Difference between revisions of "UKCA Chemistry and Aerosol vn10.9 Tutorial 4"

Revision as of 11:04, 8 October 2018

UKCA Chemistry and Aerosol Tutorials at vn10.9

What you will do in this tutorial

In this tutorial you will learn how to make the required changes in Rose and in UKCA to include new chemical tracers. As you learn how to do this you will add two new tracers to the UKCA tutorial suite you have already been running.

Task 4.1: Add new tracers into Rose and UKCA

TASK4.1: Add in two new tracers in to slots 64 and 65 for the StratTrop chemistry scheme. The tracer in slot 64 will be called ALICE and the tracer in slot 65 will be called BOB and initialise these tracers to 1.000000e-12. You should also output these two tracers through the UPA stream in STASH as 3-hour means. In UKCA, you should set the conversion factor for each of these to 1.0.

Make a branch

As UKCA is a framework, it must have the infrastructure around it to allow it to work, with the infrastructure being the UM itself. In this tutorial you will add in two new chemical tracers. In this past this was done in two steps, but in Rose this must be done in a single step from vn10.6 onwards. Even though these tutorials are at vn10.4, we will follow the same steps as for vn10.6.

For this tutorial you will need to make a new branch in the usual way. You should do this now.

You will have learned how to make UM branches in the NCAS-CMS FCM Tutorial. However, now you should use um.x_tr as the source of your branch.

For example, first you should make a ticket on the Met Office SRS Trac pages (login required) and then make the branch like so

fcm branch-create --type dev -k ticket_number your_branch_name fcm:um.x_tr@vn10.9

before checking-out your branch by

fcm checkout fcm:um.x_br/dev/userid/vn10.9_your_branch_name

More information on FCM can be found at the NCAS-CMS FCM pages or the FCM User Guide

Metadata

In Rose, the GUI appearance is controlled by metadata, and it is possible to edit this metadata to add new variables to panels. We will not do this in this tutorial, but you will need to change where Rose looks for metadata, as the STASHmaster_A is also metadata.

Using your new metadata within Rose

To pick-up the metadata changes, you should make sure that the meta path in um points to

um-atmos/vn10.9

If you were making changes to commit to the trunk, you would use um-atmos/HEAD, but here we will use um-atmos/vn10.9.

From now on, when you want to open your Rose suite for editing, instead of doing it through rosie, you should instead open the job for editing by going to your $HOME/roses/[SUITE-ID] directory, and opening it using the command

rose edit -M /path/to/vn10.9_your_branch_name/rose-meta

If you don't do this, the STASHmaster changes will not be picked up, and you won't be able to select the tracers.

Rose Changes

Include your branch for code changes

Although we haven't made any code changes yet, you will (at some point) need to include your branch in Rose so that the UKCA code changes can be picked-up and compiled. To do this go to fcm_make $\rightarrow$ env $\rightarrow$ Sources and add a new branch by clicking the plus symbol in the um_sources section. You should then put

/path/to/vn10.9_your_branch_name

if you wish to run from a working copy, and

branches/dev/[your MOSRS username]/vn10.9_your_branch_name

if you want to run from the repository. You can specify specific revision numbers by putting @REV at the end of this line (where REV is the revision number, e.g. 12345 etc.).

STASHmaster_A

In Rose-based jobs, adding new UKCA tracers is done through editing the STASHmaster_A file directly. Take a look at the STASHmaster_A file, found in

/path/to/vn10.9_your_branch_name/rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A

This is a large file, as it contains all the possible STASH items. Scroll down the file until you get to section 34, and you will see how the tracers are defined. The key entries to consider are highlighted in red. All entried are fixed-width, so when editing the file, ensure not to change the spacing, otherwise you will get errors.

#===============================================================================
# Section 34 UKCA Chemistry
#===============================================================================
#
1|    1 |   34 |    1 |O3 MASS MIXING RATIO AFTER TIMESTEP |
2|    2 |    0 |    1 |    1 |    2 |   40 |   11 |    0 |    0 |    0 |    0 |
3| 000000000000000000000000111110 | 00000000000000000001 |    1 |
4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |
5|    0 | 2101 |    0 |   65 |    0 |    0 |    0 |    0 |    0 |
#

The meaning of these entries is:

First Line:

34: The STASH section, in this case Section 34, UKCA prognostics.
1: The STASH item, in this case, the first item in s34, ozone.
O3 MASS MIXING RATIO AFTER TIMESTEP: The name of the field in the STASHmaster file. This can be anything descriptive, but it isn't read by the model, and is only considered in Rose (or e.g. Xconv).

Second Line:

2: The Space Code, which tells the UM whether the field should be held in the restart dump or not. For prognostics, this should be 2 (which means that they should be stored in the restart dump), but for diagnostics that are only passed to output files, this should be 0.

Third Line:

000000000000000000000000111110: These are Options Codes which determine which scheme the STASH field (i.e. tracer in this case) are valid for. These are counted from the right, n1 to n30, and for UKCA only the first 8 are used. These have the following meaning:
- n1: Age-of-air tracer (ageair) or aerosol tracers
- n2: Standard Tropospheric Chemistry scheme using the Backward Euler solver (trop)
- n3: Regional Air Quality Chemistry scheme using the Backward Euler solver (raq)
- n4: Tropospheric Chemistry with Isoprene scheme using the Newton-Raphson solver (tropisop)
- n5: Stratospheric-Tropospheric Chemistry using the Newton-Raphson solver (strattrop, also know as CheST)
- n6: Standard Stratospheric Chemistry using the Newton-Raphson solver (strat)
- n7: Offline-oxidants scheme (to drive GLOMAP-mode) using the Newton-Raphson solver (offline)
- n8: Offline-oxidants scheme (to drive GLOMAP-mode) using the Newton-Raphson solver (offline_be)

Therefore, looking at the option code for ozone (s34i001), it is valid for the trop, raq, tropisop, strattrop, and strat chemistry schemes.

