UKCA - User contributions [en]

UKCA

2026-07-10T12:41:40Z

Nla27:

Minutes of the code management group meeting 2026-07-09

2026-07-09T10:06:55Z

Nla27:

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 9th July 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:''' MS, MD, AJH, AJ

'''Cambridge:''' NLA, RW

'''Leeds:''' DG, MR

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:''' PMJ

'''NEXT MEETING WILL BE THURSDAY 10TH SEPTEMBER 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke. Coding needed to get changes in. Have a way forward.
#* DG hasn't had time due to UKESM1.3 etc. After Summer should have more time.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it. AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September.
#* AJH may put the 2 things together. At the moment are word documents. Lfric_apps documentation is moving along slowly and there are a lot of gaps, but is in markdown (.md) format. Should move science into UKCA, then smaller docs in UM and lfric_apps for interface documentation.
#* MR - readthedocs might be better received by the academic community.
#* RW - should be hosted in UKCA - GitHub good at doing static documentation that can be rebuilt in Actions.
#* AJ - ACP 'living papers'?
#* Split into 2 actions - RADAER API (AJH) and wider documentation more generally (??)
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (ongoing) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
#* MD: GitHub user guide for Monsoon – the Monsoon3 user guide is linked from the ‘Community’ tab on Monsoon Teams channel: [https://code.metoffice.gov.uk/doc/monsoon3/github.html GitHub — Monsoon3 User Guide 1.0 documentation]
#* '''closed'''
# (ongoing) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified. Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing.
#* MD has asked May Chim whether she would be able to add the fix over the summer after the expected release.
#* ongoing
# (ongoing) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
#* periodic exercise - '''closed'''
# (ongoing) AJH, MD, and PMJ to discuss method for checking diagnostic KGOs with NetCDF files.
#* AJH has been assisting the AQ team with some issues. Will catch-up with PMJ offline.
#* ongoing

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

RW is kindly doing the VM partner testing this release (UM14.2).

Matt Naylor is developing 3D chunking.

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|| 161 || Error using diagnostic 50-332 with chem version 132 ("RXN NOT FOUND J H2SO4 PHOTON -> SO3 OH") || || || Mohit says "I believe this means that for chem_schemes=121+ the reaction no longer yields just SO3 and OH? This would mean that there is a bug in asad_flux_dat where this extra product is not included in set of reactions for chem_scheme 121+." For 121+ the reaction now also yields H as well as SO3 and OH (see ukca_chem_master). Found in vn13.9 || DG tried to turn it on but it didn't work. Potentially do with '''#128'''
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| ||
|-
|}

MR - Helen Burns has been working with paeloscientists - may have found a bug, will investigate and may report it.

== A.O.B. & D.N.M. (NLA) ==

Please fill in the UKESM survey: https://forms.gle/KB9QJQEwJys2BSgWA

Please fill the NERC/UKRI Atmospheric Science Forward Look review form: https://engagementhub.ukri.org/nerc-research-and-skills-directorate/atmospheric-science-forward-look/

Minutes of the code management group meeting 2026-07-09

2026-07-09T09:59:48Z

Nla27:

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 9th July 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:''' MS, MD, AJH, AJ

'''Cambridge:''' NLA, RW

'''Leeds:''' DG, MR

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:''' PMJ

'''NEXT MEETING WILL BE THURSDAY 10TH SEPTEMBER 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke. Coding needed to get changes in. Have a way forward.
#* DG hasn't had time due to UKESM1.3 etc. After Summer should have more time.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it. AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September.
#* AJH may put the 2 things together. At the moment are word documents. Lfric_apps documentation is moving along slowly and there are a lot of gaps, but is in markdown (.md) format. Should move science into UKCA, then smaller docs in UM and lfric_apps for interface documentation.
#* MR - readthedocs might be better received by the academic community.
#* RW - should be hosted in UKCA - GitHub good at doing static documentation that can be rebuilt in Actions.
#* AJ - ACP 'living papers'?
#* Split into 2 actions - RADAER API (AJH) and wider documentation more generally (??)
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (ongoing) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
#* MD: GitHub user guide for Monsoon – the Monsoon3 user guide is linked from the ‘Community’ tab on Monsoon Teams channel: [https://code.metoffice.gov.uk/doc/monsoon3/github.html GitHub — Monsoon3 User Guide 1.0 documentation]
#* '''closed'''
# (ongoing) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified. Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing.
#* MD has asked May Chim whether she would be able to add the fix over the summer after the expected release.
#* ongoing
# (ongoing) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
#* periodic exercise - '''closed'''
# (ongoing) AJH, MD, and PMJ to discuss method for checking diagnostic KGOs with NetCDF files.
#* AJH has been assisting the AQ team with some issues. Will catch-up with PMJ offline.
#* ongoing

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

RW is kindly doing the VM partner testing this release (UM14.2).

Matt Naylor is developing 3D chunking.

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|| 161 || Error using diagnostic 50-332 with chem version 132 ("RXN NOT FOUND J H2SO4 PHOTON -> SO3 OH") || || || Mohit says "I believe this means that for chem_schemes=121+ the reaction no longer yields just SO3 and OH? This would mean that there is a bug in asad_flux_dat where this extra product is not included in set of reactions for chem_scheme 121+." For 121+ the reaction now also yields H as well as SO3 and OH (see ukca_chem_master). Found in vn13.9 || DG tried to turn it on but it didn't work. Potentially do with '''#128'''
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| ||
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Please fill in the UKESM survey: https://forms.gle/KB9QJQEwJys2BSgWA

Minutes of the code management group meeting 2026-07-09

2026-07-09T08:58:27Z

Nla27:

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 9th July 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:'''

'''Cambridge:'''

'''Leeds:'''

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:''' PMJ

'''NEXT MEETING WILL BE THURSDAY 10TH SEPTEMBER 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke. Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it. AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (ongoing) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
#* MD: GitHub user guide for Monsoon – the Monsoon3 user guide is linked from the ‘Community’ tab on Monsoon Teams channel: [https://code.metoffice.gov.uk/doc/monsoon3/github.html GitHub — Monsoon3 User Guide 1.0 documentation]
# (ongoing) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified. Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing.
#* MD has asked May Chim whether she would be able to add the fix over the summer after the expected release.
# (ongoing) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
# (ongoing) AJH, MD, and PMJ to discuss method for checking diagnostic KGOs with NetCDF files.

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|| 161 || rror using diagnostic 50-332 with chem version 132 ("RXN NOT FOUND J H2SO4 PHOTON -> SO3 OH") || || || Mohit says "I believe this means that for chem_schemes=121+ the reaction no longer yields just SO3 and OH? This would mean that there is a bug in asad_flux_dat where this extra product is not included in set of reactions for chem_scheme 121+." For 121+ the reaction now also yields H as well as SO3 and OH (see ukca_chem_master). Found in vn13.9 ||
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| ||
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-07-09

2026-07-09T08:57:39Z

Nla27:

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 9th July 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:'''

'''Cambridge:'''

'''Leeds:'''

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:''' PMJ

'''NEXT MEETING WILL BE THURSDAY 10TH SEPTEMBER 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke. Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it. AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (ongoing) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
#* MD: GitHub user guide for Monsoon – the Monsoon3 user guide is linked from the ‘Community’ tab on Monsoon Teams channel: [https://code.metoffice.gov.uk/doc/monsoon3/github.html GitHub — Monsoon3 User Guide 1.0 documentation]
# (ongoing) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified. Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testingChim whether she would be able to add the fix over the summer after the expected release.
# (ongoing) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
# (ongoing) AJH, MD, and PMJ to discuss method for checking diagnostic KGOs with NetCDF files.

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|| 161 || rror using diagnostic 50-332 with chem version 132 ("RXN NOT FOUND J H2SO4 PHOTON -> SO3 OH") || || || Mohit says "I believe this means that for chem_schemes=121+ the reaction no longer yields just SO3 and OH? This would mean that there is a bug in asad_flux_dat where this extra product is not included in set of reactions for chem_scheme 121+." For 121+ the reaction now also yields H as well as SO3 and OH (see ukca_chem_master). Found in vn13.9 ||
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| ||
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Code management group minutes

2026-07-07T09:16:05Z

Nla27:

* [[Minutes_of_the_code_management_group_meeting_15/5/2012|Minutes of meeting held 15/5/2012 in Cambridge]]
* [[Minutes_of_the_code_management_group_meeting_19/7/2012|Minutes of teleconference meeting held 19/7/2012]]
* [http://www.ukca.ac.uk/wiki/images/b/b5/UKCA_CMG_06Sept2012_final_3.pdf Minutes of teleconference meeting held 06/9/2012] ([[File:UKCA_CMG_06Sept2012_final_3.pdf]])
* [[Code management group minutes 24Oct2012|Minutes of the meeting held on 24th Oct 2012]]
* [[Code management group minutes 4Dec2012|Minutes of the meeting held on 4 Dec 2012]]
* [[Notes_of_the_code_management_group_meeting_21/3/2013|Notes of the code management group meeting 21/3/2013]]
* [[Minutes_of_the_code_management_group_meeting_22/5/2013|Minutes of teleconference meeting held on 22/5/2013]]
* [[Minutes_of_the_code_management_group_meeting_9/7/2013|Minutes of teleconference meeting held on 9/7/2013]]
* [[Minutes_of_the_code_management_group_meeting_3/9/2013|Minutes of teleconference meeting held on 3/9/2013]]
* [[Minutes_of_the_code_management_group_meeting_17/10/2013|Minutes of teleconference meeting held on 17/10/2013]]
* [[Minutes_of_the_code_management_group_meeting_14/02/2014|Minutes of teleconference meeting held on 14/02/2014]]
* [[Actions_from_the_code_management_group_meeting_18/03/2014|Actions from teleconference meeting held on 18/03/2014]]
* [[Minutes_of_the_code_management_group_meeting_26/06/2014|Minutes from teleconference meeting held on 26/06/2014]]
* [[Minutes_of_the_code_management_group_meeting_16/09/2014|Minutes from teleconference meeting held on 16/09/2014]]
* [[Minutes of the code management group meeting 11/12/2014]]
* [[Minutes of the code management group meeting 2015-03-04]]
* [[Minutes of the code management group meeting 2015-04-23: LFRic Coupling]]
* [[Minutes of the code management group meeting 2015-05-06]]
* [[Minutes of the code management group meeting 2015-09-18]]
* [[Minutes of the code management group meeting 2016-01-12]]
* [[Minutes of the code management group meeting 2016-07-22]]
* [[Minutes of the code management group meeting 2016-09-23]]
* [[Minutes of the code management group meeting 2017-07-14]]
* [[Minutes of the code management group meeting 2017-10-19]]
* [[Minutes of the code management group meeting 2018-02-21]]
* [[Minutes of the code management group meeting 2018-04-17]] ({{pdf|jwcrp_workplan_v1.pdf|JWCRP Workplan}})
* [[Minutes of the code management group meeting 2018-06-19]]
* [[Minutes of the code management group meeting 2018-09-05]]
* [[Minutes of the code management group meeting 2018-11-12]]
* [[Minutes of the code management group meeting 2019-01-25]]
* [[Minutes of the code management group meeting 2019-04-01]]
* [[Minutes of the code management group meeting 2019-06-13]]
* [[Minutes of the code management group meeting 2019-09-16]]
* [[Minutes of the code management group meeting 2019-11-04]]
* [[Minutes of the code management group meeting 2020-01-14]]
* [[Minutes of the code management group meeting 2020-03-20]]
* [[Minutes of the code management group meeting 2020-05-05]]
* [[Minutes of the code management group meeting 2020-09-11]]
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[[Category:Minutes]]

Minutes of the code management group meeting 2026-07-10

2026-07-07T09:15:48Z

Nla27: Nla27 moved page Minutes of the code management group meeting 2026-07-10 to Minutes of the code management group meeting 2026-07-09

#REDIRECT [[Minutes of the code management group meeting 2026-07-09]]

Minutes of the code management group meeting 2026-07-09

2026-07-07T09:15:48Z

Nla27: Nla27 moved page Minutes of the code management group meeting 2026-07-10 to Minutes of the code management group meeting 2026-07-09

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 9th July 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:'''

'''Cambridge:'''

'''Leeds:'''

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 10TH SEPTEMBER 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke. Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it. AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (ongoing) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
# (ongoing) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified. Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (ongoing) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
# (ongoing) AJH, MD, and PMJ to discuss method for checking diagnostic KGOs with NetCDF files.

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|| 161 || rror using diagnostic 50-332 with chem version 132 ("RXN NOT FOUND J H2SO4 PHOTON -> SO3 OH") || || || Mohit says "I believe this means that for chem_schemes=121+ the reaction no longer yields just SO3 and OH? This would mean that there is a bug in asad_flux_dat where this extra product is not included in set of reactions for chem_scheme 121+." For 121+ the reaction now also yields H as well as SO3 and OH (see ukca_chem_master). Found in vn13.9 ||
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| ||
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-07-09

2026-07-07T09:14:18Z

Nla27:

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 9th July 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:'''

'''Cambridge:'''

'''Leeds:'''

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 10TH SEPTEMBER 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke. Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it. AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (ongoing) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
# (ongoing) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified. Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (ongoing) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
# (ongoing) AJH, MD, and PMJ to discuss method for checking diagnostic KGOs with NetCDF files.

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|| 161 || rror using diagnostic 50-332 with chem version 132 ("RXN NOT FOUND J H2SO4 PHOTON -> SO3 OH") || || || Mohit says "I believe this means that for chem_schemes=121+ the reaction no longer yields just SO3 and OH? This would mean that there is a bug in asad_flux_dat where this extra product is not included in set of reactions for chem_scheme 121+." For 121+ the reaction now also yields H as well as SO3 and OH (see ukca_chem_master). Found in vn13.9 ||
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| ||
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-07-09

2026-07-07T09:13:38Z

Nla27: /* Issues/PRs */

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 9th July 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:'''

'''Cambridge:'''

'''Leeds:'''

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 10TH SEPTEMBER 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke. Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it. AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (ongoing) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
# (ongoing) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified. Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (ongoing) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
# (ongoing) AJH, MD, and PMJ to discuss method for checking diagnostic KGOs with NetCDF files.

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|| 161 || rror using diagnostic 50-332 with chem version 132 ("RXN NOT FOUND J H2SO4 PHOTON -> SO3 OH") || || || Mohit says "I believe this means that for chem_schemes=121+ the reaction no longer yields just SO3 and OH? This would mean that there is a bug in asad_flux_dat where this extra product is not included in set of reactions for chem_scheme 121+." For 121+ the reaction now also yields H as well as SO3 and OH (see ukca_chem_master). Found in vn13.9 ||
|-
|}

DG - small bug in STASH diagnostics at chem version 132

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

PMJ - looking to send full domain and use ASAD/NR for RAQ, but taking time. Want to be able to use parallelisations there.

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

AJH hasn't got microplastics rose-stem test working yet, will make time later. Is not sure what is going on. CH can provide input on that.

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| ||
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-07-09

2026-07-07T09:13:12Z

Nla27: Created page with "Code management group minutes ==Teleconference Details== '''Thursday 9th July 2026, 10.00am - 11.30am GMT''' '''Meeting via Teams - see link in calendar invitation''' '''Met Office:''' '''Cambridge:''' '''Leeds:''' '''Canterbury:''' '''CSIRO:''' '''Apologies:''' '''NEXT MEETING WILL BE THURSDAY 10TH SEPTEMBER 2026, 10.00-11.30 GMT''' == Actions from this meeting == == Actions from the Last Meeting == # (ongoing) GM/..."

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 9th July 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:'''

'''Cambridge:'''

'''Leeds:'''

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 10TH SEPTEMBER 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke. Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it. AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (ongoing) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
# (ongoing) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified. Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (ongoing) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
# (ongoing) AJH, MD, and PMJ to discuss method for checking diagnostic KGOs with NetCDF files.

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

Generally, people have found GitHub OK to work with, but found trac easier to navigate.

* Need to be on reviewers list to be able to make edits to other PRs and also add links. AJH to contact SSD team. May be due to UKCA being BSD-3 and open source. Could perhaps make a change to the CONTRIBUTORS.md and then add people to be able to edit once that has been done.

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|| 161 || rror using diagnostic 50-332 with chem version 132 ("RXN NOT FOUND J H2SO4 PHOTON -> SO3 OH") || || || Mohit says "I believe this means that for chem_schemes=121+ the reaction no longer yields just SO3 and OH? This would mean that there is a bug in asad_flux_dat where this extra product is not included in set of reactions for chem_scheme 121+." For 121+ the reaction now also yields H as well as SO3 and OH (see ukca_chem_master). Found in vn13.9 ||
|-
|}

DG - small bug in STASH diagnostics at chem version 132

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

PMJ - looking to send full domain and use ASAD/NR for RAQ, but taking time. Want to be able to use parallelisations there.

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

AJH hasn't got microplastics rose-stem test working yet, will make time later. Is not sure what is going on. CH can provide input on that.

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| ||
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Code management group minutes

2026-07-07T09:04:17Z

Nla27:

Minutes of the code management group meeting 2026-05-14

2026-05-14T10:51:56Z

Nla27: /* Actions from this meeting */

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 14th May 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:''' MS, MD, AJH, PMJ, JCK,

'''Cambridge:''' LA, RW

'''Leeds:''' DG

'''Canterbury:''' CH

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke. Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it. AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (ongoing) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
# (ongoing) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified. Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (ongoing) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
# (ongoing) AJH, MD, and PMJ to discuss method for checking diagnostic KGOs with NetCDF files.

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke.
#* Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it.
#* AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
#* Ongoing
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
#* Ongoing
# (this happened - not sure if follow up is required) NLA to mention MASS issues at the next MMG
#* Waiting for new MASS
# (new) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
#* Ongoing
# (new) AJH to request UKCA tags for lfric_apps and UM , so that we are able to keep track of all UKCA GitHub pull requests and issues at the next CMG meeting.
#* Closed - done
# (new) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified.
#* Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (new) AJH has contacted the LFRic core team to inform them of the obsolete instructions for building lfric core with FCM.
#* There may be an automated system for making instructions.
#* Closed
# (new) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
#* Ongoing
# (new) AJH and Pedro to discuss method for checking diagnostic KGOs with NetCDF files.
#* AJH, MD, PMJ to catch-up offline
#* ongoing

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

Generally, people have found GitHub OK to work with, but found trac easier to navigate.

* Need to be on reviewers list to be able to make edits to other PRs and also add links. AJH to contact SSD team. May be due to UKCA being BSD-3 and open source. Could perhaps make a change to the CONTRIBUTORS.md and then add people to be able to edit once that has been done.

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 155 || OMP dynamic scheduling race condition || [https://code.metoffice.gov.uk/trac/ukca/ticket/321 ukca:#321] || || When using OpenMP with dynamic, as opposed to the standard static, scheduling, checksums were failing with lfric_apps. This indicates a race condition likely within the ASAD chemical package and so would affect the UM as well as LFRic. Further testing is needed. AJH will make some time to run it with the thread santizer || RW to double-check notes - bug we introduced. Can be '''closed'''. Need LFRic tests with dynamic scheduling.
|-
|| 156 || Bug in Lfric copy of ''ukca_volcanic_so2'', <tt>true_latitude, true_longitude</tt> used without allocating. Fails on ARCHER2 with CCE compiler || [https://github.com/MetOffice/lfric_apps/pull/133 lfric_apps:PR133] || Mohit Dalvi || Since lfric_apps-vn2.2 Temporarily allocate ''true-latitude'', ''true_longitude'', ''weight_volc_vertdist'' [https://code.metoffice.gov.uk/trac/lfric_apps/changeset/9670/main/trunk/interfaces/physics_schemes_interface/source/legacy/ukca_interface/ukca_volcanic_so2.F90 lfric_apps:#965] removed UM dependencies i.e. ''trignometric_mod'' without providing alternative source for the arrays || Fixed in LFRic, CLOSE - UM below.
|-
|| 157 || Bug in calculation of aerosol AOD from LFRic || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/1089 lfric_apps:#1089] GitHub [https://github.com/MetOffice/lfric_apps/issues/41 lfric_apps:#41] || Alan J Hewitt || Since lfric vn2.2 FCM [https://code.metoffice.gov.uk/trac/lfric_apps/log/main/branches/dev/alanjhewitt/git_migration_AOD_bug git_migration_AOD_bug] Github [https://github.com/alanjhewitt/lfric_apps/tree/AOD_bug AOD_bug] aerosol AOD was developed in [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/440 lfric_apps:#440] and it looked fine at low resolution. Running at high resolution identified an addressing error. Fix has been developed and will be in review for Jan 2026 deadline. || Closed
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|}

DG - small bug in STASH diagnostics at chem version 132

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

PMJ - looking to send full domain and use ASAD/NR for RAQ, but taking time. Want to be able to use parallelisations there.

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

AJH hasn't got microplastics rose-stem test working yet, will make time later. Is not sure what is going on. CH can provide input on that.

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| NLA || NLA & RW are submitting to SSI RSMF for the Box Model
|-
|| AJH || LFRic PS49 milestone including aerosols (GLOMAP), deadline is Summer 2027. Lots of different groups now interested. Might be aiming to turn off the UM at the start of 2028.
|-
|}

== A.O.B. & D.N.M. (NLA) ==

DG - UKCA meeting in July.

Minutes of the code management group meeting 2026-05-14

2026-05-14T10:51:43Z

Nla27:

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 14th May 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:''' MS, MD, AJH, PMJ, JCK,

'''Cambridge:''' LA, RW

'''Leeds:''' DG

'''Canterbury:''' CH

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke. Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it. AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (ongoing) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
#* Ongoing
# (ongoing) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified. Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (ongoing) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
# (ongoing) AJH, MD, and PMJ to discuss method for checking diagnostic KGOs with NetCDF files.

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke.
#* Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it.
#* AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
#* Ongoing
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
#* Ongoing
# (this happened - not sure if follow up is required) NLA to mention MASS issues at the next MMG
#* Waiting for new MASS
# (new) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
#* Ongoing
# (new) AJH to request UKCA tags for lfric_apps and UM , so that we are able to keep track of all UKCA GitHub pull requests and issues at the next CMG meeting.
#* Closed - done
# (new) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified.
#* Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (new) AJH has contacted the LFRic core team to inform them of the obsolete instructions for building lfric core with FCM.
#* There may be an automated system for making instructions.
#* Closed
# (new) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
#* Ongoing
# (new) AJH and Pedro to discuss method for checking diagnostic KGOs with NetCDF files.
#* AJH, MD, PMJ to catch-up offline
#* ongoing

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

Generally, people have found GitHub OK to work with, but found trac easier to navigate.

* Need to be on reviewers list to be able to make edits to other PRs and also add links. AJH to contact SSD team. May be due to UKCA being BSD-3 and open source. Could perhaps make a change to the CONTRIBUTORS.md and then add people to be able to edit once that has been done.

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 155 || OMP dynamic scheduling race condition || [https://code.metoffice.gov.uk/trac/ukca/ticket/321 ukca:#321] || || When using OpenMP with dynamic, as opposed to the standard static, scheduling, checksums were failing with lfric_apps. This indicates a race condition likely within the ASAD chemical package and so would affect the UM as well as LFRic. Further testing is needed. AJH will make some time to run it with the thread santizer || RW to double-check notes - bug we introduced. Can be '''closed'''. Need LFRic tests with dynamic scheduling.
|-
|| 156 || Bug in Lfric copy of ''ukca_volcanic_so2'', <tt>true_latitude, true_longitude</tt> used without allocating. Fails on ARCHER2 with CCE compiler || [https://github.com/MetOffice/lfric_apps/pull/133 lfric_apps:PR133] || Mohit Dalvi || Since lfric_apps-vn2.2 Temporarily allocate ''true-latitude'', ''true_longitude'', ''weight_volc_vertdist'' [https://code.metoffice.gov.uk/trac/lfric_apps/changeset/9670/main/trunk/interfaces/physics_schemes_interface/source/legacy/ukca_interface/ukca_volcanic_so2.F90 lfric_apps:#965] removed UM dependencies i.e. ''trignometric_mod'' without providing alternative source for the arrays || Fixed in LFRic, CLOSE - UM below.
|-
|| 157 || Bug in calculation of aerosol AOD from LFRic || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/1089 lfric_apps:#1089] GitHub [https://github.com/MetOffice/lfric_apps/issues/41 lfric_apps:#41] || Alan J Hewitt || Since lfric vn2.2 FCM [https://code.metoffice.gov.uk/trac/lfric_apps/log/main/branches/dev/alanjhewitt/git_migration_AOD_bug git_migration_AOD_bug] Github [https://github.com/alanjhewitt/lfric_apps/tree/AOD_bug AOD_bug] aerosol AOD was developed in [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/440 lfric_apps:#440] and it looked fine at low resolution. Running at high resolution identified an addressing error. Fix has been developed and will be in review for Jan 2026 deadline. || Closed
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|}

DG - small bug in STASH diagnostics at chem version 132

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

PMJ - looking to send full domain and use ASAD/NR for RAQ, but taking time. Want to be able to use parallelisations there.

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

AJH hasn't got microplastics rose-stem test working yet, will make time later. Is not sure what is going on. CH can provide input on that.

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| NLA || NLA & RW are submitting to SSI RSMF for the Box Model
|-
|| AJH || LFRic PS49 milestone including aerosols (GLOMAP), deadline is Summer 2027. Lots of different groups now interested. Might be aiming to turn off the UM at the start of 2028.
|-
|}

== A.O.B. & D.N.M. (NLA) ==

DG - UKCA meeting in July.

Minutes of the code management group meeting 2026-05-14

2026-05-14T10:49:57Z

Nla27:

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 14th May 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:''' MS, MD, AJH, PMJ, JCK,

'''Cambridge:''' LA, RW

'''Leeds:''' DG

'''Canterbury:''' CH

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke.
#* Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it.
#* AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
#* Ongoing
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
#* Ongoing
# (this happened - not sure if follow up is required) NLA to mention MASS issues at the next MMG
#* Waiting for new MASS
# (new) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
#* Ongoing
# (new) AJH to request UKCA tags for lfric_apps and UM , so that we are able to keep track of all UKCA GitHub pull requests and issues at the next CMG meeting.
#* Closed - done
# (new) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified.
#* Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (new) AJH has contacted the LFRic core team to inform them of the obsolete instructions for building lfric core with FCM.
#* There may be an automated system for making instructions.
#* Closed
# (new) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
#* Ongoing
# (new) AJH and Pedro to discuss method for checking diagnostic KGOs with NetCDF files.
#* AJH, MD, PMJ to catch-up offline
#* ongoing

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

Generally, people have found GitHub OK to work with, but found trac easier to navigate.

* Need to be on reviewers list to be able to make edits to other PRs and also add links. AJH to contact SSD team. May be due to UKCA being BSD-3 and open source. Could perhaps make a change to the CONTRIBUTORS.md and then add people to be able to edit once that has been done.

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 155 || OMP dynamic scheduling race condition || [https://code.metoffice.gov.uk/trac/ukca/ticket/321 ukca:#321] || || When using OpenMP with dynamic, as opposed to the standard static, scheduling, checksums were failing with lfric_apps. This indicates a race condition likely within the ASAD chemical package and so would affect the UM as well as LFRic. Further testing is needed. AJH will make some time to run it with the thread santizer || RW to double-check notes - bug we introduced. Can be '''closed'''. Need LFRic tests with dynamic scheduling.
|-
|| 156 || Bug in Lfric copy of ''ukca_volcanic_so2'', <tt>true_latitude, true_longitude</tt> used without allocating. Fails on ARCHER2 with CCE compiler || [https://github.com/MetOffice/lfric_apps/pull/133 lfric_apps:PR133] || Mohit Dalvi || Since lfric_apps-vn2.2 Temporarily allocate ''true-latitude'', ''true_longitude'', ''weight_volc_vertdist'' [https://code.metoffice.gov.uk/trac/lfric_apps/changeset/9670/main/trunk/interfaces/physics_schemes_interface/source/legacy/ukca_interface/ukca_volcanic_so2.F90 lfric_apps:#965] removed UM dependencies i.e. ''trignometric_mod'' without providing alternative source for the arrays || Fixed in LFRic, CLOSE - UM below.
|-
|| 157 || Bug in calculation of aerosol AOD from LFRic || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/1089 lfric_apps:#1089] GitHub [https://github.com/MetOffice/lfric_apps/issues/41 lfric_apps:#41] || Alan J Hewitt || Since lfric vn2.2 FCM [https://code.metoffice.gov.uk/trac/lfric_apps/log/main/branches/dev/alanjhewitt/git_migration_AOD_bug git_migration_AOD_bug] Github [https://github.com/alanjhewitt/lfric_apps/tree/AOD_bug AOD_bug] aerosol AOD was developed in [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/440 lfric_apps:#440] and it looked fine at low resolution. Running at high resolution identified an addressing error. Fix has been developed and will be in review for Jan 2026 deadline. || Closed
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|}

DG - small bug in STASH diagnostics at chem version 132

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

PMJ - looking to send full domain and use ASAD/NR for RAQ, but taking time. Want to be able to use parallelisations there.

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

AJH hasn't got microplastics rose-stem test working yet, will make time later. Is not sure what is going on. CH can provide input on that.

