Difference between revisions of "UKCA Chemistry and Aerosol Tutorial 12"

Latest revision as of 15:58, 9 January 2015

Back to UKCA Chemistry and Aerosol Tutorials

What you will learn in this Tutorial

In this tutorial you will learn about how to quantify the radiative effects of aerosol simulated by GLOMAP-mode in UM-UKCA.

In the first task you will update your copy of the UKCA tutorial job to request radiative fluxes allowing the radiative flux perturbation (or effective radiative forcing) to be diagnosed based on difference in the fluxes between a pair of UM-UKCA jobs with some difference (e.g. pre-industrial and present-day emissions jobs).

The second task involves configuring a copy of the UKCA tutorial job to run in double-call configuration whereby the aerosol radiative effects can be diagnosed at each radiation timestep.

Task 12.1: Update your copy of the UKCA tutorial job to diagnose Top Of the Atmosphere (TOA) radiative fluxes

In this task you will add STASH requests for SW and LW outgoing radiative fluxes at the top of the atmosphere to enable the radiative forcing from a particular change to be diagnosed.

The user should note however that to illustrate the task we are adding these requests to the UKCA tutorial job which is just a 1-day simulation.

One would need to average the flux-difference between the pair of simulations over an appropriate timescale (e.g. multi-annual monthly-means) in order to diagnose an effective radiative forcing appropriately.

Noting the above caveat, proceed and add daily-mean STASH requests for section 1 item 208 (all-sky outgoing short wave flux at the top-of-the-atmosphere) and section 2 item 205 (all-sky outgoing long wave flux at the top-of-the-atmosphere) to your copy of the UKCA tutorial job (xkvxe).

The radiative fluxes are 2-dimensional diagnostics (longitude by latitude) so you should use the DIAG domain profile in this case. For daily-means use the TDAYM time profile. Again, since we require the daily-mean fluxes to be output to the .pa file you should request the diagnostics with the UPA usage profile.

The Figure below shows the daily-mean SW and LW all-sky TOA radiative fluxes from the UKCA tutorial job for 1st December 1999 (gmann job xkwhc).

Example Output

Example output for Task12.1 can be found on ARCHER in the following directory:

/work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Task12.1

Task 12.2 Configure the UKCA tutorial job to run as a double-call job diagnosing aerosol radiative effects

In this task you will copy your copy of the standard tutorial job (xjrnk) and configure it to run with double-call to the radiation scheme to diagnose the radiative effects of the aerosol simulated by GLOMAP in UM-UKCA.

The UM has been coded to allow the user to diagnose radiative effects of a particular forcing agent by calling the radiation scheme twice with one of the calls setting the agent's concentration to zero. Special forcing STASH items are included within the UM which store the difference in the radiative fluxes between the two radiation calls.

In the UMUI go to Atmosphere --> Scientific Parameters and Sections --> Section by section choices and then choose Section 1: SW radiation.

In the SW Radiation UMUI panel that opens, you see that at the top there is an "Options for multiple calls to radiation" button-selector.

The UKCA tutorial job is set to "Timestepping scheme" which is the recommended way of running the model. In this configuration the UM has a single call to the radiation scheme every radiation timestep (here 3 hours) with a 2nd reduced-call being applied on other timesteps (for more details see Manners et al., QJRMS 2009). The single-call option is the same as the Timestepping scheme but does not apply the reduced radiation call on interim timesteps.

The other option supported here is to select "Diagnose radiative forcings" which activates the double-call approach where the radiation scheme is called twice on each radiation timestep with and without the forcing agent.

By default, if one selects the Diagnose radiative forcings option, then the model diagnoses the radiative forcing based on the advancing call including the forcing agent as usual, and the species is set to zero in the 2nd diagnostic call to the radiation.

This operation is applied via the SLWForc panel which is available after selecting the Gen2 follow-on window. See that it is possible to individually select each of the CLASSIC aerosol types to diagnose their radiative effects whereas for GLOMAP-mode it only makes sense to diagnose the effects over all the types considered since the different types become internally mixed within each size class. Note that the user needs to be very careful to specify exactly how the effects should be applied in the second radiation call and this is specified in the Call2 follow-on window.