Fifth Line:

2101: This is the PP Field Code and should be unique to each tracer. Here these begin counting at 2101 (s34i001) and end at 2356 (s34i256).

So to make a STASH entry for a single tracer called ALICE in slot s34i064 that is only valid in the StratTrop scheme, the STASHmaster_A entry would look like

#
1|    1 |   34 |   64 |ALICE MASS MIXING RATIO AFTER TSTEP |
2|    2 |    0 |    1 |    1 |    2 |   40 |   11 |    0 |    0 |    0 |    0 |
3| 000000000000000000000000010000 | 00000000000000000001 |    1 |
4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |
5|    0 | 2164 |    0 |   65 |    0 |    0 |    0 |    0 |    0 |
#

Remember: You need to add 2 tracers, ALICE in s34i064 and BOB in s34i065.

You should make these changes to STASHmaster_A, and then fcm commit these changes. This is important, otherwise ARCHER will not be able to see the changes you have made once you have included your new STASHmaster_A file in Rose.

Section 51

All STASH entries in Section 34 need a corresponding pressure-level field to be added to section 51. The equivalent STASHmaster_A entry for s51 ozone is:

#
#===============================================================================
# Section 51 UKCA Chemistry on pressure levels
#===============================================================================
#
1|    1 |   51 |    1 |O3 MASS MIXING RATIO ON PRESS LEVS  |
2|    0 |    0 |    1 |    1 |    3 |    1 |    2 |    0 |    0 |    0 |    1 |
3| 000000000000000000000000111110 | 00000000000000000001 |    3 |
4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |
5|    0 | 2101 |    0 |    8 |    0 |    0 |    0 |    0 |    0 |
#

You will notice that there are a number of changes to various codes, and this is to do with defining the grid that the diagnostic is valid on, whether it can be held in the dump, etc. For more information on what these codes mean, please see Appendix C in UMDP C4, which can be obtained from the SRS here (password required). When making a new entry, the easiest thing to do is copy an existing entry and make the required changes to the item, name, PP field code, and option codes.

Remember: You need to add 2 tracers, ALICE in s34i064 and BOB in s34i065.

Help text

You should also add appropriate help text into the vn10.4_your_branch_name/rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf file, e.g.

[stashmaster:code(34064)]
description=ALICE MASS MIXING RATIO AFTER TIMESTEP
help=UKCA Tutiorial Tracer ALICE Mass Mixing Ratio in kg/kg(Air)

and

[stashmaster:code(51064)]
description=ALICE  MASS MIX RATIO ON PRESS LEVS
help=UKCA Tutiorial Tracer ALICE Mass Mixing Ratio in kg/kg(Air)
    =on pressure levels

Remember: You need to add 2 tracers, ALICE in s34i064 and BOB in s34i065.

Use your new STASHmaster file in Rose

Before you make these changes you should first save and close your suite.

To get Rose to recognise your STASHmaster file, you will need to make a number of changes:

Point the um metadata to um-atmos/HEAD and edit Rose using rose edit -M /path/to/vn10.9_your_branch_name/rose-meta (you should already be doing this after following the instructions in the metadata section above.
You need to open the $HOME/roses/[SUITE-ID]/app/um/rose-app.conf file in a text editor (e.g. vim, emacs, nedit etc.) and add the line STASHMASTER=STASHmaster inside the [env] block
You need to open the $HOME/roses/[SUITE-ID]/rose-suite.conf file in a text editor and add the following lines at the top of the file:

[file:app/um/file/STASHmaster]
source=fcm:um.xm_br/dev/[your MOSRS userid]/vn10.9_your_branch_name/rose-meta/um-atmos/HEAD/etc/stash/STASHmaster@HEAD

You need to ensure that you have committed your STASHmaster_A changes, otherwise your new tracer(s) will not be seen at run-time during the reconfiguration or atmosphere steps.

You may wish to now fcm commit your suite changes. You can now re-open your suite.

Initialise your new tracer(s)

Your new tracer(s) is a prognostic variable, as therefore the UM requires prior knowledge of the values it has to be able to run properly. To do this you need to go to um $\rightarrow$ namelist $\rightarrow$ Reconfiguration and Ancillary Control $\rightarrow$ Configure ancils and initialise dump fields. Here you will see a list of fields. You can change the order of these by e.g. STASH number, as this often makes it easier to view.

To add new fields, right click anywhere within the table and click Add new section. This will make a new entry with index 1, if you add another entry, it will be given index 2 etc.. Right-click on this and click on View namelist:items(X) (where X is the index number). This will open a new tab where you can select the STASH section and item for the field you want to initialise using the drop-down menus. Some UKCA tracers need to be given full 3D initial conditions in ancillary file format. However, for this example we will initialise the tracer to a small number, $1.000000\times 10^{-12}$ . To do this, select the radio button for Set to a specified constant value and put 1.000000e-12 in the dialog box labelled user_prog_rconst at the bottom of the panel.

You will need to do this for each of the tracers you are adding (you can also clone existing entries). When you have finished, you will need to go to the STASH Requests panel (see the STASH tutorial) and run the TidyStashTransform macro to correctly generate the required index value for each tracer initialisation.