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| NLA || NLA & RW are submitting to SSI RSMF for the Box Model
|-
|| AJH || LFRic PS49 milestone including aerosols (GLOMAP), deadline is Summer 2027. Lots of different groups now interested. Might be aiming to turn off the UM at the start of 2028.
|-
|}

== A.O.B. & D.N.M. (NLA) ==

DG - UKCA meeting in July.

Minutes of the code management group meeting 2026-05-14

2026-05-14T10:22:28Z

Nla27:

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 14th May 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:''' MS, MD, AJH, PMJ, JCK,

'''Cambridge:''' LA, RW

'''Leeds:''' DG

'''Canterbury:''' CH

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke.
#* Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it.
#* AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
#* Ongoing
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
#* Ongoing
# (this happened - not sure if follow up is required) NLA to mention MASS issues at the next MMG
#* Waiting for new MASS
# (new) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
#* Ongoing
# (new) AJH to request UKCA tags for lfric_apps and UM , so that we are able to keep track of all UKCA GitHub pull requests and issues at the next CMG meeting.
#* Closed - done
# (new) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified.
#* Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (new) AJH has contacted the LFRic core team to inform them of the obsolete instructions for building lfric core with FCM.
#* There may be an automated system for making instructions.
#* Closed
# (new) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
#* Ongoing
# (new) AJH and Pedro to discuss method for checking diagnostic KGOs with NetCDF files.
#* AJH, MD, PMJ to catch-up offline
#* ongoing

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

Generally, people have found GitHub OK to work with, but found trac easier to navigate.

* Need to be on reviewers list to be able to make edits to other PRs and also add links. AJH to contact SSD team. May be due to UKCA being BSD-3 and open source. Could perhaps make a change to the CONTRIBUTORS.md and then add people to be able to edit once that has been done.

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 155 || OMP dynamic scheduling race condition || [https://code.metoffice.gov.uk/trac/ukca/ticket/321 ukca:#321] || || When using OpenMP with dynamic, as opposed to the standard static, scheduling, checksums were failing with lfric_apps. This indicates a race condition likely within the ASAD chemical package and so would affect the UM as well as LFRic. Further testing is needed. AJH will make some time to run it with the thread santizer || RW to double-check notes - bug we introduced. Can be '''closed'''. Need LFRic tests with dynamic scheduling.
|-
|| 156 || Bug in Lfric copy of ''ukca_volcanic_so2'', <tt>true_latitude, true_longitude</tt> used without allocating. Fails on ARCHER2 with CCE compiler || [https://github.com/MetOffice/lfric_apps/pull/133 lfric_apps:PR133] || Mohit Dalvi || Since lfric_apps-vn2.2 Temporarily allocate ''true-latitude'', ''true_longitude'', ''weight_volc_vertdist'' [https://code.metoffice.gov.uk/trac/lfric_apps/changeset/9670/main/trunk/interfaces/physics_schemes_interface/source/legacy/ukca_interface/ukca_volcanic_so2.F90 lfric_apps:#965] removed UM dependencies i.e. ''trignometric_mod'' without providing alternative source for the arrays || Fixed in LFRic, CLOSE - UM below.
|-
|| 157 || Bug in calculation of aerosol AOD from LFRic || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/1089 lfric_apps:#1089] GitHub [https://github.com/MetOffice/lfric_apps/issues/41 lfric_apps:#41] || Alan J Hewitt || Since lfric vn2.2 FCM [https://code.metoffice.gov.uk/trac/lfric_apps/log/main/branches/dev/alanjhewitt/git_migration_AOD_bug git_migration_AOD_bug] Github [https://github.com/alanjhewitt/lfric_apps/tree/AOD_bug AOD_bug] aerosol AOD was developed in [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/440 lfric_apps:#440] and it looked fine at low resolution. Running at high resolution identified an addressing error. Fix has been developed and will be in review for Jan 2026 deadline. || Closed
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|}

DG - small bug in STASH diagnostics at chem version 132

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

PMJ - looking to send full domain and use ASAD/NR for RAQ, but taking time. Want to be able to use parallelisations there.

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

AJH hasn't got microplastics rose-stem test working yet, will make time later. Is not sure what is going on. CH can provide input on that.

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| NLA || NLA & RW are submitting to SSI RSMF for the Box Model
|-
|| AJH || LFRic PS49 milestone including aerosols (GLOMAP), deadline is Summer 2027. Lots of different groups now interested. Might be aiming to turn off the UM at the start of 2028.
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-05-14

2026-05-14T09:22:23Z

Nla27: /* Actions from the Last Meeting */

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 14th May 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:''' MS, MD, AJH, PMJ, JCK,

'''Cambridge:''' LA, RW

'''Leeds:''' DG

'''Canterbury:''' CH

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke.
#* Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it.
#* AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
#* Ongoing
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
#* Ongoing
# (this happened - not sure if follow up is required) NLA to mention MASS issues at the next MMG
#* Waiting for new MASS
# (new) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
#* Ongoing
# (new) AJH to request UKCA tags for lfric_apps and UM , so that we are able to keep track of all UKCA GitHub pull requests and issues at the next CMG meeting.
#* Closed - done
# (new) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified.
#* Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (new) AJH has contacted the LFRic core team to inform them of the obsolete instructions for building lfric core with FCM.
#* There may be an automated system for making instructions.
#* Closed
# (new) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
#* Ongoing
# (new) AJH and Pedro to discuss method for checking diagnostic KGOs with NetCDF files.
#* AJH, MD, PMJ to catch-up offline
#* ongoing

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 155 || OMP dynamic scheduling race condition || [https://code.metoffice.gov.uk/trac/ukca/ticket/321 ukca:#321] || || When using OpenMP with dynamic, as opposed to the standard static, scheduling, checksums were failing with lfric_apps. This indicates a race condition likely within the ASAD chemical package and so would affect the UM as well as LFRic. Further testing is needed. AJH will make some time to run it with the thread santizer ||
|-
|| 156 || Bug in Lfric copy of ''ukca_volcanic_so2'', <tt>true_latitude, true_longitude</tt> used without allocating. Fails on ARCHER2 with CCE compiler || [https://github.com/MetOffice/lfric_apps/pull/133 lfric_apps:PR133] || Mohit Dalvi || Since lfric_apps-vn2.2 Temporarily allocate ''true-latitude'', ''true_longitude'', ''weight_volc_vertdist'' [https://code.metoffice.gov.uk/trac/lfric_apps/changeset/9670/main/trunk/interfaces/physics_schemes_interface/source/legacy/ukca_interface/ukca_volcanic_so2.F90 lfric_apps:#965] removed UM dependencies i.e. ''trignometric_mod'' without providing alternative source for the arrays ||
|-
|| 157 || Bug in calculation of aerosol AOD from LFRic || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/1089 lfric_apps:#1089] GitHub [https://github.com/MetOffice/lfric_apps/issues/41 lfric_apps:#41] || Alan J Hewitt || Since lfric vn2.2 FCM [https://code.metoffice.gov.uk/trac/lfric_apps/log/main/branches/dev/alanjhewitt/git_migration_AOD_bug git_migration_AOD_bug] Github [https://github.com/alanjhewitt/lfric_apps/tree/AOD_bug AOD_bug] aerosol AOD was developed in [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/440 lfric_apps:#440] and it looked fine at low resolution. Running at high resolution identified an addressing error. Fix has been developed and will be in review for Jan 2026 deadline. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| NLA || NLA & RW are submitting to SSI RSMF for the Box Model
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-05-14

2026-05-14T09:21:49Z

Nla27:

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 14th May 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:''' MS, MD, AJH, PMJ, JCK,

'''Cambridge:''' LA, RW

'''Leeds:''' DG

'''Canterbury:''' CH

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke.
#* Coding needed to get changes in. Have a way forward.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it.
#* AJH working on the RADAER API. Have made notes in a different document, and then will merge into single document. Expected around September
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
#* Ongoing
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
#* Ongoing
# (this happened - not sure if follow up is required) NLA to mention MASS issues at the next MMG
#* Waiting for new MASS
# (new) NLA / MD to put a link to Monsoon3 guide to GitHub in the minutes
#* Ongoing
# (new) AJH to request UKCA tags for lfric_apps and UM , so that we are able to keep track of all UKCA GitHub pull requests and issues at the next CMG meeting.
#* Closed - done
# (new) MD is developing workaround for Bug in Lfric copy of ukca_volcanic_so2. However, this will not add functionality in lfric. A developer for this needs to be identified.
#* Lodged in LFRic, confirmed with May Chim and is happy to do for UM, but may have issues with testing
# (new) AJH has contacted the LFRic core team to inform them of the obsolete instructions for building lfric core with FCM.
#* There may be an automated system for making instructions.
#* Closed
# (new) AJH to tidy up the priority table. Some items are now complete and should be marked as such.
#* Ongoing
# (new) AJH and Pedro to discuss method for checking diagnostic KGOs with NetCDF files.
#* Closed

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 155 || OMP dynamic scheduling race condition || [https://code.metoffice.gov.uk/trac/ukca/ticket/321 ukca:#321] || || When using OpenMP with dynamic, as opposed to the standard static, scheduling, checksums were failing with lfric_apps. This indicates a race condition likely within the ASAD chemical package and so would affect the UM as well as LFRic. Further testing is needed. AJH will make some time to run it with the thread santizer ||
|-
|| 156 || Bug in Lfric copy of ''ukca_volcanic_so2'', <tt>true_latitude, true_longitude</tt> used without allocating. Fails on ARCHER2 with CCE compiler || [https://github.com/MetOffice/lfric_apps/pull/133 lfric_apps:PR133] || Mohit Dalvi || Since lfric_apps-vn2.2 Temporarily allocate ''true-latitude'', ''true_longitude'', ''weight_volc_vertdist'' [https://code.metoffice.gov.uk/trac/lfric_apps/changeset/9670/main/trunk/interfaces/physics_schemes_interface/source/legacy/ukca_interface/ukca_volcanic_so2.F90 lfric_apps:#965] removed UM dependencies i.e. ''trignometric_mod'' without providing alternative source for the arrays ||
|-
|| 157 || Bug in calculation of aerosol AOD from LFRic || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/1089 lfric_apps:#1089] GitHub [https://github.com/MetOffice/lfric_apps/issues/41 lfric_apps:#41] || Alan J Hewitt || Since lfric vn2.2 FCM [https://code.metoffice.gov.uk/trac/lfric_apps/log/main/branches/dev/alanjhewitt/git_migration_AOD_bug git_migration_AOD_bug] Github [https://github.com/alanjhewitt/lfric_apps/tree/AOD_bug AOD_bug] aerosol AOD was developed in [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/440 lfric_apps:#440] and it looked fine at low resolution. Running at high resolution identified an addressing error. Fix has been developed and will be in review for Jan 2026 deadline. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| NLA || NLA & RW are submitting to SSI RSMF for the Box Model
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-05-14

2026-05-11T12:48:03Z

Nla27: /* Round (virtual) Table of current activities, plans */

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 14th May 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:'''

'''Cambridge:'''

'''Leeds:'''

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (new) AJH to chair next meeting
# (new) NLA to mention MASS issues at the next MMG
# (new) NLA to put a link to Monsoon3 guide to GitHub in the minutes

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 155 || OMP dynamic scheduling race condition || [https://code.metoffice.gov.uk/trac/ukca/ticket/321 ukca:#321] || || When using OpenMP with dynamic, as opposed to the standard static, scheduling, checksums were failing with lfric_apps. This indicates a race condition likely within the ASAD chemical package and so would affect the UM as well as LFRic. Further testing is needed. AJH will make some time to run it with the thread santizer ||
|-
|| 156 || Bug in Lfric copy of ''ukca_volcanic_so2'', <tt>true_latitude, true_longitude</tt> used without allocating. Fails on ARCHER2 with CCE compiler || [https://github.com/MetOffice/lfric_apps/pull/133 lfric_apps:PR133] || Mohit Dalvi || Since lfric_apps-vn2.2 Temporarily allocate ''true-latitude'', ''true_longitude'', ''weight_volc_vertdist'' [https://code.metoffice.gov.uk/trac/lfric_apps/changeset/9670/main/trunk/interfaces/physics_schemes_interface/source/legacy/ukca_interface/ukca_volcanic_so2.F90 lfric_apps:#965] removed UM dependencies i.e. ''trignometric_mod'' without providing alternative source for the arrays ||
|-
|| 157 || Bug in calculation of aerosol AOD from LFRic || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/1089 lfric_apps:#1089] GitHub [https://github.com/MetOffice/lfric_apps/issues/41 lfric_apps:#41] || Alan J Hewitt || Since lfric vn2.2 FCM [https://code.metoffice.gov.uk/trac/lfric_apps/log/main/branches/dev/alanjhewitt/git_migration_AOD_bug git_migration_AOD_bug] Github [https://github.com/alanjhewitt/lfric_apps/tree/AOD_bug AOD_bug] aerosol AOD was developed in [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/440 lfric_apps:#440] and it looked fine at low resolution. Running at high resolution identified an addressing error. Fix has been developed and will be in review for Jan 2026 deadline. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| NLA || NLA & RW are submitting to SSI RSMF for the Box Model
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-05-14

2026-05-11T12:47:37Z

Nla27: /* Open Bugs */

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 14th May 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:'''

'''Cambridge:'''

'''Leeds:'''

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (new) AJH to chair next meeting
# (new) NLA to mention MASS issues at the next MMG
# (new) NLA to put a link to Monsoon3 guide to GitHub in the minutes

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side Also has problems with GLOMAP-clim ||
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 155 || OMP dynamic scheduling race condition || [https://code.metoffice.gov.uk/trac/ukca/ticket/321 ukca:#321] || || When using OpenMP with dynamic, as opposed to the standard static, scheduling, checksums were failing with lfric_apps. This indicates a race condition likely within the ASAD chemical package and so would affect the UM as well as LFRic. Further testing is needed. AJH will make some time to run it with the thread santizer ||
|-
|| 156 || Bug in Lfric copy of ''ukca_volcanic_so2'', <tt>true_latitude, true_longitude</tt> used without allocating. Fails on ARCHER2 with CCE compiler || [https://github.com/MetOffice/lfric_apps/pull/133 lfric_apps:PR133] || Mohit Dalvi || Since lfric_apps-vn2.2 Temporarily allocate ''true-latitude'', ''true_longitude'', ''weight_volc_vertdist'' [https://code.metoffice.gov.uk/trac/lfric_apps/changeset/9670/main/trunk/interfaces/physics_schemes_interface/source/legacy/ukca_interface/ukca_volcanic_so2.F90 lfric_apps:#965] removed UM dependencies i.e. ''trignometric_mod'' without providing alternative source for the arrays ||
|-
|| 157 || Bug in calculation of aerosol AOD from LFRic || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/1089 lfric_apps:#1089] GitHub [https://github.com/MetOffice/lfric_apps/issues/41 lfric_apps:#41] || Alan J Hewitt || Since lfric vn2.2 FCM [https://code.metoffice.gov.uk/trac/lfric_apps/log/main/branches/dev/alanjhewitt/git_migration_AOD_bug git_migration_AOD_bug] Github [https://github.com/alanjhewitt/lfric_apps/tree/AOD_bug AOD_bug] aerosol AOD was developed in [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/440 lfric_apps:#440] and it looked fine at low resolution. Running at high resolution identified an addressing error. Fix has been developed and will be in review for Jan 2026 deadline. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| NLA || Submitting to SSI RSMF for the Box Model
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-05-14

2026-05-11T12:47:08Z

Nla27: /* Open Bugs */

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 14th May 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:'''

'''Cambridge:'''

'''Leeds:'''

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (new) AJH to chair next meeting
# (new) NLA to mention MASS issues at the next MMG
# (new) NLA to put a link to Monsoon3 guide to GitHub in the minutes

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side || Also has problems with GLOMAP-clim
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 155 || OMP dynamic scheduling race condition || [https://code.metoffice.gov.uk/trac/ukca/ticket/321 ukca:#321] || || When using OpenMP with dynamic, as opposed to the standard static, scheduling, checksums were failing with lfric_apps. This indicates a race condition likely within the ASAD chemical package and so would affect the UM as well as LFRic. Further testing is needed. || AJH will make some time to run it with the thread santizer
|-
|| 156 || Bug in Lfric copy of ''ukca_volcanic_so2'', <tt>true_latitude, true_longitude</tt> used without allocating. Fails on ARCHER2 with CCE compiler || [https://github.com/MetOffice/lfric_apps/pull/133 lfric_apps:PR133] || Mohit Dalvi || Since lfric_apps-vn2.2 Temporarily allocate ''true-latitude'', ''true_longitude'', ''weight_volc_vertdist'' [https://code.metoffice.gov.uk/trac/lfric_apps/changeset/9670/main/trunk/interfaces/physics_schemes_interface/source/legacy/ukca_interface/ukca_volcanic_so2.F90 lfric_apps:#965] removed UM dependencies i.e. ''trignometric_mod'' without providing alternative source for the arrays ||
|-
|| 157 || Bug in calculation of aerosol AOD from LFRic || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/1089 lfric_apps:#1089] GitHub [https://github.com/MetOffice/lfric_apps/issues/41 lfric_apps:#41] || Alan J Hewitt || Since lfric vn2.2 FCM [https://code.metoffice.gov.uk/trac/lfric_apps/log/main/branches/dev/alanjhewitt/git_migration_AOD_bug git_migration_AOD_bug] Github [https://github.com/alanjhewitt/lfric_apps/tree/AOD_bug AOD_bug] aerosol AOD was developed in [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/440 lfric_apps:#440] and it looked fine at low resolution. Running at high resolution identified an addressing error. Fix has been developed and will be in review for Jan 2026 deadline. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| NLA || Submitting to SSI RSMF for the Box Model
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-05-14

2026-05-11T12:46:30Z

Nla27: /* Bugs/Bugfixes (NLA) */

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 14th May 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:'''

'''Cambridge:'''

'''Leeds:'''

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (new) AJH to chair next meeting
# (new) NLA to mention MASS issues at the next MMG
# (new) NLA to put a link to Monsoon3 guide to GitHub in the minutes

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side || Also has problems with GLOMAP-clim
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 155 || OMP dynamic scheduling race condition || [https://code.metoffice.gov.uk/trac/ukca/ticket/321 ukca:#321] || || When using OpenMP with dynamic, as opposed to the standard static, scheduling, checksums were failing with lfric_apps. This indicates a race condition likely within the ASAD chemical package and so would affect the UM as well as LFRic. Further testing is needed. || AJH will make some time to run it with the thread santizer
|-
|| 156 || Bug in Lfric copy of ''ukca_volcanic_so2'', <tt>true_latitude, true_longitude</tt> used without allocating. Fails on ARCHER2 with CCE compiler || [https://github.com/MetOffice/lfric_apps/pull/133 lfric_apps:PR133] || Mohit Dalvi || Since lfric_apps-vn2.2 Temporarily allocate ''true-latitude'', ''true_longitude'', ''weight_volc_vertdist'' [https://code.metoffice.gov.uk/trac/lfric_apps/changeset/9670/main/trunk/interfaces/physics_schemes_interface/source/legacy/ukca_interface/ukca_volcanic_so2.F90 lfric_apps:#965] removed UM dependencies i.e. ''trignometric_mod'' without providing alternative source for the arrays ||
|-
|| 157 || Bug in calculation of aerosol AOD from LFRic || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/1089 lfric_apps:#1089] GitHub [https://github.com/MetOffice/lfric_apps/issues/41 lfric_apps:#41] || Alan J Hewitt || Since lfric vn2.2 FCM [https://code.metoffice.gov.uk/trac/lfric_apps/log/main/branches/dev/alanjhewitt/git_migration_AOD_bug git_migration_AOD_bug] Github [https://github.com/alanjhewitt/lfric_apps/tree/AOD_bug AOD_bug] aerosol AOD was developed in [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/440 lfric_apps:#440] and it looked fine at low resolution. Running at high resolution identified an addressing error. Fix has been developed and will be in review for Jan 2026 deadline. ||
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || May Chim? || Since UM vn13.9 Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' ||
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes || || In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. Since UM vn11.x Should be turned Off in rose metadata for Strat schemes ||
|-
|| 160 || Mismatch in tracer names indexing across UKCA API. || || Could be related to '''#143'''. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output Since UM vn10.6? ||
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| NLA || Submitting to SSI RSMF for the Box Model
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-05-14

2026-05-11T12:42:36Z

Nla27: /* Open Bugs */

[[Code management group minutes]]

==Teleconference Details==

'''Thursday 14th May 2026, 10.00am - 11.30am GMT'''

'''Meeting via Teams - see link in calendar invitation'''

'''Met Office:'''

'''Cambridge:'''

'''Leeds:'''

'''Canterbury:'''

'''CSIRO:'''

'''Apologies:'''

'''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT'''

== Actions from this meeting ==

== Actions from the Last Meeting ==

# (ongoing) GM/DG to update table on UKCA wiki documenting [[GLOMAP versions]]. DG/GM to consider the code and lodging process for GLOMAP developments and consider a suitable rose-stem test supported by NLA. GM Will work with DG to get a subset to commit. AJH to review. Graham has found code needed for meteoric smoke.
# (ongoing) AJH on update API document to UM13.6 release. NLA to provide feedback before it is be circulated. There is a comprehensive overhaul for 13.7. AJH to make document available for wider information/comment - see [https://code.metoffice.gov.uk/trac/ukca/wiki/APIandUnifiedModelDependencies here]. AJH won't do anything with API until GitHub release is out, and then will add some things to it.
# (ongoing) ALL look at [https://code.metoffice.gov.uk/trac/um/ticket/6203 um:#6203 showing other unprotected rose-stem options] and think about any code/settings they are interested in. May be able to use GitHub actions.
# (ongoing) ALL to consider ordering of the [[Priorities|Progress with Priorities table]] and highlight things that should be higher priority, and any other tasks that need to be included.
# (new) AJH to chair next meeting
# (new) NLA to mention MASS issues at the next MMG
# (new) NLA to put a link to Monsoon3 guide to GitHub in the minutes

== Issues/PRs ==

'''REMEMBER TO LINK UKCA IN YOUR UM AND LFRIC_APPS (& OTHER REPO) ISSUES/PRs'''

=== Issues ===

* [https://github.com/MetOffice/ukca/issues UKCA]
* [https://github.com/MetOffice/um/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

=== Pull Requests ===

* [https://github.com/MetOffice/ukca/pulls UKCA]
* [https://github.com/MetOffice/um/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 UM - Linked UKCA]
* [https://github.com/MetOffice/lfric_apps/pulls?q=is%3Aissue%20state%3Aopen%20label%3A%22Linked%20UKCA%22 lfric_apps - Linked UKCA]

== Progress with Priorities (NLA) ==

'''ACTION REQUEST FROM UKCA SCIENCE & MANAGEMENT BOARD:''' CMG to provide list of priorities & their status, with particular thought to UKESM2 changes that will be required.

'''[[Priorities|Progress with Priorities table]]'''

== Bugs/Bugfixes (NLA) ==

==== [[Bugfixes_(new_approach)|Open Bugs]] ====

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|#
!style="text-align:top;rowspan:2";|Description
!style="text-align:top;rowspan:2";|Ticket
!style="text-align:top;rowspan=2";|Owner
!style="text-align:top;rowspan=2";|Comments
!style="text-align:top;rowspan=2";|Comments from this meeting
|-
| 124 || H2 and N2 cannot be set for RCP and WMOA1 scenario routines || [https://code.metoffice.gov.uk/trac/um/ticket/5620 UM:#5620] [https://code.metoffice.gov.uk/trac/um/log/main/branches/dev/mohitdalvi/vn13.8.1_ukca_rcp_read_h2_n2 vn13.8.1_ukca_rcp_read_h2_n2] || Mohit || Values are hard-wired in the code and cannot be changed without a branch. N2 values seem to be read from namelist (for UM, and RCP scenarios). Branch adds possibility to read H2 from either RCP or namelist. Will probably require updating all UKCA-chem apps to maintain KGO. ''More testing required'' MD has done a little bit of work. N2 is read from namelist, but can now read from RCP file for H2 ||
|-
| 128 || Bug in UKCA stratospheric chemistry diagnostics || [https://code.metoffice.gov.uk/trac/um/ticket/5839 UM:#5839] || Luke Abraham || The indexing/values of diagnostics m01s50i101-i104 are incorrect. Fixes provided for vn11.1 and vn11.7. May affect CMIP6 diagnostics Does this need fixing for CMIP7? Need to discuss with CDDS/diagnostics team as might break existing workflow. ||
|-
|| 143 || Error in print statements from UKCA_TRACERS_COPY_FROM_UM || Not yet || ??? || The final species listed in the diagnostic print statement seems to have very large concentrations (O(1E+08)) compared to others in the ppm-ppt range. Does not seem to affect model output. Reported by James Weber. ||
|-
|| 144 || interchangeable use of specific humidity and water vapour mixing ratio || [https://code.metoffice.gov.uk/trac/um/ticket/6813 #6813] || John Hemmings and ??? ||UKCA includes calculations of relative humidity, clear-sky relative humidity and saturation vapour pressure. Relative humidity calculations should be based on water vapour mass mixing ratio but are in part based on specific humidity. Also, the calculation of saturation vapour pressure is derived from saturation mixing ratio but uses a formula for deriving SVP from saturation specific humidity. This interchangeable use of specific humidity (ratio for moist air) and mixing ratio (ratio for dry air) in existing configurations introduces small numerical errors in UM and LFRic model runs. These bugs were identified at UM version vn12.2 and have been highlighted by comments in code lodged with UM ticket [https://code.metoffice.gov.uk/trac/um/ticket/6660 #6660] (in ukca_main1-ukca_main1.F90 and atmos_ukca_humidity_mod.F90). All UKCA configurations are affected. Alan - This should be fixed by Met Office. I will speak with Anthony and Alistair about resourcing to fix this. It requires good understanding of humidity to work through this problem, otherwise I would have done this myself. When we pass stuff through the argument list, the name changes which makes things complicated. Should we pass a structure with all the humidity fields in? There is a UKCA bespoke version of humidity calculations for non-UM applications. Internal Met Office problem - will need to find someone to fix it. AJH to talk with AJ and Alistair Sellar. GM can cross-check. Ticket has 2 parts. JH suggests doing it in 2 tickets, 1 technical, 1 bug fix. JH could do technical part (either as callback routines or separate fields). Then would need UM & LFRic tickets for the bug fix, as calculations could be done in the parent or as callback routine. Some work has been done - technical change has been done in ukca:#245. Went in at UM13.9. This option is now used by the UM and LFRic. Buggy calculations are now outside of UKCA - will require UM and LFRic changes to fix those. Might not be a large amount of work, but problem needs to be well understood. Also consider what field is being passed in the tracer list - currently q but should be mixing ratio. Some has been fixed - bug has been shifted outside of UKCA. Don't know of anyone working on it currently. Someone will need to go through and check we are passing the correct one - need someone on aerosol side and on chemistry side || Also has problems with GLOMAP-clim
|-
|| 153 || bug in 2D photolysis || || || While working on developments for the new photolysis API, we’ve noticed a likely error in the current implementation of the 2D photolysis. The 2D photolysis files are tabulated by day of year at 5-day resolution, amongst other variables. The interpolation to the actual day of year is currently done in the read subroutine ([https://code.metoffice.gov.uk/trac/um/browser/main/trunk/src/control/ukca_interface/ukca_phot2d.F90 read2d_opt or read2d_orig]). However, this subroutine is only called once on the first timestep. For multi-day runs, the photolysis rates will not be updated as the day of year increases. Since nobody is using the 2D photolysis at the moment this is likely of low to no impact. Might be used by NUAQ BD or VB will know more - PMJ will ask ||
|-
|| 154 || bug in tropospheric heterogeneous chemistry || || || Within GLOMAP the <tt>wetdp</tt> variable is defined as the wet diameter in m. However, in <tt>ukca_trop_hetchem</tt> this is used as a radius in cm. This results in a factor of 50x error. Steve Turnock might be using this. NLA to contact ST and YG about this. ||
|-
|| 155 || OMP dynamic scheduling race condition || [https://code.metoffice.gov.uk/trac/ukca/ticket/321 ukca:#321] || || When using OpenMP with dynamic, as opposed to the standard static, scheduling, checksums were failing with lfric_apps. This indicates a race condition likely within the ASAD chemical package and so would affect the UM as well as LFRic. Further testing is needed. || AJH will make some time to run it with the thread santizer
|-
|| 156 || Bug in Lfric copy of ''ukca_volcanic_so2'', <tt>true_latitude, true_longitude</tt> used without allocating. Fails on ARCHER2 with CCE compiler || [https://github.com/MetOffice/lfric_apps/pull/133 lfric_apps:PR133] || || Since lfric_apps-vn2.2 || Temporarily allocate ''true-latitude'', ''true_longitude'', ''weight_volc_vertdist'' || [https://code.metoffice.gov.uk/trac/lfric_apps/changeset/9670/main/trunk/interfaces/physics_schemes_interface/source/legacy/ukca_interface/ukca_volcanic_so2.F90 lfric_apps:#965] removed UM dependencies i.e. ''trignometric_mod'' without providing alternative source for the arrays || '''OPEN''' || Mohit Dalvi
|-
|| 157 || Bug in calculation of aerosol AOD from LFRic || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/1089 lfric_apps:#1089] GitHub [https://github.com/MetOffice/lfric_apps/issues/41 lfric_apps:#41] || || Since lfric vn2.2 || FCM [https://code.metoffice.gov.uk/trac/lfric_apps/log/main/branches/dev/alanjhewitt/git_migration_AOD_bug git_migration_AOD_bug] Github [https://github.com/alanjhewitt/lfric_apps/tree/AOD_bug AOD_bug] || aerosol AOD was developed in [https://code.metoffice.gov.uk/trac/lfric_apps/ticket/440 lfric_apps:#440] and it looked fine at low resolution. Running at high resolution identified an addressing error. Fix has been developed and will be in review for Jan 2026 deadline. || '''OPEN''' || Alan J Hewitt
|-
|| 158 || While analysing #156, it was noticed that in the UM version of `ukca_volcanic_SO2` the array ''weight_volc_vertdist'' is being populated without being allocated. || || || Since UM vn13.9 || Needs to be allocated as ''weight_volc_vertdist(l2-l1+1)'' and deallocated in each iteration over ''nreupt'' || || '''OPEN''' || May Chim?
|-
|| 159 || Logical '''l_ukca_prescribech4''' should not be active in ''Strat'' schemes. In ''ukca_add_emiss'' the logical enables overwriting of CH4 surface values with prescribed concentrations. However, later on in the routine this action is repeated in a section specific to 'Strat' schemes, where use of prescribed vs emitted CH4 is governed by ''l_ukca_emisdrvn_ch4'', thus over-ridding the first logical. || || || Since UM vn11.x || Should be turned Off in rose metadata for Strat schemes || || '''OPEN''' ||
|-
|| 160 || Could be related to '''#143'''. Mismatch in tracer names indexing across UKCA API. Printing from ''UKCA_TRACER_COPY_TO/FROM_UM'', and comparing ''all_tracers_names'' vs ''tr_names'' shows {{pdf|ukca_tracer_name_index.pdf|misalignment}} in names of species. ''Note:'' this may be just limited to the population of ''tr_names'' array as any actual misalignment would have been noticed for radiative feedback as well as tracers/ diagnostics in output || || || Since UM vn10.6? || || || '''OPEN''' ||
|-
|}

== [[Redundant code|Redundant Code]] (NLA) ==

==== Code for deletion ====

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant code|REDUNDANT CODE]] TABLE AND NOT THIS PAGE'''

=== Desirable Science not tested ===

'''PLEASE REMEMBER TO EDIT THE ORIGINAL [[Redundant_code#Table_of_code_still_desired_but_which_is_not_tested|SCIENCE NOT TESTED TABLE]] AND NOT THIS PAGE'''

'''See also the complete list of [[Unprotected_Options|unprotected rose-stem options]]'''

{| class="wikitable" border = "1px"
!style="text-align:top;|#
!style="text-align:top;|Description
!style="text-align:top;|Ticket
!style="text-align:top;|Remarks
!style="text-align:top;|Owner
|-
| 1 || Use of tropospheric (2D) look-up table photolysis || || Still useful to compare against FastJX. May be used for a "fast" configuration. Will be doen as part of photolysis refactoring ||
|-
| 2 || TropIsop chemistry configuration || || May be useful in a "fast" configuration & to drive GLOMAP-mode. Useful for low-top configurations. ||
|-
| 3 || Strat chemistry configuration || || Useful for stratospheric studies, particularly with a high model top. || Luke Abraham
|-
|}

== Round (virtual) Table of current activities, plans ==

{| class="wikitable" border = "1px"
!style="text-align:top;rowspan:2";|Person
!style="text-align:top;rowspan:2";|Activity
|-
|| NLA || Submitting to SSI RSMF for the Box Model
|-
|}

== A.O.B. & D.N.M. (NLA) ==

Minutes of the code management group meeting 2026-05-14

2026-05-11T12:40:26Z

Nla27: Created page with "Code management group minutes ==Teleconference Details== '''Thursday 14th May 2026, 10.00am - 11.30am GMT''' '''Meeting via Teams - see link in calendar invitation''' '''Met Office:''' '''Cambridge:''' '''Leeds:''' '''Canterbury:''' '''CSIRO:''' '''Apologies:''' '''NEXT MEETING WILL BE THURSDAY 9TH JULY 2026, 10.00-11.30 GMT''' == Actions from this meeting == == Actions from the Last Meeting == # (ongoing) GM/DG to up..."

