UKCA Chemistry and Aerosol vn10.4 Tutorial 11

UKCA Chemistry and Aerosol Tutorials at vn10.4

Tutorial 12

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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; Turnock et al., 2015; Turnock et al., 2016; Zanchettin et al., 2016).

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 shift from the current operational aerosol scheme in C-IFS over to GLOMAP-mode is scheduled to take place during 2018.

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 both of these other 2 host model frameworks (TOMCAT and C-IFS-GLOMAP).

In this 7-mode configuration (known as setup 8), GLOMAP runs with all 7 modes activated, with 2 being pure dust modes and the other 5 containing mixtures of different aerosol components (sulphate, black carbon, organic matter, sea-salt and dust).

With this GLOMAP setup 8, the model runs has 7 number mixing ratios (one for each mode) and has a total of 19 component mass mixing ratios over all the different types.

As mentioned in task 10 however, when GLOMAP is run within UM-UKCA, dust is usually 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 further reduced to cover just the sulphate and sea-salt components in 4 modes (known as setup 1), which was the initial configuration used for interactive stratospheric aerosol simulations (e.g. Dhomse et al., 2014).

The GLOMAP scheme has been run in the TOMCAT CTM in a range of configurations, including one specifically designed to track two separate components for organic matter (OM), with the I_MODE_SETUP=4 configuration designed to have one component track the primary OM in each mode and a separate OM component to track secondary organic matter 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 OM components in the GLOMAP modes

Take a copy of the suite you generated from Task 10 with the GLOMAP AOD diagnostics added. This was your copy of the standard ARCHER v10.4 UKCA tutorial suite (u-ai071). The task is to change the aerosol settings from the standard GLOMAP aerosol configuration (setup 2) to instead use the 2-component OM configuration (setup 4).

To run the 2-component GLOMAP configuration, you will need to add in an additional branch to the suite (which supports that) and also make change to the Rose GUI metadata for the suite, so that an extra option for I_MODE_SETUP=4 is made available within the "GLOMAP configuration" selection-button.

First, add in the extra branch. Go to the fcm_make app (4th from the top) and then click on "env" then "Sources" which then shows you the 4 branches that are already used in the UKCA tutorial job. These 4 branches are to enable additional settings over and above what was present in the UM trunk code at v10.4.

To add in the extra branch click the plus sign and then paste the following into the new entry that appears after you click the plus:

branches/dev/grahammann/vn10.4_support_GLOMAPsetup4_for_2cptOM@32212

This is picking up the code-changes from revision 32212 of the branch I put together to enable UM-UKCA to correctly allign with the code that is present for GLOMAP setup 4 (and adds a few bits that were missing in the v10.4 trunk).

Next we'll need to change the GLOMAP setup. In the Rose GUI, you need to open the UM app (click on the right-hand-pointing triangle at the bottom next to "um") and then similarly click on "namelist" then "UM Science settings" and finally you can then select "Section 34: UKCA" to view which options have been selected in this particular UKCA tutorial job.

Scrolling down you will eventually see the UKCA aerosol settings and you'll see "i_mode_setup" with the description "Set aerosol species and modes". In the aerosol configuration used by the job you can see I_MODE_SETUP has been set to 2. Which corresponds to the "standard GLOMAP setup" explained and illustrated above.

You see also that there are alternative options there that can change the aerosol setup to 1 (sulphate and sea-salt in 4 modes), 6 (dust-only in 2 modes) and 8 (sulphate, sea-salt, BC, POM and dust in 7 modes).

In our case, we actually want a different set-up though to any of these standard 4 options -- to activate to use the 2-component organic matter configuration. Of course one needs to know that that configuration is actually available in the code, and although this is explained in the UMDP, it turns out that, at this version, the I_MODE_SETUP=1, 6 and 8 configurations are not supported, and we recommend you do not select those options without corresponding closely with the GLOMAP development team at Leeds.

In order to do this requires to point the Rose GUI to an updated version of the metadata that provides the information for the different panels in the GUI. At the moment the metadata used in the job tells that UM that the only options available are I_MODE_SETUP=1, 2, 6 and 8. But with the changes implemented in the branch above, it will then be possible to also run the model with I_MODE_SETUP=4 (which is the GLOMAP configuration that we want to run with).

The metadata for the UM app within the Rose GUI panel is specified in the first panel selections in the GUI. Instead of clicking on the right-hand-pointing triangle, click on the word um and then you should see a panel with only one entry that says "meta" with the text set as:

/home/grenville/meta/ga7_vn10.4

This is pointing to a rose-meta.conf file that specifies the metadata for the UM app. It is off Grenville Lister's directory because there were things that were decided were required to be added (chosen according to some priorities or requirements) to the functionality of that UM app at that particular time.

In preparation for this task I have update those Rose selections to additionally allow the user to select the option 4 as well as those 1, 2, 6 and 8.