We strongly recommend only making changes to the default settings after discussing with relevant experts within NCAS or the Met Office.

Although the default UM setting for the double-call is to set the species mixing ratio to zero in the diagnostic call, it is often very useful to be able to suppress the fast feedbacks from the forcing agent in question by reversing the operation of the double-call including the aerosol radiative effects only in the diagnostic call and setting the species mixing ratio to zero in the advancing call.

With this double-call radiative forcing configuration, the difference in radiative fluxes between the two calls provides the aerosol radiative perturbation with respect to an atmosphere containing no aerosols. One can diagnose the present-day to pre-industrial aerosol radiative forcing by taking the difference between two parallel double-call simulations with aerosol and precursor emissions set to 1850 and 2000. All other forcing agents, such as greenhouse gases or land-use change, remain fixed at a reference time period.

Often nudging to meteorological re-analysis winds and temperatures is applied in tandem with the double-call configuration in which case the composition-climate model is being run in a similar way to an offline chemistry-transport model. This approach has been used extensively in aerosol forcing intercomparisons (e.g. the AeroCom direct forcing experiments, Myhre et al., 2013, ACP) with the radiative forcings diagnosed from each model with fast feedbacks disabled.

To run UM-UKCA with this double-call radiative forcing configuration, you will need to add an extra FCM branch to the job and also add an extra hand-edit in the UMUI to configure the double-call.

So first, in the FCM panel, add an entry to point to revision 17632 of the following FCM branch:

  fcm:um-br/dev/gmann/vn8.4_RADAERupdates_for_dblcalaerforc/src

Then, in the hand-edits panel in the UMUI add the hand-edit to configure the double-call:

  ~gmann/umui_jobs/hand_edits/vn8.4/c2c_dustADE_glomapADEandAIE1_v84.ed

One of the things the hand-edit sets is the value of a switch C2C_AER_DIAGCAL which controls whether the setting of the forcing agent to zero is applied on the advancing call or the diagnostic call. You see that the hand-edit sets C2C_AER_DIAGCAL to .TRUE. so that the forcing agent is set to zero on the diagnostic call.

When the double-call forcing configuration is selected in the SW (or LW) radiation panels it synchronises to the setting in the LW (or SW) panel and a submitted job adds a series of other C2C switches to the RADFCDIA namelist in the file CNTLATM according to the buttons selected in the SLWForc panel.

In our double-call forcing job however, we will keep the SLWForc" UMUI panel unchanged with all C2C switched set to be false.

Instead we are using the above hand-edit to set the values of the C2C switches in CNTLATM.

If you view the c2c_dustADE_glomapADEandAIE1_v84.ed hand-edit you see it changes the C2C_DUST_D, C2C_UKCA_D and C2C_UKCA_I switches to be true so that the model is configured to diagnose the flux-difference (forcing) based on including the direct radiative effects from the total of the CLASSIC simulated dust combined with the direct and (1st) indirect effects from the GLOMAP simulated aerosol properties.

Configuring the radiation scheme for the double-call requires more than just selecting the Diagnose radiative forcings option.

You will need to update your job making also the following changes:

First, in the SW radiation window change the Number of times a day ot calculate increments (Diagnostic) from 24 to 8. This reverts the diagnostic call to only be carried out on radiation timesteps (3 hourly) rather than every hour as the reduced-radiation-call was applied in the timestepping configuration. Make the same change in the Section 2: LW radiation window.

Second, in the "Gen2" follow-on window for the SW radiation, change the Diagnostic File to be the same shortwave spectral file as for the Prognostic File. I.e. change spec_sw_cloud3_0 to spec_sw_ga3_0. Do the same for the Gen2 follow-on window under the LW radiation panel changing the Diagnostic File from spec_lw_cloud3_0 to spec_lw_ga3_0.

Finally, in the Call2 follow-on window (from the SW or LW Radiation panels) the radiation settings for the double-call need to be set to match those used in the main model. In order to achieve this, in the make the following changes:

change the method for representing horizontal water content variability from Homogeneous to McICA.
change the option for overlapping clouds from Maximum-random to Exponential-random.
switch on the button to include SW absorption by O2
switch on the buttons to include LW absorption by CFC113, CFC114, CFC11, CFC12, HCFC22, HCFC125, HFC134A, CH4 and N2O.

