Difference between revisions of "UKCA Chemistry and Aerosol Tutorial 11"
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==What you will learn in this Tutorial== |
==What you will learn in this Tutorial== |
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| + | In this tutorial you will learn about the GLOMAP-mode aerosol module and how it tracks different aerosol types within several size classes. You will understand the standard configuration used in the UKCA jobs so far whereby the mass mixing ratios of sulphate, sea-salt, black carbon and organic matter in each mode are transported via separate tracers. GLOMAP-mode is an aerosol microphysics scheme and therefore, as well as transporting the mass of several components in the modes, the scheme also transports the number concentrations of particles in each mode. |
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| − | In this tutorial you will learn about the UKCA diagnostics package and the different diagnostics that you can output using it. You will also learn how to add new diagnostics from the new reactions and deposition that you have added. |
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| + | Task 10 already introduced the basic concepts behind the GLOMAP-mode aerosol microphysics scheme and how it differs from the mass-based CLASSIC scheme which preceded UKCA. |
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| − | ==Task 11.1: Output new diagnostics== |
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| + | Initially developed in the TOMCAT CTM environment (see Manktelow et al., 2007; Mann et al., 2010; Mann et al., 2012), the GLOMAP code then became the aerosol module for the UKCA sub-model of the UM (see Bellouin et al., 2013; Kipling et al., 2013; West et al., 2014; Mann et al., 2014; Dhomse et al., 2014). |
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| − | <span style="color:green">'''TASK 11.1:''' Output diagnostics of the reaction <math>\textrm{ALICE} + \textrm{OH} \longrightarrow \textrm{BOB}</math> to STASH code '''34461''', the dry deposition of '''ALICE''' to STASH code '''34462''', and the wet deposition of '''BOB''' to '''34463'''. They should be outputted as a daily mean to the '''pb/UPB''' stream.</span> |
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| + | GLOMAP is now also implemented into the ECMWF Integrated Forecasting System as part of the "Composition IFS" module (C-IFS) where it will be used in combination with data assimilation of satellite Aerosol Optical Depth to provide forecasts and re-analyses of atmospheric composition and boundary conditions for regional air quality models. |
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| − | {| class="collapsible collapsed wikitable" |
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| − | |- |
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| − | ! Hint |
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| − | |- |
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| − | | Remember to use the correct sampling frequency. |
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| − | |- |
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| − | |} |
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| − | |||
| − | '''Note:''' If you were unable to successfully complete [[UKCA & UMUI Tutorial 10#Task 10.1: Add wet deposition of a species|Task 10.1]] , then please take a copy of the '''j''' job from the Tutorial experiment (''Tutorial: solution to Task 10.1 - add new wet deposition'') and work from there, as this will allow you to only make the changes required for this task. |
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| + | The GLOMAP-mode code allows several alternative "aerosol configurations" to be run using the same set of FORTRAN subroutines. |
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| − | ==Adding New UKCA Diagnostics== |
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| + | In section 12 of the UKCA UMDP, Table 18 shows the standard configuration for GLOMAP in all 3 of these modelling frameworks (TOMCAT, UM-UKCA and C-IFS-GLOMAP). |
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| − | If you are using one of the chemistry schemes that uses ASAD (e.g. ''CheT/TropIsop'', ''CheS/Strat'', ''CheST/StratTrop'') then you can make use of the ASAD Reaction Flux Diagnostics module (held in '''asad_chem_flux_diags.F90'''). These allow you to straight-forwardly output new reaction and deposition fluxes. |
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| + | There the model runs with 7 modes each containing mixtures of up to 5 different aerosol components (sulphate, black carbon, organic matter, sea-salt and dust). |
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| − | To output new diagnostics you will first need to define them in the '''asad_flux_dat.F90''' module, and then create new STASHmaster file specifications for them. |
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| + | In the full configuration (known as setup 8) the model runs has 7 number mixing ratios (one for each mode) and a total of 19 component mass mixing ratios. |
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| − | During this tutorial you will be tasked with outputting the reaction and deposition fluxes that you have added in to your branch. |
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| + | When GLOMAP is run within UM-UKCA, dust is handled by the existing 6-bin UM scheme, and GLOMAP is configured to use the "5-mode configuration" (known as setup 2) covering only 4 of the above 5 components (sulphate, black carbon, organic matter and sea-salt). |
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| − | ==Flux Definitions in asad_flux_dat.F90== |
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| + | The scheme can also be reduced to cover just the sulphate and sea-salt components in 4 modes (known as setup 1) or extended to track two separate components for organic matter (OM) to track the mass of primary OM and secondary OM in each mode. |
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| − | Within the '''asad_flux_dat.F90''' module the diagnostics are defined in blocks with the format |
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| + | Section 12.2 of the UMDP has a more detailed explaination of these configurations with Table 19 showing how these 4 different ''GLOMAP-mode setups'' map onto the model tracers. |
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| − | asad_flux_defn(<span style="color:blue">'Diagnostic type'</span>,<span style="color:red">STASH code</span>,<span style="color:blue">'Diagnostic specification'</span>,<span style="color:brown">Mask</span>,Reaction number,<span style="color:magenta">Number of species</span>, & |
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| − | (/'<span style="color:purple">Species</span>/<span style="color:green">Reactant 1</span>','<span style="color:green">Reactant 2</span>'/), & |
