

===<tt>fcm_make</tt>===

This section controls which fcm branches are used by the model, and also what compiler settings are used etc. You should go to '''fcm_make <math>\rightarrow</math> env <math>\rightarrow</math> Sources'''  to see what branches are being used. During the course of these tutorials you will make a branch and add it here to complete the tutorial tasks. You can add both relative paths to the repository (starting with <tt>branches/</tt>) and absolute paths to a working copy (starting with <tt>/home/</tt>).

===<tt>ukca</tt>===

Click the arrow by '''ukca''' to view the list of sections. We'll be most interested in the '''namelist''' section, which contains all the settings that configure the science that can be done by UKCA. Take a look through the panels and sub-panels in this section to get a feel for how it is organised.

==Viewing Output==

===gnuplot===

<gallery widths=400px heights=350px>
Image:T01_gnuplot.png|Plotting O3 concentrations using Gnuplot
Image:T01_o3_002.png|O3 mass-mixing ratio plotted using gnuplot
</gallery>

The quickest and easiest way to plot UKCA box model output is using '''[http://www.gnuplot.info/ Gnuplot]''', which is a relatively simple command-line plotting tool. The box model outputs tracer concentrations and chemical reaction fluxes every timestep to the files '''<tt>tracer_out.csv</tt>''' and '''<tt>flux_out.csv</tt>''' respectively.

To plot these files, change into your suite's cylc-run directory and navigate to the ukca directory in work, e.g.

 cd /home/vagrant/cylc-run/u-ds042/runN/work/1/ukca

then load gnuplot by typing

 gnuplot

To plot the tracer file, type

 plot "tracer_out.csv" using 1:3 with linespoints

which can be shortened to

 p "tracer_out.csv" u 1:3 w lp

The file can be saved from the export menu on the plot itself. Additional options for the [http://gnuplot.info/docs_5.5/loc9418.html <tt>set</tt> command] can be used to define labels, titles, change how the axis labels look, e.g.

 gnuplot> set title "O3 MMR"
 gnuplot> set xlabel "timestep number"
 gnuplot> set ylabel "mass mixing ratio /kg kg^{-1}"
 gnuplot> set format y "%.2t*10^{%+03T}"
 gnuplot> unset key
 gnuplot> p 'tracer_out.csv' u 1:3 w lp

The ordering of the species in the <tt>tracer_out.csv</tt> can be seen by opening it in e.g. a simple spreadsheet program like '''[http://www.gnumeric.org/ Gnumeric]'''. You may need to install this first using

 sudo apt install gnumeric

before opening the file

 gnumeric tracer_out.csv

The column number is given in the first line with the tracer name in the line below. You could also open the file in <tt>emacs</tt> and then <tt>M-x toggle-truncate-lines</tt>. An example of this header for the StratTrop chemistry with GLOMAP-mode aerosols is

<pre style="white-space: pre;">
 # COL    1,               2,               3,               4,               5,               6,               7,               8,               9,              10,              11,              12,              13,              14,              15,              16,              17,              18,              19,              20,              21,              22,              23,              24,              25,              26,              27,              28,              29,              30,              31,              32,              33,              34,              35,              36,              37,              38,              39,              40,              41,              42,              43,              44,              45,              46,              47,              48,              49,              50,              51,              52,              53,              54,              55,              56,              57,              58,              59,              60,              61,              62,              63,              64,              65,              66,              67,              68,              69,              70,              71,              72,              73,              74,              75,              76,              77,              78,              79,              80,              81,              82,              83,              84,              85,              86,              87,              88,              89,              90,              91,              92,              93,              94,              95,              96
 # Timestep,           O(3P),              O3,               N,              NO,             NO3,             NO2,            N2O5,          HO2NO2,           HONO2,            H2O2,             CH4,              CO,            HCHO,           MeOOH,               H,             H2O,              OH,             HO2,              Cl,           Cl2O2,             ClO,            OClO,              Br,             BrO,            BrCl,          BrONO2,             N2O,             HCl,            HOCl,             HBr,            HOBr,          ClONO2,           CFCl3,          CF2Cl2,            MeBr,            HONO,            C2H6,           EtOOH,           MeCHO,             PAN,            C3H8,         n-PrOOH,         i-PrOOH,           EtCHO,           Me2CO,      MeCOCH2OOH,            PPAN,          MeONO2,            C5H8,           ISOOH,            ISON,            MACR,         MACROOH,            MPAN,           HACET,            MGLY,            NALD,           HCOOH,          MeCO3H,          MeCO2H,              H2,            MeOH,             DMS,             SO2,           H2SO4,             MSA,            DMSO,             NH3,             CS2,             COS,             H2S,             SO3,        Monoterp,         Sec_Org,       Nuc_SOL_N,      Nuc_SOL_SU,       Ait_SOL_N,      Ait_SOL_SU,      Ait_SOL_BC,      Ait_SOL_OM,       Acc_SOL_N,      Acc_SOL_SU,      Acc_SOL_BC,      Acc_SOL_OM,      Acc_SOL_SS,       Cor_SOL_N,      Cor_SOL_SU,      Cor_SOL_BC,      Cor_SOL_OM,      Cor_SOL_SS,       Ait_INS_N,      Ait_INS_BC,      Ait_INS_OM,      Nuc_SOL_OM,      PASSIVE O3
</pre>