All that remains then is to add in the extra STASH requests for the double-call forcing diagnostics and to note a change to the operation of the Aerosol Optical Depth diagnostics.

The approach taken to index the STASH numbers for the radiative forcing items (the flux-difference between the two radiation calls) is to apply an offset of +200 to the item number to the corresponding item for the conventional radiative fluxes.

In task 12.1 we added STASH requests for the all-sky TOA outgoing SW and LW radiative fluxes which are referenced in STASH as section 1 item 208 and section 2 item 205.

To request the all-sky TOA outgoing SW and LW radiative forcings (between the two radiation calls) the corresponding item numbers are section 1 item 408 and section 2 item 405. Unfortunately however, at UM v8.4, section 2 item 405 is not available from the UMUI. In this task we will therefore request instead the clear-sky TOA outgoing SW and LW radiative forcing diagnostics (section 1 item 409 and section 2 item 406). Note also that one needs to request both the radiation flux and radiation forcing diagnostic in these runs so you should add 4 daily-mean STASH requests for section 1 items 209 and 409 and section 2 items 206 and 406.

Go to the STASH Specification of Diagnostic requirements window and add the daily-mean (TDAYM) requests for both of these flux-forcing pairs of diagnostics. As in Task 10.1, the domain profile should be set as DIAG and the usage profile as UPA.

Since we have now configured the model to run with GLOMAP aerosol set to zero in the advancing call, the conventional AOD diagnostics introduced in tutorial 10 (section 2 items 300 to 305) will now contain zero values when the model is run.

The UM therefore has a second set of AOD diagnostics giving the aerosol optical depth as calculated in the diagnostic call.

The approach for the double-call AOD diagnostics is the same as for the forcing diags, i.e. to apply an offset of +200 to the item number to find the corresponding AOD item in the diagnostic call.

The double-call GLOMAP AOD diagnostics are therefore found in section 2 items 500 to 505.

At v8.4 it is necessary to add an extra user-STASHmaster file to enable these STASH items to be requested in the job. In the User-STASHmaster files. Diags, Progs & Ancils window off the STASH panel you need to add in the following file

 ~gmann/stashfiles/dblecall_aods_only.stash

You will also need to add the hand-edit

~gmann/umui_jobs/hand_edits/vn8.4_nosulphateAOD.ed

which removes the CLASSIC sulphate AOD as it causes a crash in the double-call forcing configuration. You should also remove this STASH number (2-284) as well as the mineral dust optical depth (2-285) from the STASH requests panel. This causes a crash on ARCHER, but not on MONSooN.

If you view that file you see that as well as providing the STASH settings for the GLOMAP double-call AOD diagnostics for each mode, it also provides the information to the UMUI to allow double-call AOD diagnostics to be requested for each of the CLASSIC aerosol types.

Once you have have added the dblecall_aods_only.stash user-STASHmaster file you should proceed to the STASH Specification of Diagnostic requirements window and add daily-mean (TDAYM) requests for the double-call GLOMAP AODs (section 2 items 500 to 505) with usage profile UPA and domain profile DIAG_AOT.

The simulation will then output daily-mean SW and LW clear-sky forcings and double-call AOD diagnostics to the .pa file for your UM-UKCA job.

The Figure below shows daily-mean TOA SW-clearsky and LW-clearsky radiative effect fields for the double-call-modified version of the UKCA tutorial (gmann job xkwhi).

Worked Solution

A worked solution to Task 12.2 can be found in job xjrnn. Sample output from a copy of this job can be found on ARCHER in the directory