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| − | (/'<span style="color:green">Product 1</span>','<span style="color:green">Product 2</span>','<span style="color:green">Product 3</span>','<span style="color:green">Product 4</span>'/)), & |
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| + | In this task you will take a copy of the standard UKCA job (which uses GLOMAP-mode setup 2, MS2) and change it to use GLOMAP-mode setup 4 (MS4) to track two separate organic matter (OM) components rather than the usual 1. With the 2-component OC configuration, the model tracks primary (emitted) organic carbon in the usual OM component and secondary organic matter (formed following oxidation in the atmosphere) separately in a 2nd OM component. |
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| − | Which have the following meaning: |
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| + | ==Task 11.1: Understand how the GLOMAP aerosol module tracks aerosol species and modes== |
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| − | ===Diagnostic Type=== |
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| + | <span style="color:black">'''TASK 11.1:''' Read section 12 (page 32) of the [[Documentation|v8.4 UM Documentation Paper]] and refer to Tables 18, 19 and 20 on pages 33, 34 and 35. |
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| − | This is a '''three character string''' which defines what type of diagnostic is being requested. This can take the values |
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| + | ==Task 11.2: Run a copy of the standard UKCA job which tracks two OC components in the GLOMAP modes== |
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| − | * '''RXN''' to output the flux through a reaction (in moles/gridcell/s) |
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| − | * '''DEP''' to output the deposition flux of a species (in moles/gridcell/s) |
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| − | * '''EMS''' to output the emission flux into a species (in moles/gridcell/s) |
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| − | * '''NET''' to output the net chemical tendency of a species (in moles/gridcell/s) |
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| − | * '''STE''' to output the net dynamical tendency of a species (in moles/gridcell/s) |
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| − | * '''MAS''' to output the mass of the atmosphere (in kg/gridcell) |
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| − | * '''PSC''' to output polar stratospheric cloud diagnostics (1 when the gridcell contains a PSC, 0 otherwise - monthly mean field will be a fraction in range 0 → 1) |
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| − | * '''TPM''' to output the tropospheric mask (1 for troposphere, 0 otherwise - monthly mean field will be a fraction in range 0 → 1) |
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| − | * '''OUT''' to output a tracer in mmr. Only really useful if the field is masked to give the tropospheric concentration only (see the discussion of the '''Mask''' option) |
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| − | * '''RTE''' to output the rate of a reaction (in gridcell/s) |
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| + | Copy your copy of the standard UKCA tutorial job (xjrnk) from the UMUI and change the settings from the default UM-UKCA configuration for GLOMAP (setup 2) to instead use the 2-component OM configuration (setup 4). |
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| − | ===STASH Code=== |
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| + | To run the 2-component GLOMAP configuration, you will need to change an existing hand-edit in the UMUI to specify that you wish to run the model with additional aerosol tracers switched on, and change the switch controlling the GLOMAP setups from 2 to 4. |
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| − | This is a '''5 digit integer''' defining the STASH code that the diagnostic will be outputted to (e.g. 34301). Currently this must be in '''section 34'''. |
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| + | First, open the hand-edits panel in the UMUI and find the line specifying to use the hand-edit |
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| − | ===Diagnostic Specification=== |
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| + | ~mdalvi/umui_jobs/hand_edits/vn8.4/config_plume_scav_on_st.ed |
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| + | If you open this file in an editor you can get an idea of what the hand-edit does. |
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| − | This is a '''one character string''' which is needed to further define what diagnostic is required. If it isn't needed then it should just be set to '''X''' or left blank. |
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| + | The hand-edit begins by introducing a new logical variable and parameter for the convective scavenging module in UKCA. |
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| − | * ''RXN'' |
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| − | ** '''B''' to output the flux through a bimolecular reaction |
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| − | ** '''T''' to output the flux through a termolecular reaction |
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| − | ** '''H''' to output the flux through a heterogeneous reaction |
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| − | ** '''J''' to output the flux through a photolysis reaction |
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| − | * ''DEP'' |
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| − | ** '''D''' to output the dry deposition flux |
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| − | ** '''W''' to output the wet deposition flux |
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| − | * ''EMS'' |
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| − | ** '''S''' to output a surface emission (2D) |
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| − | ** '''A''' to output aircraft emissions (3D) |
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| − | ** '''L''' to output lightning emissions (3D) |
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| − | ** '''V''' to output volcanic SO2 emissions (3D) |
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| − | ** '''T''' to output SO2 emissions (3D) |
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| − | * ''PSC'' |
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| − | ** '''1''' to output the fraction of Type 1 PSCs |
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| − | ** '''2''' to output the fraction of Type 2 PSCs |
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| − | * ''RTE'' |
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| − | ** '''B''' to output the rate of a bimolecular reaction |