Output your new tracers

To output your tracers, go to the STASH panel and output your tracers as described in the What is STASH? tutorial.

Remember: You need to add 2 tracers, ALICE in s34i064 and BOB in s34i065.

Required UKCA Code Changes

`ukca_nmspec_mod.F90`

Inside UKCA there is a master mapping array that tells the UKCA code which transported species are placed into a particular item number in section 34. At vn10.9 these are contained in the first 256 slots.

This array is called nm_spec, and it can be found in ukca_nmspec_mod.F90. At vn10.9, it looks like this:

nm_spec(1:a_max_ukcavars) = (/                                     &
'O3        ','NO        ','NO3       ','NO2       ','N2O5      ',  &
'HO2NO2    ','HONO2     ','H2O2      ','CH4       ','CO        ',  & !10
'HCHO      ','MeOOH     ','HONO      ','C2H6      ','EtOOH     ',  &
'MeCHO     ','PAN       ','C3H8      ','n-PrOOH   ','i-PrOOH   ',  & !20
'EtCHO     ','Me2CO     ','MeCOCH2OOH','PPAN      ','MeONO2    ',  &
'O3_S      ','C5H8      ','ISOOH     ','ISON      ','MACR      ',  & !30
'MACROOH   ','MPAN      ','HACET     ','MGLY      ','NALD      ',  &
'HCOOH     ','MeCO3H    ','MeCO2H    ','H2O       ','ISO2      ',  & !40
'Cl        ','ClO       ','Cl2O2     ','OClO      ','Br        ',  &
'BrO       ','BrCl      ','BrONO2    ','N2O       ','HCl       ',  & !50
'HOCl      ','HBr       ','HOBr      ','ClONO2    ','CFCl3     ',  &
'CF2Cl2    ','MeBr      ','N         ','O(3P)     ','MACRO2    ',  & !60
'MeCl      ','CF2ClBr   ','CCl4      ','CF2ClCFCl2','CHF2Cl    ',  &
'MeCCl3    ','CF3Br     ','H2OS      ','CH2Br2    ','H2        ',  & !70
'DMS       ','SO2       ','H2SO4     ','MSA       ','DMSO      ',  &
'NH3       ','CS2       ','COS       ','H2S       ','H         ',  & !80
'OH        ','HO2       ','MeOO      ','EtOO      ','MeCO3     ',  &
'n-PrOO    ','i-PrOO    ','EtCO3     ','MeCOCH2OO ','MeOH      ',  & !90
'Monoterp  ','Sec_Org   ','SESQUITERP','SO3       ','AROM      ',  &
'O(3P)_S   ','O(1D)_S   ','NO2       ','BrO       ','HCl       ',  & !100
'Nuc_SOL_ND','Nuc_SOL_SU','Ait_SOL_ND','Ait_SOL_SU','Ait_SOL_BC',  &
'Ait_SOL_OC','Acc_SOL_ND','Acc_SOL_SU','Acc_SOL_BC','Acc_SOL_OC',  & !110
'Acc_SOL_SS','Acc_SOL_DU','Cor_SOL_ND','Cor_SOL_SU','Cor_SOL_BC',  &
'Cor_SOL_OC','Cor_SOL_SS','Cor_SOL_DU','Ait_INS_ND','Ait_INS_BC',  & !120
'Ait_INS_OC','Acc_INS_ND','Acc_INS_DU','Cor_INS_ND','Cor_INS_DU',  &
'Nuc_SOL_OC','Ait_SOL_SS','Nuc_SOL_SO','Ait_SOL_SO','Acc_SOL_SO',  & !130
'Cor_SOL_SO','Nuc_SOL_NH','Ait_SOL_NH','Acc_SOL_NH','Cor_SOL_NH',  &
'Nuc_SOL_NT','Ait_SOL_NT','Acc_SOL_NT','Cor_SOL_NT','XXX       ',  & !140
'Anth_Prec ','Bio_Prec  ','Anth_Cond ','Bio_Cond  ','XXX       ',  &
'XXX       ','XXX       ','XXX       ','PASSIVE O3','AGE OF AIR',  & !150
'RETIRED   ','RETIRED   ','RETIRED   ','RETIRED   ','RETIRED   ',  & 
'RETIRED   ','RETIRED   ','RETIRED   ','RETIRED   ','RETIRED   ',  & !160
'RETIRED   ','RETIRED   ','RETIRED   ','RETIRED   ','RETIRED   ',  & 
'RETIRED   ','RETIRED   ','RETIRED   ','RETIRED   ','RETIRED   ',  & !170
'RETIRED   ','RETIRED   ','XXX       ','XXX       ','XXX       ',  & 
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & !180
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & 
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & !190
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & 
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & !200
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & 
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & !210
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & 
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & !220
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & 
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & !230
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & 
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & !240
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & 
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & !250
'XXX       ','XXX       ','XXX       ','XXX       ','XXX       ',  & 
'XXX       '                                                       & !256
 /)

This array is case sensitive and each string is a fixed length of 10 characters, with the whitespace being made up of spaces and not another tpye of white space (e.g. tabs).

When adding new tracers you should not overwrite tracers that are already in use by the chemistry scheme that you are using (e.g. StratTrop etc.), and it is best to also take care and avoid tracers in use by other schemes, if possible. You can see the tracers used by each scheme by looking in the chch_defs array at the top of the ukca_chem_master.F90 module.

Here you should put a new species, 'ALICE ', into tracer slot 64 (current specified as 'CF2ClCFCl2', which is not in use by any scheme at the moment).