/work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Task12.2

Written by Graham Mann 2014

@@ Line 3: / Line 3: @@
 ==What you will learn in this Tutorial==
+In this tutorial you will learn about how to quantify the radiative effects of aerosol simulated by GLOMAP-mode in UM-UKCA.
-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.
+In the first task you will update your copy of the UKCA tutorial job to request radiative fluxes allowing the radiative flux perturbation (or effective radiative forcing) to be diagnosed based on difference in the fluxes between a pair of UM-UKCA jobs with some difference (e.g. pre-industrial and present-day emissions jobs).
-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.
+The second task involves configuring a copy of the UKCA tutorial job to run in ''double-call configuration'' whereby the aerosol radiative effects can be diagnosed at each radiation timestep.
-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).
+==Task 12.1: Update your copy of the UKCA tutorial job to diagnose Top Of the Atmosphere (TOA) radiative fluxes==
-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.
+In this task you will add STASH requests for SW and LW outgoing radiative fluxes at the top of the atmosphere to enable the radiative forcing from a particular change to be diagnosed.
-The GLOMAP-mode code allows several alternative "aerosol configurations" to be run using the same set of FORTRAN subroutines.
+The user should note however that to illustrate the task we are adding these requests to the UKCA tutorial job which is just a 1-day simulation.
-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).
+One would need to average the flux-difference between the pair of simulations over an appropriate timescale (e.g. multi-annual monthly-means) in order to diagnose an effective radiative forcing appropriately.
-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).
+Noting the above caveat, proceed and add daily-mean STASH requests for section 1 item 208 (all-sky outgoing short wave flux at the top-of-the-atmosphere) and section 2 item 205 (all-sky outgoing long wave flux at the top-of-the-atmosphere) to your copy of the UKCA tutorial job (xkvxe).
-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.
+The radiative fluxes are 2-dimensional diagnostics (longitude by latitude) so you should use the DIAG domain profile in this case.
-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).
+For daily-means use the TDAYM time profile.
+Again, since we require the daily-mean fluxes to be output to the .pa file you should request the diagnostics with the UPA usage profile.
+The Figure below shows the daily-mean SW and LW all-sky TOA radiative fluxes from the UKCA tutorial job for 1st December 1999 (gmann job xkwhc).
-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.
+[[File:idl_dailySWandLWradfluxesTOAallsky_xkwhc.jpg]]
-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.
+===Example Output===
-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.
+Example output for Task12.1 can be found on ARCHER in the following directory:
-==Task 11.1: Understand how the GLOMAP aerosol module tracks aerosol species and modes==
+ /work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Task12.1
-<span style="color:black">'''TASK 10.1:''' 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.
-==Task 11.2: Run a copy of the standard UKCA job which tracks two OC components in the GLOMAP modes==
+==Task 12.2 Configure the UKCA tutorial job to run as a ''double-call'' job diagnosing aerosol radiative effects==
-Copy your copy of the standard UKCA tutorial job (xkvxe) 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).
+In this task you will copy your copy of the standard tutorial job (<code>'''xjrnk'''</code>) and configure it to run with ''double-call'' to the radiation scheme to diagnose the radiative effects of the aerosol simulated by GLOMAP in UM-UKCA.
+The UM has been coded to allow the user to diagnose radiative effects of a particular
-To run the 2-component GLOMAP configuration, you will need to change the hand-edits in the UMUI to specify that you wish to run the model with additional aerosol tracers switched on.
+forcing agent by calling the radiation scheme twice with one of the calls setting the
+agent's concentration to zero. Special ''forcing'' STASH items are included within the
+UM which store the difference in the radiative fluxes between the two radiation calls.
+In the UMUI go to Atmosphere --> Scientific Parameters and Sections --> Section by section choices
-First, open the hand-edits panel in the UMUI and find the line specifying to use the hand-edit
+and then choose ''Section 1: SW radiation''.
-   ~mdalvi/umui_jobs/hand_edits/vn8.4/config_plume_scav_on_st.ed
+In the SW Radiation UMUI panel that opens, you see that at the top
-If you open this file (read-only) in an editor you can get an idea of what the hand-edit does.