Code management group minutes

2026-05-11T12:33:04Z

Nla27:

UKCA Chemistry and Aerosol UMvn13.9 Tutorial 17

2026-03-19T14:15:13Z

Nla27:

UKCA Chemistry and Aerosol UMvn13.9 Tutorial 16

2026-03-19T14:14:52Z

Nla27:

UKCA Chemistry and Aerosol UMvn13.9 Tutorial 15

2026-03-19T14:14:01Z

Nla27:

UKCA Chemistry and Aerosol UMvn13.9 Tutorial 8

2026-03-19T14:11:48Z

Nla27:

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

{| class="wikitable" border = "1px"
|-
| Difficulty || '''MEDIUM'''
|-
| Time to Complete || '''1-2 hours'''
|-
| Video instructions || https://www.youtube.com/watch?v=aysibeNdLUY&t=10030s
|}

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

==What you will do in this tutorial==

In this tutorial you will learn how to add new chemical reactions to UKCA. You will then include a reaction involving the chemical tracers you added in the last tutorial, ALICE and BOB.

==Adding new Chemical Reactions==

UKCA uses the ASAD chemical integration software package, which can be easily extended by a user. ASAD could in principle use many different solvers, although currently it uses a symbolic Backward Euler solver with Newton-Raphson iteration, which is known within UKCA as the ''"Newton Raphson"''. Further details on the solver implementation can be found in [https://gmd.copernicus.org/articles/11/3089/2018/ Esentürk ''et al.'' (2018)][1].

ASAD considers four different types of chemical reactions: bimolecular reactions, termolecular reactions, heterogeneous reactions, and photolysis reactions. During this tutorial you will be tasked with adding a new reaction into your UKCA branch.

'''References'''
# Esentürk, E., Abraham, N. L., Archer-Nicholls, S., Mitsakou, C., Griffiths, P., Archibald, A., and Pyle, J.: Quasi-Newton methods for atmospheric chemistry simulations: implementation in UKCA UM vn10.8, Geosci. Model Dev., 11, 3089–3108, https://doi.org/10.5194/gmd-11-3089-2018, 2018.

== Code Changes ==

=== <tt>src/science/core/chemistry/ukca_chem_master.F90</tt> ===

You will need to add your reaction(s) to the appropriate array within the <tt>ukca_chem_master.F90</tt> module. Details covering what is required for each reaction type are below.

=== <tt>src/control/core/top_level/ukca_config_defs_mod.F90</tt> ===

Within the <tt>IF</tt> blocks for each chemistry scheme are variables called '''<tt>nr_therm</tt>''' (for all bimolecular, termolecular, and heterogeneous reactions) and '''<tt>nr_phot</tt>''' (for photolysis reactions). When adding reactions you should increment the appropriate variable for each chemistry scheme altered.

==Biomolecular Reactions==

For most bimolecular reactions, it is sufficient to provide the <math>k_{0}</math>, <math>\alpha</math>, and <math>\beta</math> coefficients that are used to compute the rate coefficient <math>k</math> from the Arrhenius expression

<math>
k = k_{0} \left(\frac{T}{300}\right)^{\alpha} \textrm{exp} \left(\frac{-\beta}{T}\right)
</math>

===Bimolecular Reaction Definition===

The bimolecular reactions are defined in the '''<tt>ukca_chem_master.F90</tt>''' module using the '''<tt>ratb_t1</tt>''' Fortran type specification, and are held in arrays. At the end of this routine the '''<tt>ratb_defs_master</tt>''' array is created from these, and if that scheme is selected in UKCA these reactions are copied across into the master '''<tt>ratb_defs</tt>''' array.

The format of this '''<tt>ratb_t1</tt>''' type (defined in '''<tt>ukca_chem_defs_mod.F90</tt>''') is

ratb_t1(N, 'Reactant 1','Reactant 2','Product 1 ','Product 2 ','Product 3 ',&
'Product 4 ', <math>k_{0}</math>, <math>\alpha</math>, <math>\beta</math>, Fraction of Product 1 produced, Fraction of Product 2 produced,
Fraction of Product 3 produced, Fraction of Product 4 produced, SCHEME, QUALIFIER, DISQUALIFIER, VN), &

If fractional products are not required for a reaction, then the ''fraction of each product'' formed should be set to 0.00. If fractional products are required for any one of the products then the fraction of each product formed should be set to its correct value.

The settings for <tt>N</tt>, <tt>SCHEME</tt>, <tt>QUALIFIER</tt>, <tt>DISQUALIFIER</tt>, and <tt>VN</tt> are the same as in the [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_7#src.2Fscience.2Fcore.2Fchemistry.2Fukca_chem_master.F90|adding new tracers tutorial]], although here '''<tt>N</tt>''' should be incremented for each new '''reaction''', where there might be the same reaction specified several times with changes to reaction rates or even species.

The specifications of the individual reactions are done as, e.g.

! B060 JPL2011
ratb_t1(60,'HO2 ','NO ','OH ','NO2 ',' ', &
' ',3.30e-12, 0.00, -270.00, 0.00, 0.00, 0.00, 0.00,st+r,0,0,107), &
! updates for 121 - st only
ratb_t1(60,'HO2 ','NO ','OH ','NO2 ',' ', &
' ',3.44e-12, 0.00, -260.00, 0.00, 0.00, 0.00, 0.00,st,0,0,121), &
ratb_t1(60,'HO2 ','NO ','OH ','NO2 ',' ', &
' ',3.50e-12, 0.00, -250.00, 0.00, 0.00, 0.00, 0.00,s,0,0,107), &
ratb_t1(60,'HO2 ','NO ','OH ','NO2 ',' ', &
' ',3.60e-12, 0.00, -270.00, 0.00, 0.00, 0.00, 0.00,ti+t+cs,0,0,107),&
! CS2
ratb_t1(60,'HO2 ','NO ','OH ','NO2 ',' ', &
' ',3.45e-12, 0.00, -270.00, 0.00, 0.00, 0.00, 0.00,cs,0,0,119), &
! B060a added Alex
! Not in TI, S, ST and R schemes
ratb_t1(60,'HO2 ','NO ','HONO2 ',' ',' ', &
' ',3.60e-12, 0.00, -270.00, 0.00, 0.00, 0.00, 0.00,t,0,0,107), &

! B062 IUPAC2001
ratb_t1(62,'HO2 ','O3 ','OH ','O2 ',' ', &
' ',2.03e-16, 4.57, -693.00, 0.0, 0.0,0.0,0.0,ti+t+st+r+cs,0,0,107), &
! updates for 121 - st only
ratb_t1(62,'HO2 ','O3 ','OH ','O2 ',' ', &
' ',1.00e-14, 0.00, 490.00, 0.0, 0.0,0.0,0.0,st,0,0,121), &
ratb_t1(62,'HO2 ','O3 ','OH ','O2 ','O2 ', &
' ',2.03e-16, 4.57, -693.00, 0.00, 0.00, 0.00, 0.00,s,0,0,107), &

! B204
ratb_t1(204,'DMSO ','OH ','SO2 ',' ',' ', &
' ',5.80e-11, 0.00, 0.00, 0.60, 0.00, 0.00, 0.00, ol+r,a,0,107), &
ratb_t1(204,'DMSO ','OH ','SO2 ','MSA ',' ', &
' ',5.80e-11, 0.00, 0.00, 0.60, 0.40, 0.00, 0.00, ti,a,0,107), &
ratb_t1(204,'DMSO ','OH ','SO2 ','MSA ',' ', &
' ',5.80e-11, 0.00, 0.00, 0.60, 0.40, 0.00, 0.00, st,a,0,117), &
! updates for 121
ratb_t1(204,'DMSO ','OH ','SO2 ','MSA ',' ', &
' ',6.10e-12, 0.00, -800.00, 0.60, 0.40, 0.00, 0.00, st,a,0,121), &

* The first reaction above takes its kinetic data from '''[http://jpldataeval.jpl.nasa.gov/ NASA's Jet Propulsion Laboratory]'''. The rate for this can be found on page 1-10 (with further description on page 1-51) of the [http://jpldataeval.jpl.nasa.gov/pdf/JPL%2010-6%20Final%2015June2011.pdf JPL2011 document].
* The second reaction in these examples takes its kinetic data from '''[http://iupac.pole-ether.fr/ IUPAC]'''. Going to this website, this reaction is defined [http://iupac.pole-ether.fr/htdocs/datasheets/pdf/HOx15_HO2_O3.pdf here].
* The third reaction shows the use of fractional products.
* Other reactions may take their rates from the '''[http://chmlin9.leeds.ac.uk/MCM/ Master Chemical Mechanism]'''.

You can see that in the instances above, different chemistry schemes use slightly different rates or species, as may be required by the scheme and species considered.

When adding new reactions you will need to increment the size of the array holding the <tt>ratb_t1</tt> type ('''<tt>n_bimol_master</tt>'''). Due to the large number of bimolecular reactions, the array containing them has been broken up into several blocks. If you are not adding new reactions to the last block (for instance, if you are adding a variation on an existing reaction) you will need to increment the '''stride''' as well, e.g.

n_ratb_s = n_ratb_e+1
n_ratb_e = n_ratb_s+49
ratb_defs_master(n_ratb_s:n_ratb_e) = (/ &

would become

n_ratb_s = n_ratb_e+1
n_ratb_e = n_ratb_s+50
ratb_defs_master(n_ratb_s:n_ratb_e) = (/ &

If there is a reaction that is an exception to the general Arrhenius equation then special code needs to be placed in the '''<tt>asad_bimol.F90</tt>''' routine, which is held in the <tt>UKCA/</tt> source-code directory.

==Termolecular Reactions==

As well as defining reactions involving a third body, the termolecular rate definition can also be used to define unimolecular reactions.

The pressure and temperature dependent rate, <math>k</math>, of a termolecular reaction is given by

<math>
k = \left(\frac{k_{0}\left[M\right]}{1+k_{0}\left[M\right]/k_{\infty}}\right)F_{c}^{\left(1+\left[\textrm{log}_{10}\left(\frac{k_{0}\left[M\right]}{k_{\infty}}\right)\right]^{2}\right)^{-1}}
</math>

where the low pressure rate constant <math>k_{0}</math> is given by

<math>
k_{0} = k_{1} \left(\frac{T}{300}\right)^{{\alpha}_{1}} \textrm{exp} \left(\frac{-{\beta}_{1}}{T}\right)
</math>

and the high pressure rate constant <math>k_{\infty}</math> is given by

<math>
k_{\infty} = k_{2} \left(\frac{T}{300}\right)^{{\alpha}_{2}} \textrm{exp} \left(\frac{-{\beta}_{2}}{T}\right)
</math>

===Termolecular Reaction Definition===

The termolecular reactions are defined in the '''<tt>ukca_chem_master.F90</tt>''' module using the '''<tt>ratt_t1</tt>''' Fortran type specification and are held in the '''<tt>ratt_defs_master</tt>''' array.

To format of this '''<tt>ratt_t1</tt>''' type is

ratt_t(N,'Reactant 1','Reactant 2','Product 1 ','Product 2 ', <math>f</math>, &
<math>k_{1}</math>, <math>{\alpha}_{1}</math>, <math>{\beta}_{1}</math>, <math>k_{2}</math>, <math>{\alpha}_{2}</math>, <math>{\beta}_{2}</math>, Fraction of Product 1 produced, Fraction of Product 2 produced,SCHEME,QUALIFIER,
DISQUALIFIER,VN), &

and as in <tt>rabt_t1</tt>, where the fraction of a product should be set to 0.0 if this functionality does not need to be used.

The settings for <tt>N</tt>, <tt>SCHEME</tt>, <tt>QUALIFIER</tt>, <tt>DISQUALIFIER</tt>, and <tt>VN</tt> are the same as in the [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_7#src.2Fscience.2Fcore.2Fchemistry.2Fukca_chem_master.F90|adding new tracers tutorial]], although here '''<tt>N</tt>''' should be incremented for each new '''reaction''', where there might be the same reaction specified several times with changes to reaction rates or even species.

The <math>f</math> value is used to define the <math>F_{c}</math> value by

<blockquote>
If <math>f < 1.0</math> then <math>F_{c} = f</math> 
else <math>F_{c} = \textrm{exp}\left(-T/f\right)</math>
</blockquote>

as <math>F_{c}</math> may or may not be highly temperature dependent.

Examples of these reactions are

! T004 JPL 2011
ratt_t1(4,'O(1D) ','N2 ','N2O ','m ', 0.0, &
2.80e-36, -0.90, 0.00, 0.00e+00, 0.0, 0.0, 0.0, 0.0, st+cs,0,0,107), &
! update for 121
ratt_t1(4,'O(1D) ','N2 ','N2O ','m ', 0.60, &
2.80e-36, -0.90, 0.00, 0.00e+00, 0.0, 0.0, 0.0, 0.0, st+cs,0,0,121), &
! JPL 2003
ratt_t1(4,'O(1D) ','N2 ','N2O ','m ', 0.0, &
3.50e-37, -0.60, 0.00, 0.00e+00, 0.0, 0.0, 0.0, 0.0, s,0,0,107) , &

To add new termolecular reactions you will need to append equivalent lines for the new reactions to the end of the '''<tt>ratt_defs_master</tt>''' array (increasing the array size '''<tt>n_ratt_master</tt>''' accordingly). If there is any special code that needs to be added, this should be placed in the '''<tt>asad_trimol.F90</tt>''' routine, which is held in the <tt>UKCA/</tt> source-code directory.

==Heterogeneous Reactions==

Heterogeneous reactions are those that occur on aerosol surfaces. There is no functional form defined for these reactions, with special code needed to be added for each case.

===Heterogeneous Reaction Definition===

The heterogeneous reactions are defined in the '''<tt>ukca_chem_master.F90</tt>''' module using the '''<tt>rath_t1</tt>''' Fortran type specification, usually in one array ('''<tt>rath_defs_master</tt>''').

To format of this '''<tt>rath_t1</tt>''' type is

rath_t(N,'Reactant 1','Reactant 2','Product 1 ','Product 2 ','Product 3 ',&
'Product 4 ', Fraction of Product 1 produced, Fraction of Product 2 produced, Fraction of Product 3 produced,
Fraction of Product 4 produced,SCHEME,QUALIFIER,DISQUALIFIER,VN), &

i.e. there is no rate information provided. For reactions on PSCs special code has been added to the routines in '''<tt>ukca_hetero_mod.F90</tt>''', and for other reactions there is code in '''<tt>asad_hetero.F90</tt>'''.

The settings for <tt>N</tt>, <tt>SCHEME</tt>, <tt>QUALIFIER</tt>, <tt>DISQUALIFIER</tt>, and <tt>VN</tt> are the same as in the [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_7#src.2Fscience.2Fcore.2Fchemistry.2Fukca_chem_master.F90|adding new tracers tutorial]], although here '''<tt>N</tt>''' should be incremented for each new '''reaction''', where there might be the same reaction specified several times with changes to reaction rates or even species.

Examples of this type are

rath_t1(5,'N2O5 ','HCl ','Cl ','NO2 ','HONO2 ', &
' ', 0.000, 0.000, 0.000, 0.000, s+st+cs,hp,0,107), &
rath_t1(6,'ClONO2 ','HBr ','BrCl ','HONO2 ',' ', &
' ', 0.000, 0.000, 0.000, 0.000, s+st+cs,eh,0,111), &

To add new heterogeneous reactions you will need to append equivalent lines for the new reactions to the end of the <tt>rath_defs_master</tt> array (increasing the array size '''<tt>n_het_master</tt>''' accordingly), before adding code to either '''<tt>ukca_hetero_mod.F90</tt>''' (for stratospheric reactions) or '''<tt>asad_hetero.F90</tt>''' (for tropospheric reactions).

In the above block you can also see the use of the chemical mechanism version specification.

==Photolysis Reactions==

These define a reaction where a chemical compound is broken down by photons. There is no functional form defined for this type of reaction. Instead, either (in the troposphere) input files are used to define the reaction rates for each species, while (in the stratosphere) on-line look-up tables are generated for the rates for each species, or a separate photolysis code, '''Fast-JX''', is used to interactively calculate the rate of reaction throughout the the whole atmosphere (for Fast-JX). These interactive schemes are preferred as they take the effect of aerosols or clouds into account at each timestep, allowing for more feedbacks to be investigated. In the upper stratosphere there are some wavelength regions that Fast-JX does not consider, and so the 3D on-line look-up tables are also used for these regions.

===Tropospheric Off-Line Photolysis===

If Fast-JX is not being used, then the off-line two-dimensional (zonally average) tropospheric photolysis is used (for all schemes). It is based on the work of Hough (1988)[2] and Law ''et al'' (1998)[3].

This scheme makes use of datafiles which define the reaction rate for a particular species (e.g. H2O2), or if no rate is known, a '''nil''' rate can be used. For vn10.4 these files can be found in

$UMDIR/vn11.8/ctldata/UKCA/tropdata/photol

To use this scheme set the value of <tt>i_ukca_photol</tt> by clicking '''2D Photolysis Scheme'''. You will then need to give the location of the files (above). The code controlling this scheme is held in '''<tt>ukca_phot2d.F90</tt>'''.

It is advised that this scheme is no longer used, and Fast-JX interactive photolysis should be used instead.

'''References'''
# Hough, A. M.: The calculation of photolysis rates for use in global modelling studies, Tech. rep., UK Atomic Energy Authority, Harwell, Oxon., UK, 1988
# Law, K., Plantevin, P., Shallcross, D., Rogers, H., Pyle, J., Grouhel, C., Thouret, V., and Marenco, A.: Evaluation of modeled O3 using Measurement of Ozone by Airbus In-Service Aircraft (MOZAIC) data, J. Geophys. Res., 103, 25721–25737, 1998

===Stratospheric Look-Up Table Photolysis===

In a chemistry scheme which has stratospheric chemistry, such as ''CheS/Strat'' and ''CheST/StratTrop'', if interactive photolysis is not used, then above 300hPa the look-up table approach of Lary and Pyle (1991)[4] is used (below 300hPa the tropospheric scheme described above is used). To use this scheme set the value of <tt>i_ukca_photol</tt> by clicking '''2D Photolysis Scheme'''. The code for this scheme is held in '''<tt>ukca_strat_update.F90</tt>'''.

'''References'''
# <li value="4"> Lary, D. and Pyle, J.: Diffuse-radiation, twilight, and photochemistry, J. Atmos. Chem., 13, 393–406, 1991.</li>

===Interactive Photolysis===

The original Fast-J scheme (Wild ''et al'', 2000)[5] uses 7 different wavelength bins appropriate for the troposphere, and the updated Fast-JX scheme (Neu et al, 2007)[6] adds up to an extra 11 bins allowing use in the stratosphere. At present only Fast-JX is available, although some previous UM versions used the older Fast-J scheme as well.

To use this scheme set the value of '''<tt>i_ukca_photol</tt>''' by clicking '''FastJ-X'''. You will then need to give the location of several input data files used by this scheme.

Further details on how the the Fast-JX scheme is used in UKCA, can be found in [http://www.geosci-model-dev.net/6/161/2013/gmd-6-161-2013.html Telford ''et al'' (2013)][7].

The Fast-JX data files are held in

$UMDIR/vn11.8/ctldata/UKCA/fastj

on ARCHER.

'''References'''
# Wild, O., Zhu, X., and Prather, M.: Fast-J: accurate simulation of in- and below-cloud photolysis in tropospheric chemical models, J. Atmos. Chem., 37, 245–282, doi:10.1023/A:1006415919030, 2000</li>
# Neu, J., Prather, M., and Penner, J.: Global atmospheric chemistry: integrating over fractional cloud cover, J. Geophys. Res., 112, D11306, 12 pp., doi:10.1029/2006JD008007, 2007
# Telford, P. J., Abraham, N. L., Archibald, A. T., Braesicke, P., Dalvi, M., Morgenstern, O., O'Connor, F. M., Richards, N. A. D., and Pyle, J. A.: Implementation of the Fast-JX Photolysis scheme (v6.4) into the UKCA component of the MetUM chemistry-climate model (v7.3), Geosci. Model Dev., 6, 161-177, doi:10.5194/gmd-6-161-2013, 2013.

===Photolysis Reaction Definition===

The photolysis reactions are defined in the '''<tt>ukca_chem_master.F90</tt>''' module using the '''<tt>ratj_t1</tt>''' Fortran type specification and held in the '''<tt>ratj_defs_master</tt>''' array.

To format of this '''<tt>ratj_t1</tt>''' type is

ratj_t1(N,'Reactant 1','Reactant 2','Product 1 ','Product 2 ','Product 3 ',&
'Product 4 ', Fraction of Product 1 produced, Fraction of Product 2 produced, Fraction of Product 3 produced,
Fraction of Product 4 produced, Quantum Yield, Look-up Label,SCHEME,QUALIFIER,DISQUALIFIER,VN), &

The '''Look-Up Label''' is used to define the file used for the 2D photolysis, and is used by Fast-JX to find the correct values for each species in the input data files. This is a 10-character string, although only the first '''7''' characters are read by Fast-JX. ''Reactant 2'' will always be ''PHOTON''.

The settings for <tt>N</tt>, <tt>SCHEME</tt>, <tt>QUALIFIER</tt>, <tt>DISQUALIFIER</tt>, and <tt>VN</tt> are the same as in the [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_7#src.2Fscience.2Fcore.2Fchemistry.2Fukca_chem_master.F90|adding new tracers tutorial]], although here '''<tt>N</tt>''' should be incremented for each new '''reaction''', where there might be the same reaction specified several times with changes to reaction rates or even species.

Examples of this type are

! 3
! This should produce H+ CHO -> H + HO2 + CO in ST scheme.
ratj_t1(3,'HCHO ','PHOTON ','HO2 ','HO2 ','CO ', &
' ', 0.0,0.0,0.0,0.0, 100.000,'jhchoa ',ti+t+st+r+cs,0,0,107),&
! CS2
ratj_t1(3,'HCHO ','PHOTON ','HO2 ','HO2 ','CO ', &
' ', 0.0,0.0,0.0,0.0, 100.000,'jforma ',cs,0,0,119), &
ratj_t1(3,'HCHO ','PHOTON ','H ','CO ','HO2 ', &
' ', 0.0,0.0,0.0,0.0, 100.000,'jhchoa ',s,0,0,107) , &
! 4
ratj_t1(4,'HCHO ','PHOTON ','H2 ','CO ',' ', &
' ', 0.0,0.0,0.0,0.0, 100.0,'jhchob ',ti+s+t+st+r+cs,0,0,107),&
! CS2
ratj_t1(4,'HCHO ','PHOTON ','H2 ','CO ',' ', &
' ', 0.0,0.0,0.0,0.0, 100.0,'jformb ',cs,0,0,119), &

To add new photolysis reactions you will need to append equivalent lines for the new reactions to the end of the <tt>ratj_defs_master</tt> array (increasing the array size '''<tt>n_ratj_master</tt>''' accordingly), adding new files/code as necessary as described above.

==Task 8.1: Add a bimolecular reaction==

'''TASK 8.1:''' You should now add in the bimolecular reaction of '''ALICE''' with '''OH''' to form '''BOB''' and an optional '''''secondary organic compound''''' (labelled in UKCA as '''Sec_Org''') when aerosol chemistry is included. You should add this to both the StratTrop and CRI-Strat schemes using version '''131'''. This reaction is given by:

<math>
\textrm{ALICE} + \textrm{OH} \longrightarrow \textrm{BOB} + \textrm{Sec}\_\textrm{Org}
</math>

{| class="wikitable" border = "1px"
!style="text-align:top;"|Parameter
!style="text-align:top;"|Value
|-
| <math>k_{0}</math> || 2.70E-11
|-
| <math>\alpha</math> || 0.00
|-
| <math>\beta</math> || -390.00
|}

{| class="collapsible collapsed wikitable"
|-
! Hint
|-
| As <tt>Sec_Org</tt> is part of the aerosol chemistry, when it is included the reaction should be given the '''a''' qualifier. When it is not included the reaction should have the '''a''' as a disqualifier.
|-
| You should increment the value of <tt>n_bimol_master</tt> by the number of different reaction lines added.
|-
| You should increment the value of <tt>nr_therm</tt> accordingly.
|}

=== Python notebook ===

The Jupyter notebook

Tutorials/UMvn13.9/notebooks/BoxModel_T08.ipynb

and can be viewed online here

* [https://github.com/theabro/ukca_scripts/blob/master/Tutorials/UMvn13.9/notebooks/BoxModel_T08.ipynb BoxModel_T08.ipynb]

can be used to plot ALICE and BOB for this exercise.