The <tt>flux_out.csv</tt> file has a more complicated header as it also gives all the chemical reactants and products, e.g.

<pre style="white-space: pre;">
# Timestep, UKCA reaction fluxes (units = molecules.cm^-3.s^-1)
# COL    1,               2,               3,               4,               5,               6,               7,               8,               9,              10,              11,              12,              13,              14,              15,              16,              17,              18,              19,              20,              21,              22,              23,              24,              25,              26,              27,              28,              29,              30,              31,              32,              33,              34,              35,              36,              37,              38,              39,              40,              41,              42,              43,              44,              45,              46,              47,              48,              49,              50,              51,              52,              53,              54,              55,              56,              57,              58,              59,              60,              61,              62,              63,              64,              65,              66,              67,              68,              69,              70,              71,              72,              73,              74,              75,              76,              77,              78,              79,              80,              81,              82,              83,              84,              85,              86,              87,              88,              89,              90,              91,              92,              93,              94,              95,              96,              97,              98,              99,             100,             101,             102,             103,             104,             105,             106,             107,             108,             109,             110,             111,             112,             113,             114,             115,             116,             117,             118,             119,             120,             121,             122,             123,             124,             125,             126,             127,             128,             129,             130,             131,             132,             133,             134,             135,             136,             137,             138,             139,             140,             141,             142,             143,             144,             145,             146,             147,             148,             149,             150,             151,             152,             153,             154,             155,             156,             157,             158,             159,             160,             161,             162,             163,             164,             165,             166,             167,             168,             169,             170,             171,             172,             173,             174,             175,             176,             177,             178,             179,             180,             181,             182,             183,             184,             185,             186,             187,             188,             189,             190,             191,             192,             193,             194,             195,             196,             197,             198,             199,             200,             201,             202,             203,             204,             205,             206,             207,             208,             209,             210,             211,             212,             213,             214,             215,             216,             217,             218,             219,             220,             221,             222,             223,             224,             225,             226,             227,             228,             229,             230,             231,             232,             233,             234,             235,             236,             237,             238,             239,             240,             241,             242,             243,             244,             245,             246,             247,             248,             249,             250,             251,             252,             253,             254,             255,             256,             257,             258,             259,             260,             261,             262,             263,             264,             265,             266,             267,             268,             269,             270,             271,             272,             273,             274,             275,             276,             277,             278,             279,             280,             281,             282,             283,             284,             285,             286,             287,             288,             289,             290,             291,             292,             293,             294,             295,             296,             297,             298,             299,             300,             301,             302,             303,             304,             305,             306,             307,             308,             309,             310
#   PROD 1,           Cl2O2,          HO2NO2,             PAN,            PPAN,            MPAN,            N2O5,           EtOOH,            H2O2,            HCHO,            HCHO,          HO2NO2,           HONO2,           MeCHO,           MeCHO,           MeOOH,            N2O5,             NO2,             NO3,             NO3,              O2,              O3,              O3,             PAN,            HONO,           EtCHO,           Me2CO,         n-PrOOH,         i-PrOOH,      MeCOCH2OOH,            PPAN,          MeONO2,           ISOOH,            ISON,            MACR,            MPAN,         MACROOH,         MACROOH,           HACET,            MGLY,            NALD,          MeCO3H,            BrCl,             BrO,          BrONO2,          BrONO2,              O2,            OClO,              NO,            HOBr,             N2O,             H2O,          ClONO2,          ClONO2,             HCl,            HOCl,           Cl2O2,           CFCl3,          CF2Cl2,            MeBr,             CH4,             CO2,          HO2NO2,             CS2,             COS,           H2SO4,             SO3,              Br,              Br,              Br,              Br,              Br,             BrO,             BrO,             BrO,             BrO,             BrO,             BrO,             BrO,          CF2Cl2,           CFCl3,              Cl,              Cl,              Cl,              Cl,              Cl,              Cl,              Cl,              Cl,              Cl,              Cl,              