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| − | ** '''T''' to output the rate of a termolecular reaction |
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| − | ** '''H''' to output the rate of a heterogeneous reaction |
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| − | ** '''J''' to output the rate of a photolysis reaction |
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| + | But the relevant section of the hand-edit for this task is the where it edits the file ''SIZES'' setting the values of the array ''TC_UKCA'' which specifies which of the UKCA tracers are switched on (=1) or off (=0). |
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| − | ===Mask=== |
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| + | The order of the tracers here matches that specified in the code in the array ''nm_spec'' in the routine ''ukca_init.F90''. |
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| − | This is a '''logical''' which defines whether only the tropospheric values of the diagnostic are outputted ('''.TRUE.''') or not ('''.FALSE.'''). It is calculated every timestep. |
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| + | If you look in that file (e.g. checkout the package branch used in the model) you can check which tracers and switched on and off. |
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| − | For the ''STE'' diagnostic this is required if you wish to output the diagnosed stratosphere-troposphere exchange of a species. For the ''OUT'' diagnostic this can be used to output only the tropospheric concentration of a tracer. This is also used in the calculation of the of the ''TPM'' diagnostic. |
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| + | In the standard tracer configuration for UKCA specified in this ''config_plume_scav_on_st.ed'' hand-edit, tracers ''Ait_SOL_OC'' (index 106), ''Acc_SOL_OC'' (110), ''Cor_SOL_OC'' (116), ''Ait_INS_OC'' (121) and ''Nuc_SOL_OC'' (126) are set to 1 but tracers ''Nuc_SOL_SO'' (128), ''Ait_SOL_SO'' (129), ''Acc_SOL_SO'' (130) and ''Cor_SOL_SO'' (131) are set to zero. |
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| − | ===Reaction number=== |
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| + | To run with the 2-component OC configuration, the additional "SO" tracers to store the 2nd organic matter component in each mode need to be switched on. |
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| − | This is an '''integer''', and should only be used in the special case of there being two (or more) reactions with the exactly the same reactants and products, but with different rate coefficients. In this case the first reaction in the list would be given number '''1''' and the second '''2''' etc. If this is not needed then it should be set to '''0''' (which will be usual for most reactions). |
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| + | Also, the hand-edit needs to change the value of ''I_MODE_SETUP'' via the GLOMAP UMUI panel (labelled ''MODE'') from the selection of Atmosphere-->Model Configuration--> UKCA --> MODE and the button-selector ''Set Aerosol Species and Modes''). |
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| − | ===Number of Species=== |
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| + | Currently, there are two options for ''Set Aerosol Species and Modes'' which are ''H2SO4, NaCl in 4 modes'' for GLOMAP setup 1 (MS1) and ''H2SO4, NaCl, BC and OC in 5 modes'' for GLOMAP setup 2 (MS2), which set the value of ''I_MODE_SETUP'' to be 1 or 2 accordingly. |
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| − | This is an '''integer''', and should give the total number of species, so this will be '''1''' for diagnostics such as ''DEP'', ''STE'', ''NET'' etc., which only consider a single species, and the '''total number of reactants and products''' for diagnostics ''RXN'' and ''RTE''. |
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| + | The UMUI does not yet have the option to automatically select GLOMAP setup 4 (''I_MODE_SETUP''=4). |
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| − | ===Species=== |
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| + | So that also needs to done via the hand-edit. |
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| + | The hand-edit edits the file ''CNTLATM'' to change the switch ''I_MODE_SETUP'' from the value of 2 set in the UMUI to instead be set to 4 for the 2-component OC configuration. |
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| − | This is a '''10-character string''' giving the exact name of the species that the diagnostic should be considered for (including capitalisation). This is only used for the ''DEP'', ''EMS'', ''NET'', ''STE'', and ''OUT''. For the ''RXN'' and ''RTE'' diagnostics the full list of reactants and products should be given (see below). For the ''MAS'', ''PSC'', and ''TPM'' diagnostics this isn't needed and could either be set to '''XXX''' or left blank. If it is needed the other reactant/product slots should be left blank. |
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| + | An equivalent hand-edit for the 2-component OC configuration to apply these changes has already been produced which you can find in the file: |
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| − | ===Reactants and Products=== |
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| + | ~gmann/stashfiles/config_plume_scav_on_st_MS4.ed |
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| + | You can use a graphical difference tool like tkdiff or xxdiff to see the differences between the two files. |
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| − | These are '''10-character strings''', and should be as the reaction is defined in the '''ukca_chem_<span style="color:blue">scheme</span>.F90''' modules. |
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| + | You see that running with the standard configuration of GLOMAP (I_MODE_SETUP=2) requires 83 tracers in the UKCA CheST configuration, with 20 coming from GLOMAP. |
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| − | ===Addition of Diagnostics=== |
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| + | To run with the 2-component OM configuration of GLOMAP (I_MODE_SETUP=4) and the UKCA CheST chemistry required 3 addititional aerosol tracers, giving 86 in total. |
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| − | If you define more than one diagnostic to be output to the same STASH code, then the diagnostic routines will sum these diagnostics together. This can be useful (e.g., if you wanted to output the sum of all NO+RO2 reactions to one STASH item), but can be problematic if you accidentally output two fields to the same STASH code, as this will give strange results! |