===Solution to Task 8.1: Add a bimolecular reaction===

You were asked to:

* ''You should now add in the bimolecular reaction of '''ALICE''' with '''OH''' to form '''BOB''' and an optional '''''secondary organic compound''''' (labelled in UKCA as '''Sec_Org''') when aerosol chemistry is included. You should add this to both the StratTrop and CRI-Strat schemes using version '''131'''. This reaction is given by:''

<math>
\textrm{ALICE} + \textrm{OH} \longrightarrow \textrm{BOB} + \textrm{Sec}\_\textrm{Org}
</math>

{| class="wikitable" border = "1px"
!style="text-align:top;"|Parameter
!style="text-align:top;"|Value
|-
| <math>k_{0}</math> || 2.70E-11
|-
| <math>\alpha</math> || 0.00
|-
| <math>\beta</math> || -390.00
|}

<gallery widths=400px heights=350px>
Image:T04_alicebob_001.png|Evolution of ALICE and BOB during the simulation
Image:T04_alicebobflux_001.png|Flux through the ALICE+OH->BOB+Sec_Org reaction
</gallery>

The changes to UKCA are:

* https://code.metoffice.gov.uk/trac/ukca/changeset/7771/main/branches/dev/lukeabraham/um13.9_ukca_tutorial_solutions

Index: src/control/core/top_level/ukca_config_defs_mod.F90
===================================================================
--- src/control/core/top_level/ukca_config_defs_mod.F90 (revision 7770)
+++ src/control/core/top_level/ukca_config_defs_mod.F90 (revision 7771)
@@ -363,7 +363,7 @@
'C2H6 ','C3H8 ','Me2CO ','MeCHO ', &
'C5H8 ','MeOH ','NO_aircrft']
n_chem_tracers = 73 ! No chem tracers
- nr_therm = 220 ! thermal reactions
+ nr_therm = 221 ! thermal reactions
nr_phot = 55 ! photolytic (ATA)

ELSE ! If using aerosol chemistry
@@ -391,9 +391,9 @@
END IF
n_chem_tracers = 73 ! No chem tracers
IF (ukca_config%l_ukca_trophet) THEN
- nr_therm = 241 ! thermal reactions
+ nr_therm = 242 ! thermal reactions
ELSE
- nr_therm = 239 ! thermal reactions
+ nr_therm = 240 ! thermal reactions
END IF
nr_phot = 59 ! photolytic (ATA)

@@ -455,7 +455,7 @@
IF (ukca_config%i_ukca_chem_version >= 119) THEN ! CRI-Strat 2 w/o aerosol
n_chem_tracers = 173 ! advected chemical tracers (+9, -4)
n_aero_tracers = 0 ! DMS, SO2... aerosol precursor species
- nr_therm = 625 ! thermal reactions (+45 bimol, +8 termol)
+ nr_therm = 626 ! thermal reactions (+45 bimol, +8 termol)
nr_phot = 135 ! photolytic reacs
ELSE ! CRI-Strat without aerosol
n_chem_tracers = 166 ! advected chemical tracers
@@ -480,9 +480,9 @@
n_aero_tracers = 17 ! DMS, SO2... aerosol precursor species
nr_phot = 137 ! photolytic reacs
IF (ukca_config%l_ukca_trophet) THEN
- nr_therm = 644 ! thermal reactions (+45 bimol, +8 termol)
+ nr_therm = 645 ! thermal reactions (+45 bimol, +8 termol)
ELSE
- nr_therm = 646 ! thermal reactions (+45 bimol, +8 termol)
+ nr_therm = 647 ! thermal reactions (+45 bimol, +8 termol)
END IF
ELSE ! CRI-Strat with aerosol
n_chem_tracers = 166 ! advected chemical tracers
Index: src/science/core/chemistry/ukca_chem_master.F90
===================================================================
--- src/science/core/chemistry/ukca_chem_master.F90 (revision 7770)
+++ src/science/core/chemistry/ukca_chem_master.F90 (revision 7771)
@@ -107,7 +107,7 @@
INTEGER, PARAMETER :: n_het_master = 18 ! number of heterogeneous reactions
INTEGER, PARAMETER :: n_dry_master = 162 ! number of dry deposition reactions
INTEGER, PARAMETER :: n_wet_master = 160 ! number of wet deposition reactions
-INTEGER, PARAMETER :: n_bimol_master = 1212 ! number of bimolecular reactions
+INTEGER, PARAMETER :: n_bimol_master = 1214 ! number of bimolecular reactions
INTEGER, PARAMETER :: n_ratj_master = 183 ! number of photolysis reactions
INTEGER, PARAMETER :: n_ratt_master = 116 ! number of termolecular reactions

@@ -6237,7 +6237,13 @@
' ',3.93e-15, 0.00, 1913.00, 0.54, 0.00, 0.00, 0.00,r,0,0,107), &
! B745 - updates for 121
ratb_t1(745,'HO2 ','EtCO3 ','OH ','EtOO ','CO2 ', &
-' ',1.89e-13, 0.00, -1040.00, 0.00, 0.00, 0.00, 0.00,st,0,0,121) &
+' ',1.89e-13, 0.00, -1040.00, 0.00, 0.00, 0.00, 0.00,st,0,0,121), &
+! B746 - updates for 121 (ALICE & BOB tutorials) - aerosol chemistry
+ratb_t1(746,'ALICE ','OH ','BOB ','Sec_Org ',' ', &
+' ',2.70e-11, 0.00, -390.00, 0.00, 0.00, 0.00, 0.00,st+cs,a,0,121),&
+! B746 - updates for 121 (ALICE & BOB tutorials) - no aerosol chemistry
+ratb_t1(746,'ALICE ','OH ','BOB ',' ',' ', &
+' ',2.70e-11, 0.00, -390.00, 0.00, 0.00, 0.00, 0.00,st+cs,0,a,121) &
]

!----------------------------------------------------------------------

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task08.1/Task08.1_ukca.patch

Sample output from this task can be found here:

Tutorials/UMvn13.9/sample_output/Task08.1/

==Task 8.2: Change the initial condition of ALICE==

As both ALICE and BOB were initialised to very small concentrations (1.0e-15) and there are no emissions in the Box Model, ALICE is converted to BOB almost immediately.

'''TASK 8.2:''' You should now provide an initial conditions of '''ALICE''', setting it to 1.0e-9.

{| class="collapsible collapsed wikitable"
|-
! Hint
|-
| You will either need to edit the file specified by '''<tt>tracer_in_filename</tt>''', or make a copy of this, edit it to add the initialisation, and then use this new file in your Rose suite.
|}

As this is just an input file change you do not need to recompile.

===Solution to Task 8.2: Change the initial condition of ALICE===

You were asked to:

* ''You should now provide an initial conditions of '''ALICE''', setting it to 1.0e-9.''

<gallery widths=400px heights=350px>
Image:T04_alicebob_002.png|Evolution of ALICE and BOB during the simulation
Image:T04_alicebobflux_002.png|Flux through the ALICE+OH->BOB+Sec_Org reaction
</gallery>

The changes to Rose are:

* https://code.metoffice.gov.uk/trac/roses-u/changeset/337644/d/s/0/4/2/trunk

Index: app/ukca/file/chem_tracer_pars_STwGMaero_EqTropopause
===================================================================
--- app/ukca/file/chem_tracer_pars_STwGMaero_EqTropopause (revision 337643)
+++ app/ukca/file/chem_tracer_pars_STwGMaero_EqTropopause (revision 337644)
@@ -23,6 +23,7 @@
3.0000e-22 Monoterp
5.0000e-24 Sec_org
5.0000e-23 SO3
+1.0000e-09 ALICE
2.0000e-15 Nuc_SOL_N
4.0000e-11 Nuc_SOL_SU
2.0000e-17 Ait_SOL_N

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task08.2/Task08.2_rose.patch

Sample output from this task can be found here:

Tutorials/UMvn13.9/sample_output/Task08.2/

==Task 8.3: Use this reaction with a different chemistry scheme==

'''TASK 8.3:''' Now test that this reaction works with the CRI-Strat scheme without GLOMAP-mode aerosols included.

{| class="collapsible collapsed wikitable"
|-
! Solution
|-
| Change the value of <tt>i_ukca_chem</tt> to be '''<tt>59</tt>''' (CRI-Strat)
|-
| (Optional) set the value of <tt>l_ukca_mode</tt> to be '''False'''
|-
| Change the value of <tt>l_ukca_chem_aero</tt> to be '''False'''
|-
| Change the value of <tt>l_ukca_het_psc</tt> to be '''False'''
|}

This is just one example - you may also want to test this scheme with other combinations of StratTrop and CRI-Strat chemistry schemes, with and without GLOMAP-mode aerosols.

'''Note''' that changing these setting will automatically make lots of other changes to variables within Rose. '''''You do not need to worry about these additional changes.'''''

As this is just a namelist change you do not need to recompile.

===Worked Solution to Task 8.3: Use this reaction with a different chemistry scheme===

You were asked to:

* ''Now test that this reaction works with the CRI-Strat scheme without GLOMAP-mode aerosols included.''

<gallery widths=400px heights=350px>
Image:T04_alicebob_003.png|Evolution of ALICE and BOB during the simulation
Image:T04_alicebobflux_003.png|Flux through the ALICE+OH->BOB reaction
</gallery>

You were given the hints:

* ''Change the value of <tt>i_ukca_chem</tt> to be '''<tt>59</tt>''' (CRI-Strat)''
* ''(Optional) set the value of <tt>l_ukca_mode</tt> to be '''False'''''
* ''Change the value of <tt>l_ukca_chem_aero</tt> to be '''False'''''
* ''Change the value of <tt>l_ukca_het_psc</tt> to be '''False'''''

'''Note''' that here <tt>Sec_Org</tt> is now no longer a product of the reaction.

The changes to Rose are:

* https://code.metoffice.gov.uk/trac/roses-u/changeset/337645/d/s/0/4/2/trunk

Index: app/ukca/rose-app.conf
===================================================================
--- app/ukca/rose-app.conf (revision 337644)
+++ app/ukca/rose-app.conf (revision 337645)
@@ -479,14 +479,14 @@
!!i_ageair_reset_method=1
!!i_inferno_emi=
!!i_mode_bln_param_method=0
-i_mode_nzts=15
-i_mode_setup=2
-i_ukca_activation_scheme=0
-i_ukca_chem=51
+!!i_mode_nzts=15
+!!i_mode_setup=2
+!!i_ukca_activation_scheme=0
+i_ukca_chem=59
i_ukca_chem_version=121
i_ukca_conserve_method=3
-i_ukca_dms_flux=1
-i_ukca_hetconfig=0
+!!i_ukca_dms_flux=1
+!!i_ukca_hetconfig=0
!!i_ukca_hiorder_scheme=0
i_ukca_light_param=0
!!i_ukca_nwbins=20
@@ -510,8 +510,8 @@
!!l_dust_mp_slinn_impc_scav=.false.
l_environ_jo2=.false.
l_environ_jo2b=.false.
-l_mode_bhn_on=.true.
-l_mode_bln_on=.false.
+!!l_mode_bhn_on=.true.
+!!l_mode_bln_on=.false.
!!l_no3_prod_in_aero_step=.false.
l_ukca=.true.
l_ukca_ageair=.false.
@@ -519,7 +519,7 @@
!!l_ukca_aie2=.false.
l_ukca_asad_columns=.true.
l_ukca_asad_full=.false.
-l_ukca_chem_aero=.true.
+l_ukca_chem_aero=.false.
!!l_ukca_classic_hetchem=.false.
!!l_ukca_coarse_no3_prod=.true.
l_ukca_ddep_lev1=.false.
@@ -527,59 +527,59 @@
l_ukca_debug_asad=.true.
l_ukca_dry_dep_so2wet=.false.
!!l_ukca_dust=.false.
-l_ukca_emsdrvn_ch4=.false.
+!!l_ukca_emsdrvn_ch4=.false.
!!l_ukca_fine_no3_prod=.true.
l_ukca_h2o_feedback=.false.
-l_ukca_het_psc=.true.
+l_ukca_het_psc=.false.
l_ukca_ibvoc=.false.
-l_ukca_inferno=.false.
+!!l_ukca_inferno=.false.
!!l_ukca_inferno_ch4=.false.
l_ukca_intdd=.true.
l_ukca_intph=.false.
-l_ukca_limit_nat=.false.
+!!l_ukca_limit_nat=.false.
l_ukca_linox_scaling=.false.
-l_ukca_mode=.true.
+!!l_ukca_mode=.false.
l_ukca_prescribech4=.false.
!!l_ukca_prim_moc=.false.
-l_ukca_primbcoc=.false.
+!!l_ukca_primbcoc=.false.
!!l_ukca_primdu=.false.
-l_ukca_primss=.false.
-l_ukca_primsu=.false.
+!!l_ukca_primss=.false.
+!!l_ukca_primsu=.false.
l_ukca_qch4inter=.false.
l_ukca_quasinewton=.false.
-l_ukca_radaer=.false.
+!!l_ukca_radaer=.false.
!!l_ukca_radaer_sustrat=.false.
l_ukca_radch4=.false.
-l_ukca_radf11=.false.
-l_ukca_radf113=.false.
-l_ukca_radf12=.false.
-l_ukca_radf22=.false.
+!!l_ukca_radf11=.false.
+!!l_ukca_radf113=.false.
+!!l_ukca_radf12=.false.
+!!l_ukca_radf22=.false.
l_ukca_radn2o=.false.
l_ukca_rado3=.false.
l_ukca_ro2_ntp=.true.
l_ukca_ro2_perm=.true.
-l_ukca_sa_clim=.false.
-l_ukca_scale_biom_aer_ems=.false.
+!!l_ukca_sa_clim=.false.
+!!l_ukca_scale_biom_aer_ems=.false.
!!l_ukca_scale_marine_pom_ems=.false.
!!l_ukca_scale_sea_salt_ems=.false.
-l_ukca_scale_seadms_ems=.false.
+!!l_ukca_scale_seadms_ems=.false.
!!l_ukca_scale_soa_yield_isop=.false.
-l_ukca_scale_soa_yield_mt=.false.
+!!l_ukca_scale_soa_yield_mt=.false.
l_ukca_set_trace_gases=.true.
!!l_ukca_sfix=.false.
-l_ukca_so2ems_expvolc=.false.
+!!l_ukca_so2ems_expvolc=.false.
!!l_ukca_so2ems_plumeria=.false.
!!l_ukca_src_in_conservation=.true.
-l_ukca_trophet=.false.
+!!l_ukca_trophet=.false.
!!l_ukca_use_background_aerosol=.false.
lightnox_scale_fac=0.5
!!marine_pom_ems_scaling=0
!!max_ageair_reset_height=0.0
!!max_ageair_reset_level=0
-mode_activation_dryr=37.5
-mode_aitsol_cvscav=0.5
-mode_incld_so2_rfrac=0.25
-mode_parfrac=2.5
+!!mode_activation_dryr=37.5
+!!mode_aitsol_cvscav=0.5
+!!mode_incld_so2_rfrac=0.25
+!!mode_parfrac=2.5
!!nerupt=0
!!nit=0
nrsteps=45
@@ -640,7 +640,7 @@
l_fix_ukca_impscav=.false.
!!l_fix_ukca_offox_h2o_fac=.false.
l_fix_ukca_water_content=.false.
-l_improve_aero_drydep=.false.
+!!l_improve_aero_drydep=.false.
!!l_improve_cv_cons=.false.
l_methox_fix=.true.

@@ -649,5 +649,5 @@
!!a_convect_segments=-99
!!a_convect_trac_seg_size=1
ukca_chem_seg_size=1
-ukca_mode_seg_size=1
+!!ukca_mode_seg_size=1
ussp_seg_size=1

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task08.3/Task08.3_rose.patch

Sample output from this task can be found here:

Tutorials/UMvn13.9/sample_output/Task08.3/

==Checklist==

: ☐ Add the new reaction into the correct reaction type array in <tt>ukca_chem_master.F90</tt>, incrementing the size of the array accordingly.
: ☐ Increment the value of <tt>nr_therm</tt> and/or <tt>nr_phot</tt> in <tt>ukca_config_defs_mod.F90</tt>.
: ☐ If required, add special code to the <tt>asad_bimol.F90</tt>, <tt>asad_trimol.F90</tt>, <tt>ukca_hetero_mod.F90</tt>, or <tt>asad_hetero.F90</tt> routines.
: ☐ For photolysis reactions, further work is required to calculate new cross sections. Code will also need to be added to <tt>ukca_strat_update.F90</tt>.
: ☐ Add initialisations of your new tracers if required.
: ☐ Test your new chemistry with different chemistry schemes and aerosol options as necessary.

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

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

UKCA Chemistry and Aerosol UMvn13.9 Tutorial 6

2026-03-19T14:11:06Z

Nla27:

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

{| class="wikitable" border = "1px"
|-
| Difficulty || '''HARD'''
|-
| Time to Complete || '''2 or more hours'''
|-
| Video instructions || https://www.youtube.com/watch?v=aysibeNdLUY&t=6351s
|}

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

==What you will learn in this Tutorial==

In this tutorial you will learn how to output and process aerosol diagnostics from UKCA.

===Python===

In this Tutorial you will make extensive use of Python to process the UM output. Instructions as to how to use this are in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_5#Using_python_to_regrid_your_emissions|Tutorial 5]].

Example python scripts are provided for each Task, and you should take the time to read through these and understand what they are doing. None of these scripts plot any of the output, so as an extension to these tasks you could try extending the scripts to plot the output from python directly, rather than visualising via Xconv. Further information (and examples) on how Iris plots can be found here:

* https://scitools-iris.readthedocs.io/en/latest/userguide/plotting_a_cube.html
* https://scitools-iris.readthedocs.io/en/latest/generated/gallery/general/plot_global_map.html

==Task 6.1: Output aerosol diagnostics==

'''TASK 6.1:''' Output the following aerosol and radiation diagnostics to a new '''UPL''' output stream that reinitialises every 3 hours. You should make a new ''time profile'' (called TRAD) to only output these on '''radiation timesteps'''. You will also need to make a new ''domain profile'' (called D3DAR) for s02i530 and s02i540, to '''output these on both model levels and pseudo levels'''.

{| class="collapsible collapsed wikitable"
|-
! Hint
|-
| Incoming and outgoing radiation are single-level fields that should be output using the DIAG profile.
|-
| Remember to output your aerosol diagnostics on the AOT pseudo levels using the DIAGAOT profile.
|}

{| class="wikitable" border = "1px"
!style="text-align:top;"|STASH Section
!style="text-align:top;"|STASH Item
!style="text-align:top;"|STASH Name
|- style="background:lightgrey;"
| 1 || 207 || INCOMING SW RAD FLUX (TOA): ALL TSS
|- style="background:lightgrey;"
| 1 || 208 || OUTGOING SW RAD FLUX (TOA)
|- style="background:lightgrey;"
| 2 || 205 || OUTGOING LW RAD FLUX (TOA)
|-
| 2 || 285 || MINERAL DUST OPTICAL DEPTH IN RADN.
|-
| 2 || 300 || AITKEN MODE (SOLUBLE) OPTICAL DEPTH
|-
| 2 || 301 || ACCUM MODE (SOLUBLE) OPTICAL DEPTH
|-
| 2 || 302 || COARSE MODE (SOLUBLE) OPTICAL DEPTH
|-
| 2 || 303 || AITKEN MODE (INSOL) OPTICAL DEPTH
|-
| 2 || 304 || ACCUM MODE (INSOL) OPTICAL DEPTH
|-
| 2 || 305 || COARSE MODE (INSOL) OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 585 || MINERAL DUST ABS. OPICAL DEPTH
|- style="background:lightgrey;"
| 2 || 240 || AITKEN (SOLUBLE) ABS OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 241 || ACCUM (SOLUBLE) ABS OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 242 || COARSE (SOLUBLE) ABS OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 243 || AITKEN (INSOL) ABS OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 244 || ACCUM (INSOL) ABS OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 245 || COARSE (INSOL) ABS OPTICAL DEPTH
|-
| 2 || 530 || UKCA 3D AEROSOL EXTINCTION
|-
| 2 || 540 || CLASSIC 3D AEROSOL EXTINCTION
|}

==Radiation Timesteps==

The number of shortwave radiation timesteps per day is given by '''<tt>i_sw_radstep_perday_prog</tt>''', found in '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> UM Science Settings <math>\rightarrow</math> Section 01 - 02 Radiation <math>\rightarrow</math> Shortwave'''. The equivalent for longwave is '''<tt>i_lw_radstep_perday_prog</tt>''', found in '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> UM Science Settings <math>\rightarrow</math> Section 01 - 02 Radiation <math>\rightarrow</math> Longwave'''.

In the UKCA training suite, both of these are set to '''16''', i.e. a call every 90 minutes. This value is very configuration dependent - sometimes radiation is called every hour (24), sometimes every 3 hours (8) etc. You should check the settings in your suite if you need to consider any of the radiation diagnostics.

==Making new STASH profiles==

While we have covered outputting and analysing diagnostics in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_4|Tutorial 4]] and [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_5|Tutorial 5]] you were only making use of existing settings for the different "profiles" that define how the diagnostics are considered in space and time.

Here you will learn how to make new '''time''', '''domain''', and '''usage''' profiles.

===Time profiles===

[[Image:UM11.8_newtime.png|thumb|300px|right|The new time panel in Rose.]]
To make a new time profile, go to: '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> STASH Requests and Profiles <math>\rightarrow</math> Time Profiles'''. This contains a list of existing time profiles, with names like ''<tt>t3hmn_039ecafe</tt>'' etc.

To make a new time profile, you should:

# Right-click anywhere on the list and click the green plus symbol ('''+''') named '''Add new section'''
#: This will make a new blank line (usually labelled '''1''', the next '''2''' etc.) with a red '''X''' next to it.
# Right-click this new line and click '''View namelist'''.
# Fill-in the values as required for what you want to do.
# When you have finished, you will need to run the When you have finished, you will need to run the '''stashindices.TidyStashTransform''' macro by going to the '''Metadata <math>\rightarrow</math> um''' drop-down menu. This will rename the new profile into the correct format.

====Example: Output on Radiation Timesteps====

You will have discovered that there are 16 radiation timesteps per day, but to work out how to output diagnostics you need to know many model timesteps per day there are. This can be found at: '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Top Level Model Control <math>\rightarrow</math> Model Domain and Timestep'''. The number is given by the variable '''<tt>steps_per_periodim</tt>''', which is defined as the number of steps per period given (in seconds) by '''<tt>secs_per_periodim</tt>'''. For one day, this value is 86400 (24h x 60m x 60s).

In the UKCA training suite, <tt>secs_per_periodim</tt>=86400, and <tt>steps_per_periodim</tt>=48. This means that there are 48 timesteps per day, i.e. each timestep is '''30 minutes'''.

We can combine this with the number of radiation timesteps per day (16), to calculate that '''radiation is called every third model timestep''' (48/16 = 3) in this configuration. We can now fill-in the values in the new time profile accordingly, e.g.

* '''<tt>ityp</tt>:''' No time processing
* '''<tt>tim_name</tt>:''' e.g. TRAD
* '''<tt>unt3</tt>:''' Timesteps (1)
* '''<tt>iopt</tt>:''' Regular intervals
* '''<tt>istr</tt>:''' 1 (i.e. start on first timestep)
* '''<tt>iend</tt>:''' -1 (i.e. never stop outputting)
* '''<tt>ifre</tt>:''' 3 (i.e. output every third timestep)

We need to start at timestep 1, as radiation is called on the first timestep, and then called every third model timestep after that. In contrast, the UKCA Newton-Raphson chemical solver is first called on the first hour, and then every hour after that. For the UKCA training suite this would mean that <tt>istr</tt>=2 and <tt>ifre</tt>=2, but for standard UKCA runs at N96eL85 with a 20-minute timestep this would have <tt>istr</tt>=3 and <tt>ifre</tt>=3.

===Domain profiles===

[[Image:Vn10.9_newdom.png|thumb|300px|right|The new domain panel in Rose.]]
To make a new domain profile, go to: '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> STASH Requests and Profiles <math>\rightarrow</math> Domain Profiles'''. This contains a list of existing domain profiles, with names like ''<tt>dallth_1e2e730d</tt>'' etc.

To make a new domain profile, you should:

# Right-click anywhere on the list and click the green plus symbol ('''+''') named '''Add new section'''
#: This will make a new blank line (usually labelled '''1''', the next '''2''' etc.) with a red '''X''' next to it.
# Right-click this new line and click '''View namelist'''.
# Fill-in the values as required for what you want to do.
# When you have finished, you will need to run the When you have finished, you will need to run the '''stashindices.TidyStashTransform''' macro by going to the '''Metadata <math>\rightarrow</math> um''' drop-down menu. This will rename the new profile into the correct format.

====Example: Output AOT pseudo levels on all model theta levels====

Aerosol diagnostics are defined on a series of 6 '''pseudo levels''', corresponding to 0.38, 0.44, 0.55, 0.67, 0.87, and 1.02 microns. You will therefore need to output on your data on all of these. For some diagnostics, such as AOD, these are defined on a single level, but others, such as extinction, are a 3D field over the whole atmosphere. Therefore, to output the 3D aerosol extinction we need to make a new profile over all model (theta grid) levels, ''and'' all 6 pseudo levels.

We can now fill-in the values in the new domain profile accordingly, e.g.

* '''<tt>dom_name</tt>:''' e.g. D3DAR
* '''<tt>iopl</tt>:''' Variable derived on model theta levels (Charney-Phillips Grid) (2)
* '''<tt>ilevs</tt>:''' provide range <nowiki>[</nowiki>bottom and top level numbers<nowiki>]</nowiki>
* '''<tt>ilevb</tt>:''' 1 (i.e. 20m level)
* '''<tt>ilevt</tt>:''' 38 (i.e. highest level)
* '''<tt>plt</tt>:''' Radiation bands for calculating aerosol optical depth (4)
: This will then insert a new option below (<tt>pslist</tt>) to allow you to specify the bands you require.
* '''<tt>pslist</tt>:''' press the green plus symbol ('''+''') 5 times, and enter the numbers 1 to 6 in each of the boxes to output all AOT pseudo levels.
* '''<tt>iopa</tt>:''' Full model area (1)
* '''<tt>imsk</tt>:''' Land and sea points
* '''<tt>imn</tt>:''' None (0)
* '''<tt>iwt</tt>:''' None
* '''<tt>ts</tt>:''' false

===Usage profiles===

[[Image:Vn10.9_newuse.png|thumb|300px|right|The new usage panel in Rose.]]
Making new usage profiles is not as straight-forward as for time and domain profiles, as these are used to output diagnostics to different output files (and possibly to climate mean files). To see what output streams are available, go to: '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> Model Output Streams'''. In the UKCA training suite, only '''pp0''' is active. As part of this tutorial you will need to make a new output stream.

For most modern UM jobs, climate meaning is off. However, to look at climate meaning, go to: '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> Dumping and Meaning'''. This is controlled by the logical '''<tt>l_meaning_sequence</tt>''', which in the UKCA training suite is set to '''false''' (i.e. no climate meaning). If this is set to ''true'' then various settings will need to be chosen, such as the reference time, the frequency of files, and which files to output.

To view the usage profiles, go to: '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> STASH Requests and Profiles <math>\rightarrow</math> Usage Profiles'''. This contains a list of existing domain profiles, with names like ''<tt>upa_ffb3f00b</tt>'' etc. If you look at the '''upa''' namelist (by right-clicking on it and clicking '''view namelist''') you can see that this corresponds with the ''pp0'' output stream. For this tutorial you will make a new usage profile and link it to your new output stream.

It is also possible to write diagnostics to a '''tag''', which can then be read by other parts of the code. This is how UKCA couples to the UM, via tag=98. This can be seen in the '''upukca''' usage profile.

When you take a copy of an existing configuration it is unlikely that you will need to make any changes to any (or make new) usage profiles. However, if you do want to make a new usage profile, you should first make a new output stream:

# Go to '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> Model Output Streams''' and right-click anywhere on the list and click the green plus symbol ('''+''') named '''Add new section'''.
#: This will make a new blank line (usually labelled '''1''', the next '''2''' etc.) with a red '''X''' next to it.
# Right-click this new line and click '''View namelist'''.
# Fill-in the values as required for what you want to do.
# When you have finished, you will need to rename this output stream via the right-hand menu by right-clicking on the entry.
# Then go to '''um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> STASH Requests and Profiles <math>\rightarrow</math> Usage Profiles''', right-click anywhere on the list and click the green plus symbol ('''+''') named '''Add new section'''.
#: This will make a new blank line (usually labelled '''1''', the next '''2''' etc.) with a red '''X''' next to it.
# Right-click this new line and click '''View namelist'''.
# Fill-in the values as required for what you want to do.
# When you have finished, you will need to run the When you have finished, you will need to run the '''stashindices.TidyStashTransform''' macro by going to the '''Metadata <math>\rightarrow</math> um''' drop-down menu. This will rename the new profile into the correct format.

'''Note''' that if you are making a new usage profile that is not associated with a ''tag'', you may also need to make changes to the output streams. This could be quite involved.

====Example: Make a new UPL usage profile and corresponding pp11 output stream====

You will need to make the model output stream first, as described above and then fill in the values as below to make a stream and reinitialises every 3 hours. Note that text beginning with <tt>$</tt>, e.g. <tt>$ROSE_DATAC</tt> are ''environment variables'' used within Rose that usually point to directory paths or auto-generated names. For example, ${RUNID} will resolve as the suite-id.