Cl,              Cl,              Cl,             ClO,             ClO,             ClO,             ClO,             ClO,             ClO,             ClO,           EtCO3,           EtCO3,            EtOO,            EtOO,               H,               H,               H,               H,               H,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,             HO2,            MeBr,            MeBr,            MeBr,           MeCO3,           MeCO3,       MeCOCH2OO,       MeCOCH2OO,            MeOO,            MeOO,            MeOO,               N,               N,               N,            N2O5,              NO,              NO,              NO,              NO,              NO,              NO,             NO2,             NO2,             NO3,             NO3,             NO3,             NO3,             NO3,             NO3,             NO3,           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(1D),           O(3P),           O(3P),           O(3P),           O(3P),           O(3P),           O(3P),           O(3P),           O(3P),           O(3P),           O(3P),           O(3P),           O(3P),           O(3P),              O3,              O3,              O3,              O3,              O3,              O3,              O3,            OClO,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,              OH,          i-PrOO,          i-PrOO,          n-PrOO,          n-PrOO,             CS2,             CS2,             DMS,             DMS,            DMSO,             H2S,             H2S,             COS,             COS,             SO2,             SO3,        Monoterp,        Monoterp,        Monoterp,            MeOO,            MeOO,            EtOO,            EtOO,          n-PrOO,          n-PrOO,          i-PrOO,          i-PrOO,           MeCO3,           EtCO3,       MeCOCH2OO,       MeCOCH2OO,            ISO2,          MACRO2,          MACRO2,             HO2,           O(3P),           O(3P),           O(3P),           O(1D),             BrO,             ClO,             ClO,               H,             HO2,             HO2,              OH,              OH,              OH,           MeCO3,           EtCO3,          MACRO2,             NO2,              NO,             SO2,             DMS,             DMS,          ClONO2,          ClONO2,            HOCl,            N2O5,            N2O5,             SO2,             SO2,             SO2
#   PROD 2,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,           Cl2O2,            HCHO,             HO2,              O3,            OClO,             BrO,             ClO,             ClO,             ClO,             HO2,              NO,              OH,           O(1D),           O(1D),             CH4,           Cl2O2,          ClONO2,              H2,            H2O2,            HCHO,             HO2,             HO2,            HOCl,           MeOOH,             NO3,              O3,            OClO,             ClO,             ClO,             ClO,             HO2,            MeOO,              NO,             NO3,              NO,             NO3,              NO,             NO3,             HO2,             HO2,             HO2,             NO2,              O3,           EtCO3,           EtCO3,            EtOO,             HO2,            ISO2,          MACRO2,           MeCO3,           MeCO3,           MeCO3,       MeCOCH2OO,            MeOO,            MeOO,              NO,             NO3,              O3,          i-PrOO,          n-PrOO,              Cl,           O(1D),              OH,              NO,             NO3,              NO,             NO3,              NO,              NO,             NO3,              NO,             NO2,              O2,             H2O,            ISO2,            ISO2,          MACRO2,          MACRO2,             NO3,              O3,             NO3,              O3,              Br,            C5H8,           EtCHO,            HCHO,            MGLY,           Me2CO,           MeCHO,             CH4,             CH4,             CH4,             CO2,              H2,             H2O,             HBr,             HBr,             HCl,             HCl,             HCl,              N2,             N2O,             N2O,              O2,              O3,              O3,             BrO,             ClO,          ClONO2,            H2O2,             HBr,             HCl,             HO2,            HOCl,             NO2,             NO3,              O3,            OClO,              OH,            C5H8,            C5H8,            C5H8,            MACR,            MACR,            MACR,            MACR,              NO,            C2H6,            C3H8,            C3H8,            C5H8,             CH4,              CO,             ClO,             ClO,          ClONO2,           EtCHO,           EtOOH,           EtOOH,              H2,            H2O2,           HACET,             HBr,            HCHO,           HCOOH,             HCl,             HO2,          HO2NO2,            HOCl,            HONO,           HONO2,            ISON,           ISOOH,            MACR,            MACR,         MACROOH,            MGLY,            MPAN,           Me2CO,           Me2CO,           MeCHO,          MeCO2H,          MeCO3H,      MeCOCH2OOH,      MeCOCH2OOH,            MeOH,          MeONO2,           MeOOH,           MeOOH,            NALD,             NO3,              O3,            OClO,              OH,             PAN,            PPAN,         i-PrOOH,         i-PrOOH,         n-PrOOH,         n-PrOOH,              NO,             NO3,              NO,             NO3,           O(3P),              OH,              OH,             NO3,              OH,           O(3P),              OH,           O(3P),              OH,              O3,             H2O,              OH,              O3,             NO3,             RO2,             RO2,             RO2,             RO2,             RO2,             RO2,             RO2,             RO2,             RO2,             RO2,             RO2,             RO2,             RO2,             RO2,             RO2,           EtCO3,              O2,              NO,             NO2,              N2,             NO2,             ClO,             NO2,              O2,             HO2,             NO2,              NO,             NO2,              OH,             NO2,             NO2,             NO2,             NO3,              NO,              OH,              OH,              OH,             H2O,             HCl,             HCl,             H2O,             HCl,            H2O2,              O3,              O3
#  REACT 1,             ClO,             NO2,           MeCO3,           EtCO3,          MACRO2,             NO2,           MeCHO,              OH,             HO2,              H2,             HO2,              OH,            MeOO,             CH4,             HO2,             NO3,              NO,              NO,             NO2,           O(3P),              O2,              O2,           