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| + | If you compare against ''config_plume_scav_on_st.ed'', you see that in ''config_plume_scav_on_st_MS4.ed'' TC_UKCA tracers 128, 129, 130 and 131 are set to 1 for the SO components in each of the soluble modes and the nucleation soluble OC mmr is no longer required as it has been replaced with SO mmr. |
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| − | ===Changes to asad_flux_dat.F90=== |
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| + | So to configure your copy of your initial UKCA tutorial job to run with 2-component OM, change the line in the UMUI hand-edits panel to point to |
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| − | After you have defined your new diagnostics at the top of this module, you will need to make sure that they have been added correctly to the '''asad_chemical_fluxes''' array, which is defined in the '''ASAD_LOAD_DEFAULT_FLUXES''' subroutine held in the '''asad_flux_dat.F90'''. |
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| + | ~gmann/stashfiles/config_plume_scav_on_st_MS4.ed |
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| + | rather than |
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| − | ==STASHmaster file== |
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| + | ~mdalvi/umui_jobs/hand_edits/vn8.4/config_plume_scav_on_st.ed |
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| + | |||
| + | Similarly, you also need to use an updated version of the RADAER hand-edit ''raderv2_vn84_ARCHER.ed'' to allow the 2-component OM configuration of GLOMAP to couple to the UM radiation scheme. |
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| + | For this replace the hand-edit |
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| − | While the diagnostics are defined in '''asad_flux_dat.F90''' they are turned on by requesting the item through STASH. To do this you will need to make a new STASHmaster file for diagnostics that you have defined yourself. The easiest option is to copy an existing diagnostic specification from the ''STASHmaster_A'' file, which is located at |
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| + | ~ukca/hand_edits/VN8.4/raderv2_vn84_ARCHER.ed |
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| + | with the version for GLOMAP setup 4: |
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| − | /work/n02/n02/hum/vn8.2/ctldata/STASHmaster/STASHmaster_A |
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| + | ~gmann/stashfiles/raderv2_vn84_MS4_ARCHER.ed |
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| + | The update to the hand-edit adds STASH requests to make available to RADAER the values of the partial volumes from the 2nd OM components at each radiation timestep to ensure they are included when calculating the GLOMAP aerosol optical properties. |
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| − | on HECToR, and at |
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| + | To be able to add STASH requests for the additional OM components you also need to change the User-STASHmaster file in Atmosphere --> STASH --> User STASHmaster files, Diags, Progs and Ancils from |
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| − | /projects/um1/vn8.2/ctldata/STASHmaster/STASHmaster_A |
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| + | ~ukca/userprestash/VN8.4/UKCA_Tr_StratTropAeroMODE.prestash |
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| + | to instead use |
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| − | on MONSooN. |
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| + | ~gmann/stashfiles/UKCA_Tr_StratTropAeroMODE_MS4.prestash |
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| + | Once you have done this you should then add daily-mean STASH requests for section 34 items 128, 129, 130 and 131 for the SO component mmr's in each soluble mode as you already did for the OC mmr items in Task 10. |
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| − | ===2D Diagnostic Fields=== |
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| + | Finally, since you have asked the model to run with new tracers, you also need to specify how these should be initialised. |
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| − | If you are outputting a 2D field such as a surface emission or a dry deposition field (e.g. you are using the old 2D dry deposition scheme) then the fact that this is a 2D surface field is defined in the STASHmaster entry, which looks like this e.g. |
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| + | Go to the Initialisation of User Prognostics panel off the STASH window. |
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| + | Scroll down until you see items 34128, 34129, 34130, 34131 and set the ''Option'' column to 3 so that these tracers are initialised to zero values for an NRUN. |
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| + | ===Worked Solution=== |
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| − | # |
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| − | 1| 1 | 34 | <span style="color:red">321</span> |<span style="color:red">Ox BUDGET: O3 DRY DEPOSITION (2D)</span> | |
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| − | 2| 0 | 0 | 1 | 1 | 5 | -1 | -1 | 0 | 0 | 0 | 0 | |
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| − | 3| 000000000000000000000000000000 | 00000000000000000001 | 3 | |
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| − | 4| 1 | 0 | -99 -99 -99 -99 -99 -99 -99 -99 -99 -99 | |
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| − | 5| 0 | 1871 | 1 | 129 | 0 | 0 | 0 | 0 | 0 | |
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| − | # |
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| + | The worked solution to this task can be found in job <code>'''xjrnm'''</code>. Sample output can be found on ARCHER in the directory |
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| − | However, you can always output a surface diagnostic using a STASHmaster file that defines a 3D field, it is just that only the surface values will be non-zero (if the full field is output). |
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| + | /work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Task11.2 |
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| − | You will need to edit the two elements in <span style="color:red">red</span> to match your new diagnostic. |
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| + | ==Task 11.3 Examine the simulated total organic carbon in the original and two-cpt OC configurations== |
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| − | ===3D Diagnostic Fields=== |
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| + | In the above Task 11.2 you ran a 2-component OC version of the UKCA tutorial job (<code>'''xjrnk'''</code>). |
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| − | A 3D diagnostic field has slightly different values for some of the elements of the STASHmaster definition. These can been seen by comparing the specification above with the one below |