* '''<tt>file_id</tt>:''' e.g. pp11
* '''<tt>filename</tt>:''' e.g. $ROSE_DATAC/$RUNID.pp11
* '''<tt>packing</tt>:''' (here we will use the same as UPA) 'New Climate' (5)
* '''<tt>reserved_headers</tt>:''' here we will set this to a large enough number, e.g. 16000. Sometimes you will get error messages telling you that "the number of fields exceeds reserved headers", and a solution to this is to increase this number further.
* '''<tt>l_reinit</tt>:''' True
: This will then give you the following options for reinitialisation of the file. It will also remove the <tt>filename</tt> attribute which may not be needed but is best to provide.
* '''<tt>filename_base</tt>:''' e.g. $DATAM/${RUNID}a.pl%C
* '''<tt>reinit_unit</tt>:''' 'Hours' (1)
* '''<tt>reinit_start</tt>:''' 0 (i.e. start straight away)
* '''<tt>reinit_end</tt>:''' -1 (i.e. never stop)
* '''<tt>reinit_step</tt>:''' 3

This will just have a name of e.g. '1' at this point. To rename this to e.g. 'pp11' you will need to find it in the list on the right-hand panel under "Model Output Streams", right-click it, select "rename a section", and change the e.g.

namelist:nlstcall_pp(1)

to be

namelist:nlstcall_pp(pp11)

Now you need to make your new usage profile as described above, and fill in the values as below to use this new model output stream, e.g.

* '''<tt>use_name</tt>:''' e.g. UPL
* '''<tt>locn</tt>:''' To be written to a FF output stream with supplied file ID (3)
: This will then give you the option below (<tt>file_id</tt>) to allow you to specify the output stream ID you defined above
* '''<tt>file_id</tt>:''' e.g. pp11 (as you defined above)

The run the TidyStashTransform macro to give this usage profile a correct name.

===Using your new profiles===

Once you have made your new profiles you should then use them in the usual way when outputting diagnostics, as covered in [[UKCA_Chemistry_and_Aerosol_vn11.8_Tutorial_3#STASH_Panel|Tutorial 3]].

When all your new STASH is set-up, you can use the Validator Macros to check if the names are correct, or if there are any unused STASH items etc. To run this, go to '''Metadata <math>\rightarrow</math> Check all Validator Macros''' from the drop-down menu. You can also check for ''fail-if'' or ''warn-if'' issues. However, these won't warn of incorrect domain requests (i.e. requesting pressure-levels for diagnostics only defined on a single level), so some care should still be taken.

==Solution to Task 6.1==

You were given the task

* ''Output the following aerosol and radiation diagnostics to a new '''UPL''' output stream that reinitialises every 3 hours. You should make a new ''time profile'' (called TRAD) to only output these on '''radiation timesteps'''. You will also need to make a new ''domain profile'' (called D3DAR) for s02i530 and s02i540, to '''output these on both model levels and pseudo levels'''.''

{| class="wikitable" border = "1px"
!style="text-align:top;"|STASH Section
!style="text-align:top;"|STASH Item
!style="text-align:top;"|STASH Name
|- style="background:lightgrey;"
| 1 || 207 || INCOMING SW RAD FLUX (TOA): ALL TSS
|- style="background:lightgrey;"
| 1 || 208 || OUTGOING SW RAD FLUX (TOA)
|- style="background:lightgrey;"
| 2 || 205 || OUTGOING LW RAD FLUX (TOA)
|-
| 2 || 285 || MINERAL DUST OPTICAL DEPTH IN RADN.
|-
| 2 || 300 || AITKEN MODE (SOLUBLE) OPTICAL DEPTH
|-
| 2 || 301 || ACCUM MODE (SOLUBLE) OPTICAL DEPTH
|-
| 2 || 302 || COARSE MODE (SOLUBLE) OPTICAL DEPTH
|-
| 2 || 303 || AITKEN MODE (INSOL) OPTICAL DEPTH
|-
| 2 || 304 || ACCUM MODE (INSOL) OPTICAL DEPTH
|-
| 2 || 305 || COARSE MODE (INSOL) OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 585 || MINERAL DUST ABS. OPICAL DEPTH
|- style="background:lightgrey;"
| 2 || 240 || AITKEN (SOLUBLE) ABS OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 241 || ACCUM (SOLUBLE) ABS OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 242 || COARSE (SOLUBLE) ABS OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 243 || AITKEN (INSOL) ABS OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 244 || ACCUM (INSOL) ABS OPTICAL DEPTH
|- style="background:lightgrey;"
| 2 || 245 || COARSE (INSOL) ABS OPTICAL DEPTH
|-
| 2 || 530 || UKCA 3D AEROSOL EXTINCTION
|-
| 2 || 540 || CLASSIC 3D AEROSOL EXTINCTION
|}

and were given the hints

:* ''Incoming and outgoing radiation are single-level fields that should be output using the DIAG profile.''
:* ''Remember to output your aerosol diagnostics on the AOT pseudo levels using the DIAGAOT profile.''

The specific Rose changes made are:

* https://code.metoffice.gov.uk/trac/roses-u/changeset/337623/d/u/5/1/6/trunk

The specific Rose changes made are:

Index: app/um/rose-app.conf
===================================================================
--- app/um/rose-app.conf (revision 337614)
+++ app/um/rose-app.conf (revision 337623)
@@ -1679,6 +1679,18 @@
reinit_unit=2
reserved_headers=16000

+[namelist:nlstcall_pp(pp11)]
+file_id='pp11'
+!!filename='$ROSE_DATAC/$RUNID.pp11'
+filename_base='$DATAM/${RUNID}a.pl%C'
+l_reinit=.true.
+packing=5
+reinit_end=-1
+reinit_start=0
+reinit_step=3
+reinit_unit=1
+reserved_headers=16000
+
[!namelist:nlstcall_pp(pp2)]
file_id='pp2'
!!filename='$ROSE_DATAC/$RUNID.pp2'
@@ -3423,6 +3435,40 @@
ukca_mode_seg_size=4
ussp_seg_size=32

+[namelist:umstash_domain(d3dar_17f7e88a)]
+dom_name='D3DAR'
+!!iest=0
+ilevs=1
+imn=0
+imsk=1
+!!inth=0
+iopa=1
+iopl=2
+!!isth=0
+!!iwst=0
+iwt=0
+!!l_spml_ts=.false.
+levb=1
+!!levlst=0
+levt=38
+plt=4
+pslist=1,2,3,4,5,6
+!!rlevlst=0
+!!spml_bot=0
+!!spml_ew=0
+!!spml_ns=0
+!!spml_top=0
+!!tblim=0
+!!tblimr=0
+!!telim=0
+!!tnlim=0
+ts=.false.
+!!tslim=0
+!!tsnum=0
+!!ttlim=0
+!!ttlimr=0
+!!twlim=0
+
[namelist:umstash_domain(dallrh_0496a967)]
dom_name='DALLRH'
!!iest=0
@@ -3704,6 +3750,22 @@
tim_name='TALLTS'
use_name='UPUKCA'

+[namelist:umstash_streq(01207_a27dd756)]
+dom_name='DIAG'
+isec=1
+item=207
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(01208_3171c632)]
+dom_name='DIAG'
+isec=1
+item=208
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
[namelist:umstash_streq(01235_3511dd9f)]
dom_name='DIAG'
isec=1
@@ -3712,6 +3774,78 @@
tim_name='TALLTS'
use_name='UPUKCA'

+[namelist:umstash_streq(02205_f31b05b3)]
+dom_name='DIAG'
+isec=2
+item=205
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02240_428b5acd)]
+dom_name='DIAGAOT'
+isec=2
+item=240
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02241_83ebc205)]
+dom_name='DIAGAOT'
+isec=2
+item=241
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02242_5a8d74dc)]
+dom_name='DIAGAOT'
+isec=2
+item=242
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02243_b109987d)]
+dom_name='DIAGAOT'
+isec=2
+item=243
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02244_4874edcf)]
+dom_name='DIAGAOT'
+isec=2
+item=244
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02245_87d0662f)]
+dom_name='DIAGAOT'
+isec=2
+item=245
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02285_8370d4a7)]
+dom_name='DIAGAOT'
+isec=2
+item=285
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02300_4fd94c8e)]
+dom_name='DIAGAOT'
+isec=2
+item=300
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
[namelist:umstash_streq(02301_0f7c5f4a)]
dom_name='DIAGAOT'
isec=2
@@ -3720,6 +3854,70 @@
tim_name='T3HMN'
use_name='UPA'

+[namelist:umstash_streq(02301_5045b5d3)]
+dom_name='DIAGAOT'
+isec=2
+item=301
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02302_3c823c55)]
+dom_name='DIAGAOT'
+isec=2
+item=302
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02303_875ad30f)]
+dom_name='DIAGAOT'
+isec=2
+item=303
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02304_a6a633dd)]
+dom_name='DIAGAOT'
+isec=2
+item=304
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02305_43befd1e)]
+dom_name='DIAGAOT'
+isec=2
+item=305
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02530_a52da11d)]
+dom_name='D3DAR'
+isec=2
+item=530
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02540_025da8d5)]
+dom_name='D3DAR'
+isec=2
+item=540
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
+[namelist:umstash_streq(02585_c0486d2f)]
+dom_name='DIAGAOT'
+isec=2
+item=585
+package=''
+tim_name='TRAD'
+use_name='UPL'
+
[namelist:umstash_streq(03025_c8768f77)]
dom_name='DIAG'
isec=3
@@ -4190,6 +4388,25 @@
!!unt2=2
unt3=1

+[namelist:umstash_time(trad_acd872d3)]
+!!iedt=0
+iend=-1
+ifre=3
+!!intv=0
+!!ioff=0
+iopt=1
+!!isam=0
+!!isdt=0
+!!iser=0
+istr=1
+!!itimes=0
+ityp=1
+!!lts0=.false.
+tim_name='TRAD'
+!!unt1=1
+!!unt2=1
+unt3=1
+
[namelist:umstash_use(upa_ffb3f00b)]
file_id='pp0'
locn=3
@@ -4256,6 +4473,12 @@
!!macrotag=0
use_name='UPK'

+[namelist:umstash_use(upl_b3d59e31)]
+file_id='pp11'
+locn=3
+!!macrotag=0
+use_name='UPL'
+
[namelist:umstash_use(upukca_bde064da)]
!!file_id=''
locn=6

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task06.1/Task06.1_ukca.patch

Sample output from this task can be found at

Tutorials/UMvn13.9/sample_output/Task06.1/

If you open the '''.pl''' file in Xconv, you should see the following additional fields:

0 : 96 72 1 2 field200: INCOMING SW RAD FLUX (TOA): ALL TSS
1 : 96 72 1 2 field201: OUTGOING SW RAD FLUX (TOA)
2 : 96 72 1 2 olr: OUTGOING LW RAD FLUX (TOA)
3 : 96 72 6 2 unspecified: AITKEN (SOLUBLE) ABS OPTICAL DEPTH
4 : 96 72 6 2 unspecified: ACCUM (SOLUBLE) ABS OPTICAL DEPTH
5 : 96 72 6 2 unspecified: COARSE (SOLUBLE) ABS OPTICAL DEPTH
6 : 96 72 6 2 unspecified: AITKEN (INSOL) ABS OPTICAL DEPTH
7 : 96 72 6 2 unspecified: ACCUM (INSOL) ABS OPTICAL DEPTH
8 : 96 72 6 2 unspecified: COARSE (INSOL) ABS OPTICAL DEPTH
9 : 96 72 6 2 unspecified: MINERAL DUST OPTICAL DEPTH IN RADN.
10 : 96 72 6 2 unspecified: AITKEN MODE (SOLUBLE) OPTICAL DEPTH
11 : 96 72 6 2 unspecified: ACCUM MODE (SOLUBLE) OPTICAL DEPTH
12 : 96 72 6 2 unspecified: COARSE MODE (SOLUBLE) OPTICAL DEPTH
13 : 96 72 6 2 unspecified: AITKEN MODE (INSOL) OPTICAL DEPTH
14 : 96 72 6 2 unspecified: ACCUM MODE (INSOL) OPTICAL DEPTH
15 : 96 72 6 2 unspecified: COARSE MODE (INSOL) OPTICAL DEPTH
16 : 96 72 38 2 unspecified: UKCA 3D AEROSOL EXTINCTION
17 : 96 72 38 2 unspecified: UKCA 3D AEROSOL EXTINCTION
18 : 96 72 38 2 unspecified: UKCA 3D AEROSOL EXTINCTION
19 : 96 72 38 2 unspecified: UKCA 3D AEROSOL EXTINCTION
20 : 96 72 38 2 unspecified: UKCA 3D AEROSOL EXTINCTION
21 : 96 72 38 2 unspecified: UKCA 3D AEROSOL EXTINCTION
22 : 96 72 38 2 unspecified: CLASSIC 3D AEROSOL EXTINCTION
23 : 96 72 38 2 unspecified: CLASSIC 3D AEROSOL EXTINCTION
24 : 96 72 38 2 unspecified: CLASSIC 3D AEROSOL EXTINCTION
25 : 96 72 38 2 unspecified: CLASSIC 3D AEROSOL EXTINCTION
26 : 96 72 38 2 unspecified: CLASSIC 3D AEROSOL EXTINCTION
27 : 96 72 38 2 unspecified: CLASSIC 3D AEROSOL EXTINCTION
28 : 96 72 6 2 unspecified: MINERAL DUST ABS. OPICAL DEPTH

==Task 6.2: Calculate aerosol optical depth==

'''TASK 6.2:''' Calculate the aerosol optical depth at 0.55 microns on the second radiation timestep.

{| class="collapsible collapsed wikitable"
|-
! Hint
|-
| The UM calculates optical depth diagnostics on 6 pseudo levels corresponding to 0.38, 0.44, 0.55, 0.67, 0.87, and 1.02 microns, therefore 0.55 microns is pseudo level 3.
|}

'''Note:''' You will need to use the CLASSIC mineral dust optical depth diagnostic, as the configuration used in these tutorials does not use modal dust. Likewise, the insoluble accumulation and coarse mode diagnostics will be zero as these modes are not used in the configuration used here.

===Python notebook===

To calculate the total aerosol optical depth at 0.55 microns, you should sum up the contribution from the different aerosol components.

Example python notebooks to do this have been provided at

Tutorials/UMvn13.9/notebooks/iris_UM-UKCA_T062.ipynb

and can be seen online here

* [https://github.com/theabro/ukca_scripts/blob/master/Tutorials/UMvn13.9/notebooks/iris_UM-UKCA_T062.ipynb iris_UM-UKCA_T062.ipynb]

==Solution to Task 6.2 ==

<gallery widths=300px heights=200px>
Image:UM139_T062_aod.png|0.55 micron AOD calculated from the component aerosol AOD diagnostics.
</gallery>

You were asked to

* ''Calculate the aerosol optical depth at 0.55 microns on the second radiation timestep.''

and were given the hint

:* ''The UM calculates optical depth diagnostics on 6 pseudo levels corresponding to 0.38, 0.44, 0.55, 0.67, 0.87, and 1.02 microns, therefore 0.55 microns is pseudo level 3.''

You should make use of the python notebook provided to do this.

Sample output from this task can be found at

Tutorials/UMvn13.9/sample_output/Task06.2/

==Task 6.3: Calculate the single-scattering albedo==

'''TASK 6.3:''' Calculate the single-scattering albedo at 0.55 microns on the second radiation timestep, defined as: 

<math>
1 - \left(\frac{\textrm{Absorption}\ \textrm{Aerosol}\ \textrm{Optical}\ \textrm{Depth}}{\textrm{Aerosol}\ \textrm{Optical}\ \textrm{Depth}}\right)
</math>

===Python notebook===

To calculate the single-scattering albedo at 0.55 microns, you should sum up the contribution to AAOD and AOD from the different aerosol components.

Example python notebooks to do this have been provided at

Tutorials/UMvn13.9/notebooks/iris_UM-UKCA_T063.ipynb

and can be seen online here

* [https://github.com/theabro/ukca_scripts/blob/master/Tutorials/UMvn13.9/notebooks/iris_UM-UKCA_T063.ipynb iris_UM-UKCA_T063.ipynb]

==Solution to Task 6.3 ==

<gallery widths=300px heights=200px>
Image:UM139_T063_ssa.png|0.55 micron single-scattering albedo.
</gallery>

You were asked to

* ''Calculate the single-scattering albedo at 0.55 microns on the second radiation timestep, defined as:''

<math>
1 - \left(\frac{\textrm{Absorption}\ \textrm{Aerosol}\ \textrm{Optical}\ \textrm{Depth}}{\textrm{Aerosol}\ \textrm{Optical}\ \textrm{Depth}}\right)
</math>

You should use the python notebook provided to do this.

Sample output from this task can be found at

Tutorials/UMvn13.9/sample_output/Task06.3/

==Task 6.4: Calculate the top of the atmosphere net downward radiative flux==

'''TASK 6.4:''' Calculate the net downward top of the atmosphere radiative flux on the second radiation timestep.

===Python notebook===

To calculate the net TOA downward radiative flux, you should sum up the outgoing contributions from shortwave and longwave radiation, and take this away from the incoming shortwave radiative flux.

Example python notebooks to do this have been provided at

Tutorials/UMvn13.9/notebooks/iris_UM-UKCA_T064.ipynb

and can be seen online here

* [https://github.com/theabro/ukca_scripts/blob/master/Tutorials/UMvn13.9/notebooks/iris_UM-UKCA_T064.ipynb iris_UM-UKCA_T064.ipynb]

==Solution to Task 6.4 ==

<gallery widths=300px heights=200px>
Image:UM139_T064_toa.png|Net downward TOA radiative flux.
</gallery>

You were asked to

* ''Calculate the net downward top of the atmosphere radiative flux on the second radiation timestep.''

You should use the python notebook provided to do this.

Sample output from this task can be found at

Tutorials/UMvn13.9/sample_output/Task06.4/

==Task 6.5: Calculate aerosol optical depth from the 3D aerosol extinction==

'''TASK 6.5:''' Using the 3D aerosol extinction, calculate the 0.55 micron aerosol optical depth on the second radiation timestep, and compare this to your AOD from Task 6.2.

{| class="collapsible collapsed wikitable"
|-
! Hint
|-
| You will need to include contributions from both UKCA and CLASSIC (due to the dust scheme).
|-
| Remember to correctly calculate the grid-cell heights.
|}

===Python notebook===

To calculate the AOD from the aerosol extinction, you will need to integrate this in the column. To do this you should first multiply by the height of each grid-cell before summing-up.

Example python notebooks to do this have been provided at

Tutorials/UMvn13.9/notebooks/iris_UM-UKCA_T065.ipynb

and can be seen online here

* [https://github.com/theabro/ukca_scripts/blob/master/Tutorials/UMvn13.9/notebooks/iris_UM-UKCA_T065.ipynb iris_UM-UKCA_T065.ipynb]

These scripts will also difference the two different methods.

==Solution to Task 6.5 ==

<gallery widths=300px heights=200px>
Image:UM139_T065_aod.png|0.55 micron AOD calculated from the 3D extinction diagnostics.
Image:UM139_T065_aod_diff.png|Difference in AODs calculated by the two methods.
</gallery>

You were asked to

* ''Using the 3D aerosol extinction, calculate the 0.55 micron aerosol optical depth on the second radiation timestep, and compare this to your AOD from Task 6.2.''

and were given the hints

:* ''You will need to include contributions from both UKCA and CLASSIC (due to the dust scheme).''
:* ''Remember to correctly calculate the grid-cell heights.''

You should use the python notebook provided to do this.

Sample output from this task can be found at

Tutorials/UMvn13.9/sample_output/Task06.5/

==Checklist==

: ☐ Make new time and domain profiles as needed.
: ☐ Run the TidyStashTransform transform macro.
: ☐ Output your diagnostics in STASH at: um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> STASH Requests and Profiles <math>\rightarrow</math> STASH Requests.
: ☐ When adding new aerosol diagnostics, remember to output on pseudo levels if appropriate.
: ☐ Run the TidyStashTransform transform macro again for the diagnostic requests.
: ☐ Save your suite.
: ☐ In the <tt>roses/[SUITE-ID]</tt> directory, run <tt>fcm commit</tt> to commit your changes to the repository.
: ☐ Python can be used to process and visualise Unified Model output.

[[UKCA Chemistry and Aerosol UMvn13.9 Tutorial 7|Tutorial 7]]

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

UKCA Chemistry and Aerosol UMvn13.9 Tutorial 5

2026-03-19T14:10:37Z

Nla27:

UKCA Chemistry and Aerosol UMvn13.9 Tutorial 1

2026-03-19T14:09:34Z

Nla27:

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

{| class="wikitable" border = "1px"
|-
| Difficulty || '''EASY'''
|-
| Time to Complete || '''Under 1 hour'''
|-
| Video instructions || https://www.youtube.com/watch?v=aysibeNdLUY&t=711s
|}

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

==What you will learn in this tutorial==

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

==Copying and Running an Existing Rose Suite==

{| class="wikitable" border = "1px"
!style="text-align:top;|Machine
!style="text-align:top;|UM Version/Configuration
!style="text-align:top;|Suite ID
|-
| vm || UMvn13.9 UKCA Box Model || '''[https://code.metoffice.gov.uk/trac/roses-u/browser/d/r/4/0/7/trunk u-dr407]'''
|-
|}

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

Then copy the rose suite by:

rosie copy u-dr407

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

description=Copy of u-dr407/trunk@328566
owner=lukeabraham
project=ukca
title=Cylc 8 UMvn13.9 UKCA Box Model

# Make changes ABOVE these lines.
# The "owner", "project" and "title" fields are compulsory.
# Any KEY=VALUE pairs can be added. Known fields include:
# "access-list", "description" and "sub-project".

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

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

cd roses/u-ab123

then open the suite by typing

rose edit &

and pressing return. You run the suite for the first time by typing

cylc vip

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

vagrant@vagrant:~/roses/u-ds042$ cylc vip
$ cylc validate /home/vagrant/roses/u-ds042
Valid for cylc-8.4.3
$ cylc install /home/vagrant/roses/u-ds042
INSTALLED u-ds042/run1 from /home/vagrant/roses/u-ds042
$ cylc play u-ds042/run1

▪ ■ Cylc Workflow Engine 8.4.3
██ Copyright (C) 2008-2025 NIWA
▝▘ & British Crown (Met Office) & Contributors

INFO - Extracting job.sh to /home/vagrant/cylc-run/u-ds042/run1/.service/etc/job.sh
u-ds042/run1: vagrant PID=347531

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

cylc tui

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

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

cylc-gui

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

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

This starts the graphical Cylc server, and you then need to connect to it as described '''[[UKCA_Chemistry_and_Aerosol_Tutorials:_Python_notebooks_with_Cylc|here]]'''.

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

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

For this suite to run you need the UKCA branch

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

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

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

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

To re-run a suite, you can <tt>cylc vip</tt> again, but this will make a new run, located in a different <tt>~/cylc_run/'''[SUITE-ID]'''/run'''X'''</tt> directory. This will also do a fresh build, which may take time and could fill up the disk on your machine. To rerun in the existing directory you can make any desired changes and then, e.g. from within your <tt>roses/'''[SUITE-ID]'''</tt>

cylc vr --yes ${PWD##*/}
cylc trigger --flow=new ${PWD##*/}//1/'''TASK'''

where '''<tt>TASK</tt>''' is, e.g. <tt>fcm_make</tt> or <tt>ukca</tt>. If you want to rebuild and then rerun you would trigger the <tt>fcm_make</tt> task which will then automatically run the <tt>ukca</tt> task when the <tt>fcm_make</tt> task has finished. If you don't need to rebuild at all you could just run the <tt>ukca</tt> task straight away.

The <tt>--yes</tt> on the reinstall prevents a y/n prompt and means it will run straight away, and the <tt>--flow=new</tt> means that the suite will start again and ignore that it completed successfully. If you are not in your e.g. <tt>~/roses/'''[SUITE-ID]'''</tt> directory you should replace '''<tt>${PWD##*/}</tt>''' with the suite-id (e.g. <tt>u-ab123</tt> etc.).

If a suite did not complete a task successfully it is possible to re-trigger that task directly in the TUI or GUI from the options menu of that task.

'''You may prefer to re-run a suite using these above methods, rather than <tt>cylc vip</tt>, as it may save time and reduce disk space with rebuilding.'''

==Version Control==

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

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

and then type

'''fcm commit'''

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

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

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

==Output Directory Structure==

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

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

Within this directory there are several directories, including:

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

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

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

===Notes===

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

==Exploring Rose==

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

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

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

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

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

==Viewing Output==

Example output from the UKCA box model training suite can be found at

Tutorials/UMvn13.9/sample_output/Box_Base

===gnuplot===

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

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

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

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

then load gnuplot by typing

gnuplot

To plot the tracer file, type

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

which can be shortened to

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

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

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

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

sudo apt install gnumeric

before opening the file

gnumeric tracer_out.csv

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

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

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

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

===Jupyter Notebook===

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

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

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

and can be viewed online here

* [https://github.com/theabro/ukca_scripts/blob/master/Tutorials/UMvn13.9/notebooks/BoxModel_T01-02.ipynb BoxModel_T01-02.ipynb]

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

Connect to the notebook using

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

==Checklist==

: ☐ Copy suites using <tt>rosie copy</tt>
: ☐ Run suites using <tt>cylc</tt> commands
: ☐ Plot output using gnuplot or python

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

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

UKCA Chemistry and Aerosol Tutorials: Python notebooks with Cylc

2026-03-19T14:08:39Z

Nla27:

UKCA Chemistry and Aerosol Tutorials: Configuring X2Go for AWS

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Nla27: /* Connecting via Amazon DCV */

UKCA Chemistry and Aerosol Tutorials: Configuring X2Go for AWS

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UKCA Chemistry and Aerosol Tutorials: Configuring X2Go for AWS

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File:DCV disconnect.png

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File:DCV clipboard sync.png

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Nla27: Ubuntu login page with clipboard tool selected

== Summary ==
Ubuntu login page with clipboard tool selected

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2026-03-10T13:41:08Z

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UKCA Chemistry and Aerosol Tutorials: Configuring X2Go for AWS

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UKCA Chemistry and Aerosol Tutorials: Configuring X2Go for AWS

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UKCA Chemistry and Aerosol Tutorials: Configuring X2Go for AWS

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UKCA

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Nla27: /* UKCA source available on GitHub */

UKCA

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UKCA

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UKCA

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Nla27:

==='''Welcome to the UKCA Wiki'''===
__NOTOC__
UKCA is a joint NCAS-Met Office programme part of the NERC-Met Office Joint Climate and Weather Research Programme (JWCRP). Project partners are the Hadley Centre and the Universities of Cambridge, Leeds and Oxford. Our objective is to develop, evaluate and make available a UK community atmospheric chemistry-aerosol global model suitable for a range of topics in climate and environmental change research.

[[Image:NCAS_logo_RGB.png|221px]] [[Image:Ukmo_logo.gif]] [[Image:Leeds_uni_logo.gif]] [[Image:Unicam_logo.gif]][[Image:2274_ox_brand_blue_rev_rect.png|221px]]

=== UKCA/UKESM Science Advances Meeting, Friday March 26th, 2021. ===

The slides for this meeting are available [https://www.ukca.ac.uk/wiki/index.php/Meetings/UKESM_UKCA_science_advances_2021 here].

=== UKCA User Survey - June 2021 ===

We invite all users of UKCA to complete the '''[https://forms.gle/rLLmHA5C4Tkv9xvcA UKCA User Survey 2020]'''.

===UKCA Training - January 2026===

The NCAS '''Introduction to UKCA''' course took place on the 14th-16th January 2026 at Fairbairn House in Leeds (NCAS HQ). This covered using [[UKCA_Chemistry_and_Aerosol_Tutorials_at_UMvn13.9|UKCA at UM13.9]], and photos from the course are available on [https://www.linkedin.com/posts/national-centre-for-atmospheric-science_studyscience-studywithus-activity-7423033850211053569-JMSq LinkedIn]

===Composition-Climate Interaction Meeting===

The Seventh Annual Composition-Climate Interaction meeting will took place on 20 - 21 March 2019 at the UK Met Office, Exeter, EX1 3PB. The meeting is supported by the UK Met Office, with administrative support kindly provided by the National Centre for Atmospheric Science (NCAS).

The meeting aims were to bring together UK scientists from universities, research centres and the Met Office working on all aspects of atmospheric composition and the interaction with climate and the Earth system, including atmospheric chemistry, aerosols and land surface interactions. The event provided an opportunity to present and discuss the latest UK research on all aspects of atmospheric composition. Invited and open presentations covered new science with the UKCA model, other chemistry-climate models, the UK’s Earth System Model and/or other Earth System Models. A poster session allowed further presentation and discussion on a wide range of research in this area.

There were four oral sessions with the following themes:

* Atmospheric composition in the Earth System
* Atmosphere-biosphere interactions
* Regional-scale composition and interactions
* Model evaluation and observational constraints

* AerChemMIP: There was also a side meeting on the morning of the 20 March 2019, before the start of the main meeting, dedicated to the organisation of the UK community simulations for the CMIP6 project AerChemMIP.

Following the main composition-climate meeting, the new UKCA working groups met on the afternoon of 21 March.

===== See Also =====
<div style="column-count:2;-moz-column-count:2;-webkit-column-count:2">

* [http://ncas.nerc.ac.uk NCAS]
* [http://www.metoffice.gov.uk The Met Office]
* [http://www.see.leeds.ac.uk/research/icas/ University of Leeds School of Earth and Environment]
* [http://www.atm.ch.cam.ac.uk/ University of Cambridge Centre for Atmospheric Science]
* [http://www.atm.ox.ac.uk/ University of Oxford Atmospheric, Oceanic and Planetary Physics]
</div>

UKCA Chemistry and Aerosol UMvn13.9 Tutorial 7

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Nla27: /* Make a branch */

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

{| class="wikitable" border = "1px"
|-
| Difficulty || '''MEDIUM'''
|-
| Time to Complete || '''1-2 hours'''
|-
| Video instructions || https://www.youtube.com/watch?v=aysibeNdLUY&t=8487s
|}

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

==What you will do in this tutorial==

In this tutorial you will learn how to make a branch to allow you to include UKCA code changes within the Box Model. You will then include 2 new chemical tracers, ALICE and BOB. '''You should continue using your UKCA box model suite (i.e. NOT a UM suite) that you last used in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_2|Tutorial 2]].'''