Remember: You need to add 2 tracers, ALICE in s34i064 and BOB in s34i065.

`ukca_chem_master.F90`

We will go through changes that need to be made for the StratTrop chemistry scheme (defined in the file ukca_chem_master.F90, using the code ST), but equivalent changes would need to be made for others, e.g. TropIsop or Strat. For this example we will only refer to this scheme.

In this file the list of species used in chemistry is defined by the array chch_defs_master. The list of species is held in a derived type, of the format:

chch_t1( N,'SPECIES   ',  X,'TYPE      ','FAMILY    ',  D,  W,  E, SCHEME, QUALIFIER, DISQUALIFIER, VN),  &

Where:

N is an integer. The value should be incremented for each new species that is added.
'SPECIES ' is the name of the species, e.g. 'O3 '
X number of odd atoms
'TYPE      ' describes whether the species is
a tracer ('TR        ')

a steady-state species ('SS        ')

a constant ('CT        ')

a constant field ('CF        ').
For SS, CT, and CF, special code will need to be added.
'FAMILY ' is the family that the species belongs to. This field is not currently used.
D is 1 if the species is dry-deposited, and 0 otherwise.
W is 1 if the species is wet-deposited, and 0 otherwise.
E is 1 if the species is emitted, and 0 otherwise. This field is not currently used.
SCHEME defines the chemistry scheme used, e.g.:
ST = Stratosphere-Troposphere scheme

T = Troposphere scheme

S = Stratosphere scheme

R = RAQ scheme

OL = Offline-oxidants scheme

TI = Troposphere-Isoprene scheme
- If the same species is used in multiple schemes these are added, e.g. ST+S+TI etc.
QUALIFIER (and DISQUALIFIER) defines lines to add (or remove) on top of the base chemistry scheme depending on if certain additional options have been chosen, e.g.
0 = no qualifier/disqualifer used

A = Aerosol chemistry additions required to run GLOMAP-mode

TH = Tropospheric heterogeneous reactions

HP = Heterogeneous PSC chemistry

ES = Extended stratospheric reactions
- As with the SCHEME codes, these are also additive if required, e.g. A+TH etc.
VN gives the model version the addition is added at. This is future functionality that will allow for multiple rates to be included in the source-code. This is currently not used, so please set to 107.

Therefore to add-in the ALICE species, we should insert a line similar to this one

chch_t1(116,'ALICE     ',1,'TR        ','          ',0,0,0,ST,0,0,107),&

into chch_defs_master, remembering to also increment the size of this array, given by n_chch_master

Remember: You need to add 2 tracers, ALICE in s34i064 and BOB in s34i065.

`ukca_setd1defs.F90`

In ukca_setd1defs.F90 you will find code blocks which set values for various parameters depending on the scheme used. In this example you will need to scroll down to the section which defines the StratTrop (also known as CheST) chemistry, which is located in the Stratospheric Chemistry section and is referenced by using the L_ukca_strattrop logical.

The IF block tests against L_ukca_strattrop and L_ukca_achem (which determines whether or not you require the additional chemistry used to drive the GLOMAP-mode aerosol scheme). You should increment the value of n_chem_tracers by the number of chemical tracers that you are adding in both sections of the IF block, as this tracer is not defined to be for aerosol chemistry only. If your additional tracers are aerosol chemistry additions then you should increment the value of n_aero_tracers.

If you are adding to a different chemistry scheme then you will need to make these changes accordingly.

Remember: You need to add 2 tracers, ALICE in s34i064 and BOB in s34i065.

`ukca_constants.F90`

The unit of the tracers is kg(species)/kg(air) (i.e. mass mixing ratio, or mmr), but inside UKCA these species are converted to volume mixing ratio (or vmr). To enable UKCA to do this you will need to add the conversion factor(s) for your new tracer(s) into the code. This is done in the ukca_constants.F90 module.

Open this file and add the required conversion factor(s). The naming convention for these is M_species is the molecular mass of the new species in g/mol, and C_species for the converson factor from vmr to mmr (calculated as M_species/M_air, where M_air=28.97). In actuality, only the C_species listing is always required, although you may need to add the M_species value later if you are emitting into the new species that you are adding.

For example:

REAL, PARAMETER :: C_ALICE      = 1.0000

Remember: You need to add 2 tracers, ALICE in s34i064 and BOB in s34i065.

`ukca_cspecies.F90`

After you have added in the C_species conversion factors, you will need to tell UKCA to use them for your species. To do this you need to edit the ukca_cspecies.F90 module, which contains code which contructs the c_species array of conversion factors for the advected tracers. This contains a subroutine called ukca_calc_cspecies which has a long block of code that you need to edit to add an entry like this:

WHERE (advt == 'ALICE     ') c_species = C_ALICE

The advt array is automatically generated by UKCA at run-time from the chch_defs_scheme chemistry scheme definition you edited earlier, so your new tracer(s) will exist within it. You need to add in a new line for each of your tracers which sets the value of the c_species array to your individual C_species parameter. Add the line(s) in at the end of the block.

Remember: You need to add 2 tracers, ALICE in s34i064 and BOB in s34i065.