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| + | You can also refer to the worked solution <code>'''xjrnm'''</code> which I have configured in this way. |
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| + | See that <code>'''xjrnl'''</code> was the same as the UKCA tutorial job <code>'''xjrnk'''</code> except that I have added the extra STASH requests as in Task 10.3. |
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| + | So by now you should have equivalent standard (as <code>'''xjrnl'''</code>) and 2-component OM (as <code>'''xjrnm'''</code>) versions of the UKCA tutorial job. |
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| − | # |
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| + | In these jobs you have requested numerous daily-mean fields to be output in the .pa files. |
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| − | 1| 1 | 34 | <span style="color:red">321</span> |<span style="color:red">Ox BUDGET: O3 DRY DEPOSITION (3D)</span> | |
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| − | 2| 0 | 0 | 1 | 1 | 2 | 10 | 11 | 0 | 0 | 0 | 0 | |
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| − | 3| 000000000000000000000000000000 | 00000000000000000001 | 3 | |
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| − | 4| 1 | 0 | -99 -99 -99 -99 -99 -99 -99 -99 -99 -99 | |
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| − | 5| 0 | 1871 | 0 | 65 | 0 | 0 | 0 | 0 | 0 | |
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| − | # |
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| + | So in your /work/n02/n02/ directory on ARCHER you should have '''jobid'''a.pa19991201 files for your standard and 2-component OM jobs. |
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| − | You will need to edit the two elements in <span style="color:red">red</span> to match your new diagnostic. |
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| + | Included in the extra STASH requests are the mass mixing ratios of OC (the standard organic component) and SO (the 2nd organic component) in each mode. |
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| − | ===STASHmaster file format=== |
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| + | The OC mmrs are STASH section 34, items 126 (nucleation mode), 106 (Aitken-soluble), 110 (accumn-soluble), 116 (coarse-soluble) and 121 (Aitken-insoluble). |
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| − | As well as defining the STASH items in your new user STASHmaster file, you will also need to include the correct preamble and an end of file specifier. These are |
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| + | The SO mmrs are STASH section 34, items 128 (nucleation mode), 129 (Aitken-soluble), 130 (accumn-soluble), 131 (coarse-soluble). |
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| − | Preamble: |
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| + | These STASH item numbers and the details of the standard and 2-component GLOMAP configurations can be found in the UKCA UMDP section 12 Tables 19 and 20. |
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| − | H1| SUBMODEL_NUMBER=1 |
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| − | H2| SUBMODEL_NAME=ATMOS |
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| − | H3| UM_VERSION=8.2 |
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| − | # |
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| − | #|Model |Sectn | Item |Name | |
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| − | #|Space |Point | Time | Grid |LevelT|LevelF|LevelL|PseudT|PseudF|PseudL|LevCom| |
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| − | #| Option Codes | Version Mask | Halo | |
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| − | #|DataT |DumpP | PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PCA | |
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| − | #|Rotate| PPF | USER | LBVC | BLEV | TLEV |RBLEVV| CFLL | CFFF | |
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| − | # |
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| + | Note that there is no SO in the Aitken-insoluble mode as this contains only primary carbonaceous particles. |
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| − | which is also helpful in describing what the elements in the STASH specification are. |
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| + | Any SO or OC condensing onto the particles in the insoluble modes is immediately transferred over to the corresponding soluble mode following the "condensation-ageing" approach used by the model. This OC or SO condensing onto the insoluble particles is a kind of "coating" for the particles making the particles hygroscopic/soluble. |
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| + | You could also try adding STASH requests for the mmr of the gas phase species MONOTER and SEC_ORG (STASH section 34, items 91 and 92). |
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| − | End of file specifier: |
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| + | As an example I have put here a link to a pdf {{pdf|GlobalMap_2cptOM.pdf|OMcomparison}} showing global maps comparing surface OM fields between the worked solutions <code>'''xjrnl'''</code> (top-left, labelled as <code>xkwhg</code>) and <code>'''xjrnm'''</code> (top-right, labelled as <code>xkwhh</code>). |
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| − | # |
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| − | 1| -1 | -1 | -1 |END OF FILE MARK | |
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| − | 2| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
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| − | 3| 000000000000000000000000000000 | 00000000000000000000 | 0 | |
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| − | 4| 0 | 0 | -99 -99 -99 -99 -30 -99 -99 -99 -99 -99 | |
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| − | 5| 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | |
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| − | # |
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| + | Page 1 of the pdf compares the "total POM mmr" at the surface which is the total particulate organic matter (POM) summing up the mass of OC and SO in each mode. |
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| − | ===UMUI Changes=== |
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| + | Pages 2 and 3 show comparisons of "total POM1 mmr" and "total POM2 mmr" which are the sum of the 1st and 2nd organic component over all the modes. |
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| − | After you have made your STASHmaster file with the required diagnostics, you should add it to the UMUI in '''Model Selection → Atmosphere → STASH → User-STASHmaster files. Diags, Progs & Ancils'''. You will also need to give it an initial value in '''Model Selection → Atmosphere → STASH → Initialisation of User Prognostics''' (you can just set it to '''zero''', i.e. '''3''' in the '''Option''' column). After you have done this you can select the diagnostic in the '''Model Selection → Atmosphere → STASH → STASH. Specification of Diagnostics requirements''' panel. |