If you change the text set in that box to instead be set as:

/home/gmann/meta/ga7_vn10.4_MS4updated

it will then know that that particular option is available, and the GUI will display it (whereas it didn't with the above path specified).

To get an idea of what is different about the rose-meta.conf file, that then allows the user to choose that option, you could use a graphical difference engine like "tkdiff" or "xxdiff" to compare the rose-meta.conf in those two directories.

tkdiff /home/grenville/meta/ga7_vn10.4/rose-meta.conf /home/gmann/meta/ga7_vn10.4_MS4updated/rose-meta.conf

By doing this, you see that the functionality that was added in the file off Grenville Lister's directory was to enable a new switch to allow the user to scale up or down how much NOx is emitted from lightning sources.

In the hand-edit for the MS4updated version of this, the code has actually provided a replacement for the existing metadata that enabled that switch for different values of I_MODE_SETUP which now allows to take 5 alternative values (1, 2, 4, 6 and 8) instead of the existing 4.

Once you have activated the new meta data you may not be able to see it until you have de-selected the "u-" (Edit --> Data Source in Rose GUI) and re-selected it again -- alternatively you may need to save and exit the GUI and open it back up again.

But once it's refreshed it should be fine to go ahead and select that I_MODE_SETUP=4 option rather than the previous (default) setting of I_MODE_SETUP=2.

When these buttons are selected, the code itself does several things automatically to only activate those tracers required to be switched on.

At previous versions of the UM, one needed to set several hand-edits to 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). But at v10.4 this is done automatically within the code itself, based on what is set in the so-called "STASHmaster_A" file which specifies all the different prognostic and diagnostic variables that are set.

This STASHmaster_A is a very complicated file and it will not be possible to explain all aspects of what it does -- but suffice it to say that it contains a sequence of 6-line segments for each prognostic or diagnostic variable with several different fields within it specifying particular information about that particular prognostic/diagnostic.

All the UKCA prognostic variables can be found in section 34 in items 1-150. All the diagnostics explained in Task 10 (such as the AOD for each mode) can also be found here. The reason it is relevant to explain this here is that, at v10.4, the way the main UKCA tracers are specified as on or off is now done from within one of the fields in the STASHmaster entry for these variables.

In particular, which of the GLOMAP tracers are switched ON (i.e. are transported and made available during run-time) is set from the 30-character string on the 3rd line of the (known as an "option code").

This is tricky and you won't need to remember the details of this -- but just know that is how the model specifies which tracers are on or off for the particular chosen value of I_MODE_SETUP.

And I think it is worth seeing in the STASHmaster and in the code where this is done. For this reason, I recommend at this point that you do an "FCM checkout" of the v10.4 branch that was added above to your local space on PUMA.

If you haven't already, you should create an "FCM" directory off your home directory on PUMA and, after cd'ing into that directory run the following command to "check-out" the code to a "user working copy" in your directory that you can then refer to:

fcm checkout fcm:um.x_br/dev/grahammann/vn10.4_support_GLOMAPsetup4_for_2cptOM

That checks-out the whole contents of that branch to your ~/FCM/ directory and may take a few minutes to complete (although sometimes it's much quicker).

If you then cd into that branch "vn10.4_support_GLOMAPsetup4_for_2cptOM" and then into the following directory:

cd rose-meta/um-atmos/HEAD/etc/stash/STASHmaster

you will see the STASHmaster_A file.

It's a big file but if you go to line 14028 (e.g. use capital-G in vi) you see section 34 item 101 and on the 3rd line you see the 30-character string of zeros and ones for nucleation mode (soluble) number is set as "100000000000000000000010001011".

The way the model has been coded is to pick up the values of 1 or 0 near the end of this "option code" and use these to specify which tracers are switched on. In short, the nth character from the right-hand side species whether the tracer is switched on for I_MODE_SETUP=n.

You see that the 29th and 30th characters are set to "1" which means that the tracer is included for I_MODE_SETUP=1 and I_MODE_SETUP=2. You'll recall that the only other values for I_MODE_SETUP that are allowed to be selected at this model version (in the unchanged base job that is) are I_MODE_SETUP=6 (2mode dust-only) and I_MODE_SETUP=8 (the "full" setup with all 7 modes active). And you see that the 6th-from-the-right is a zero which means that the nucleation mode number tracer is not included in that I_MODE_SETUP=6 configuration (dust-only). But you see that the 8th-from-the-right is set to "1" which means that the tracer is included for I_MODE_SETUP=8 (the "full" set-up with all 7 modes active).

In this task we are actually activating an extra GLOMAP set-up -- we will change the STASHmaster to a new one which then allows the user to select I_MODE_SETUP=4 as an option with support from the notes from this UKCA tutorial task. And you see that there is a 1 also set in the 4th character from the end so that this and the other required GLOMAP tracers are switched ON for I_MODE_SETUP=4.