MeCO3,              OH,            EtOO,           MeCO3,           EtCHO,           Me2CO,           MeCO3,           EtCO3,             HO2,              OH,             NO2,           MeCO3,          MACRO2,              OH,           HACET,           MeCO3,           MeCO3,            HCHO,            MeOO,              Br,              Br,              Br,             BrO,           O(3P),           O(3P),               N,              OH,              N2,              OH,              Cl,             ClO,               H,              OH,              Cl,              Cl,              Cl,              Br,            MeOO,              CO,              OH,             COS,              CO,             SO3,             SO2,            BrCl,             HBr,             HBr,             BrO,             BrO,              Br,              Br,              Br,            BrCl,            HOBr,              Br,              Br,              Cl,              Cl,             HCl,              Cl,              Cl,             HCl,             HCl,             HCl,             ClO,             HCl,              Cl,             HCl,             ClO,             ClO,             ClO,              Cl,              Cl,              Cl,            HOCl,              Cl,              Cl,              Cl,            EtOO,            EtOO,           MeCHO,           MeCHO,              H2,           O(3P),              OH,              OH,              OH,              O2,              O3,           EtOOH,            H2O2,           ISOOH,         MACROOH,          MeCO2H,          MeCO3H,              OH,      MeCOCH2OOH,            HCHO,           MeOOH,              OH,              OH,              OH,         i-PrOOH,         n-PrOOH,              Br,              Br,              Br,            MeOO,            MeOO,           MeCO3,           MeCO3,             HO2,          MeONO2,             HO2,              N2,             N2O,              NO,           HONO2,            ISON,             NO2,            MGLY,             NO2,             NO2,             NO2,              NO,             NO3,             BrO,            ISON,           HONO2,           HONO2,           MeCO3,           HONO2,           HONO2,            HCHO,            HCHO,              OH,           O(3P),              OH,              OH,             HBr,              OH,               H,           O(3P),              OH,           O(3P),              N2,              NO,           O(3P),              O2,              O2,              O2,              Cl,             ClO,              OH,              OH,              OH,              OH,              OH,              NO,              O2,              O2,              O2,              O2,             HO2,            MACR,            MeOO,            MGLY,            MGLY,              OH,              OH,             NO2,             H2O,          i-PrOO,          n-PrOO,            ISO2,             H2O,               H,             HCl,             HO2,            HOCl,             H2O,             H2O,             H2O,             H2O,             H2O,            MGLY,             H2O,             H2O,             CO2,             H2O,             H2O,             H2O,             ClO,             H2O,             H2O,           HACET,            MACR,          MACRO2,          MACRO2,          MACRO2,           MeCO3,           HACET,             H2O,             H2O,             H2O,            MeOO,           MeCO3,             H2O,              OH,             HO2,            HCHO,             H2O,             H2O,            HCHO,             HO2,             HO2,            HOCl,             H2O,            HCHO,           MeCHO,           Me2CO,          i-PrOO,           EtCHO,          n-PrOO,           Me2CO,           Me2CO,           EtCHO,           EtCHO,              CO,             COS,             SO2,             SO2,             SO2,              OH,             SO2,              CO,             CO2,             SO3,           H2SO4,         Sec_Org,         Sec_Org,         Sec_Org,             HO2,            MeOH,             HO2,           MeCHO,             HO2,           EtCHO,             HO2,           Me2CO,          MeCO2H,                ,            HCHO,           HACET,            MACR,           HACET,             HO2,              OH,              O3,             NO2,             NO3,             N2O,          BrONO2,           Cl2O2,          ClONO2,             HO2,            H2O2,          HO2NO2,            HONO,           HONO2,            H2O2,             PAN,            PPAN,            MPAN,            N2O5,             NO2,             SO3,            DMSO,             SO2,            HOCl,              Cl,              Cl,           HONO2,              Cl,                ,                ,
#  REACT 2,             ClO,             HO2,             NO2,             NO2,             NO2,             NO3,             HO2,              OH,             HO2,              CO,             NO2,             NO2,             HO2,              CO,            HCHO,             NO2,           O(3P),              O2,           O(3P),           O(3P),           O(1D),           O(3P),             NO2,              NO,             HO2,            MeOO,             HO2,             HO2,            HCHO,             NO2,            HCHO,            MACR,            MACR,            HCHO,             NO2,             HO2,              CO,            HCHO,              CO,              CO,              OH,              Cl,           O(3P),             NO3,             NO2,           O(1D),             ClO,           O(3P),              Br,           O(1D),               H,             NO3,             NO2,              Cl,              Cl,              Cl,              Cl,              Cl,               H,               H,           O(3P),             NO3,             SO2,             SO2,              OH,           O(3P),              Cl,              CO,              O2,              O2,             ClO,              Br,              Cl,            OClO,              O2,              O2,             NO2,             HO2,             ClO,              Cl,            MeOO,              Cl,              Cl,               H,             HO2,              CO,              OH,              O2,              Cl,            MeOO,             NO2,              O2,             ClO,              Cl,              Cl,            OClO,              O2,            HCHO,             NO2,              O2,             CO2,             CO2,             HO2,             HO2,              O2,             H2O,              OH,              NO,              O2,                ,                ,                ,                ,                ,                ,              O3,                ,            MeOO,                ,                ,                ,             NO2,             NO2,              O2,                ,                ,             HCl,              