To be able to make UKCA code changes you will need to make a work with the UKCA code repository on the Met Office Science Repository Service (MOSRS), located here

* https://code.metoffice.gov.uk/trac/ukca/

==Working with the UKCA repository==

===Making a ticket===

To work with the UKCA code you will need to first make a new "ticket" on the UKCA trac pages on MOSRS, located here:

* https://code.metoffice.gov.uk/trac/ukca/newticket

You should ensure that:

* The '''Milestone''' is set to '''Not for builds'''. If you were developing a code change for the trunk then this would be set to the code version you wanted the change to be available from. You can also select yourself as the owner in the '''Owner''' drop-down menu.
* Once the ticket is created you click '''Modify Ticket''' and then select '''Start work''' and then '''Submit changes'''. This will make the ticket active and owned by you if you haven't already done so.

An example ticket can be seen at

* https://code.metoffice.gov.uk/trac/ukca/ticket/33

The ticket is useful to be able to keep a log of your progress with the ticket as well as being able to hold trac wiki pages that can be used to present results and documentation.

In these tutorials we will have tickets and branches for both the UKCA and UM, so you will need to keep track of both.

===Make a branch===

Once you have a ticket you are able to make a branch on the UKCA repository. You should do this in your terminal

fcm branch-create --type dev -k ticket_number your_branch_name fcm:ukca.x_tr@um13.9

{| class="wikitable" border = "1px"
!style="text-align:top;|Setting
!style="text-align:top;|Description
|-
| '''<tt>ticket_number</tt>''' || This is the number of the ticket that you have just created, e.g. 33 etc.
|-
| '''<tt>your_branch_name</tt>''' || This is a descriptive name for your branch, e.g. <tt>ukca_tutorials</tt>. You '''should not''' also include a revision/version number here.
|-
| '''<tt>REV</tt>''' i.e. <tt>um13.9</tt> || This is the trunk revision we are branching from. For these tutorials it is '''<tt>um13.9</tt>'''.
|}

Once you have run this command you will be placed into a text editor (as when you copied your Rose suite) to provide a commit message, e.g.


--Add your commit message ABOVE - do not alter this line or those below--
--FCM message (will be inserted automatically)--
#33: Created /main/branches/dev/lukeabraham/um13.9_ukca_tutorial_solutions from /main/trunk@6356.
--Change summary (not part of commit message)--
A <nowiki>https://code.metoffice.gov.uk/svn/ukca/main/branches/dev/lukeabraham/um13.9_ukca_tutorial_solutions</nowiki>

You should put a descriptive commit message, e.g. something like

#33 lukeabraham creating branch for UKCA tutorials

The <tt>#33</tt> will resolve as a link on the trac webpages, allowing you to easily find the ticket, and providing your name is useful to keep track of who made changes. Now you should '''save''' and '''quit''' the text editor. In the terminal, you will then be presented with

[info] Source: <nowiki>https://code.metoffice.gov.uk/svn/ukca/main/trunk@6356</nowiki> (6356)
[info] vim: starting commit message editor...
Change summary:
--------------------------------------------------------------------------------
A <nowiki>https://code.metoffice.gov.uk/svn/ukca/main/branches/dev/lukeabraham/um13.9_ukca_tutorial_solutions</nowiki>
--------------------------------------------------------------------------------
Commit message is as follows:
--------------------------------------------------------------------------------
#33 lukeabraham creating branch for UKCA tutorials
#33: Created /main/branches/dev/lukeabraham/um13.9_ukca_tutorial_solutions from /main/trunk@6356.
--------------------------------------------------------------------------------
Create the branch?
Enter "y" or "n" (or just press <return> for "n")

You should now type '''y''' and press '''return'''. This will create the branch.

Now change directory to one where you want to copy your branch to, e.g. '''cd''' and then '''return''' to take you back to your home directory. You should then select the full URL of the branch and check it out using the command

fcm co

e.g.

fcm co <nowiki>https://code.metoffice.gov.uk/svn/ukca/main/branches/dev/</nowiki>'''[YOUR MOSRS USERNAME]'''/um13.9_'''[YOUR BRANCH NAME]'''

You can then '''cd''' into this directory. The UKCA source code is held within the '''<tt>src</tt>''' directory. The code is organised in the following directory structure, with a number of Fortran source files in each directory and sub-directory

├── control
│ ├── core
│ │ ├── diagnostics
│ │ ├── interface
│ │ ├── misc
│ │ └── top_level
│ ├── glomap_clim
│ │ └── interface
│ ├── legacy
│ ├── photolysis
│ │ └── interface
│ └── shared
└── science
├── core
│ ├── aerosols
│ │ ├── activation
│ │ ├── deposition
│ │ └── glomap
│ ├── chemistry
│ │ ├── asad
│ │ └── deposition
│ └── emissions
├── glomap_clim
├── photolysis
│ ├── fastjx
│ ├── stratospheric
│ │ └── photolib
│ └── tropospheric
├── plumeria
└── radaer

===Use your branch in your suite===

Although we have not made any code changes yet, we will include our branch in our Rose suite now so that the changes will get picked-up the next time we run. To do this, go to the '''fcm_make <math>\rightarrow</math> env <math>\rightarrow</math> Sources''' panel. You will need to click the green plus symbol ('''+''' for the '''<tt>ukca_sources</tt>''' to add a new line, and then copy and paste the path to the working directory of your branch, e.g.

/home/vagrant/um13.9_ukca_tutorial_solutions

It is also possible to specify the repository location on the MOSRS using

branches/dev/'''[YOUR MOSRS USERNAME]'''/um13.9_'''[YOUR BRANCH NAME]'''@'''[REV]'''

where the @'''[REV]''' (which is optional) is a revision of the branch, e.g. 6356. If a revision is not specified then the latest revision is used. However, this requires you to commit your code before it is picked-up by the model, and so for code development it is often easier to point to a working copy.

The change to the suite is now, e.g.

Index: app/fcm_make/rose-app.conf
===================================================================
--- app/fcm_make/rose-app.conf (revision 337465)
+++ app/fcm_make/rose-app.conf (working copy)
@@ -30,6 +30,6 @@
thread_utils=false
timer_version=3A
ukca_rev=$BASE_UKCA_REV
-ukca_sources=/home/vagrant/um13.9_ukca_box
+ukca_sources=/home/vagrant/um13.9_ukca_box /home/vagrant/um13.9_ukca_tutorial_solutions
um_rev=$BASE_UM_REV
um_sources=

So it is uses 2 branches, the new one and the original <tt>/home/vagrant/um13.9_ukca_box</tt> branch that contains the control routines for the box model. You need both branches for the remainder of these tutorials.

==Include your new chemical tracers==

Before we can consider any chemical reactions with new species, we first need to include these as UKCA chemical tracers. This is done in 4 places:

# In the <tt>ukca_chem_master.F90</tt> routine, to add them to the master species list
# In the <tt>ukca_config_defs_mod.F90</tt> routine, to tell the relevant chemical mechanism how many chemical tracers it has
# In the <tt>ukca_constants.F90</tt> routine, to define conversion factors for each species from mass-mixing ratio to mole fraction
# In the <tt>ukca_cspecies.F90</tt> routine, to assign these conversion factors to the correct place in the master list of conversion factors

===Task 7.1: Include ALICE and BOB===

'''TASK 7.1:''' Include ALICE and BOB as chemical tracers for both the StratTrop and CRI-Strat schemes. You should set the conversion factor for each of these to 1.0. You should test this in your existing box model suite.

'''Note''' that your box model suite should currently be set to CRI-Strat chemistry without aerosols or heterogeneous chemistry. You should not change this at this time as it is useful to test your new chemistry under different conditions.

===<tt>src/science/core/chemistry/ukca_chem_master.F90</tt>===

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

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

Where:

* '''<tt>N</tt>''' is an integer. The value should be incremented for each new '''species''' that is added so that each species has a unique number, but there can be several entries for each species.
* '''<tt>'SPECIES   '</tt>''' is the name of the species, e.g. <tt>'O3        '</tt>
* '''<tt>X</tt>''' is number of odd atoms. This field is not currently used so please set it to <tt>1</tt>.
* '''<tt>'TYPE      '</tt>''' describes whether the species is
*: a tracer (<tt>'TR        '</tt>)
*: an RO2 tracer (<tt>'OO        '</tt>)
*: a steady-state species (<tt>'SS        '</tt>)
*: a constant (<tt>'CT        '</tt>)
*: a constant field (<tt>'CF        '</tt>).
*:: For SS, CT, and CF, special code will need to be added.
* '''<tt>'FAMILY    '</tt>''' is the family that the species belongs to. This field is not currently used.
* '''<tt>D</tt>''' is '''1''' if the species is dry-deposited, and '''0''' otherwise.
* '''<tt>W</tt>''' is '''1''' if the species is wet-deposited, and '''0''' otherwise.
* '''<tt>SCHEME</tt>''' defines the chemistry scheme used, e.g.:
*: <tt>st</tt> = Stratosphere-Troposphere scheme
*: <tt>t</tt> = Troposphere scheme
*: <tt>s</tt> = Stratosphere scheme
*: <tt>r</tt> = RAQ scheme
*: <tt>ol</tt> = Offline-oxidants scheme
*: <tt>ti</tt> = Troposphere-Isoprene scheme
*: <tt>cs</tt> = CRI-Strat scheme
** If the same species is used in multiple schemes these are added, e.g. <tt>st+s+ti+cs</tt> etc.
* '''<tt>QUALIFIER</tt>''' and '''<tt>DISQUALIFIER</tt>''' define 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
*: <tt>a</tt> = Aerosol chemistry additions required to run GLOMAP-mode
*: <tt>th</tt> = Tropospheric heterogeneous reactions
*: <tt>hp</tt> = Heterogeneous PSC chemistry
*: <tt>es</tt> = Extended stratospheric reactions
*: <tt>ci</tt> = use a 3-D CO2 tracer
*: <tt>eh</tt> = Extended heterogeneous chemistry
*: <tt>rn</tt> = RO2 a non-transported prognostic (StratTrop and CRI-Strat chemistry only)
*: <tt>rp</tt> = RO2 permutation chemistry (StratTrop and CRI-Strat chemistry only)
*: <tt>cs2</tt> = used for changes from CRI-Strat version 1 to CRI-Strat version 2 chemistry
*: <tt>ce</tt> = used for emissions-driven CH4
*: <tt>rm</tt> = used to remove reactions from older mechanisms
** As with the '''<tt>SCHEME</tt>''' codes, these are also additive if required, e.g. <tt>a+th</tt> etc.
* '''<tt>VN</tt>''' 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. '''The current standard version in UKESM1.1 is <tt>117</tt>, but for these tutorials we are using <tt>121</tt>.'''

The latest version is 132, but in this tutorial we will be adding our chemistry to version 121. If you were incrementing on top of 132, the next version to use would be 140 as we are developing at um13.9 for the um14.0 release.

Therefore to add-in the ALICE and BOB species, we should insert lines similar to this

! 285
chch_t1(285,'ALICE ',1,'TR ',' ',0,0,st+cs,0,0,121), &
! 286
chch_t1(286,'BOB ',1,'TR ',' ',0,0,st+cs,0,0,121) &

into '''<tt>chch_defs_master</tt>''', remembering to also '''increment the size of this array, given by <tt>n_chch_master</tt>'''.

===<tt>src/control/core/top_level/ukca_config_defs_mod.F90</tt>===

In '''<tt>ukca_config_defs_mod.F90</tt>''' 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 sections that define the '''StratTrop''' and '''CRI-Strat''' chemistry schemes. When adding tracers you will need to increment the value of '''<tt>n_chem_tracers</tt>'''.

For StratTrop this is located in the ''Stratospheric Chemistry'' section and is referenced by using the '''<tt>ukca_config%l_ukca_strattrop</tt>''' logical. For CRI-Strat this is located in the ''CRI-Strat and CRI-Strat 2 chemistry'' section controlled by '''<tt>ukca_config%l_ukca_cristrat</tt>''' logical. Note also for CRI-Strat there is an additional check on the chemistry version number used, as if this is greater than 119 we are using CRI-Strat version 2.

The IF blocks test against <tt>ukca_config%l_ukca_achem</tt> (which determines whether or not you require the additional chemistry used to drive the GLOMAP-mode aerosol scheme). You should increment the value of '''<tt>n_chem_tracers</tt>''' by the number of chemical tracers that you are adding (i.e. 2) in '''both''' sections of these IF blocks, as this tracer is not defined to be for aerosol chemistry only. If your additional tracers were only aerosol chemistry additions then you would increment the value of '''<tt>n_aero_tracers</tt>'''. '''Note''' that as we are using a chemical version of '''121''' we only need to increment the value for CRI-Strat2.

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

===<tt>src/science/core/chemistry/ukca_constants.F90</tt>===

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 mole fraction or volume mixing ratio ('''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 '''<tt>ukca_constants.F90</tt>''' module.

Open this file and add the required conversion factor(s). The naming convention for these is:

* '''m_species''' for the molecular mass of the new species in g/mol
* '''c_species''' for the converson factor from vmr to mmr

The c_species conversion factor calculated as m_species/M_air, where M_air=28.97). In actuality, only the c_species listing is always required, although you will need to add the M_species value later if you are emitting into the new species that you are adding.

For these new species we can add the following blocks, as we have been told to use a conversion factor of 1:

REAL, PARAMETER :: c_alice = 1.000
REAL, PARAMETER :: c_bob = 1.000

===<tt>src/science/core/chemistry/ukca_cspecies.F90</tt>===

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 constructs the '''c_species''' array of conversion factors for the advected tracers. This contains a subroutine called <tt>ukca_calc_cspecies</tt> which has a long block of code that you need to edit to add entries like this:

WHERE (advt == 'ALICE ') c_species = c_alice
WHERE (advt == 'BOB ') c_species = c_bob

The '''advt''' array is automatically generated by UKCA at run-time from the <tt>chch_defs_master</tt> 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.

As the <tt>c_species</tt> conversion factors are defined in the <tt>ukca_constants</tt> module you will need to explicitly add them to the

USE ukca_constants, ONLY: ...

statement at the top of the module.

===Run your Rose Suite===

You should now run your suite and see what happens with ALICE and BOB. As you have not made any changes (other than to include your UKCA branch) you can run it using

cylc vr --yes ${PWD##*/}
cylc trigger --flow=new ${PWD##*/}//1/fcm_make

which will build and then run. If there are any compile errors you can use the Cylc GUI to view these, make your code changes, and then re-trigger the <tt>fcm_make</tt> process through the GUI menu.

'''Note''' that initial conditions of ALICE and BOB do not need to be specified at this stage as any species that does not have a concentration explicitly given in '''<tt>tracer_in_filename</tt>''' uses the value given by '''<tt>tracer_nullval</tt>''', currently set to '''1e-15'''.

===Worked Solution to Task 7.1===

You were given the task:

* ''Include ALICE and BOB as chemical tracers for both the StratTrop and CRI-Strat schemes. You should set the conversion factor for each of these to 1.0. You should test this in your existing box model suite.''

<gallery widths=400px heights=350px>
Image:T03_alice_001.png
Image:T03_bob_001.png
</gallery>

As there is no chemistry occurring for species, and they are initialised to very small values, they will maintain there values throughout the simulation.

The changes to Rose are:

* https://code.metoffice.gov.uk/trac/roses-u/changeset/337635/d/s/0/4/2/trunk

Index: app/fcm_make/rose-app.conf
===================================================================
--- app/fcm_make/rose-app.conf (revision 337465)
+++ app/fcm_make/rose-app.conf (revision 337635)
@@ -30,6 +30,6 @@
thread_utils=false
timer_version=3A
ukca_rev=$BASE_UKCA_REV
-ukca_sources=/home/vagrant/um13.9_ukca_box
+ukca_sources=/home/vagrant/um13.9_ukca_box /home/vagrant/um13.9_ukca_tutorial_solutions
um_rev=$BASE_UM_REV
um_sources=

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task07.1/Task07.1_rose.patch

The changes to UKCA are:

* https://code.metoffice.gov.uk/trac/ukca/changeset/7770/main/branches/dev/lukeabraham/um13.9_ukca_tutorial_solutions

Index: src/control/core/top_level/ukca_config_defs_mod.F90
===================================================================
--- src/control/core/top_level/ukca_config_defs_mod.F90 (revision 7769)
+++ src/control/core/top_level/ukca_config_defs_mod.F90 (revision 7770)
@@ -362,7 +362,7 @@
['NO ','CH4 ','CO ','HCHO ', &
'C2H6 ','C3H8 ','Me2CO ','MeCHO ', &
'C5H8 ','MeOH ','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)

@@ -389,7 +389,7 @@
ELSE
n_aero_tracers = 12
END IF
- n_chem_tracers = 71 ! No chem tracers
+ n_chem_tracers = 73 ! No chem tracers
IF (ukca_config%l_ukca_trophet) THEN
nr_therm = 241 ! thermal reactions
ELSE
@@ -453,7 +453,7 @@
ELSE IF (ukca_config%l_ukca_cristrat) THEN
IF (.NOT. ukca_config%l_ukca_achem) THEN ! Without aerosol
IF (ukca_config%i_ukca_chem_version >= 119) THEN ! CRI-Strat 2 w/o aerosol
- n_chem_tracers = 171 ! advected chemical tracers (+9, -4)
+ n_chem_tracers = 173 ! advected chemical tracers (+9, -4)
n_aero_tracers = 0 ! DMS, SO2... aerosol precursor species
nr_therm = 625 ! thermal reactions (+45 bimol, +8 termol)
nr_phot = 135 ! photolytic reacs
@@ -476,7 +476,7 @@
'MeCO2H ','HOCH2CHO ','NO_aircrft']
ELSE ! With aerosol
IF (ukca_config%i_ukca_chem_version >= 119) THEN ! CRI-Strat 2 with aerosol
- n_chem_tracers = 171 ! advected chemical tracers (+9, -4)
+ n_chem_tracers = 173 ! advected chemical tracers (+9, -4)
n_aero_tracers = 17 ! DMS, SO2... aerosol precursor species
nr_phot = 137 ! photolytic reacs
IF (ukca_config%l_ukca_trophet) THEN
Index: src/science/core/chemistry/ukca_chem_master.F90
===================================================================
--- src/science/core/chemistry/ukca_chem_master.F90 (revision 7769)
+++ src/science/core/chemistry/ukca_chem_master.F90 (revision 7770)
@@ -103,7 +103,7 @@
! later ones

! Define size of master chemistry
-INTEGER, PARAMETER :: n_chch_master = 357 ! number of known species
+INTEGER, PARAMETER :: n_chch_master = 359 ! number of known species
INTEGER, PARAMETER :: n_het_master = 18 ! number of heterogeneous reactions
INTEGER, PARAMETER :: n_dry_master = 162 ! number of dry deposition reactions
INTEGER, PARAMETER :: n_wet_master = 160 ! number of wet deposition reactions
@@ -919,7 +919,11 @@
! 283
chch_t1(283,'MACO3 ',1,'OO ',' ',0,0,cs,rp,0,119), &
! 284
-chch_t1(284,'SEC_ORG_I ',1,'TR ',' ',1,1,st,a,0,132) &
+chch_t1(284,'SEC_ORG_I ',1,'TR ',' ',1,1,st,a,0,132), &
+! 285
+chch_t1(285,'ALICE ',1,'TR ',' ',0,0,st+cs,0,0,121), &
+! 286
+chch_t1(286,'BOB ',1,'TR ',' ',0,0,st+cs,0,0,121) &
]

Index: src/science/core/chemistry/ukca_constants.F90
===================================================================
--- src/science/core/chemistry/ukca_constants.F90 (revision 7769)
+++ src/science/core/chemistry/ukca_constants.F90 (revision 7770)
@@ -372,6 +372,10 @@
! Same as Sec_org
REAL, PARAMETER :: c_cri = 5.1782

+! define conversion factors for tutorial species
+REAL, PARAMETER :: c_alice = 1.000
+REAL, PARAMETER :: c_bob = 1.000
+
! molecular masses in g/mol of emitted species,
! for budget calculations
REAL, PARAMETER :: m_ho2 = 33.007
Index: src/science/core/chemistry/ukca_cspecies.F90
===================================================================
--- src/science/core/chemistry/ukca_cspecies.F90 (revision 7769)
+++ src/science/core/chemistry/ukca_cspecies.F90 (revision 7770)
@@ -184,7 +184,7 @@
c_txcarb22, c_ru12pan, c_rtn26pan, c_aroh14, c_aroh17, c_arnoh14, &
c_arnoh17, c_anhy, c_cri,c_dhpcarb9, c_hpucarb12, c_hucarb9, c_iepox, &
c_hmml, c_dhpr12ooh, c_dhcarb9, c_ru12no3, c_ru10no3, c_dhpr12o2, &
- c_ru10ao2, c_maco3
+ c_ru10ao2, c_maco3, c_alice, c_bob

USE asad_mod, ONLY: advt, nadvt, speci, jpctr, jpspec
@@ -466,6 +466,10 @@
WHERE (advt == 'PASSIVE O3') c_species = 1.0
WHERE (advt == 'AGE OF AIR') c_species = 1.0

+! tutorial species
+WHERE (advt == 'ALICE ') c_species = c_alice
+WHERE (advt == 'BOB ') c_species = c_bob
+
! non-advected tracers
c_na_species=0.0
WHERE (nadvt == 'OH ') c_na_species = c_oh

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task07.1/Task07.1_ukca.patch

Sample output from this task can be found here:

Tutorials/UMvn13.9/sample_output/Task07.1/

===Task 7.2: Test your changes in another chemistry scheme===

'''TASK 7.2:''' Change the chemistry and aerosol settings to test these changes with StratTrop chemistry, GLOMAP-mode aerosols, and with heterogeneous chemistry turned back on.

{| class="collapsible collapsed wikitable"
|-
! Solution
|-
| Change the value of <tt>i_ukca_chem</tt> to be '''<tt>51</tt>''' (StratTrop)
|-
| Change the value of <tt>l_ukca_chem_aero</tt> to be '''True'''
|-
| Ensure that the value of <tt>l_ukca_mode</tt> is '''True'''
|-
| Change the value of <tt>l_ukca_het_psc</tt> to be '''True'''
|}

'''Note''' that changing these setting will automatically make lots of other changes to variables within Rose. '''''You do not need to worry about these additional changes.'''''

As you are only making namelist changes there is no need to recompile your box model.

====Worked Solution to Task 7.2====

You were asked to:

* ''Change the chemistry and aerosol settings to test these changes with StratTrop chemistry, GLOMAP-mode aerosols, and with heterogeneous chemistry turned back on.''

The changes to Rose are:

* https://code.metoffice.gov.uk/trac/roses-u/changeset/337643/d/s/0/4/2/trunk

Index: app/ukca/rose-app.conf
===================================================================
--- app/ukca/rose-app.conf (revision 337635)
+++ app/ukca/rose-app.conf (revision 337643)
@@ -479,14 +479,14 @@
!!i_ageair_reset_method=1
!!i_inferno_emi=
!!i_mode_bln_param_method=0
-!!i_mode_nzts=15
-!!i_mode_setup=2
-!!i_ukca_activation_scheme=0
-i_ukca_chem=59
+i_mode_nzts=15
+i_mode_setup=2
+i_ukca_activation_scheme=0
+i_ukca_chem=51
i_ukca_chem_version=121
i_ukca_conserve_method=3
-!!i_ukca_dms_flux=1
-!!i_ukca_hetconfig=0
+i_ukca_dms_flux=1
+i_ukca_hetconfig=0
!!i_ukca_hiorder_scheme=0
i_ukca_light_param=0
!!i_ukca_nwbins=20
@@ -510,8 +510,8 @@
!!l_dust_mp_slinn_impc_scav=.false.
l_environ_jo2=.false.
l_environ_jo2b=.false.
-!!l_mode_bhn_on=.true.
-!!l_mode_bln_on=.false.
+l_mode_bhn_on=.true.
+l_mode_bln_on=.false.
!!l_no3_prod_in_aero_step=.false.
l_ukca=.true.
l_ukca_ageair=.false.
@@ -519,7 +519,7 @@
!!l_ukca_aie2=.false.
l_ukca_asad_columns=.true.
l_ukca_asad_full=.false.
-l_ukca_chem_aero=.false.
+l_ukca_chem_aero=.true.
!!l_ukca_classic_hetchem=.false.
!!l_ukca_coarse_no3_prod=.true.
l_ukca_ddep_lev1=.false.
@@ -527,59 +527,59 @@
l_ukca_debug_asad=.true.
l_ukca_dry_dep_so2wet=.false.
!!l_ukca_dust=.false.
-!!l_ukca_emsdrvn_ch4=.false.
+l_ukca_emsdrvn_ch4=.false.
!!l_ukca_fine_no3_prod=.true.
l_ukca_h2o_feedback=.false.
-l_ukca_het_psc=.false.
+l_ukca_het_psc=.true.
l_ukca_ibvoc=.false.
-!!l_ukca_inferno=.false.
+l_ukca_inferno=.false.
!!l_ukca_inferno_ch4=.false.
l_ukca_intdd=.true.
l_ukca_intph=.false.
-!!l_ukca_limit_nat=.false.
+l_ukca_limit_nat=.false.
l_ukca_linox_scaling=.false.
-!!l_ukca_mode=.false.
+l_ukca_mode=.true.
l_ukca_prescribech4=.false.
!!l_ukca_prim_moc=.false.
-!!l_ukca_primbcoc=.false.
+l_ukca_primbcoc=.false.
!!l_ukca_primdu=.false.
-!!l_ukca_primss=.false.
-!!l_ukca_primsu=.false.
+l_ukca_primss=.false.
+l_ukca_primsu=.false.
l_ukca_qch4inter=.false.
l_ukca_quasinewton=.false.
-!!l_ukca_radaer=.false.
+l_ukca_radaer=.false.
!!l_ukca_radaer_sustrat=.false.
l_ukca_radch4=.false.
-!!l_ukca_radf11=.false.
-!!l_ukca_radf113=.false.
-!!l_ukca_radf12=.false.
-!!l_ukca_radf22=.false.
+l_ukca_radf11=.false.
+l_ukca_radf113=.false.
+l_ukca_radf12=.false.
+l_ukca_radf22=.false.
l_ukca_radn2o=.false.
l_ukca_rado3=.false.
l_ukca_ro2_ntp=.true.
l_ukca_ro2_perm=.true.
-!!l_ukca_sa_clim=.false.
-!!l_ukca_scale_biom_aer_ems=.false.
+l_ukca_sa_clim=.false.
+l_ukca_scale_biom_aer_ems=.false.
!!l_ukca_scale_marine_pom_ems=.false.
!!l_ukca_scale_sea_salt_ems=.false.
-!!l_ukca_scale_seadms_ems=.false.
+l_ukca_scale_seadms_ems=.false.
!!l_ukca_scale_soa_yield_isop=.false.
-!!l_ukca_scale_soa_yield_mt=.false.
+l_ukca_scale_soa_yield_mt=.false.
l_ukca_set_trace_gases=.true.
!!l_ukca_sfix=.false.
-!!l_ukca_so2ems_expvolc=.false.
+l_ukca_so2ems_expvolc=.false.
!!l_ukca_so2ems_plumeria=.false.
!!l_ukca_src_in_conservation=.true.
-!!l_ukca_trophet=.false.
+l_ukca_trophet=.false.
!!l_ukca_use_background_aerosol=.false.
lightnox_scale_fac=0.5
!!marine_pom_ems_scaling=0
!!max_ageair_reset_height=0.0
!!max_ageair_reset_level=0
-!!mode_activation_dryr=37.5
-!!mode_aitsol_cvscav=0.5
-!!mode_incld_so2_rfrac=0.25
-!!mode_parfrac=2.5
+mode_activation_dryr=37.5
+mode_aitsol_cvscav=0.5
+mode_incld_so2_rfrac=0.25
+mode_parfrac=2.5
!!nerupt=0
!!nit=0
nrsteps=45
@@ -640,7 +640,7 @@
l_fix_ukca_impscav=.false.
!!l_fix_ukca_offox_h2o_fac=.false.
l_fix_ukca_water_content=.false.
-!!l_improve_aero_drydep=.false.
+l_improve_aero_drydep=.false.
!!l_improve_cv_cons=.false.
l_methox_fix=.true.