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| + | You can see from the example that the "total POM2 mmr" in <code>'''xjrnl'''</code> is zero everywhere. |
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| − | ==Time Validity== |
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| + | That's because in this job GLOMAP has the standard configuration with just one organic component. |
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| + | By contrast the "total POM2 mmr" for <code>'''xjrnm'''</code> has considerable concentrations in vegetated continental regions. |
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| − | When outputting UKCA reaction and deposition fluxes, you need to consider what time-points these diagnostics are valid at. Tracer fields are valid at all timesteps, but for reaction fluxes this is not the case. For all the chemistry schemes which use ASAD/Newton-Raphson (''CheT/TropIsop'', ''CheS/Strat'', and ''CheST/StratTrop''), the UKCA chemical timestep is every hour. |
||
| + | In this "I_MODE_SETUP=4" configuration, the "SEC_ORG" species (which contains the secondary organics from monoterpene oxidation) condenses into the "SO" component, whereas in <code>'''xjrnl'''</code> SEC_ORG condenses into the "OC" component. |
||
| + | The bottom left panel on each page shows a global map of the ratio of the field for the two model runs. |
||
| − | This means that when you output this diagnostic through STASH you need to change the ''sampling frequency''. To do this, go to the STASH panel in the UMUI ('''Model Selection → Atmosphere → STASH → STASH. Specification of Diagnostic requirements''') and '''copy''' the '''time profile''' you would like to use for the diagnostic to a new profile (giving it a similar, but slightly different name) and then change the '''sampling frequency''' to be |
||
| + | One can use this kind of approach to track the fraction of the OM that is biogenic and anthropogenic. |
||
| + | Note however that we initialised the SO mmr's to zero at the start of the 1-day run. |
||
| − | * '''Frequency (every)''' to be '''3''' |
||
| + | So the OC1 mmrs will be spinning down and the SO mmrs will be spinning up. |
||
| − | * '''Offset''' to be '''2''' |
||
| + | The daily-mean values are averaging over values on each the 1-hour timesteps over which the UKCA chemistry and aerosol processes are integrated. |
||
| + | So although the ratio shown in the bottom-left on page 2 is indicative of the biogenic fraction it should be treated with caution as the fields will not have spun-up/down yet. |
||
| + | This task illustrates how one can separate out the aerosol mass from different sources and track them separately via a different aerosol component. |
||
| − | This will then sample the diagnostic on the UKCA timesteps. If you don't sample the diagnostic using this sampling frequency, then the output may be incorrect. |
||
| + | One could also introduce a 2nd gas phase species like "SEC_ORG" to track different types of SOA. |
||
| − | The following diagnostics are valid on '''all timesteps''': |
||
| + | For example one could configure the model so that such a 2nd "SEC_ORG2" species held semi-volatile oxidised organic species with very low volatility oxidised organics held in the usual "SEC_ORG" species. |
||
| + | ''Written by [[User:Gmann | Graham Mann]] 2014'' |
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| − | * ''MAS'' |
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| − | * ''OUT'' |
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| − | * ''TPM'' |
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| − | * ''STE'' |
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| − | * ''EMS'' |
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| − | |||
| − | The following diagnostics are only valid on '''chemical timesteps''': |
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| − | |||
| − | * ''RXN'' |
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| − | * ''DEP'' |
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| − | * ''RTE'' |
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| − | * ''PSC'' |
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| − | |||
| − | ==Solution to Task 11.1: Output new diagnostics== |
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| − | |||
| − | Please see [[Solution to UKCA & UMUI Tutorial 11 Task 11.1 |this page]] for a solution to [[#Task 11.1: Output new diagnostics|Task 11.1]]. |
||
| − | |||
| − | ---- |
||
| − | ''Written by [[User:Nla27 | Luke Abraham]] 2014'' |
||
Latest revision as of 15:08, 7 January 2016
Back to UKCA Chemistry and Aerosol Tutorials
What you will learn in this Tutorial
In this tutorial you will learn about the GLOMAP-mode aerosol module and how it tracks different aerosol types within several size classes. You will understand the standard configuration used in the UKCA jobs so far whereby the mass mixing ratios of sulphate, sea-salt, black carbon and organic matter in each mode are transported via separate tracers. GLOMAP-mode is an aerosol microphysics scheme and therefore, as well as transporting the mass of several components in the modes, the scheme also transports the number concentrations of particles in each mode.
Task 10 already introduced the basic concepts behind the GLOMAP-mode aerosol microphysics scheme and how it differs from the mass-based CLASSIC scheme which preceded UKCA.
Initially developed in the TOMCAT CTM environment (see Manktelow et al., 2007; Mann et al., 2010; Mann et al., 2012), the GLOMAP code then became the aerosol module for the UKCA sub-model of the UM (see Bellouin et al., 2013; Kipling et al., 2013; West et al., 2014; Mann et al., 2014; Dhomse et al., 2014).
GLOMAP is now also implemented into the ECMWF Integrated Forecasting System as part of the "Composition IFS" module (C-IFS) where it will be used in combination with data assimilation of satellite Aerosol Optical Depth to provide forecasts and re-analyses of atmospheric composition and boundary conditions for regional air quality models.
The GLOMAP-mode code allows several alternative "aerosol configurations" to be run using the same set of FORTRAN subroutines.
In section 12 of the UKCA UMDP, Table 18 shows the standard configuration for GLOMAP in all 3 of these modelling frameworks (TOMCAT, UM-UKCA and C-IFS-GLOMAP).
There the model runs with 7 modes each containing mixtures of up to 5 different aerosol components (sulphate, black carbon, organic matter, sea-salt and dust).
In the full configuration (known as setup 8) the model runs has 7 number mixing ratios (one for each mode) and a total of 19 component mass mixing ratios.