OH,             H2O,             CO2,             CO2,            HCHO,            HCHO,            HCHO,                ,            HCHO,           O(3P),           O(3P),           O(3P),           HONO2,                ,            MACR,            HCHO,           MeCO3,             NO2,                ,             NO2,                ,             NO2,                ,           EtCO3,             HO2,              CO,       MeCOCH2OO,           MeCO3,              H2,             HO2,            MeOO,             CO2,               H,              OH,           O(3P),              Br,             ClO,             HCl,              Cl,              N2,              O2,              NO,              O2,           O(3P),              O2,              Br,              O2,             NO3,             HO2,              Br,              Cl,              O2,             ClO,              O2,             NO2,              O2,             ClO,               H,              OH,            HCHO,           HCOOH,           HCOOH,           HCOOH,           MeCO3,           MeCO3,             ClO,            EtOO,             H2O,             H2O,                ,            MeOO,             CO2,              O2,              Cl,             NO3,           EtCO3,            EtOO,           MeCHO,               H,             HO2,             HO2,              Br,             HO2,             H2O,              Cl,                ,             NO2,             H2O,             NO2,             NO3,            NALD,              OH,                ,                ,                ,              CO,             NO2,       MeCOCH2OO,       MeCOCH2OO,           MeCO3,                ,                ,       MeCOCH2OO,            MGLY,            HCHO,             NO2,            HCHO,            MeOO,              CO,             NO2,              O2,              O2,           O(3P),             NO2,             NO2,              OH,             H2O,             H2O,             H2O,             HO2,             HO2,             HO2,             HO2,             SO2,             SO2,                ,                ,             MSA,             SO2,             H2O,             SO2,             SO2,                ,             H2O,                ,                ,                ,            HCHO,            HCHO,           MeCHO,                ,           EtCHO,                ,           Me2CO,                ,            MeOO,            EtOO,           MeCO3,            MGLY,            HCHO,            MGLY,                ,            EtOO,                ,                ,                ,                ,                ,                ,                ,                ,              O2,                ,                ,                ,                ,                ,                ,                ,                ,             NO2,             HO2,             HO2,            MeOO,           HONO2,              Cl,              Cl,           HONO2,             NO2,                ,                ,
#  REACT 3,                ,                ,                ,                ,                ,                ,              OH,                ,              CO,                ,                ,                ,              CO,                ,              OH,                ,                ,                ,                ,                ,                ,                ,                ,                ,              CO,                ,              OH,              OH,              OH,                ,             NO2,            HCHO,            HCHO,              CO,                ,              OH,            MGLY,             HO2,             HO2,             NO2,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,              O2,              Cl,                ,                ,                ,                ,                ,                ,                ,               H,                ,              O2,             HO2,                ,                ,                ,              O2,              O2,                ,                ,                ,                ,                ,                ,             ClO,                ,              Cl,             NO3,                ,                ,             HO2,                ,                ,              OH,                ,                ,                ,                ,              O2,              O2,                ,                ,             HO2,                ,             NO2,             NO2,             NO2,             NO2,             NO2,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,             NO2,             NO2,             NO2,             NO2,             NO2,                ,             NO2,                ,                ,                ,                ,                ,            HCHO,             HO2,           HACET,                ,                ,              O2,                ,                ,                ,                ,              CO,           HONO2,                ,                ,                ,             HO2,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,           O(3P),                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,          MACRO2,              CO,             HO2,             HO2,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,              OH,                ,                ,                ,                ,              CO,               H,                ,                ,              O2,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,             H2O,              OH,                ,             NO2,                ,                ,                ,                ,             H2O,             H2O,                ,                ,              OH,                ,             NO2,             NO2,             NO2,             NO2,             SO2,                ,                ,                ,                ,              OH,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,             HO2,            HCHO,                ,             CO2,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,           HONO2,             H2O,                ,           HONO2,                ,                ,
#  REACT 4,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,             HO2,             HO2,             HO2,                ,             HO2,            HCHO,                ,                ,             HO2,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,             HO2,                ,              CO,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,           MeCO3,            H2O2,              CO,              CO,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,           O(3P),                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,              CO,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,                ,
</pre>