Run your suite

Now that you have made the required changes to Rose and in your branch, please run your suite. You may find that it fails on the, fcm_make2, recon, or atmos jobs. To find the errors and see output, you should either right-click the failed task in Gcylc and view the output, or go to the

/home/n02/n02/[your ARCHER userid]/cylc-run/[SUITE-ID]

directory on ARCHER. Within this there are a number of directories. To see the log files, cd into

log/job/1/[JOB NAME]/NN

and view the job.err or job.out files. When the suite successfully runs, the fieldsfile output can usually be found in

/work/n02/n02/[your ARCHER userid]/cylc-run/[SUITE-ID]/work/1/atmos/

Numerical Noise

Numerical noise in the ALICE tracer (s34i064)
Numerical noise in the BOB tracer (s34i065)

When your suite has run successfully, and you view the fields for your new tracer(s) in Xconv, you may find that they have a speckled appearance, rather than being constant. This is due to numerical noise that has been introduced as the tracer is run through the UKCA chemical solver. Once the field is converted to 32-bit this should disappear. It will also cease to become apparent when emissions and reactions are applied to these tracers.

Solution to Task 4.1

You were given the task

Add in two new tracers in to slots 64 and 65 for the StratTrop chemistry scheme. The tracer in slot 64 will be called ALICE and the tracer in slot 65 will be called BOB and initialise these tracers to 1.000000e-12. You should also output these two tracers through the UPA stream in STASH as 3-hour means. In UKCA, you should set the conversion factor for each of these to 1.0.

For a working Rose suite that has completed this task, please see

ARCHER: u-as292@59818
vm: u-as297@59815

The specific Rose changes made are:

ARCHER:

Index: app/um/rose-app.conf
===================================================================
--- app/um/rose-app.conf	(revision 59777)
+++ app/um/rose-app.conf	(revision 59818)
@@ -1,4 +1,4 @@
-meta=um-atmos/vn10.9
+meta=um-atmos/HEAD
 
 [command]
 default=um-atmos
@@ -24,6 +24,7 @@
 RECON_KEEP_MPP_STDOUT=true
 RUNID=atmos
 SPECTRAL_FILE_DIR=$UM_INSTALL_DIR/vn$VN/ctldata/spectral/ga7
+STASHMASTER=STASHmaster
 
 [file:$DATAM]
 mode=mkdir
@@ -644,6 +645,18 @@
 !!user_prog_ancil_stash_req=0
 !!user_prog_rconst=0
 
+[namelist:items(3e9a6939)]
+ancilfilename=
+domain=1
+!!interval=0
+!!netcdf_varname=
+!!period=1
+source=6
+stash_req=34064
+update_anc=.false.
+!!user_prog_ancil_stash_req=0
+user_prog_rconst=1.000000e-12
+
 [namelist:items(4a4f86c3)]
 ancilfilename='$UM_INSTALL_DIR/ancil/atmos/n48e/orca1/seaice/reynolds/1981_2012_360/v1/qrclim.seaice'
 domain=1
@@ -728,6 +741,18 @@
 !!user_prog_ancil_stash_req=
 user_prog_rconst=1.000000e-12
 
+[namelist:items(c3e3b7ad)]
+ancilfilename=
+domain=1
+!!interval=0
+!!netcdf_varname=
+!!period=1
+source=6
+stash_req=34065
+update_anc=.false.
+!!user_prog_ancil_stash_req=0
+user_prog_rconst=1.000000e-12
+
 [namelist:items(c54d9b29)]
 ancilfilename='$UM_INSTALL_DIR/ancil/atmos/n48e/orca1/land_sea_mask/etop01/v1/qrparm.mask'
 domain=1
@@ -3295,6 +3320,22 @@
 tim_name='T3HMN'
 use_name='UPA'
 
+[namelist:umstash_streq(34064_487e535d)]
+dom_name='DALLTH'
+isec=34
+item=64
+package=
+tim_name='T3HMN'
+use_name='UPA'
+
+[namelist:umstash_streq(34065_6dc07351)]
+dom_name='DALLTH'
+isec=34
+item=65
+package=
+tim_name='T3HMN'
+use_name='UPA'
+
 [namelist:umstash_streq(34106_ebb7bb67)]
 dom_name='DALLTH'
 isec=34
Index: app/fcm_make/rose-app.conf
===================================================================
--- app/fcm_make/rose-app.conf	(revision 59777)
+++ app/fcm_make/rose-app.conf	(revision 59818)
@@ -42,4 +42,4 @@
 stash_version=1A
 timer_version=3A
 um_rev=vn10.9
-um_sources=
+um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46535
Index: rose-suite.conf
===================================================================
--- rose-suite.conf	(revision 59777)
+++ rose-suite.conf	(revision 59818)
@@ -1,3 +1,6 @@
+[file:app/um/file/STASHmaster]
+source=fcm:um.xm_br/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns/rose-meta/um-atmos/HEAD/etc/stash/STASHmaster@HEAD
+
 [jinja2:suite.rc]
 ARCHER_GROUP='n02-chem'
 ARCHER_QUEUE='short'

vm:

Index: app/um/rose-app.conf
===================================================================
--- app/um/rose-app.conf	(revision 59775)
+++ app/um/rose-app.conf	(revision 59815)
@@ -1,4 +1,4 @@
-meta=um-atmos/vn10.9
+meta=um-atmos/HEAD
 
 [command]
 default=um-atmos
@@ -26,6 +26,7 @@
 RECON_STDOUT_FILE=pe_output/atmos.fort6.pe
 RUNID=atmos
 SPECTRAL_FILE_DIR=$UMDIR/vn$VN/ctldata/spectral/ga7
+STASHMASTER=STASHmaster
 UM_THREAD_LEVEL=MULTIPLE
 
 [file:$DATAM]
@@ -647,6 +648,18 @@
 !!user_prog_ancil_stash_req=0
 !!user_prog_rconst=0
 