@@ -649,5 +649,5 @@
!!a_convect_segments=-99
!!a_convect_trac_seg_size=1
ukca_chem_seg_size=1
-!!ukca_mode_seg_size=1
+ukca_mode_seg_size=1
ussp_seg_size=1

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task07.2/Task07.2_rose.patch

Sample output from this task can be found here:

Tutorials/UMvn13.9/sample_output/Task07.2/

==Checklist==

: ☐ Make a ticket at the UKCA trac pages
: ☐ Make a UKCA branch
: ☐ Include this branch within your Rose suite
: ☐ Make your code changes to <tt>ukca_chem_master.F90</tt>, <tt>ukca_config_defs_mod.F90</tt>, <tt>ukca_constants.F90</tt>, and <tt>ukca_cspecies.F90</tt>
: ☐ Ensure that you are using the correct value of <tt>i_ukca_chem_version</tt>
: ☐ Test with multiple chemistry schemes as required

[[UKCA Chemistry and Aerosol UMvn13.9 Tutorial 8|Tutorial 8]]

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

UKCA Chemistry and Aerosol UMvn13.9 Tutorial 10

2026-01-13T13:51:19Z

Nla27: /* Diagnostics */

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

{| class="wikitable" border = "1px"
|-
| Difficulty || '''HARD'''
|-
| Time to Complete || '''2 or more hours'''
|-
| Video instructions || https://www.youtube.com/watch?v=aysibeNdLUY&t=13444s
|}

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

==What you will learn in this Tutorial==

This is a continuation of what you learned in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_5|Tutorial 5]], where you regridded a set of emissions to the UM grid and included them for an existing tracers. During this tutorial you will make new UKCA netCDF emissions files and then you will learn how to add new emissions into UKCA so that they emit into one of your new tracers.

At the end of the [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_9|previous tutorial]] you will now know how to create new tracers in the UM for use by UKCA. However, while the chemical reaction(s) added in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_8|tutorial 8]] are active, as the tracers have been initialised to very small values these are not behaving as could be expected. This tutorial will teach you how to create an emissions file that the UKCA will read, and that you can then tell UKCA to use and emit into your tracer(s). These emissions will then become the higher concentrations that will drive the new chemistry.

This example only deals with a single field. For a more detailed examples on changing emissions for all species, please see the [[Emissions for ACSIS]] webpage.

==Task 10.1: Create a new NetCDF emissions file ==

'''Task 10.1:''' In the <pre>Tutorials/UMvn13.9/Task10.1</pre> directory there is the file '''Emissions_of_ALICE.nc''' which is a 0.5x0.5 degree resolution surface emission field. You should regrid this file to the '''N48 ENDGame grid''', and output it as a netCDF file that has the required netCDF metadata for a climatological surface emission without any diurnal cycle.

You should take the script you used in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_5|Tutorial 5]] and adapt it to work with this new file and new species that is being emitted into.

{| class="collapsible collapsed wikitable"
|-
! Hints
|-
| Remember to change the location of the <tt>emiss</tt> file.
|-
| Remember to change the values of the attributes <tt>var_name</tt>, <tt>long_name</tt>, and <tt>tracer_name</tt>.
|-
| Remember to change the name of the output file set by <tt>outpath</tt>.
|}

==Solution to Task10.1==

You were given the task:

* ''In the <pre>Tutorials/UMvn13.9/Task10.1</pre> directory there is the file '''Emissions_of_ALICE.nc''' which is a 0.5x0.5 degree resolution surface emission field. You should regrid this file to the '''N48 ENDGame grid''', and output it as a netCDF file that has the required netCDF metadata for a climatological surface emission without any diurnal cycle.''

and were given the hints:

* ''Remember to change the location of the <tt>emiss</tt> file.''
* ''Remember to change the values of the attributes <tt>var_name</tt>, <tt>long_name</tt>, and <tt>tracer_name</tt>.''
* ''Remember to change the name of the output file set by <tt>outpath</tt>.''

It should be straight-forward adapt your existing script to work for ALICE. If you are having problems, a solution script can be found at

* '''[https://github.com/theabro/ukca/blob/master/Tutorials/UMvn13.9/notebooks/Solutions/iris_UM-UKCA_T101.ipynb Solution to Task 10.1]'''

Once the file has been regridded, you should see the output looking like this:

<gallery widths=300px heights=200px>
Image:UM139_alice_05x05.png|ALICE emissions prior to regridding.
Image:UM139_alice_n48e.png|ALICE emissions after regridding.
</gallery>

A file that has been produced by the above script can be found at

Tutorials/UMvn13.9/sample_output/Task10.1/ukca_emiss_ALICE.nc

==Task 10.2: make the required code changes to add your emission into UKCA==

'''TASK 10.2:''' You should now make the UKCA code changes to add your emission into the '''ALICE''' tracer. Use STASH code <tt>s50i315</tt> for the diagnostic and output this to the '''UPA''' stream as a 3-hour mean.

{| class="collapsible collapsed wikitable"
|-
! Hint
|-
| You will need to add-in the molar mass of ALICE. You can calculate this from the mass of air and the conversion factor defined in [[UKCA_Chemistry_and_Aerosol_UMvn13.0_Tutorial_7#Task_7.1:_Include_ALICE_and_BOB|Task 7.1]]. You will need to add code to allow a diagnostic of the emission to be output.
|}

==Rose changes==

===Include your new emissions file===

You should include your new emissions file as you did in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_5#Rose_changes|Task 5.2]].

===Diagnostics===

You should make your STASHmaster_A entry and add this to the STASH panel as you have done in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_4|Tutorial 4]] and [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_5|Tutorial 5]]. Be careful when you make this entry. You should ensure that the option codes are valid for the chemistry scheme you are using (StratTrop). There are other STASH entries that define the levels used, so if you copy an existing STASHmaster entry, ensure that it is for a surface emission.

You won't need to make any changes to the location of the STASHmaster file '''so long as you commit your changes prior to running the suite'''.

Note that here you are making the diagnostic entry before you have made code changes that will populate this field, which are done below.

==Code changes==

Code changes are split between changes that need to be made to the UM and those that are made to UKCA.

===UKCA code changes===

====Code changes to use the new emissions====

=====<tt>src/control/core/top_level/ukca_config_defs_mod.F90</tt>=====

You will need to edit the '''<tt>em_chem_spec</tt>''' array for the scheme that you are using to include the new species that you are emitting into. By convention, these are ordered as 2D fields followed by 3D fields, with chemical emissions first and then aerosol emissions, although this order is unimportant other than the fact that the 2D emissions should be placed before the 3D emissions of '''<tt>'SO2_nat'</tt>''', '''<tt>'BC_biomass'</tt>''', '''<tt>'OC_biomass'</tt>''', and '''<tt>'NO_aircrft'</tt>''' if these are present.

If the tracer is purely chemical and is always on (i.e. is not included only when aerosol chemistry is turned on) then you will need to put this in both <tt>em_chem_spec</tt> arrays (i.e. one for the chemistry scheme without aerosols and one with aerosols). Also remember to increment this size of the '''<tt>em_chem_spec</tt>''' array, given by '''<tt>n_chem_emissions</tt>''' variable.

For this example you will need to make changes for StratTrop ''and'' CRI-Strat (version 2) schemes, both with an without aerosol chemistry.

=====<tt>src/science/core/chemistry/ukca_constants.F90</tt>=====

You will need to define the '''<tt>M_species</tt>''' for the emitted species, e.g. <tt>m_alice</tt>. The value of this should be consistent with the '''<tt>C_species</tt>''' value set in the [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_7#src.2Fscience.2Fcore.2Fchemistry.2Fukca_constants.F90 | adding new tracers tutorial]].

=====<tt>src/science/core/chemistry/get_molmass_mod.F90</tt>=====

You will need to add to the '''<tt>species_name</tt>''' <tt>CASE</tt> statement, to include a line such as this

CASE ('ALICE ')
get_molmass = m_alice

for each new species that you are emitting into.

As the <tt>M_species</tt> conversion factors are defined in the <tt>ukca_constants</tt> module you will need to explicitly add them to the

USE ukca_constants, ONLY: ...

statement at the top of the module.

====Code changes for the emissions diagnostics====

Additionally, by default, when emitting into a new species, the code requires you to create a diagnostic for these emissions as well. These changes are also considered below.

=====<tt>src/control/core/diagnostics/ukca_emdiags_struct_mod.F90</tt>=====

This routine contains the derived type that holds the emissions fluxes for all species. You will need to add a logical (used to determine whether the output has been requested in STASH) and a pointer to a 2D or 3D array that will hold the emissions flux.

=====<tt>src/control/core/diagnostics/ukca_update_emdiagstruct_mod.F90</tt>=====

In this routine you will need to add the initialisation of the logical added in <tt>ukca_emdiags_struct_mod.F90</tt>, as well as a small block of code that copies the 2D/3D <tt>em_diags</tt> data into the newly created pointer in the derived type. The logical will also need to be set to <tt>.TRUE.</tt> if STASH output has been requested (determined by the <tt>sf(item,section)</tt> look-up array).

Here is it easiest to copy an existing code-block and make the necessary changes for your new emission.

=====<tt>src/control/core/diagnostics/ukca_emiss_diags_mod.F90</tt>=====

In this routine you will add a unique code-block for this diagnostic that copies the pointer in the derived type into the <tt>stashwork</tt> array using the <tt>copydiag</tt> or <tt>copydiag_3d</tt> routines. The <tt>stashwork</tt> array contains all the fields that will be output through STASH.

Here is it easiest to copy an existing code-block and make the necessary changes for your new emission.

=====<tt>src/science/core/emissions/ukca_emiss_ctl_mod.F90</tt>=====

The call to '''<tt>ukca_emiss_diags</tt>''' is protected by an IF statement, and you'll need to add a check to the entry in the '''<tt>sf</tt>''' array to see if the diagnostic is on. This should be of the format '''<tt>sf(N,section)</tt>''', where '''N''' is the item number of your new emissions diagnostic.

===UM code changes===

These code changes need to be made in a UM branch, and relate to the emissions diagnostics.

=====<tt>src/control/ukca_interface/get_emdiag_stash_mod.F90</tt>=====

Once you have decided on the STASH code to use, you need to add the species and 3-digit '''item''' code to this routine in the CASE statement.

=====<tt>STASHmaster_A</tt> and <tt>STASHmaster-meta.conf</tt>=====

These files are contained in the <tt>rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/</tt> directory of the UM.

You should add a diagnostic in a similar way to the [[UKCA_Chemistry_and_Aerosol_UMvn13.0_Tutorial_7#STASHmaster_A|section 34 tracers]], but in this case to '''section 50'''. It is best to copy an existing 2D (or 3D) emissions diagnostic specification into an empty slot at the end of the emissions list (e.g. section 50, item 315 for instance), and make only the required edits to that.

Once you have made these code changes you should '''commit your branch''' to ensure that these STASHmaster changes are picked-up by your suite correctly when running.

'''Note''' that 2D emissions diagnostics won't need to have a corresponding pressure-level field added in section 52. Only 3D emissions diagnostics fields will need this.

==Worked Solution to Task 10.2==

<gallery widths=300px heights=200px>
Image:UM139_s34i498_T102.png|Surface level (20m) concentrations (kg/kg) of ALICE after emissions have been applied.
Image:UM139_s34i499_T102.png|Surface level (20m) concentrations (kg/kg) of BOB after emissions have been applied.
Image:UM139_s50i315_T102.png|Emissions flux of ALICE (moles/s).
</gallery>

You were given the task

* ''You should now make the UKCA code changes to add your emission into the '''ALICE''' tracer. Use STASH code <tt>s50i315</tt> for the diagnostic and output this to the '''UPA''' stream as a 3-hour mean.''

You were given the hints

* ''You will need to add-in the molar mass of ALICE. You can calculate this from the mass of air and the conversion factor defined in [[UKCA_Chemistry_and_Aerosol_UMvn13.0_Tutorial_3#Task_3.1:_Include_ALICE_and_BOB|Task 3.1]].''
* ''You will need to add code to allow a diagnostic of the emission to be output.''

Once you have made the required code and Rose changes, you should now see that the ALICE tracer now looks a bit like the emissions field you created in [[#Task_8.1:_Create_a_new_NetCDF_emissions_file|Task 8.1]].

The specific Rose changes made are:

* https://code.metoffice.gov.uk/trac/roses-u/changeset/337770/d/u/5/1/6/trunk

Index: app/um/rose-app.conf
===================================================================
--- app/um/rose-app.conf (revision 337756)
+++ app/um/rose-app.conf (revision 337770)
@@ -3278,7 +3278,8 @@
='$UMDIR/ancil/atmos/n48e/ukca_emiss/cmip5/2000/v1/ukca_emiss_C5H8.nc',
='$UMDIR/ancil/atmos/n48e/ukca_emiss/biogenic/v1/biogenic/MEGAN-MACC_biogenic_MeOH_clim_2001-2010.nc',
='$UMDIR/ancil/atmos/n48e/ukca_emiss/cmip5/2000/v1/ukca_emiss_CO.nc',
- ='/home/vagrant/ukca_emiss_CO.nc'
+ ='/home/vagrant/ukca_emiss_CO.nc',
+ ='/home/vagrant/ukca_emiss_ALICE.nc'
ukca_h1202mmr=3.788e-13
ukca_h1211mmr=2.225e-11
ukca_h1301mmr=1.363e-11
@@ -4348,6 +4349,14 @@
tim_name='T3HMN'
use_name='UPA'

+[namelist:umstash_streq(50315_f7d499b0)]
+dom_name='DIAG'
+isec=50
+item=315
+package=''
+tim_name='T3HMN'
+use_name='UPA'
+
[namelist:umstash_streq(51001_3e6241a4)]
dom_name='DP27CCM'
isec=51

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task10.2/Task10.2_rose.patch

The specific UKCA changes made are:

* https://code.metoffice.gov.uk/trac/ukca/changeset/7784/main/branches/dev/lukeabraham/um13.9_ukca_tutorial_solutions

Index: src/control/core/diagnostics/ukca_emdiags_struct_mod.F90
===================================================================
--- src/control/core/diagnostics/ukca_emdiags_struct_mod.F90 (revision 7771)
+++ src/control/core/diagnostics/ukca_emdiags_struct_mod.F90 (revision 7784)
@@ -65,8 +65,9 @@
LOGICAL :: l_em_etcho
LOGICAL :: l_em_hoch2cho
LOGICAL :: l_em_mek
+ ! UKCA Tutorial
+ LOGICAL :: l_em_alice

-
! Pointers to hold emission diagnostics
REAL, POINTER :: em_no (:,:)
REAL, POINTER :: em_ch4 (:,:)
@@ -104,6 +105,8 @@
REAL, POINTER :: em_etcho (:,:)
REAL, POINTER :: em_hoch2cho(:,:)
REAL, POINTER :: em_mek (:,:)
+ ! UKCA Tutorial
+ REAL, POINTER :: em_alice (:,:)

END TYPE emdiags_struct

Index: src/control/core/diagnostics/ukca_emiss_diags_mod.F90
===================================================================
--- src/control/core/diagnostics/ukca_emiss_diags_mod.F90 (revision 7771)
+++ src/control/core/diagnostics/ukca_emiss_diags_mod.F90 (revision 7784)
@@ -495,6 +495,15 @@
emdiags%em_mek (:,:), row_length, rows)
END IF

+!---------------------------------------------------------------------
+! Sec 50, item 315: ALICE surface emissions for UKCA Tutorial
+item = get_emdiag_stash ('ALICE ')
+IF (sf(item, section)) THEN
+ CALL copydiag (stashwork (si(item,section,im_index): &
+ si_last(item,section,im_index)), &
+ emdiags%em_alice (:,:), row_length, rows)
+END IF
+
IF (lhook) CALL dr_hook(ModuleName//':'//RoutineName,zhook_out,zhook_handle)

RETURN
Index: src/control/core/diagnostics/ukca_update_emdiagstruct_mod.F90
===================================================================
--- src/control/core/diagnostics/ukca_update_emdiagstruct_mod.F90 (revision 7771)
+++ src/control/core/diagnostics/ukca_update_emdiagstruct_mod.F90 (revision 7784)
@@ -121,6 +121,8 @@
emdiags%l_em_etcho = .FALSE.
emdiags%l_em_hoch2cho= .FALSE.
emdiags%l_em_mek = .FALSE.
+ ! UKCA Tutorial
+ emdiags%l_em_alice = .FALSE.

l_first = .FALSE.
END IF
@@ -535,6 +537,17 @@
END IF
END IF

+! UKCA Tutorial
+CASE ('ALICE ')
+ IF (emdiags%l_em_alice) THEN
+ emdiags%em_alice (:,:) = em_diags (:,:,1)
+ ELSE
+ IF (sf(item,section)) THEN
+ ALLOCATE (emdiags%em_alice (row_length, rows))
+ emdiags%em_alice (:,:) = em_diags (:,:,1)
+ emdiags%l_em_alice = .TRUE.
+ END IF
+ END IF

CASE DEFAULT
! Report error unless this is an aerosol emission (BC_fossil:, etc)
Index: src/control/core/top_level/ukca_config_defs_mod.F90
===================================================================
--- src/control/core/top_level/ukca_config_defs_mod.F90 (revision 7771)
+++ src/control/core/top_level/ukca_config_defs_mod.F90 (revision 7784)
@@ -354,7 +354,7 @@
! =======================
ELSE IF (ukca_config%l_ukca_strattrop) THEN
IF (.NOT. ukca_config%l_ukca_achem) THEN ! If NOT using aerosol chemistry
- n_chem_emissions = 10
+ n_chem_emissions = 11
n_3d_emissions = 1 ! aircraft NOX
n_aero_tracers = 0
ALLOCATE(em_chem_spec(n_chem_emissions+n_3d_emissions))
@@ -361,13 +361,13 @@
em_chem_spec = &
['NO ','CH4 ','CO ','HCHO ', &
'C2H6 ','C3H8 ','Me2CO ','MeCHO ', &
- 'C5H8 ','MeOH ','NO_aircrft']
+ 'C5H8 ','MeOH ','ALICE ','NO_aircrft']
n_chem_tracers = 73 ! No chem tracers
nr_therm = 221 ! thermal reactions
nr_phot = 55 ! photolytic (ATA)

ELSE ! If using aerosol chemistry
- n_chem_emissions = 19 ! em_chem_spec below
+ n_chem_emissions = 20 ! em_chem_spec below
n_3d_emissions = 4 ! BC, OC, volc SO2 & aircraft NOX

! add extra allocation for microplastics (i_mode_setup 13)
@@ -376,13 +376,13 @@
END IF

ALLOCATE(em_chem_spec(n_chem_emissions+n_3d_emissions))
- em_chem_spec(1:23) = &
+ em_chem_spec(1:24) = &
['NO ','CH4 ','CO ','HCHO ', &
'C2H6 ','C3H8 ','Me2CO ','MeCHO ', &
'C5H8 ','BC_fossil ','BC_biofuel','OM_fossil ', &
'OM_biofuel','Monoterp ','MeOH ','SO2_low ', &
- 'SO2_high ','NH3 ','DMS ','SO2_nat ', &
- 'BC_biomass','OM_biomass','NO_aircrft']
+ 'SO2_high ','NH3 ','DMS ','ALICE ', &
+ 'SO2_nat ','BC_biomass','OM_biomass','NO_aircrft']
IF (ukca_config%i_ukca_chem_version >= ichem_ver132) THEN
! Include secondary organic species from isoprene oxidation (SEC_ORG_I)
n_aero_tracers = 13
@@ -463,7 +463,7 @@
nr_therm = 572 ! thermal reactions
nr_phot = 121 ! photolytic reacs
END IF
- n_chem_emissions = 26
+ n_chem_emissions = 27
n_3d_emissions = 1 ! aircraft NOX
ALLOCATE(em_chem_spec(n_chem_emissions+n_3d_emissions))
em_chem_spec = &
@@ -473,7 +473,7 @@
'BPINENE ','BENZENE ','TOLUENE ','oXYLENE ', &
'MeOH ','EtOH ','HCHO ','MeCHO ', &
'EtCHO ','Me2CO ','MEK ','HCOOH ', &
- 'MeCO2H ','HOCH2CHO ','NO_aircrft']
+ 'MeCO2H ','HOCH2CHO ','ALICE ','NO_aircrft']
ELSE ! With aerosol
IF (ukca_config%i_ukca_chem_version >= 119) THEN ! CRI-Strat 2 with aerosol
n_chem_tracers = 173 ! advected chemical tracers (+9, -4)
@@ -494,7 +494,7 @@
nr_therm = 593 ! thermal reactions
END IF
END IF
- n_chem_emissions = 34 ! em_chem_spec below
+ n_chem_emissions = 35 ! em_chem_spec below
n_3d_emissions = 4 ! BC, OC, volc SO2 & aircraft NOX

! add extra allocation for microplastics
@@ -503,7 +503,7 @@
END IF

ALLOCATE(em_chem_spec(n_chem_emissions+n_3d_emissions))
- em_chem_spec(1:38) = &
+ em_chem_spec(1:39) = &
['NO ','CH4 ','CO ','C2H6 ', &
'C3H8 ','C4H10 ','C2H4 ','C3H6 ', &
'TBUT2ENE ','C2H2 ','C5H8 ','APINENE ', &
@@ -512,8 +512,8 @@
'EtCHO ','Me2CO ','MEK ','HCOOH ', &
'MeCO2H ','HOCH2CHO ','BC_fossil ','BC_biofuel', &
'OM_fossil ','OM_biofuel','SO2_low ','SO2_high ', &
- 'NH3 ','DMS ','SO2_nat ','BC_biomass', &
- 'OM_biomass','NO_aircrft']
+ 'NH3 ','DMS ','ALICE ','SO2_nat ', &
+ 'BC_biomass','OM_biomass','NO_aircrft']

! adding microplastics to em_chem_spec
IF (ukca_config%l_ukca_mode .AND. glomap_config%i_mode_setup == 13) THEN
Index: src/science/core/chemistry/get_molmass_mod.F90
===================================================================
--- src/science/core/chemistry/get_molmass_mod.F90 (revision 7771)
+++ src/science/core/chemistry/get_molmass_mod.F90 (revision 7784)
@@ -50,7 +50,7 @@
m_nh3, m_no, m_no2, m_oclo, m_ocs, m_oxylene, &
m_so2, m_so4, m_toluene, m_c2h2, m_tbut2ene, &
m_benzene, m_etoh, m_etcho, m_mek, m_hcooh, &
- m_meco2h, m_hoch2cho, m_mp
+ m_meco2h, m_hoch2cho, m_mp, m_alice

USE ereport_mod, ONLY: ereport
USE parkind1, ONLY: jpim, jprb ! DrHook
@@ -283,6 +283,11 @@
CASE ('HOCH2CHO ')
get_molmass = m_hoch2cho

+! -----------------------------------------
+! UKCA Tutorial Tracer
+CASE ('ALICE ')
+ get_molmass = m_alice
+
! -----------------------------------------
! Others (report warning)
CASE ('AGE ')
Index: src/science/core/chemistry/ukca_constants.F90
===================================================================
--- src/science/core/chemistry/ukca_constants.F90 (revision 7771)
+++ src/science/core/chemistry/ukca_constants.F90 (revision 7784)
@@ -632,6 +632,9 @@
! - Using m_cri = 150g/mol (same as Sec_org)
REAL, PARAMETER :: m_cri = 150.0

+! UKCA Tutorial tracers - only ALICE is emitted
+REAL, PARAMETER :: m_alice = 28.97
+
! For solar calculations

REAL, PARAMETER :: fxb = 23.45 / recip_pi_over_180 ! Latitude of tropic of
Index: src/science/core/emissions/ukca_emiss_ctl_mod.F90
===================================================================
--- src/science/core/emissions/ukca_emiss_ctl_mod.F90 (revision 7771)
+++ src/science/core/emissions/ukca_emiss_ctl_mod.F90 (revision 7784)
@@ -1226,7 +1226,7 @@
sf(304,section) .OR. sf(305,section) .OR. sf(306,section) .OR. &
sf(307,section) .OR. sf(308,section) .OR. sf(309,section) .OR. &
sf(310,section) .OR. sf(311,section) .OR. sf(312,section) .OR. &
- sf(313,section) .OR. sf(314,section) ) THEN
+ sf(313,section) .OR. sf(314,section) .OR. sf(315,section) ) THEN

CALL ukca_emiss_diags (row_length, rows, model_levels, &
len_stashwork50, stashwork50)

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task10.2/Task10.2_ukca.patch

The specific UM changes made are:

* https://code.metoffice.gov.uk/trac/um/changeset/131866/main/branches/dev/lukeabraham/vn13.9_ukca_tutorial_solutions

Index: rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf
===================================================================
--- rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf (revision 131864)
+++ rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf (revision 131866)
@@ -29016,6 +29016,14 @@
=
=Available only if NetCDF emission system of UKCA is used

+[stashmaster:code(50315)]
+description=ALICE surf emissions (kg m-2 s-1)
+help=Surface emission flux of ALICE (2D)
+ =kg m-2 s-1
+ =Valid on all timesteps
+ =
+ =Available only if NetCDF emission system of UKCA is used
+
[stashmaster:code(50331)]
help=Chemical reaction flux for COS + hv => CO + SO2
=(moles/s)
Index: rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A
===================================================================
--- rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A (revision 131864)
+++ rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A (revision 131866)
@@ -29868,6 +29868,12 @@
4| 1 | 0 | -99 -99 -99 -99 -99 -99 -99 -99 -99 -99 |
5| 0 | 0 | 0 | 129 | 0 | 0 | 0 | 0 | 0 |
#
+1| 1 | 50 | 315 |ALICE surf emissions (kg m-2 s-1) |
+2| 0 | 0 | 1 | 1 | 5 | -1 | -1 | 0 | 0 | 0 | 0 |
+3| 000000000000000000010000010000 | 00000000000000000001 | 3 |
+4| 1 | 0 | -99 -99 -99 -99 -99 -99 -99 -99 -99 -99 |
+5| 0 | 0 | 0 | 129 | 0 | 0 | 0 | 0 | 0 |
+#
1| 1 | 50 | 331 |RXN FLUX: COS + hv => CO + SO2 |
2| 0 | 0 | 17 | 1 | 2 | 10 | 11 | 0 | 0 | 0 | 0 |
3| 000000000000000000110000010000 | 00000000000000000001 | 3 |
Index: src/control/ukca_interface/get_emdiag_stash_mod.F90
===================================================================
--- src/control/ukca_interface/get_emdiag_stash_mod.F90 (revision 131864)
+++ src/control/ukca_interface/get_emdiag_stash_mod.F90 (revision 131866)
@@ -175,6 +175,9 @@
CASE ('MEK ')
get_emdiag_stash = 314

+CASE ('ALICE ')
+ get_emdiag_stash = 315
+
CASE DEFAULT
! Report error
ierr = 1

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task10.2/Task10.2_um.patch

Sample output from this task can be found at

Tutorials/UMvn13.9/sample_output/Task10.2/

==Checklist==

: ☐ Obtain emissions data for the species of interest.
: ☐ Regrid the emissions to the correct MetUM resolution that you are using.
: ☐ Save these emissions as netCDF, including the required metadata that UKCA requires.
: ☐ In your suite, include this file in the <tt>ukca_em_files</tt> variable in the UKCA panel: um <math>\rightarrow</math> namelist <math>\rightarrow</math> UM Science Settings <math>\rightarrow</math> Section 34 - UKCA: UK Aerosols and Chemistry <math>\rightarrow</math> Emissions.
: ☐ Put the species being emitted into the <tt>em_chem_spec</tt> array in <tt> ukca_config_defs_mod.F90</tt>, and increment <tt>n_chem_emissions</tt>.
: ☐ Put the correct M_species value in <tt>ukca_constants.F90</tt>.
: ☐ In <tt>get_molmass_mod.F90</tt>, append the CASE statement with your new species.
: ☐ Make diagnostics output slots for your new emissions in <tt>STASHmaster_A</tt> and add help-text to <tt>STASHmaster-meta.conf</tt>.
: ☐ If required, using a text editor, open the <tt>app/um/rose-app.conf</tt> file from your <tt>roses/[SUITE-ID]</tt> directory, and add the line <tt>STASHMASTER=STASHmaster</tt> in the <tt>[env]</tt> block, then save and close the file.
: ☐ If required, using a text editor, open the <tt>rose-suite.conf</tt> file from your <tt>roses/[SUITE-ID]</tt> 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
: ☐ Point the metadata in your suite to the <tt>rose-meta/um-atmos/HEAD</tt> of your branch's working copy.
: ☐ If required, include your branch in your suite at: fcm_make <math>\rightarrow</math> env <math>\rightarrow</math> Sources.
: ☐ In <tt>get_emdiag_stash_mod.F90</tt> add the species and 3-digit item code to the CASE statement.
: ☐ In <tt>ukca_emdiags_struct_mod.F90</tt> add a logical and array pointer to the derived type for your new species.
: ☐ In <tt>ukca_update_emdiagstruct_mod.F90</tt> initialise your new derived type entries, and add a block of code to copy the emissions field into the diagnostic pointer.
: ☐ In <tt>ukca_emiss_diags_mod.F90</tt> add a code block to copy the field to the <tt>stashwork</tt> array using <tt>copydiag</tt>/<tt>copydiag_3d</tt>.
: ☐ In <tt>ukca_emiss_ctl_mod.F90</tt> add the <tt>sf(ITEM,section)</tt> check in the IF statement protecting the call to <tt>ukca_emiss_diags</tt>.
: ☐ <tt> fcm commit</tt> the changes to your branch.
: ☐ Output your emissions diagnostic in: um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> STASH Requests and Profiles <math>\rightarrow</math> STASH Requests.
: ☐ Run the TidyStashTransform transform macro.
: ☐ Save your suite.
: ☐ In the <tt>roses/[SUITE-ID]</tt> directory, run <tt>fcm commit</tt> to commit your changes to the repository.
: ☐ Run your suite.