===Jupyter Notebook===

<gallery widths=400px heights=350px>
Image:T01_o3_001.png|Ozone mass-mixing ration
Image:T01_f200_001.png|Flux through the OH+ClO->HO2+Cl reaction
</gallery>

An example Jupyter Notebook which plots both tracers and chemical reaction fluxes can be found in 

 Tutorials/UMvn13.9/notebooks/BoxModel_T01-03.ipynb

and can be viewed online here

* [https://github.com/theabro/ukca/blob/master/Tutorials/UMvn13.9/notebooks/BoxModel_T01-03.ipynb BoxModel_T01-03.ipynb] 


You can try changing the chemical species and reaction flux selected.

Connect to the notebook using

* <div style="font-size: 140%;">'''http://localhost:4801/?token=UKCATraining'''</div>

==Checklist==

: <span style="font-size:20px">☐</span> List suites using <tt>rosie go</tt>
: <span style="font-size:20px">☐</span> Copy suites using the right-click menu
: <span style="font-size:20px">☐</span> Run suites using the play button
: <span style="font-size:20px">☐</span> Plot output using gnuplot or python


[[Advanced UKCA Chemistry and Aerosol UMvn13.9 Tutorial 2|Tutorial 2]]

[[Advanced UKCA Chemistry and Aerosol Tutorials at UMvn13.9]]
----
''Written by [[User:Nla27 | Luke Abraham]] 2025''