UKCA Chemistry and Aerosol UMvn13.0 Tutorial 2: Difference between revisions

Revision as of 15:00, 14 September 2022

UKCA Chemistry and Aerosol Tutorials at UMvn13.0

Difficulty	EASY
Time to Complete	Under 1 hour
Video instructions

Remember to run mosrs-cache-password in your Rose suite and UM branch terminals.

Changing UKCA Box Model Options

This tutorial describes how to change the time settings, meteorological conditions, tracer initialisations, chemistry, and aerosol options in the UKCA Box Model.

Changing the Box Model Time Settings

The time settings for the box model can be found in the ukca $\rightarrow$ namelist $\rightarrow$ Time Settings panel and the ukca $\rightarrow$ namelist $\rightarrow$ Science Settings $\rightarrow$ Chemistry panel. The key variables are:

Panel	Variable	Description	Example
Time Settings	`model_basis_time`	The nominal start time of the model, defined as `YEAR, MONTH, DAY, HOUR, MINUTE, SECOND`	1989,09,01,00,00,00 (i.e. midnight on 1st September 1989)
Time Settings	`run_target_end`	The run length of model, defined as `YEARS, MONTHS, DAYS, HOURS, MINUTES, SECONDS`	0,0,1,0,0,0 (i.e. 1 day)
Time Settings	`steps_per_periodim`	The number of "dynamical" timesteps per "period" (a model day, containing the number of seconds given in the `secs_per_periodim` variable above)	24 (i.e. 1 hour)
Chemistry	`chem_timestep`	The number of seconds in a chemical timestep. This must be a multiple of the value of `steps_per_periodim`	3600 (i.e. 1 hour)

Task 2.1: Change the Start Time

O3 mass-mixing ratio when started from midday.

TASK 2.1: Change the start time of the model to begin at midday rather than midnight.

Solution
Change the value of `model_basis_time` to be `1989,09,01,12,00,00`

Once the run has finished, replot ozone and see how the graph has changed.

Worked Solution to Task 2.1

The changes to Rose are:

https://code.metoffice.gov.uk/trac/roses-u/changeset/236400/c/q/7/8/2/trunk

Index: app/ukca/rose-app.conf
===================================================================
--- app/ukca/rose-app.conf	(revision 236285)
+++ app/ukca/rose-app.conf	(revision 236400)
@@ -145,7 +145,7 @@
 ltimer=.true.
 !!ltimers_user=.false.
 model_analysis_mins=0
-model_basis_time=1981,09,01,00,00,00
+model_basis_time=1981,09,01,12,00,00
 num_albcs=0
 run_target_end=0,0,1,0,0,0

These differences can be found here:

Tutorials/UMvn13.0/worked_solutions/Task02.1/Task02.1_rose.patch

Task 2.2: Increase the run-length

O3 mass-mixing ratio for a 5-day run.

TASK 2.2: Increase the run length of the box model to 5 days.

Solution
Change the value of `run_target_end` to be `0,0,5,0,0,0`

Once the run has finished, replot ozone and see how the graph has changed.

Worked Solution to Task 2.2

The changes to Rose are:

https://code.metoffice.gov.uk/trac/roses-u/changeset/236409/c/q/7/8/2/trunk

Index: app/ukca/rose-app.conf
===================================================================
--- app/ukca/rose-app.conf	(revision 236400)
+++ app/ukca/rose-app.conf	(revision 236409)
@@ -147,7 +147,7 @@
 model_analysis_mins=0
 model_basis_time=1981,09,01,12,00,00
 num_albcs=0
-run_target_end=0,0,1,0,0,0
+run_target_end=0,0,5,0,0,0
 
 [namelist:nlstcall_box_options]
 flux_out_filename='flux_out.csv'

These differences can be found here:

Tutorials/UMvn13.0/worked_solutions/Task02.2/Task02.2_rose.patch

Task 2.3: Increase the run-length

O3 mass-mixing ratio for a 5-day run with a 30-minute timestep.

TASK 2.3: Change the timestep to be 30 minutes.

Solution
Change the value of `steps_per_periodim` to be `48` and `chem_timestep` to be `1800`.

Once the run has finished, replot ozone and see how the graph has changed.

Worked Solution to Task 2.3

The changes to Rose are:

https://code.metoffice.gov.uk/trac/roses-u/changeset/236413/c/q/7/8/2/trunk

Index: app/ukca/rose-app.conf
===================================================================
--- app/ukca/rose-app.conf	(revision 236409)
+++ app/ukca/rose-app.conf	(revision 236413)
@@ -178,7 +178,7 @@
 !!ppxm=1
 !!psum_filename_base='$DATAM/${RUNID}a_s'
 secs_per_periodim=86400
-steps_per_periodim=24
+steps_per_periodim=48
 