[[UKCA Chemistry and Aerosol UMvn13.9 Tutorial 11|Tutorial 11]]

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

UKCA Chemistry and Aerosol UMvn13.9 Tutorial 10

2026-01-13T13:42:58Z

Nla27: /* src/science/core/chemistry/ukca_constants.F90 */

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

{| class="wikitable" border = "1px"
|-
| Difficulty || '''HARD'''
|-
| Time to Complete || '''2 or more hours'''
|-
| Video instructions || https://www.youtube.com/watch?v=aysibeNdLUY&t=13444s
|}

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

==What you will learn in this Tutorial==

This is a continuation of what you learned in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_5|Tutorial 5]], where you regridded a set of emissions to the UM grid and included them for an existing tracers. During this tutorial you will make new UKCA netCDF emissions files and then you will learn how to add new emissions into UKCA so that they emit into one of your new tracers.

At the end of the [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_9|previous tutorial]] you will now know how to create new tracers in the UM for use by UKCA. However, while the chemical reaction(s) added in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_8|tutorial 8]] are active, as the tracers have been initialised to very small values these are not behaving as could be expected. This tutorial will teach you how to create an emissions file that the UKCA will read, and that you can then tell UKCA to use and emit into your tracer(s). These emissions will then become the higher concentrations that will drive the new chemistry.

This example only deals with a single field. For a more detailed examples on changing emissions for all species, please see the [[Emissions for ACSIS]] webpage.

==Task 10.1: Create a new NetCDF emissions file ==

'''Task 10.1:''' In the <pre>Tutorials/UMvn13.9/Task10.1</pre> directory there is the file '''Emissions_of_ALICE.nc''' which is a 0.5x0.5 degree resolution surface emission field. You should regrid this file to the '''N48 ENDGame grid''', and output it as a netCDF file that has the required netCDF metadata for a climatological surface emission without any diurnal cycle.

You should take the script you used in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_5|Tutorial 5]] and adapt it to work with this new file and new species that is being emitted into.

{| class="collapsible collapsed wikitable"
|-
! Hints
|-
| Remember to change the location of the <tt>emiss</tt> file.
|-
| Remember to change the values of the attributes <tt>var_name</tt>, <tt>long_name</tt>, and <tt>tracer_name</tt>.
|-
| Remember to change the name of the output file set by <tt>outpath</tt>.
|}

==Solution to Task10.1==

You were given the task:

* ''In the <pre>Tutorials/UMvn13.9/Task10.1</pre> directory there is the file '''Emissions_of_ALICE.nc''' which is a 0.5x0.5 degree resolution surface emission field. You should regrid this file to the '''N48 ENDGame grid''', and output it as a netCDF file that has the required netCDF metadata for a climatological surface emission without any diurnal cycle.''

and were given the hints:

* ''Remember to change the location of the <tt>emiss</tt> file.''
* ''Remember to change the values of the attributes <tt>var_name</tt>, <tt>long_name</tt>, and <tt>tracer_name</tt>.''
* ''Remember to change the name of the output file set by <tt>outpath</tt>.''

It should be straight-forward adapt your existing script to work for ALICE. If you are having problems, a solution script can be found at

* '''[https://github.com/theabro/ukca/blob/master/Tutorials/UMvn13.9/notebooks/Solutions/iris_UM-UKCA_T101.ipynb Solution to Task 10.1]'''

Once the file has been regridded, you should see the output looking like this:

<gallery widths=300px heights=200px>
Image:UM139_alice_05x05.png|ALICE emissions prior to regridding.
Image:UM139_alice_n48e.png|ALICE emissions after regridding.
</gallery>

A file that has been produced by the above script can be found at

Tutorials/UMvn13.9/sample_output/Task10.1/ukca_emiss_ALICE.nc

==Task 10.2: make the required code changes to add your emission into UKCA==

'''TASK 10.2:''' You should now make the UKCA code changes to add your emission into the '''ALICE''' tracer. Use STASH code <tt>s50i315</tt> for the diagnostic and output this to the '''UPA''' stream as a 3-hour mean.

{| class="collapsible collapsed wikitable"
|-
! Hint
|-
| You will need to add-in the molar mass of ALICE. You can calculate this from the mass of air and the conversion factor defined in [[UKCA_Chemistry_and_Aerosol_UMvn13.0_Tutorial_7#Task_7.1:_Include_ALICE_and_BOB|Task 7.1]]. You will need to add code to allow a diagnostic of the emission to be output.
|}

==Rose changes==

===Include your new emissions file===

You should include your new emissions file as you did in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_5#Rose_changes|Task 5.2]].

===Diagnostics===

You should make your STASHmaster_A entry and add this to the STASH panel as you have done in [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_4|Tutorial 4]] and [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_5|Tutorial 5]].

You won't need to make any changes to the location of the STASHmaster file '''so long as you commit your changes prior to running the suite'''.

Note that here you are making the diagnostic entry before you have made code changes that will populate this field, which are done below.

==Code changes==

Code changes are split between changes that need to be made to the UM and those that are made to UKCA.

===UKCA code changes===

====Code changes to use the new emissions====

=====<tt>src/control/core/top_level/ukca_config_defs_mod.F90</tt>=====

You will need to edit the '''<tt>em_chem_spec</tt>''' array for the scheme that you are using to include the new species that you are emitting into. By convention, these are ordered as 2D fields followed by 3D fields, with chemical emissions first and then aerosol emissions, although this order is unimportant other than the fact that the 2D emissions should be placed before the 3D emissions of '''<tt>'SO2_nat'</tt>''', '''<tt>'BC_biomass'</tt>''', '''<tt>'OC_biomass'</tt>''', and '''<tt>'NO_aircrft'</tt>''' if these are present.

If the tracer is purely chemical and is always on (i.e. is not included only when aerosol chemistry is turned on) then you will need to put this in both <tt>em_chem_spec</tt> arrays (i.e. one for the chemistry scheme without aerosols and one with aerosols). Also remember to increment this size of the '''<tt>em_chem_spec</tt>''' array, given by '''<tt>n_chem_emissions</tt>''' variable.

For this example you will need to make changes for StratTrop ''and'' CRI-Strat (version 2) schemes, both with an without aerosol chemistry.

=====<tt>src/science/core/chemistry/ukca_constants.F90</tt>=====

You will need to define the '''<tt>M_species</tt>''' for the emitted species, e.g. <tt>m_alice</tt>. The value of this should be consistent with the '''<tt>C_species</tt>''' value set in the [[UKCA_Chemistry_and_Aerosol_UMvn13.9_Tutorial_7#src.2Fscience.2Fcore.2Fchemistry.2Fukca_constants.F90 | adding new tracers tutorial]].

=====<tt>src/science/core/chemistry/get_molmass_mod.F90</tt>=====

You will need to add to the '''<tt>species_name</tt>''' <tt>CASE</tt> statement, to include a line such as this

CASE ('ALICE ')
get_molmass = m_alice

for each new species that you are emitting into.

As the <tt>M_species</tt> conversion factors are defined in the <tt>ukca_constants</tt> module you will need to explicitly add them to the

USE ukca_constants, ONLY: ...

statement at the top of the module.

====Code changes for the emissions diagnostics====

Additionally, by default, when emitting into a new species, the code requires you to create a diagnostic for these emissions as well. These changes are also considered below.

=====<tt>src/control/core/diagnostics/ukca_emdiags_struct_mod.F90</tt>=====

This routine contains the derived type that holds the emissions fluxes for all species. You will need to add a logical (used to determine whether the output has been requested in STASH) and a pointer to a 2D or 3D array that will hold the emissions flux.

=====<tt>src/control/core/diagnostics/ukca_update_emdiagstruct_mod.F90</tt>=====

In this routine you will need to add the initialisation of the logical added in <tt>ukca_emdiags_struct_mod.F90</tt>, as well as a small block of code that copies the 2D/3D <tt>em_diags</tt> data into the newly created pointer in the derived type. The logical will also need to be set to <tt>.TRUE.</tt> if STASH output has been requested (determined by the <tt>sf(item,section)</tt> look-up array).

Here is it easiest to copy an existing code-block and make the necessary changes for your new emission.

=====<tt>src/control/core/diagnostics/ukca_emiss_diags_mod.F90</tt>=====

In this routine you will add a unique code-block for this diagnostic that copies the pointer in the derived type into the <tt>stashwork</tt> array using the <tt>copydiag</tt> or <tt>copydiag_3d</tt> routines. The <tt>stashwork</tt> array contains all the fields that will be output through STASH.

Here is it easiest to copy an existing code-block and make the necessary changes for your new emission.

=====<tt>src/science/core/emissions/ukca_emiss_ctl_mod.F90</tt>=====

The call to '''<tt>ukca_emiss_diags</tt>''' is protected by an IF statement, and you'll need to add a check to the entry in the '''<tt>sf</tt>''' array to see if the diagnostic is on. This should be of the format '''<tt>sf(N,section)</tt>''', where '''N''' is the item number of your new emissions diagnostic.

===UM code changes===

These code changes need to be made in a UM branch, and relate to the emissions diagnostics.

=====<tt>src/control/ukca_interface/get_emdiag_stash_mod.F90</tt>=====

Once you have decided on the STASH code to use, you need to add the species and 3-digit '''item''' code to this routine in the CASE statement.

=====<tt>STASHmaster_A</tt> and <tt>STASHmaster-meta.conf</tt>=====

These files are contained in the <tt>rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/</tt> directory of the UM.

You should add a diagnostic in a similar way to the [[UKCA_Chemistry_and_Aerosol_UMvn13.0_Tutorial_7#STASHmaster_A|section 34 tracers]], but in this case to '''section 50'''. It is best to copy an existing 2D (or 3D) emissions diagnostic specification into an empty slot at the end of the emissions list (e.g. section 50, item 315 for instance), and make only the required edits to that.

Once you have made these code changes you should '''commit your branch''' to ensure that these STASHmaster changes are picked-up by your suite correctly when running.

'''Note''' that 2D emissions diagnostics won't need to have a corresponding pressure-level field added in section 52. Only 3D emissions diagnostics fields will need this.

==Worked Solution to Task 10.2==

<gallery widths=300px heights=200px>
Image:UM139_s34i498_T102.png|Surface level (20m) concentrations (kg/kg) of ALICE after emissions have been applied.
Image:UM139_s34i499_T102.png|Surface level (20m) concentrations (kg/kg) of BOB after emissions have been applied.
Image:UM139_s50i315_T102.png|Emissions flux of ALICE (moles/s).
</gallery>

You were given the task

* ''You should now make the UKCA code changes to add your emission into the '''ALICE''' tracer. Use STASH code <tt>s50i315</tt> for the diagnostic and output this to the '''UPA''' stream as a 3-hour mean.''

You were given the hints

* ''You will need to add-in the molar mass of ALICE. You can calculate this from the mass of air and the conversion factor defined in [[UKCA_Chemistry_and_Aerosol_UMvn13.0_Tutorial_3#Task_3.1:_Include_ALICE_and_BOB|Task 3.1]].''
* ''You will need to add code to allow a diagnostic of the emission to be output.''

Once you have made the required code and Rose changes, you should now see that the ALICE tracer now looks a bit like the emissions field you created in [[#Task_8.1:_Create_a_new_NetCDF_emissions_file|Task 8.1]].

The specific Rose changes made are:

* https://code.metoffice.gov.uk/trac/roses-u/changeset/337770/d/u/5/1/6/trunk

Index: app/um/rose-app.conf
===================================================================
--- app/um/rose-app.conf (revision 337756)
+++ app/um/rose-app.conf (revision 337770)
@@ -3278,7 +3278,8 @@
='$UMDIR/ancil/atmos/n48e/ukca_emiss/cmip5/2000/v1/ukca_emiss_C5H8.nc',
='$UMDIR/ancil/atmos/n48e/ukca_emiss/biogenic/v1/biogenic/MEGAN-MACC_biogenic_MeOH_clim_2001-2010.nc',
='$UMDIR/ancil/atmos/n48e/ukca_emiss/cmip5/2000/v1/ukca_emiss_CO.nc',
- ='/home/vagrant/ukca_emiss_CO.nc'
+ ='/home/vagrant/ukca_emiss_CO.nc',
+ ='/home/vagrant/ukca_emiss_ALICE.nc'
ukca_h1202mmr=3.788e-13
ukca_h1211mmr=2.225e-11
ukca_h1301mmr=1.363e-11
@@ -4348,6 +4349,14 @@
tim_name='T3HMN'
use_name='UPA'

+[namelist:umstash_streq(50315_f7d499b0)]
+dom_name='DIAG'
+isec=50
+item=315
+package=''
+tim_name='T3HMN'
+use_name='UPA'
+
[namelist:umstash_streq(51001_3e6241a4)]
dom_name='DP27CCM'
isec=51

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task10.2/Task10.2_rose.patch

The specific UKCA changes made are:

* https://code.metoffice.gov.uk/trac/ukca/changeset/7784/main/branches/dev/lukeabraham/um13.9_ukca_tutorial_solutions

Index: src/control/core/diagnostics/ukca_emdiags_struct_mod.F90
===================================================================
--- src/control/core/diagnostics/ukca_emdiags_struct_mod.F90 (revision 7771)
+++ src/control/core/diagnostics/ukca_emdiags_struct_mod.F90 (revision 7784)
@@ -65,8 +65,9 @@
LOGICAL :: l_em_etcho
LOGICAL :: l_em_hoch2cho
LOGICAL :: l_em_mek
+ ! UKCA Tutorial
+ LOGICAL :: l_em_alice

-
! Pointers to hold emission diagnostics
REAL, POINTER :: em_no (:,:)
REAL, POINTER :: em_ch4 (:,:)
@@ -104,6 +105,8 @@
REAL, POINTER :: em_etcho (:,:)
REAL, POINTER :: em_hoch2cho(:,:)
REAL, POINTER :: em_mek (:,:)
+ ! UKCA Tutorial
+ REAL, POINTER :: em_alice (:,:)

END TYPE emdiags_struct

Index: src/control/core/diagnostics/ukca_emiss_diags_mod.F90
===================================================================
--- src/control/core/diagnostics/ukca_emiss_diags_mod.F90 (revision 7771)
+++ src/control/core/diagnostics/ukca_emiss_diags_mod.F90 (revision 7784)
@@ -495,6 +495,15 @@
emdiags%em_mek (:,:), row_length, rows)
END IF

+!---------------------------------------------------------------------
+! Sec 50, item 315: ALICE surface emissions for UKCA Tutorial
+item = get_emdiag_stash ('ALICE ')
+IF (sf(item, section)) THEN
+ CALL copydiag (stashwork (si(item,section,im_index): &
+ si_last(item,section,im_index)), &
+ emdiags%em_alice (:,:), row_length, rows)
+END IF
+
IF (lhook) CALL dr_hook(ModuleName//':'//RoutineName,zhook_out,zhook_handle)

RETURN
Index: src/control/core/diagnostics/ukca_update_emdiagstruct_mod.F90
===================================================================
--- src/control/core/diagnostics/ukca_update_emdiagstruct_mod.F90 (revision 7771)
+++ src/control/core/diagnostics/ukca_update_emdiagstruct_mod.F90 (revision 7784)
@@ -121,6 +121,8 @@
emdiags%l_em_etcho = .FALSE.
emdiags%l_em_hoch2cho= .FALSE.
emdiags%l_em_mek = .FALSE.
+ ! UKCA Tutorial
+ emdiags%l_em_alice = .FALSE.

l_first = .FALSE.
END IF
@@ -535,6 +537,17 @@
END IF
END IF

+! UKCA Tutorial
+CASE ('ALICE ')
+ IF (emdiags%l_em_alice) THEN
+ emdiags%em_alice (:,:) = em_diags (:,:,1)
+ ELSE
+ IF (sf(item,section)) THEN
+ ALLOCATE (emdiags%em_alice (row_length, rows))
+ emdiags%em_alice (:,:) = em_diags (:,:,1)
+ emdiags%l_em_alice = .TRUE.
+ END IF
+ END IF

CASE DEFAULT
! Report error unless this is an aerosol emission (BC_fossil:, etc)
Index: src/control/core/top_level/ukca_config_defs_mod.F90
===================================================================
--- src/control/core/top_level/ukca_config_defs_mod.F90 (revision 7771)
+++ src/control/core/top_level/ukca_config_defs_mod.F90 (revision 7784)
@@ -354,7 +354,7 @@
! =======================
ELSE IF (ukca_config%l_ukca_strattrop) THEN
IF (.NOT. ukca_config%l_ukca_achem) THEN ! If NOT using aerosol chemistry
- n_chem_emissions = 10
+ n_chem_emissions = 11
n_3d_emissions = 1 ! aircraft NOX
n_aero_tracers = 0
ALLOCATE(em_chem_spec(n_chem_emissions+n_3d_emissions))
@@ -361,13 +361,13 @@
em_chem_spec = &
['NO ','CH4 ','CO ','HCHO ', &
'C2H6 ','C3H8 ','Me2CO ','MeCHO ', &
- 'C5H8 ','MeOH ','NO_aircrft']
+ 'C5H8 ','MeOH ','ALICE ','NO_aircrft']
n_chem_tracers = 73 ! No chem tracers
nr_therm = 221 ! thermal reactions
nr_phot = 55 ! photolytic (ATA)

ELSE ! If using aerosol chemistry
- n_chem_emissions = 19 ! em_chem_spec below
+ n_chem_emissions = 20 ! em_chem_spec below
n_3d_emissions = 4 ! BC, OC, volc SO2 & aircraft NOX

! add extra allocation for microplastics (i_mode_setup 13)
@@ -376,13 +376,13 @@
END IF

ALLOCATE(em_chem_spec(n_chem_emissions+n_3d_emissions))
- em_chem_spec(1:23) = &
+ em_chem_spec(1:24) = &
['NO ','CH4 ','CO ','HCHO ', &
'C2H6 ','C3H8 ','Me2CO ','MeCHO ', &
'C5H8 ','BC_fossil ','BC_biofuel','OM_fossil ', &
'OM_biofuel','Monoterp ','MeOH ','SO2_low ', &
- 'SO2_high ','NH3 ','DMS ','SO2_nat ', &
- 'BC_biomass','OM_biomass','NO_aircrft']
+ 'SO2_high ','NH3 ','DMS ','ALICE ', &
+ 'SO2_nat ','BC_biomass','OM_biomass','NO_aircrft']
IF (ukca_config%i_ukca_chem_version >= ichem_ver132) THEN
! Include secondary organic species from isoprene oxidation (SEC_ORG_I)
n_aero_tracers = 13
@@ -463,7 +463,7 @@
nr_therm = 572 ! thermal reactions
nr_phot = 121 ! photolytic reacs
END IF
- n_chem_emissions = 26
+ n_chem_emissions = 27
n_3d_emissions = 1 ! aircraft NOX
ALLOCATE(em_chem_spec(n_chem_emissions+n_3d_emissions))
em_chem_spec = &
@@ -473,7 +473,7 @@
'BPINENE ','BENZENE ','TOLUENE ','oXYLENE ', &
'MeOH ','EtOH ','HCHO ','MeCHO ', &
'EtCHO ','Me2CO ','MEK ','HCOOH ', &
- 'MeCO2H ','HOCH2CHO ','NO_aircrft']
+ 'MeCO2H ','HOCH2CHO ','ALICE ','NO_aircrft']
ELSE ! With aerosol
IF (ukca_config%i_ukca_chem_version >= 119) THEN ! CRI-Strat 2 with aerosol
n_chem_tracers = 173 ! advected chemical tracers (+9, -4)
@@ -494,7 +494,7 @@
nr_therm = 593 ! thermal reactions
END IF
END IF
- n_chem_emissions = 34 ! em_chem_spec below
+ n_chem_emissions = 35 ! em_chem_spec below
n_3d_emissions = 4 ! BC, OC, volc SO2 & aircraft NOX

! add extra allocation for microplastics
@@ -503,7 +503,7 @@
END IF

ALLOCATE(em_chem_spec(n_chem_emissions+n_3d_emissions))
- em_chem_spec(1:38) = &
+ em_chem_spec(1:39) = &
['NO ','CH4 ','CO ','C2H6 ', &
'C3H8 ','C4H10 ','C2H4 ','C3H6 ', &
'TBUT2ENE ','C2H2 ','C5H8 ','APINENE ', &
@@ -512,8 +512,8 @@
'EtCHO ','Me2CO ','MEK ','HCOOH ', &
'MeCO2H ','HOCH2CHO ','BC_fossil ','BC_biofuel', &
'OM_fossil ','OM_biofuel','SO2_low ','SO2_high ', &
- 'NH3 ','DMS ','SO2_nat ','BC_biomass', &
- 'OM_biomass','NO_aircrft']
+ 'NH3 ','DMS ','ALICE ','SO2_nat ', &
+ 'BC_biomass','OM_biomass','NO_aircrft']

! adding microplastics to em_chem_spec
IF (ukca_config%l_ukca_mode .AND. glomap_config%i_mode_setup == 13) THEN
Index: src/science/core/chemistry/get_molmass_mod.F90
===================================================================
--- src/science/core/chemistry/get_molmass_mod.F90 (revision 7771)
+++ src/science/core/chemistry/get_molmass_mod.F90 (revision 7784)
@@ -50,7 +50,7 @@
m_nh3, m_no, m_no2, m_oclo, m_ocs, m_oxylene, &
m_so2, m_so4, m_toluene, m_c2h2, m_tbut2ene, &
m_benzene, m_etoh, m_etcho, m_mek, m_hcooh, &
- m_meco2h, m_hoch2cho, m_mp
+ m_meco2h, m_hoch2cho, m_mp, m_alice

USE ereport_mod, ONLY: ereport
USE parkind1, ONLY: jpim, jprb ! DrHook
@@ -283,6 +283,11 @@
CASE ('HOCH2CHO ')
get_molmass = m_hoch2cho

+! -----------------------------------------
+! UKCA Tutorial Tracer
+CASE ('ALICE ')
+ get_molmass = m_alice
+
! -----------------------------------------
! Others (report warning)
CASE ('AGE ')
Index: src/science/core/chemistry/ukca_constants.F90
===================================================================
--- src/science/core/chemistry/ukca_constants.F90 (revision 7771)
+++ src/science/core/chemistry/ukca_constants.F90 (revision 7784)
@@ -632,6 +632,9 @@
! - Using m_cri = 150g/mol (same as Sec_org)
REAL, PARAMETER :: m_cri = 150.0

+! UKCA Tutorial tracers - only ALICE is emitted
+REAL, PARAMETER :: m_alice = 28.97
+
! For solar calculations

REAL, PARAMETER :: fxb = 23.45 / recip_pi_over_180 ! Latitude of tropic of
Index: src/science/core/emissions/ukca_emiss_ctl_mod.F90
===================================================================
--- src/science/core/emissions/ukca_emiss_ctl_mod.F90 (revision 7771)
+++ src/science/core/emissions/ukca_emiss_ctl_mod.F90 (revision 7784)
@@ -1226,7 +1226,7 @@
sf(304,section) .OR. sf(305,section) .OR. sf(306,section) .OR. &
sf(307,section) .OR. sf(308,section) .OR. sf(309,section) .OR. &
sf(310,section) .OR. sf(311,section) .OR. sf(312,section) .OR. &
- sf(313,section) .OR. sf(314,section) ) THEN
+ sf(313,section) .OR. sf(314,section) .OR. sf(315,section) ) THEN

CALL ukca_emiss_diags (row_length, rows, model_levels, &
len_stashwork50, stashwork50)

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task10.2/Task10.2_ukca.patch

The specific UM changes made are:

* https://code.metoffice.gov.uk/trac/um/changeset/131866/main/branches/dev/lukeabraham/vn13.9_ukca_tutorial_solutions

Index: rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf
===================================================================
--- rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf (revision 131864)
+++ rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster-meta.conf (revision 131866)
@@ -29016,6 +29016,14 @@
=
=Available only if NetCDF emission system of UKCA is used

+[stashmaster:code(50315)]
+description=ALICE surf emissions (kg m-2 s-1)
+help=Surface emission flux of ALICE (2D)
+ =kg m-2 s-1
+ =Valid on all timesteps
+ =
+ =Available only if NetCDF emission system of UKCA is used
+
[stashmaster:code(50331)]
help=Chemical reaction flux for COS + hv => CO + SO2
=(moles/s)
Index: rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A
===================================================================
--- rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A (revision 131864)
+++ rose-meta/um-atmos/HEAD/etc/stash/STASHmaster/STASHmaster_A (revision 131866)
@@ -29868,6 +29868,12 @@
4| 1 | 0 | -99 -99 -99 -99 -99 -99 -99 -99 -99 -99 |
5| 0 | 0 | 0 | 129 | 0 | 0 | 0 | 0 | 0 |
#
+1| 1 | 50 | 315 |ALICE surf emissions (kg m-2 s-1) |
+2| 0 | 0 | 1 | 1 | 5 | -1 | -1 | 0 | 0 | 0 | 0 |
+3| 000000000000000000010000010000 | 00000000000000000001 | 3 |
+4| 1 | 0 | -99 -99 -99 -99 -99 -99 -99 -99 -99 -99 |
+5| 0 | 0 | 0 | 129 | 0 | 0 | 0 | 0 | 0 |
+#
1| 1 | 50 | 331 |RXN FLUX: COS + hv => CO + SO2 |
2| 0 | 0 | 17 | 1 | 2 | 10 | 11 | 0 | 0 | 0 | 0 |
3| 000000000000000000110000010000 | 00000000000000000001 | 3 |
Index: src/control/ukca_interface/get_emdiag_stash_mod.F90
===================================================================
--- src/control/ukca_interface/get_emdiag_stash_mod.F90 (revision 131864)
+++ src/control/ukca_interface/get_emdiag_stash_mod.F90 (revision 131866)
@@ -175,6 +175,9 @@
CASE ('MEK ')
get_emdiag_stash = 314

+CASE ('ALICE ')
+ get_emdiag_stash = 315
+
CASE DEFAULT
! Report error
ierr = 1

These differences can be found here:

Tutorials/UMvn13.9/worked_solutions/Task10.2/Task10.2_um.patch

Sample output from this task can be found at

Tutorials/UMvn13.9/sample_output/Task10.2/

==Checklist==

: ☐ Obtain emissions data for the species of interest.
: ☐ Regrid the emissions to the correct MetUM resolution that you are using.
: ☐ Save these emissions as netCDF, including the required metadata that UKCA requires.
: ☐ In your suite, include this file in the <tt>ukca_em_files</tt> variable in the UKCA panel: um <math>\rightarrow</math> namelist <math>\rightarrow</math> UM Science Settings <math>\rightarrow</math> Section 34 - UKCA: UK Aerosols and Chemistry <math>\rightarrow</math> Emissions.
: ☐ Put the species being emitted into the <tt>em_chem_spec</tt> array in <tt> ukca_config_defs_mod.F90</tt>, and increment <tt>n_chem_emissions</tt>.
: ☐ Put the correct M_species value in <tt>ukca_constants.F90</tt>.
: ☐ In <tt>get_molmass_mod.F90</tt>, append the CASE statement with your new species.
: ☐ Make diagnostics output slots for your new emissions in <tt>STASHmaster_A</tt> and add help-text to <tt>STASHmaster-meta.conf</tt>.
: ☐ If required, using a text editor, open the <tt>app/um/rose-app.conf</tt> file from your <tt>roses/[SUITE-ID]</tt> directory, and add the line <tt>STASHMASTER=STASHmaster</tt> in the <tt>[env]</tt> block, then save and close the file.
: ☐ If required, using a text editor, open the <tt>rose-suite.conf</tt> file from your <tt>roses/[SUITE-ID]</tt> 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
: ☐ Point the metadata in your suite to the <tt>rose-meta/um-atmos/HEAD</tt> of your branch's working copy.
: ☐ If required, include your branch in your suite at: fcm_make <math>\rightarrow</math> env <math>\rightarrow</math> Sources.
: ☐ In <tt>get_emdiag_stash_mod.F90</tt> add the species and 3-digit item code to the CASE statement.
: ☐ In <tt>ukca_emdiags_struct_mod.F90</tt> add a logical and array pointer to the derived type for your new species.
: ☐ In <tt>ukca_update_emdiagstruct_mod.F90</tt> initialise your new derived type entries, and add a block of code to copy the emissions field into the diagnostic pointer.
: ☐ In <tt>ukca_emiss_diags_mod.F90</tt> add a code block to copy the field to the <tt>stashwork</tt> array using <tt>copydiag</tt>/<tt>copydiag_3d</tt>.
: ☐ In <tt>ukca_emiss_ctl_mod.F90</tt> add the <tt>sf(ITEM,section)</tt> check in the IF statement protecting the call to <tt>ukca_emiss_diags</tt>.
: ☐ <tt> fcm commit</tt> the changes to your branch.
: ☐ Output your emissions diagnostic in: um <math>\rightarrow</math> namelist <math>\rightarrow</math> Model Input and Output <math>\rightarrow</math> STASH Requests and Profiles <math>\rightarrow</math> STASH Requests.
: ☐ Run the TidyStashTransform transform macro.
: ☐ Save your suite.
: ☐ In the <tt>roses/[SUITE-ID]</tt> directory, run <tt>fcm commit</tt> to commit your changes to the repository.
: ☐ Run your suite.

[[UKCA Chemistry and Aerosol UMvn13.9 Tutorial 11|Tutorial 11]]

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