+[namelist:items(3e9a6939)]
+ancilfilename=
+domain=1
+!!interval=0
+!!netcdf_varname=
+!!period=1
+source=6
+stash_req=34064
+update_anc=.false.
+!!user_prog_ancil_stash_req=0
+user_prog_rconst=1.000000e-12
+
 [namelist:items(4a4f86c3)]
 ancilfilename='$UMDIR/ancil/atmos/n48e/orca1/seaice/reynolds/1981_2012_360/v1/qrclim.seaice'
 domain=1
@@ -731,6 +744,18 @@
 !!user_prog_ancil_stash_req=
 user_prog_rconst=1.000000e-12
 
+[namelist:items(c3e3b7ad)]
+ancilfilename=
+domain=1
+!!interval=0
+!!netcdf_varname=
+!!period=1
+source=6
+stash_req=34065
+update_anc=.false.
+!!user_prog_ancil_stash_req=0
+user_prog_rconst=1.000000e-12
+
 [namelist:items(c54d9b29)]
 ancilfilename='$UMDIR/ancil/atmos/n48e/orca1/land_sea_mask/etop01/v1/qrparm.mask'
 domain=1
@@ -3887,6 +3912,22 @@
 tim_name='T3HMN'
 use_name='UPA'
 
+[namelist:umstash_streq(34064_487e535d)]
+dom_name='DALLTH'
+isec=34
+item=64
+package=
+tim_name='T3HMN'
+use_name='UPA'
+
+[namelist:umstash_streq(34065_6dc07351)]
+dom_name='DALLTH'
+isec=34
+item=65
+package=
+tim_name='T3HMN'
+use_name='UPA'
+
 [namelist:umstash_streq(34106_ebb7bb67)]
 dom_name='DALLTH'
 isec=34
Index: app/fcm_make/rose-app.conf
===================================================================
--- app/fcm_make/rose-app.conf	(revision 59775)
+++ app/fcm_make/rose-app.conf	(revision 59815)
@@ -42,4 +42,4 @@
 stash_version=1A
 timer_version=3A
 um_rev=vn10.9
-um_sources=
+um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46535
Index: rose-suite.conf
===================================================================
--- rose-suite.conf	(revision 59775)
+++ rose-suite.conf	(revision 59815)
@@ -1,3 +1,6 @@
+[file:app/um/file/STASHmaster]
+source=fcm:um.xm_br/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns/rose-meta/um-atmos/HEAD/etc/stash/STASHmaster@HEAD
+
 [jinja2:suite.rc]
 BUILD=true
 OFFLINE=false

These ARCHER differences can be found in the file /home/ukca/Tutorial/vn10.9/worked_solutions/Task4.1/Task4.1_rose.patch on PUMA.

The specific UM changes made are:

Index: src/atmosphere/UKCA/ukca_setd1defs.F90
===================================================================
--- src/atmosphere/UKCA/ukca_setd1defs.F90	(revision 46527)
+++ src/atmosphere/UKCA/ukca_setd1defs.F90	(revision 46535)
@@ -321,7 +321,7 @@
         (/'NO        ','CH4       ','CO        ','HCHO      ', &
           'C2H6      ','C3H8      ','Me2CO     ','MeCHO     ', &
           'C5H8      ','NO_aircrft'/)
-    n_chem_tracers = 71         ! No chem tracers
+    n_chem_tracers = 73         ! No chem tracers
     nr_therm       = 220        ! thermal reactions
     nr_phot        = 55         ! photolytic (ATA)
 
@@ -337,7 +337,7 @@
           'SO2_high  ','NH3       ','DMS       ','SO2_nat   ', &
           'BC_biomass','OC_biomass','NO_aircrft'/)
     n_aero_tracers = 12
-    n_chem_tracers = 71         ! No chem tracers
+    n_chem_tracers = 73         ! No chem tracers
     IF (L_ukca_trophet) THEN
       nr_therm     = 241        ! thermal reactions
     ELSE
Index: src/atmosphere/UKCA/ukca_chem_master.F90
===================================================================
--- src/atmosphere/UKCA/ukca_chem_master.F90	(revision 46527)
+++ src/atmosphere/UKCA/ukca_chem_master.F90	(revision 46535)
@@ -79,7 +79,7 @@
 ! define below the chemistry schemes 
 
 ! define size of master chemistry
-INTEGER, PARAMETER :: n_chch_master = 148 ! number of known species
+INTEGER, PARAMETER :: n_chch_master = 150 ! number of known species
 INTEGER, PARAMETER :: n_het_master  =  10 ! number of heterogeneous reactions
 INTEGER, PARAMETER :: n_dry_master  =  57 ! number of dry deposition reactions
 INTEGER, PARAMETER :: n_wet_master  =  49 ! number of wet deposition reactions
@@ -376,7 +376,9 @@
 chch_t1(112,'TOLP1     ',1,'SS        ','          ',0,0,0,R,0,0,107),&
 chch_t1(113,'MEMALD    ',1,'TR        ','          ',0,0,0,R,0,0,107),&
 chch_t1(114,'GLY       ',1,'TR        ','          ',0,1,0,R,0,0,107),&
-chch_t1(115,'oXYLENE   ',1,'TR        ','          ',0,0,1,R,0,0,107)/)
+chch_t1(115,'oXYLENE   ',1,'TR        ','          ',0,0,1,R,0,0,107),&
+chch_t1(116,'ALICE     ',1,'TR        ','          ',0,0,0,ST,0,0,107),&
+chch_t1(117,'BOB       ',1,'TR        ','          ',0,0,0,ST,0,0,107)/)
 