 [!!namelist:oasis_send_nml]
 !!hybrid_rmp_mapping='BILINEAR'
@@ -467,7 +467,7 @@
 
 [namelist:run_ukca]
 !!biom_aer_ems_scaling=2.0
-chem_timestep=3600
+chem_timestep=1800
 !!dir_strat_aer=
 !!dts0=300
 fastjx_mode=1

These differences can be found here:

Tutorials/UMvn13.0/worked_solutions/Task02.3/Task02.3_rose.patch

Changing the Box Model Environmental Settings

The environmental conditions used by the box model are set by the variable ukca_box_nml in the ukca $\rightarrow$ namelist $\rightarrow$ Model Input and Output panel. The value corresponds to a Fortran namelist file held in the

[SUITE-ID]/app/ukca/file

directory. Currently 3 example files are provided:

File	Description
`nml_box_sfc`	A box with settings relevant for surface conditions
`nml_box_tropopause`	A box with settings relevant for conditions around the tropopause
`nml_box_strat`	A box with settings relevant for conditions in the stratosphere

You can make your own file and place it in the same directory, although remember to

fcm add nml_box_[YOUR FILE]

otherwise you will not be able to commit the file to the suite repository.

Example file: `nml_box_sfc`

!-----------------------------------------------
! Box-MODEL test NAMELIST - surface
!-----------------------------------------------

! Section to define environmental parameters for box model
&ENVIRONMENT_PARS
  latitude_1       = 30.     ! Latitude, degrees North, -90:90
  longitude_1      = 0.      ! Longitude, degrees East, 0:360
  t_theta_levels_1 = 288.15  ! Temperature, K
  p_theta_levels_1 = 100000. ! Pressure, Pa
  land_sea_mask_1  = .TRUE.  ! Land/sea mask, logical
  tstar_1          = 288.15  ! Tmperature at surface, K
  zbl_1            = 1000.   ! Height of boundary layer, m
  pstar_1          = 101325. ! Pressure at surface, Pa
  q_1              = 0.01    ! Mass fraction of water vapour in air
  qcf_1            = 0.0     ! Mass fraction of cloud ice in air
  qcl_1            = 0.0     ! Mass fraction of liquid cloud water in air
  surf_albedo_1    = 0.2     ! Surface albedo
/

! Section to define Offline Oxidant MMR values
! (only used if running with offline oxidants scheme)
&OFFLINE_OXIDANT_MMR
  O3             = 5.0000e-08
  OH             = 5.0000e-14
  HO2            = 5.0000e-12
  H2O2           = 5.0000e-10
  NO3            = 5.0000e-12
/

Task 2.4: Change the environmental conditions of the box

O3 mass-mixing ratio from a stratospheric box.

TASK 2.4: Change the environmental conditions to be in the stratosphere.

Solution
Change the value of `ukca_box_nml` to be `nml_box_strat`

Once the run has finished, replot ozone and see how the graph has changed.

Worked Solution to Task 2.4

The changes to Rose are:

https://code.metoffice.gov.uk/trac/roses-u/changeset/236419/c/q/7/8/2/trunk

Index: app/ukca/rose-app.conf
===================================================================
--- app/ukca/rose-app.conf	(revision 236413)
+++ app/ukca/rose-app.conf	(revision 236419)
@@ -156,7 +156,7 @@
 tracer_in_filename='chem_tracer_pars_STwGMaero'
 tracer_nullval=1e-15
 tracer_out_filename='tracer_out.csv'
-ukca_box_nml='nml_box_sfc'
+ukca_box_nml='nml_box_strat'

 [namelist:nlstcgen]
 dump_filename_base='$DATAM/${RUNID}a.d%z%C'

These differences can be found here:

Tutorials/UMvn13.0/worked_solutions/Task02.4/Task02.4_rose.patch

Changing the Box Model Chemistry Scheme

The model chemistry scheme used is set by the variable i_ukca_chem in the ukca $\rightarrow$ namelist $\rightarrow$ Science Settings panel. The following schemes can be used with the Box Model:

Scheme	Value	Description
`Stratospheric+Tropospheric`	51	A scheme with chemistry relevant for the troposphere and the stratosphere
`Offline Oxidants`	54	A basic scheme used to drive the GLOMAP-mode aerosol scheme
`CRI+Stratospheric`	59	A scheme with chemistry relevant for the stratosphere with a more comprehensive tropospheric chemistry scheme included

Task 2.5: Change the chemistry scheme

TASK 2.4: Use the offline-oxidants chemistry scheme to drive GLOMAP-mode

Solution
Change the value of `i_ukca_chem` to be `54` (Offline Oxidants)

Once the run has finished, plot quantities such as SO2 and the Soluble Accumulation mode sulphate to see how the values evolve during the simulation.