When GLOMAP is run within UM-UKCA, dust is handled by the existing 6-bin UM scheme, and GLOMAP is configured to use the "5-mode configuration" (known as setup 2) covering only 4 of the above 5 components (sulphate, black carbon, organic matter and sea-salt).
The scheme can also be reduced to cover just the sulphate and sea-salt components in 4 modes (known as setup 1) or extended to track two separate components for organic matter (OM) to track the mass of primary OM and secondary OM in each mode.
Section 12.2 of the UMDP has a more detailed explaination of these configurations with Table 19 showing how these 4 different GLOMAP-mode setups map onto the model tracers.
In this task you will take a copy of the standard UKCA job (which uses GLOMAP-mode setup 2, MS2) and change it to use GLOMAP-mode setup 4 (MS4) to track two separate organic matter (OM) components rather than the usual 1. With the 2-component OC configuration, the model tracks primary (emitted) organic carbon in the usual OM component and secondary organic matter (formed following oxidation in the atmosphere) separately in a 2nd OM component.
Task 11.1: Understand how the GLOMAP aerosol module tracks aerosol species and modes
TASK 11.1: Read section 12 (page 32) of the v8.4 UM Documentation Paper and refer to Tables 18, 19 and 20 on pages 33, 34 and 35.
Task 11.2: Run a copy of the standard UKCA job which tracks two OC components in the GLOMAP modes
Copy your copy of the standard UKCA tutorial job (xjrnk) from the UMUI and change the settings from the default UM-UKCA configuration for GLOMAP (setup 2) to instead use the 2-component OM configuration (setup 4).
To run the 2-component GLOMAP configuration, you will need to change an existing hand-edit in the UMUI to specify that you wish to run the model with additional aerosol tracers switched on, and change the switch controlling the GLOMAP setups from 2 to 4.
First, open the hand-edits panel in the UMUI and find the line specifying to use the hand-edit
~mdalvi/umui_jobs/hand_edits/vn8.4/config_plume_scav_on_st.ed
If you open this file in an editor you can get an idea of what the hand-edit does.
The hand-edit begins by introducing a new logical variable and parameter for the convective scavenging module in UKCA.
But the relevant section of the hand-edit for this task is the where it edits the file SIZES setting the values of the array TC_UKCA which specifies which of the UKCA tracers are switched on (=1) or off (=0).
The order of the tracers here matches that specified in the code in the array nm_spec in the routine ukca_init.F90.
If you look in that file (e.g. checkout the package branch used in the model) you can check which tracers and switched on and off.
In the standard tracer configuration for UKCA specified in this config_plume_scav_on_st.ed hand-edit, tracers Ait_SOL_OC (index 106), Acc_SOL_OC (110), Cor_SOL_OC (116), Ait_INS_OC (121) and Nuc_SOL_OC (126) are set to 1 but tracers Nuc_SOL_SO (128), Ait_SOL_SO (129), Acc_SOL_SO (130) and Cor_SOL_SO (131) are set to zero.
To run with the 2-component OC configuration, the additional "SO" tracers to store the 2nd organic matter component in each mode need to be switched on.
Also, the hand-edit needs to change the value of I_MODE_SETUP via the GLOMAP UMUI panel (labelled MODE) from the selection of Atmosphere-->Model Configuration--> UKCA --> MODE and the button-selector Set Aerosol Species and Modes).
Currently, there are two options for Set Aerosol Species and Modes which are H2SO4, NaCl in 4 modes for GLOMAP setup 1 (MS1) and H2SO4, NaCl, BC and OC in 5 modes for GLOMAP setup 2 (MS2), which set the value of I_MODE_SETUP to be 1 or 2 accordingly.
The UMUI does not yet have the option to automatically select GLOMAP setup 4 (I_MODE_SETUP=4). So that also needs to done via the hand-edit.
The hand-edit edits the file CNTLATM to change the switch I_MODE_SETUP from the value of 2 set in the UMUI to instead be set to 4 for the 2-component OC configuration.
An equivalent hand-edit for the 2-component OC configuration to apply these changes has already been produced which you can find in the file:
~gmann/stashfiles/config_plume_scav_on_st_MS4.ed
You can use a graphical difference tool like tkdiff or xxdiff to see the differences between the two files.
You see that running with the standard configuration of GLOMAP (I_MODE_SETUP=2) requires 83 tracers in the UKCA CheST configuration, with 20 coming from GLOMAP.
To run with the 2-component OM configuration of GLOMAP (I_MODE_SETUP=4) and the UKCA CheST chemistry required 3 addititional aerosol tracers, giving 86 in total.
If you compare against config_plume_scav_on_st.ed, you see that in config_plume_scav_on_st_MS4.ed TC_UKCA tracers 128, 129, 130 and 131 are set to 1 for the SO components in each of the soluble modes and the nucleation soluble OC mmr is no longer required as it has been replaced with SO mmr.
So to configure your copy of your initial UKCA tutorial job to run with 2-component OM, change the line in the UMUI hand-edits panel to point to
~gmann/stashfiles/config_plume_scav_on_st_MS4.ed
rather than
~mdalvi/umui_jobs/hand_edits/vn8.4/config_plume_scav_on_st.ed
Similarly, you also need to use an updated version of the RADAER hand-edit raderv2_vn84_ARCHER.ed to allow the 2-component OM configuration of GLOMAP to couple to the UM radiation scheme.
