Evaluation suite2

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UKCA Evaluation Suite - Version 2

This is the description for Version 2. Instructions for Version-1 can be found here

The UKCA Evaluation suite is a collection of basic assessment methods being used at various partner institutions. The package can be divided largely into three categories:

  • Tropospheric chemistry evaluation
  • Stratospheric chemistry and dynamics evaluation
  • Aerosol chemistry and processes evaluation --Not yet available for V2, use from V1

The evaluation suite can currently analyse the outputs from UM-UKCA configurations against specific observation datasets. To use the evaluation suite, the model output needs to be in the form of 12 x monthly mean pp files (UM pm stream) conforming to the UM pp file naming format (jobida.somename.pp). The Stratospheric as well as Tropospheric Chemistry suites can carry out multi-annual meaning if data for more than one year are specified as input. Each type of analysis requires a specified list of fields to be present in the pp files and there are UM STASH macro handedits to ensure that these fields are requested in the output.

For the Tropospheric and Stratospheric Chemistry part of evaluation, these fields can be added to your job by using the hand_edit:

  • /home/h02/hadzm/umui_jobs/hand_edits/vn8.2/add_ukca_eval1_diags_lxx.ed (where xx is the number of vertical levels) on the Met Office systems and
  • /home/mdalvi/umui_jobs/hand_edits/vn8.2/add_ukca_eval1_diags_lxx.ed on the Puma server.

For UM versions vn8.5-8.6, use the hand_edits:

  • /home/h02/hadzm/umui_jobs/hand_edits/vn8.5/add_ukca_eval_diags_vn85_l85.ed on the Met Office systems and
  • /home/mdalvi/umui_jobs/hand_edits/vn8.5/add_ukca_eval_diags_vn85_l85.ed on the Puma server.

For Rose (Um9.0+) configurations, the requests will have to be added manually or inherited from a base/ Release suite.

The UKCA Evaluation suite V2 is available on the Met Office Desktop, MONSooN postprocessor, ARCHER, and JASMIN (sci1,lotus).


Tropospheric Chemistry package

This currently performs the following analysis/ evaluations:

  • CO against CMDL obs
  • ClO against MLS data
  • CO, HNO3, NOx against Emmons et al dataset
  • OH using Lawrence etal (1991) method, vs ACCMIP and Parta et al Reference values.
  • O3 against Tilmes ozonesonde data at multiple locations
  • Ox budget (sources/sinks, deposition)
  • OH/CH4 ratio and CH4 lifetime vs ACCMIP multi-model values
  • Profiles of O3,HNO3,NO2,H2O2,water vap against ACE,UARS,.. data
  • Age of Air against SF6 obs
  • Tropospheric O3 and NO2 columns
  • Lightning NOx : total N and zonal mean


The tool will automatically carry out multi-annual meaning on-the-fly if more than 12 (and a multiple of 12) files are detected.
Usage:

A. Met Office desktop:
/home/h02/hadzm/eval_v2/camb_chem/eval_tropchem_spice.py -i <ppfiles> [-s STASHlist] [-m trmap]

Options
-h, --help show this help message and exit
-i Required: ppfiles (12) from the year to analyse -full path-
-s STASHLIST Optional: STASHcodes list, e.g. if using pre-vn8.5 output (diags in Section 34 vs 50)
-m TRMAPS Optional :Var<->STASH mapping file, e.g. if using pre-vn8.5 output
-f SCALE_FAC Optional : Flux multiplication factor, to account for difference in UM:UKCA call frequency (default=3.0 for 1 UM: 3 UKCA timesteps)

B. MONSooN Postprocessor:
/home/mdalvi/eval_v2/camb_chem/eval_tropchem.py -i <ppfiles> [-s STASHlist] [-m trmap]

Note: The performance on postproc01 varies, depending on the machine load.

C. JASMIN
On jasmin-sci1/sci2 or lotus

/home/users/mcdalvi/eval_v2/camb_chem/eval_tropchem_top.py -i <ppfiles> [-s STASHlist] [-m trmap]

This will launch a job on the Lotus system.