 ! Heterogeneous chemistry
 ! Columns take the following meanings:
Index: src/atmosphere/UKCA/ukca_constants.F90
===================================================================
--- src/atmosphere/UKCA/ukca_constants.F90	(revision 46527)
+++ src/atmosphere/UKCA/ukca_constants.F90	(revision 46535)
@@ -272,6 +272,10 @@
 REAL, PARAMETER :: c_isosvoc2   = 2.3473   ! as C5H8
 REAL, PARAMETER :: c_isosoa     = 4.4874   ! 130.0
 
+! UKCA Tutorial Tracers:
+REAL, PARAMETER :: c_ALICE      = 1.0000
+REAL, PARAMETER :: c_BOB        = 1.0000
+
 !     molecular masses in g/mol of emitted species,
 !     for budget calculations
 REAL, PARAMETER :: m_ho2     =  33.007
Index: src/atmosphere/UKCA/ukca_nmspec_mod.F90
===================================================================
--- src/atmosphere/UKCA/ukca_nmspec_mod.F90	(revision 46527)
+++ src/atmosphere/UKCA/ukca_nmspec_mod.F90	(revision 46535)
@@ -86,7 +86,7 @@
 'BrO       ','BrCl      ','BrONO2    ','N2O       ','HCl       ',  & !50
 'HOCl      ','HBr       ','HOBr      ','ClONO2    ','CFCl3     ',  &
 'CF2Cl2    ','MeBr      ','N         ','O(3P)     ','MACRO2    ',  & !60
-'MeCl      ','CF2ClBr   ','CCl4      ','CF2ClCFCl2','CHF2Cl    ',  &
+'MeCl      ','CF2ClBr   ','CCl4      ','ALICE     ','BOB       ',  &
 'MeCCl3    ','CF3Br     ','H2OS      ','CH2Br2    ','H2        ',  & !70
 'DMS       ','SO2       ','H2SO4     ','MSA       ','DMSO      ',  &
 'NH3       ','CS2       ','COS       ','H2S       ','H         ',  & !80
Index: src/atmosphere/UKCA/ukca_cspecies.F90
===================================================================
--- src/atmosphere/UKCA/ukca_cspecies.F90	(revision 46527)
+++ src/atmosphere/UKCA/ukca_cspecies.F90	(revision 46535)
@@ -296,6 +296,9 @@
 WHERE (advt == 'ORGNIT    ') c_species = c_orgnit
 WHERE (advt == 'PASSIVE O3') c_species = 1.0
 WHERE (advt == 'AGE OF AIR') c_species = 1.0
+! UKCA Tutorial Tracers:
+WHERE (advt == 'ALICE     ') c_species = c_ALICE
+WHERE (advt == 'BOB       ') c_species = c_BOB
 
 ! non-advected tracers
 c_na_species=0.0
Index: rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf
===================================================================
--- rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf	(revision 46527)
+++ rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf	(revision 46535)
@@ -16215,6 +16215,14 @@
 description=O3P MASS MIXING RATIO AFTER TIMESTEP
 help=Oxygen atom (ground state) Mass Mixing Ratio in kg/kg(Air)
 
+[stashmaster:code(34064)]
+description=ALICE MASS MIXING RATIO AFTER TIMESTEP
+help=UKCA Tutorial Tracer ALICE Mass Mixing Ratio in kg/kg(Air)
+
+[stashmaster:code(34065)]
+description=BOB MASS MIXING RATIO AFTER TIMESTEP
+help=UKCA Tutorial Tracer BOB Mass Mixing Ratio in kg/kg(Air)
+
 [stashmaster:code(34070)]
 description=H2 MASS MIXING RATIO AFTER TIMESTEP
 help=Hydrogen Mass Mixing Ratio in kg/kg(Air)
@@ -22480,6 +22488,16 @@
 description=O3P MASS MIXING RATIO ON PRESS LEVS
 help=Oxygen atom (ground state) Mass Mixing Ratio in kg/kg(Air)
 