+there is an "Options for multiple calls to radiation" button-selector.
+The UKCA tutorial job is set to "Timestepping scheme" which is the recommended way of running the model.
-The hand-edit begins by introducing a new logical variable and parameter for the convective scavenging module in UKCA.
+In this configuration the UM has a single call to the radiation scheme every radiation timestep (here 3 hours)
+with a 2nd reduced-call being applied on other timesteps (for more details see Manners et al., QJRMS 2009).
+The ''single-call'' option is the same as the Timestepping scheme but does not apply the reduced radiation
+call on interim timesteps.
+The other option supported here is to select "Diagnose radiative forcings" which activates the ''double-call''
-But the relevant section of the hand-edit for this task is 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).
+approach where the radiation scheme is called twice on each radiation timestep with and without the forcing agent.
+By default, if one selects the ''Diagnose radiative forcings'' option, then the model diagnoses the radiative
-The order of the tracers here matches that specified in the code in the array ''nm_spec'' in the routine ''ukca_init.F90''.
+forcing based on the ''advancing call'' including the forcing agent as usual, and the species is set to zero
+in the 2nd ''diagnostic call'' to the radiation.
+This operation is applied via the ''SLWForc'' panel which
-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.
+is available after selecting the ''Gen2'' follow-on window.  See that it is possible to individually select
+each of the CLASSIC aerosol types to diagnose their radiative effects whereas for GLOMAP-mode it only
+makes sense to diagnose the effects over all the types considered since the different types become internally
+mixed within each size class. Note that the user needs to be very careful to specify exactly how the effects
+should be applied in the second radiation call and this is specified in the ''Call2'' follow-on window.
+We strongly recommend only making changes to the default settings after discussing with relevant experts
-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.
+within NCAS or the Met Office.
+Although the default UM setting for the double-call is to set the species mixing ratio to zero in the diagnostic
-To run with the 2-component OC configuration, you need to switch on these additional "SO" tracers to store the 2nd organic matter component in each mode, and also change the switch ''I_MODE_SETUP'' in the file ''CNTLATM'' from the value of 2 specified via the UKCA-MODE UMUI panel to instead be set to 4 for GLOMAP-mode setup 4.
+call, it is often very useful to be able to suppress the fast feedbacks from the forcing agent in question by
+reversing the operation of the double-call including the aerosol radiative effects only in the diagnostic call
+and setting the species mixing ratio to zero in the advancing call.
+With this ''double-call radiative forcing'' configuration, the difference in radiative fluxes between the two calls
-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:
+provides the aerosol radiative perturbation with respect to an atmosphere containing no aerosols.
-    ~gmann/stashfiles/config_plume_scav_on_st_MS4.ed
+One can diagnose the present-day to pre-industrial aerosol radiative forcing by taking the difference between
+two parallel double-call simulations with aerosol and precursor emissions set to 1850 and 2000.
+All other forcing agents, such as greenhouse gases or land-use change, remain fixed at a reference time period.
+Often nudging to meteorological re-analysis winds and temperatures is applied in tandem with the double-call configuration
-You can use a graphical difference tool like tkdiff or xxdiff to see the differences between the two files.
+in which case the composition-climate model is being run in a similar way to an offline chemistry-transport model.
+This approach has been used extensively in aerosol forcing intercomparisons (e.g. the AeroCom direct forcing
+experiments, Myhre et al., 2013, ACP) with the radiative forcings diagnosed from each model with fast feedbacks
+disabled.
+To run UM-UKCA with this ''double-call radiative forcing'' configuration, you will need to add an extra FCM
-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.
+branch to the job and also add an extra hand-edit in the UMUI to configure the double-call.
+So first, in the FCM panel, add an entry to point to revision 17632 of the following FCM branch:
-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.
+   fcm:um-br/dev/gmann/vn8.4_RADAERupdates_for_dblcalaerforc/src
+Then, in the hand-edits panel in the UMUI add the hand-edit to configure the double-call:
-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.
+   ~gmann/umui_jobs/hand_edits/vn8.4/c2c_dustADE_glomapADEandAIE1_v84.ed