SO2 mass-mixing ratio
Soluble Accumulation mode sulphate

Worked Solution to Task 2.4

The changes to Rose are:

https://code.metoffice.gov.uk/trac/roses-u/changeset/236419/c/q/7/8/2/trunk

Index: app/ukca/rose-app.conf
===================================================================
--- app/ukca/rose-app.conf	(revision 236413)
+++ app/ukca/rose-app.conf	(revision 236419)
@@ -156,7 +156,7 @@
 tracer_in_filename='chem_tracer_pars_STwGMaero'
 tracer_nullval=1e-15
 tracer_out_filename='tracer_out.csv'
-ukca_box_nml='nml_box_sfc'
+ukca_box_nml='nml_box_strat'

 [namelist:nlstcgen]
 dump_filename_base='$DATAM/${RUNID}a.d%z%C'

These differences can be found here:

Tutorials/UMvn13.0/worked_solutions/Task02.4/Task02.4_rose.patch

Changing the Box Model Tracer Initial Values

The initial tracer values used by the box model are set by the variable tracer_in_filename in the ukca $\rightarrow$ namelist $\rightarrow$ Model Input and Output panel. The value corresponds to a Fortran namelist file held in the

[SUITE-ID]/app/ukca/file

directory. There are several example files provided, including

File	Description
`chem_tracer_pars_OffOx`	Aerosol and aerosol precursor initial condition base case for running with offline oxidents
`chem_tracer_pars_OffOx_LowAero`	Aerosol and aerosol precursor initial conditions for running with offline oxidents with initial aerosol concentrations reduced by a factor of 10
`chem_tracer_pars_ST_basic`	Initial tracer MMR values for basic StratTrop setup - only a few species MMRs defined with values typical for clean background troposphere conditions
`chem_tracer_pars_ST_urban`	Initial MMR values for all gas-phase species in StratTrop typical of clean tropospheric conditions
`chem_tracer_pars_STwGMaero`	Basic StratTrop initial gas phase concentrations with aerosol and aerosol precurser values the same as Offline Oxident base case
`chem_tracer_pars_STwGMaero_EqTropopause`	StratTrop initial gas phase concentrations typical of equatorial tropopause with aerosol and aerosol precurser values the same as Offline Oxident base case

The current file used is chem_tracer_pars_STwGMaero.

Checklist

☐ List suites using rosie go

☐ Copy suites using the right-click menu

☐ Run suites using the play button

☐ Plot output using gnuplot

Tutorial 2

Written by Luke Abraham 2022

@@ Line 251: / Line 251: @@
   [namelist:nlstcgen]
   dump_filename_base='$DATAM/${RUNID}a.d%z%C'
 These differences can be found here:
@@ Line 273: / Line 272: @@
 |}
+====Task 2.5: Change the chemistry scheme====
+<span style="color:green">'''TASK 2.4:''' Use the offline-oxidants chemistry scheme to drive GLOMAP-mode</span>
+{| class="collapsible collapsed wikitable"
+|-
+! Solution
+|-
+| Change the value of <tt>i_ukca_chem</tt> to be '''<tt>54</tt> (Offline Oxidants)'''
+|}
+Once the run has finished, plot quantities such as SO2 and the Soluble Accumulation mode sulphate to see how the values evolve during the simulation.
+<gallery widths=400px heights=350px>
+Image:T02_so2_005.png|SO2 mass-mixing ratio
+Image:T02_Acc_SOL_SU_005.png|Soluble Accumulation mode sulphate
+</gallery>
+=====Worked Solution to Task 2.4=====
+The changes to Rose are:
+* https://code.metoffice.gov.uk/trac/roses-u/changeset/236419/c/q/7/8/2/trunk
+ Index: app/ukca/rose-app.conf
+ ===================================================================
+ --- app/ukca/rose-app.conf	(revision 236413)
+ +++ app/ukca/rose-app.conf	(revision 236419)
+ @@ -156,7 +156,7 @@
+  tracer_in_filename='chem_tracer_pars_STwGMaero'
+  tracer_nullval=1e-15
+  tracer_out_filename='tracer_out.csv'
+ -ukca_box_nml='nml_box_sfc'
+ +ukca_box_nml='nml_box_strat'
+  [namelist:nlstcgen]
+  dump_filename_base='$DATAM/${RUNID}a.d%z%C'
+These differences can be found here:
+ Tutorials/UMvn13.0/worked_solutions/Task02.4/Task02.4_rose.patch
 ===Changing the Box Model Tracer Initial Values===

UKCA Chemistry and Aerosol UMvn13.0 Tutorial 2: Difference between revisions

Revision as of 15:00, 14 September 2022

Changing UKCA Box Model Options

Changing the Box Model Time Settings

Task 2.1: Change the Start Time

Worked Solution to Task 2.1

Task 2.2: Increase the run-length

Worked Solution to Task 2.2

Task 2.3: Increase the run-length

Worked Solution to Task 2.3

Changing the Box Model Environmental Settings

Example file: nml_box_sfc

Task 2.4: Change the environmental conditions of the box

Worked Solution to Task 2.4

Changing the Box Model Chemistry Scheme

Task 2.5: Change the chemistry scheme

Worked Solution to Task 2.4

Changing the Box Model Tracer Initial Values

Checklist

Example file: `nml_box_sfc`