For this replace the hand-edit
~ukca/hand_edits/VN8.4/raderv2_vn84_ARCHER.ed
with the version for GLOMAP setup 4:
~gmann/stashfiles/raderv2_vn84_MS4_ARCHER.ed
The update to the hand-edit adds STASH requests to make available to RADAER the values of the partial volumes from the 2nd OM components at each radiation timestep to ensure they are included when calculating the GLOMAP aerosol optical properties.
To be able to add STASH requests for the additional OM components you also need to change the User-STASHmaster file in Atmosphere --> STASH --> User STASHmaster files, Diags, Progs and Ancils from
~ukca/userprestash/VN8.4/UKCA_Tr_StratTropAeroMODE.prestash
to instead use
~gmann/stashfiles/UKCA_Tr_StratTropAeroMODE_MS4.prestash
Once you have done this you should then add daily-mean STASH requests for section 34 items 128, 129, 130 and 131 for the SO component mmr's in each soluble mode as you already did for the OC mmr items in Task 10.
Finally, since you have asked the model to run with new tracers, you also need to specify how these should be initialised. Go to the Initialisation of User Prognostics panel off the STASH window. Scroll down until you see items 34128, 34129, 34130, 34131 and set the Option column to 3 so that these tracers are initialised to zero values for an NRUN.
Worked Solution
The worked solution to this task can be found in job xjrnm. Sample output can be found on ARCHER in the directory
/work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Task11.2
Task 11.3 Examine the simulated total organic carbon in the original and two-cpt OC configurations
In the above Task 11.2 you ran a 2-component OC version of the UKCA tutorial job (xjrnk).
You can also refer to the worked solution xjrnm which I have configured in this way.
See that xjrnl was the same as the UKCA tutorial job xjrnk except that I have added the extra STASH requests as in Task 10.3.
So by now you should have equivalent standard (as xjrnl) and 2-component OM (as xjrnm) versions of the UKCA tutorial job.
In these jobs you have requested numerous daily-mean fields to be output in the .pa files.
So in your /work/n02/n02/ directory on ARCHER you should have jobida.pa19991201 files for your standard and 2-component OM jobs.
Included in the extra STASH requests are the mass mixing ratios of OC (the standard organic component) and SO (the 2nd organic component) in each mode.
The OC mmrs are STASH section 34, items 126 (nucleation mode), 106 (Aitken-soluble), 110 (accumn-soluble), 116 (coarse-soluble) and 121 (Aitken-insoluble).
The SO mmrs are STASH section 34, items 128 (nucleation mode), 129 (Aitken-soluble), 130 (accumn-soluble), 131 (coarse-soluble).
These STASH item numbers and the details of the standard and 2-component GLOMAP configurations can be found in the UKCA UMDP section 12 Tables 19 and 20.
Note that there is no SO in the Aitken-insoluble mode as this contains only primary carbonaceous particles. Any SO or OC condensing onto the particles in the insoluble modes is immediately transferred over to the corresponding soluble mode following the "condensation-ageing" approach used by the model. This OC or SO condensing onto the insoluble particles is a kind of "coating" for the particles making the particles hygroscopic/soluble.
You could also try adding STASH requests for the mmr of the gas phase species MONOTER and SEC_ORG (STASH section 34, items 91 and 92).
As an example I have put here a link to a pdf 
OMcomparison 
showing global maps comparing surface OM fields between the worked solutions xjrnl (top-left, labelled as xkwhg) and xjrnm (top-right, labelled as xkwhh).
Page 1 of the pdf compares the "total POM mmr" at the surface which is the total particulate organic matter (POM) summing up the mass of OC and SO in each mode.
Pages 2 and 3 show comparisons of "total POM1 mmr" and "total POM2 mmr" which are the sum of the 1st and 2nd organic component over all the modes.
You can see from the example that the "total POM2 mmr" in xjrnl is zero everywhere.
That's because in this job GLOMAP has the standard configuration with just one organic component.
By contrast the "total POM2 mmr" for xjrnm has considerable concentrations in vegetated continental regions.
In this "I_MODE_SETUP=4" configuration, the "SEC_ORG" species (which contains the secondary organics from monoterpene oxidation) condenses into the "SO" component, whereas in xjrnl SEC_ORG condenses into the "OC" component.
The bottom left panel on each page shows a global map of the ratio of the field for the two model runs. One can use this kind of approach to track the fraction of the OM that is biogenic and anthropogenic.
Note however that we initialised the SO mmr's to zero at the start of the 1-day run. So the OC1 mmrs will be spinning down and the SO mmrs will be spinning up. The daily-mean values are averaging over values on each the 1-hour timesteps over which the UKCA chemistry and aerosol processes are integrated. So although the ratio shown in the bottom-left on page 2 is indicative of the biogenic fraction it should be treated with caution as the fields will not have spun-up/down yet.
This task illustrates how one can separate out the aerosol mass from different sources and track them separately via a different aerosol component.
One could also introduce a 2nd gas phase species like "SEC_ORG" to track different types of SOA. For example one could configure the model so that such a 2nd "SEC_ORG2" species held semi-volatile oxidised organic species with very low volatility oxidised organics held in the usual "SEC_ORG" species.
Written by Graham Mann 2014