+One of the things the hand-edit sets is the value of a switch C2C_AER_DIAGCAL which controls whether the
-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
+setting of the forcing agent to zero is applied on the advancing call or the diagnostic call.
-   ~gmann/stashfiles/config_plume_scav_on_st_MS4.ed
+You see that the hand-edit sets C2C_AER_DIAGCAL to .TRUE. so that the forcing agent
+is set to zero on the diagnostic call.
+When the double-call forcing configuration is selected in the SW (or LW) radiation panels it
-rather than
+synchronises to the setting in the LW (or SW) panel and a submitted job adds a series of other ''C2C'' switches
-   ~mdalvi/umui_jobs/hand_edits/vn8.4/config_plume_scav_on_st.ed
+to the ''RADFCDIA'' namelist in the file CNTLATM according to the buttons selected in the ''SLWForc'' panel.
-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.
+In our ''double-call forcing'' job however, we will keep the ''SLWForc" UMUI panel unchanged with all
-For this replace the hand-edit
+C2C switched set to be false.
-   ~ukca/hand_edits/VN8.4/raderv2_vn84_ARCHER.ed
+Instead we are using the above hand-edit to set the values of the C2C switches in CNTLATM.
-with the version for GLOMAP setup 4:
-   ~gmann/stashfiles/raderv2_vn84_MS4_ARCHER.ed
+If you view the c2c_dustADE_glomapADEandAIE1_v84.ed hand-edit you see it changes the C2C_DUST_D,
-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.
+C2C_UKCA_D and C2C_UKCA_I switches to be true so that the model is configured to diagnose the
+flux-difference (forcing) based on including the direct radiative effects from the total of the
+CLASSIC simulated dust combined with the direct and (1st) indirect effects from the GLOMAP
+simulated aerosol properties.
+Configuring the radiation scheme for the double-call requires more than just selecting the
-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
+''Diagnose radiative forcings'' option.
-    ~ukca/userprestash/VN8.4/UKCA_Tr_StratTropAeroMODE.prestash
+You will need to update your job making also the following changes:
-to instead use
-    ~gmann/stashfiles/UKCA_Tr_StratTropAeroMODE_MS4.prestash
+First, in the SW radiation window change the ''Number of times a day ot calculate increments (Diagnostic)'' from 24 to 8.  This reverts the diagnostic call to only be carried out on radiation timesteps (3 hourly) rather than every hour as the reduced-radiation-call was applied in the timestepping configuration. Make the same change in the ''Section 2: LW radiation window''.
-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.
+Second, in the "Gen2" follow-on window for the SW radiation, change the ''Diagnostic File'' to be the same shortwave spectral file as for the ''Prognostic File''.  I.e. change ''spec_sw_cloud3_0'' to ''spec_sw_ga3_0''.  Do the same for the ''Gen2'' follow-on window under the LW radiation panel changing the ''Diagnostic File'' from ''spec_lw_cloud3_0'' to ''spec_lw_ga3_0''.
-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.
+Finally, in the ''Call2'' follow-on window (from the SW or LW Radiation panels) the radiation settings for the double-call need to be set to match those used in the main model.
-==Task 11.3 Examine the simulated total organic carbon in the original and two-cpt OC configurations==
+In order to achieve this, in the  make the following changes:
+* change the ''method for representing horizontal water content variability'' from ''Homogeneous'' to ''McICA''.
+* change the ''option for overlapping clouds'' from ''Maximum-random'' to ''Exponential-random''.
+* switch on the button  to include SW absorption by O2
+* switch on the buttons to include LW absorption by CFC113, CFC114, CFC11, CFC12, HCFC22, HCFC125, HFC134A, CH4 and N2O.
+All that remains then is to add in the extra STASH requests for the double-call forcing diagnostics and to note a change to the operation of the Aerosol Optical Depth diagnostics.
-In the above Task 11.2 you ran a 2-component OC version of the UKCA tutorial job (xkvxe).
-You can also refer to gmann job xkwhh which I have configured in this way.
-See my xkwhg was the same as the UKCA tutorial job xkvxe except that I have added the extra STASH requests as in Task 10.
+The approach taken to index the STASH numbers for the radiative forcing items (the flux-difference between the two radiation calls) is to apply an offset of +200 to the item number to the corresponding item for the conventional radiative fluxes.
-So by now you should have equivalent standard (as xkwhg) and 2-component OM (as xkwhh) versions of the UKCA tutorial job.
-In these jobs you have requested numerous daily-mean fields to be output in the .pa files.
+In task 12.1 we added STASH requests for the all-sky TOA outgoing SW and LW radiative fluxes which are referenced in STASH as section 1 item 208 and section 2 item 205.