That's different from the default specification for this tracer (in the UM trunk at v10.4) which species the option code as zero for this column 36:

"100000000000000000000010000011".

You see in the STASHmaster_A file there are the two sets of organic matter tracers, the first one being called "OC" and the second one called "SO". At some points in the model the tracers are given short-hand names of Ait_SOL_OC (item 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). But the STASHmaster_A file has their full names -- and you can see that whereas the "OC" tracers are included for both I_MODE_SETUP=2 and I_MODE_SETUP=4, the "SO" tracers are only included for I_MODE_SETUP=4.

The extra tracers for the OC2 mass mixing ratios in each are stored in STASH items 128, 129, 130 and 131 in section 34. You see that these 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.

When we changed the Rose GUI to allow the user to select I_MODE_SETUP=4, we did this by pointing the Rose GUI to an updated rose-meta.conf file in a separate directory that enabled the I_MODE_SETUP=4 option. It was this one:

/home/gmann/meta/ga7_vn10.4_MS4updated/rose-meta.conf

The reason I refresh the memory about this is to further explain that, in a sub-directory of that same "ga7_vn10.4_MS4updated" main directory, the "MS4-updated" version of the STASHmaster_A file that we added to the branch is also additionally present with the I_MODE_SETUP=4 option enabled. This copy of the "MS4-updated" STASHmaster_A file can be found at:

/home/gmann/meta/ga7_vn10.4_MS4updated/etc/stash/STASHmaster

Due to a quirk in this preliminary realisation of the Rose software (which is still in its infancy really for use with the UM), when one makes a change to the STASHmaster_A file, and one wants to use the functionality added to the STASHmaster_A in an actual suite, then one needs also to additionally to a manual copy-in of the STASHmaster_A into a sub-directory of the ~/roses/suite-id/app/um/ part of the suite that one wants to run.

I will come back to this manual copy-in later (at the appropriate time) but I thought it relevant to mention this here as we are discussing STASHmaster_A files.

Next, I advise to look in the directory src/atmosphere/UKCA of the checked-out branch. This is where all the main UKCA code can be found (including the GLOMAP routines) and also the routines for RADAER, ACTIVATE and FAST-J/JX. The reason I mention this is that I think it is worth taking a look at the routine ukca_init.F90 as this gives you some idea of how the code proceeses these different aerosol configurations and how GLOMAP acts on the different settings of I_MODE_SETUP to specify which modes and components are switched ON and OFF. Looking in ukca_init.F90 you see there is the comment that says "Call appropriate MODE setup routine". You see there that, for each different setting for I_MODE_SETUP, the code calls a different trio of "module-procedures" that together set up everything that is needed to run that particular set-up.

If you already know quite a bit about GLOMAP you could take a look at these by looking in the routine ukca_mode_setup.F90

In ukca_init.F90 you see that, for I_MODE_SETUP=2, the code specifies to call the module-procedure "ukca_mode_sussbcoc_5mode" whereas for I_MODE_SETUP=4 it calls "ukca_mode_sussbcocso_5mode". These ukca_mode_xxxx routines specify the main logical variables mode and component which specify which modes are switched on and which components are included in each mode.

Once these are set (and the associated set of arrays that specify different properties about each component), the same code can be used for many of the routines (e.g. aerosol dry deposition, sedimentation -- see the Mann et al. (2010) GMD paper and the UMDP for more info on these processes.

The other two setup indices module-procedures specify what is done for processes that exchange from the gas phase to the particle phase (principally condensation of H2SO4 or SEC_ORG into one of the aerosol components in the particle modes). The module-procedures set for example how the condensation routine UKCA_CONDEN should direct the condensation from the gas phase into particular components (by direct I mean which component the gas phase should partition into or out of).

Because of the way the code has been written (reasonably flexibly, but note this is only for tried-and-tested GLOMAP set-ups) once these three module-procedure are set, the model then has all it needs to be able to run the same code with different module-procedures that specify which modes are to be switched on and which off.

At this point, let's get back to the task in hand -- and in your job please add extra daily-mean STASH requests for these additional 4 2nd OM mmr's (the SO tracers) as you did to request the standard OM mmrs in task 10. That way you will be able to validate that there is the same amount of OM in the two-component run as in the standard single-component OM run (with also the aerosol optical properties being equivalent).

Note that whereas at v8.4 the user had to switch to a different 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, at v10.4 this is all taken care of automatically within the code.

So the AOD's calculated by RADAER will include the partial volume from each of the OC2 mmr's (items 128 to 131, which are now tracking the secondary OM) as well as the usual OC mmrs (which now only include the primary OM).

Finally, since you have asked the model to run with additional 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 4 new tracers are initialised to zero values for an NRUN (for a CRUN it automatically picks up the previous values like a model re-start -- but for an NRUN this can be specified flexibly).

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 only the very low volatility oxidised organics held in the usual "SEC_ORG" species.

Written by Graham Mann 2016