+[stashmaster:code(51064)]
+description=ALICE MASS MIXING RATIO AFTER TIMESTEP
+help=UKCA Tutorial Tracer ALICE Mass Mixing Ratio in kg/kg(Air)
+    =on pressure levels
+
+[stashmaster:code(51065)]
+description=BOB MASS MIXING RATIO AFTER TIMESTEP
+help=UKCA Tutorial Tracer BOB Mass Mixing Ratio in kg/kg(Air)
+    =on pressure levels
+
 [stashmaster:code(51070)]
 description=H2 MASS MIXING RATIO ON PRESS LEVS
 help=Hydrogen Mass Mixing Ratio in kg/kg(Air)
Index: rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A
===================================================================
--- rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A	(revision 46527)
+++ rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A	(revision 46535)
@@ -15942,6 +15942,18 @@
 4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |
 5|    0 | 2160 |    0 |   65 |    0 |    0 |    0 |    0 |    0 |
 #
+1|    1 |   34 |   64 |ALICE MASS MIXING RATIO AFTER TSTEP |
+2|    2 |    0 |    1 |    1 |    2 |   40 |   11 |    0 |    0 |    0 |    0 |
+3| 000000000000000000000000010000 | 00000000000000000001 |    1 |
+4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |
+5|    0 | 2164 |    0 |   65 |    0 |    0 |    0 |    0 |    0 |
+#
+1|    1 |   34 |   65 |BOB MASS MIXING RATIO AFTER TSTEP   |
+2|    2 |    0 |    1 |    1 |    2 |   40 |   11 |    0 |    0 |    0 |    0 |
+3| 000000000000000000000000010000 | 00000000000000000001 |    1 |
+4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |
+5|    0 | 2165 |    0 |   65 |    0 |    0 |    0 |    0 |    0 |
+#
 1|    1 |   34 |   69 |CH3OH MASS MIXING RATIO AFTER TS    |
 2|    2 |    0 |    1 |    1 |    2 |   40 |   11 |    0 |    0 |    0 |    0 |
 3| 000000000000000000000000000100 | 00000000000000000001 |    1 |
@@ -24580,6 +24592,18 @@
 4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |
 5|    0 | 2160 |    0 |    8 |    0 |    0 |    0 |    0 |    0 |
 #
+1|    1 |   51 |   64 |ALICE MMR ON PRESSURE LEVELS        |
+2|    0 |    0 |    1 |    1 |    3 |    1 |    2 |    0 |    0 |    0 |    1 |
+3| 000000000000000000000000010000 | 00000000000000000001 |    3 |
+4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |
+5|    0 | 2164 |    0 |    8 |    0 |    0 |    0 |    0 |    0 |
+#
+1|    1 |   51 |   65 |BOB MMR ON PRESSURE LEVELS          |
+2|    0 |    0 |    1 |    1 |    3 |    1 |    2 |    0 |    0 |    0 |    1 |
+3| 000000000000000000000000010000 | 00000000000000000001 |    3 |
+4|    1 |    0 | -99  -99  -99  -99  -99  -99  -99  -99  -99  -99 |
+5|    0 | 2165 |    0 |    8 |    0 |    0 |    0 |    0 |    0 |
+#
 1|    1 |   51 |   69 |CH3OH MASS MIX RATIO ON PRESS LEVS  |
 2|    0 |    0 |    1 |    1 |    3 |    1 |    2 |    0 |    0 |    0 |    1 |
 3| 000000000000000000000000000100 | 00000000000000000001 |    3 |

These differences can be found in the file /home/ukca/Tutorial/vn10.9/worked_solutions/Task4.1/Task4.1_code.patch on PUMA.

If you open the .pa file in Xconv, you should see the following fields:

 7    : 96   72   38    1     field2164: Stash code = 34064
 8    : 96   72   38    1     field2165: Stash code = 34065

Sample output from this task can be found at /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task4.1/atmosa.pa19810901_00 on ARCHER.

Checklist

☐ If required, copy an appropriate Rose suite to use to test your changes.

☐ Make a new ticket on the Met Office SRS Trac pages.

☐ Make a branch at the required MetUM version using fcm branch-create.

☐ Checkout your branch using fcm checkout.

☐ Choose slots for your new tracer(s) from the list in ukca_set_nmspec.F90, and add the correct names for them in these slots.

☐ Add the tracer(s) to the chch_defs_strattrop array in ukca_chem_master.F90.

☐ Increase the value of n_chem_tracers in ukca_setd1defs.F90.

☐ Add a C_species value for each tracer in ukca_constants.F90.

☐ Append the CASE statement in ukca_cspecies.F90 to add this value to the c_species array.

☐ fcm commit the changes to your branch.

☐ Make the required changes to branch's STASHmaster_A file, to add the new tracers.

☐ Add help text for your tracers in your branch's STASHmaster-meta.conf file.

☐ Using a text editor, open the app/um/rose-app.conf file from your roses/[SUITE-ID] directory, and add the line STASHMASTER=STASHmaster in the [env] block, then save and close the file.

☐ Using a text editor, open the rose-suite.conf file from your roses/[SUITE-ID] directory, and add the following lines to the top of the file, before saving and closing it:

[file:app/um/file/STASHmaster]
source=fcm:um.xm_br/dev/[your MOSRS userid]/vnX.Y_your_branch_name/rose-meta/um-atmos/HEAD/etc/stash/STASHmaster@HEAD

☐ Edit your suite using rose edit -M /path/to/your/branch/working/copy.

☐ Point the metadata in your suite to um-atmos/HEAD.

☐ Include your branch in your suite at: fcm_make

\rightarrow

env

\rightarrow

Sources.

☐ Initialise your tracers in your suite at: um

\rightarrow

namelist

\rightarrow

Reconfiguration and Ancillary Control

\rightarrow

Configure ancils and initialise dump fields.

☐ Output your tracers in STASH at: um

\rightarrow

namelist

\rightarrow

Model Input and Output

\rightarrow

STASH Requests and Profiles

\rightarrow

STASH Requests.

☐ Run the TidyStashTransform transform macro.

☐ Save your suite.

☐ In the roses/[SUITE-ID] directory, run fcm commit to commit your changes to the repository.

☐ Run your suite.

Tutorial 5

Written by Luke Abraham 2017

@@ Line 33: / Line 33: @@
 ====Using your new metadata within Rose====
-To pick-up the metadata changes, you should edit the '''meta''' path in '''um''' to point to
+To pick-up the metadata changes, you should make sure that the '''meta''' path in '''um''' points to
- um-atmos/HEAD
+ um-atmos/vn10.9
+If you were making changes to commit to the trunk, you would use <code>um-atmos/HEAD</code>, but here we will use <code>um-atmos/vn10.9</code>.
 From now on, when you want to open your Rose suite for editing, instead of doing it through rosie, you should instead open the job for editing by going to your <code>$HOME/roses/'''[SUITE-ID]'''</code> directory, and opening it using the command