-So in your /work/n02/n02/ directory on ARCHER you should have .pa19991201 files for your standard and 2-component OM jobs.
+To request the all-sky TOA outgoing SW and LW radiative forcings (between the two radiation calls) the corresponding item numbers are section 1 item 408 and section 2 item 405.  Unfortunately however, at UM v8.4, section 2 item 405 is not available from the UMUI.  In this task we will therefore request instead the clear-sky TOA outgoing SW and LW radiative forcing diagnostics (section 1 item 409 and section 2 item 406).  Note also that one needs to request both the radiation flux and radiation forcing diagnostic in these runs so you should add 4 daily-mean STASH requests for section 1 items 209 and 409 and section 2 items 206 and 406.
-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.
+Go to the ''STASH Specification of Diagnostic requirements'' window and add the daily-mean (TDAYM) requests for both of these flux-forcing pairs of diagnostics. As in Task 10.1, the domain profile should be set as DIAG and the usage profile as UPA.
-The OC mmrs are STASH section 34, items 126 (nucleation mode), 106 (Aitken-soluble), 110 (accumn-soluble), 116 (coarse-soluble) and 121 (Aitken-insoluble).
+Since we have now configured the model to run with GLOMAP aerosol set to zero in the advancing call, the conventional AOD diagnostics introduced in tutorial 10 (section 2 items 300 to 305) will now contain zero values when the model is run.
-The SO mmrs are STASH section 34, items 128 (nucleation mode), 129 (Aitken-soluble), 130 (accumn-soluble), 131 (coarse-soluble).
+The UM therefore has a second set of AOD diagnostics giving the aerosol optical depth as calculated in the diagnostic call.
-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.
+The approach for the double-call AOD diagnostics is the same as for the forcing diags, i.e. to apply an offset of +200 to the item number to find the corresponding AOD item in the diagnostic call.
-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.
+The double-call GLOMAP AOD diagnostics are therefore found in section 2 items 500 to 505.
-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).
+At v8.4 it is necessary to add an extra user-STASHmaster file to enable these STASH items to be requested in the job.
-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 my jobs xkwhg (top-left) and xkwhh (top-right).
+In the ''User-STASHmaster files. Diags, Progs & Ancils'' window off the STASH panel you need to add in the following file
+  ~gmann/stashfiles/dblecall_aods_only.stash
+You will also need to add the hand-edit
-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.
+ ~gmann/umui_jobs/hand_edits/vn8.4_nosulphateAOD.ed
-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.
+which removes the CLASSIC sulphate AOD as it causes a crash in the double-call forcing configuration. You should also remove this STASH number (2-284) as well as the mineral dust optical depth (2-285) from the STASH requests panel. This causes a crash on ARCHER, but not on MONSooN.
-You can see from the example that the "total POM2 mmr" in xkwhg is zero everywhere.
-That's because in this job GLOMAP has the standard configuration with just one organic component.
+If you view that file you see that as well as providing the STASH settings for the GLOMAP double-call AOD diagnostics for each mode, it also provides the information to the UMUI to allow double-call AOD diagnostics to be requested for each of the CLASSIC aerosol types.
-By contrast the "total POM2 mmr" for xkwhh 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 xkwhg SEC_ORG condenses into the "OC" component.
+Once you have have added the ''dblecall_aods_only.stash'' user-STASHmaster file you should proceed to the ''STASH Specification of Diagnostic requirements'' window and add daily-mean (TDAYM) requests for the double-call GLOMAP AODs (section 2 items 500 to 505) with usage profile UPA and domain profile DIAG_AOT.
-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.
+The simulation will then output daily-mean SW and LW clear-sky forcings and double-call AOD diagnostics to the .pa file for your UM-UKCA job.
-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.
+The Figure below shows daily-mean TOA SW-clearsky and LW-clearsky radiative effect fields for the double-call-modified version of the UKCA tutorial (gmann job xkwhi).
-This task illustrates how one can separate out the aerosol mass from different sources and track them separately via a different aerosol component.
+[[File:idl_dailyTOAradforcings_SWclearsky_LWclearsky_xkwhi.jpg]]
+===Worked Solution===
+A worked solution to Task 12.2 can be found in job <code>'''xjrnn'''</code>. Sample output from a copy of this job can be found on ARCHER in the directory
+ /work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Task12.2
-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 [[User:Gmann | Graham Mann]] 2014''