The plots will be created in: ./Plots_TC/<jobid>/


Pre-vn8.5 Model output
Add arguments: -s <mohit home>/eval_v2/camb_chem/stash_pre85.lst -m <mohit home>/eval_v2/camb_chem/ukca_stdname_pre85


vn10.3 onwards
Some of the required fields are being output via different stash codes, hence to analyse output from UM10.3+ runs add the arguments:

-s <mohit home>/eval_v2/camb_chem/stash_eval_v103.lst -m <mohit home>/eval_v2/etc/ukca_stdname_vn103

vn10.6 onwards
In addition to stash changes above, more changes, including an UKCA STASH timecode mean that the scaling factor for UM:UKCA timestep ratio no longer needs to be applied to reaction fluxes. To cover all the changes use the script:

Met Office: /home/h02/hadzm/eval_v2/camb_chem/eval_tropchem_spice106.py -i <ppfiles>

JASMIN: /home/users/mcdalvi/eval_v2/camb_chem/eval_tropchem_jas106.py -i <ppfiles>

No other commandline options are required.


Stratospheric Chemistry (toms_haloe) package

The suite currently evaluates:

  • CH4, N2O, O3, against HALOE dataset
  • O3 against a dataset compiled at NIWA for CCMVal
  • Column O3 against TOMS

The HALOE/ NIWA comparisons are currently for the months of January and July, while the Column data is based on the whole year.

Usage:

MONSooN - /home/mdalvi/eval_v2/toms_haloe/compare_toms_haloe.py < model pp files -atleast 12>

The names of all the model output files need to be passed, i.e. at least 12 for an year (note: wild cards can be used).
The tool will automatically carry out multi-annual meaning on-the-fly if more than 12 (and a multiple of 12) files are detected.


Met Office Desktop:- /home/h02/hadzm/eval_v2/toms_haloe/comp_toms_haloe_spice.py < model pp files >
JASMIN: (launch from sci1,2,3,4 onto Lotus) /home/users/mcdalvi/eval_v2/toms_haloe/comp_toms_haloe_lotus.py < model pp files >.


Outputs will be created in : ./Plots_TH/<jobid>/


ARCHER

The scripts have been modified slightly to work on ARCHER. They are designed such that output from a UM vn10.6 job or above will not require any additional arguments, other than the location of the *.pp files. Also, all Stratospheric output is saved as .pdf.

While you can use the login nodes for this, you can also log-in to the post-processing nodes by

ssh -Y espp1

Required modules

To be able to use Iris (required for both Stratospheric and Tropospheric packages), you will need to:

module load anaconda/2.2.0-python2

To run the Tropospheric chemistry package you will need to load R by

module load R/3.2.3

and load the required netCDF libraries by

module load cray-netcdf-hdf5parallel/4.4.1.1

Running the packages

For UM versions vn10.6 and above you will just need to:

  • Tropospheric Chemistry: /work/n02/n02/ukca/Eval/eval_v2/camb_chem/eval_tropchem.py -i /path/to/pp/files/*.pp [--eval_only]
  • Stratospheric Chemistry: /work/n02/n02/ukca/Eval/eval_v2/toms_haloe/compare_toms_haloe.py /path/to/pp/files/*.pp

You can use evince to view the outputted .pdf files.

If you need to run these on pre-vn10.6 versions, the equivalent to <mohit home> is /work/n02/n02/ukca/Eval for the paths to particular STASH maps etc.

The Stratospheric chemistry package takes a few minutes for a single years-worth of data. The Tropospheric chemistry package will take about 50 minutes to extract the data to netCDF and then an additional 15-20 minutes to produce the plots.

Example Data

Example data from vn10.9 can be found at

/work/n02/n02/ukca/Eval/ExampleData/u-as022

and an empty directory with the data already extracted to netCDF can be found here:

/work/n02/n02/ukca/Eval/WorkedExample/u-as022

This directory can be rsync-d to a working directory and the evaluation suite can be run using the --eval_only command which will save some time.

Required Chemistry Diagnostics

The UKCA chemistry evaluation packages require the following diagnostics (STASH section/item numbers from vn10.3 onwards):

STASH Section STASH Item STASH Name
0 010 SPECIFIC HUMIDITY AFTER TIMESTEP
0 408 PRESSURE AT THETA LEVELS AFTER TS
16 004 TEMPERATURE ON THETA LEVELS
30 451 Pressure at Tropopause Level
30 453 Height at Tropopause Level
34 001 O3 MASS MIXING RATIO AFTER TIMESTEP
34 002 NO MASS MIXING RATIO AFTER TIMESTEP
34 004 NO2 MASS MIXING RATIO AFTER TIMESTEP*
34 007 HONO2 MASS MIXING RATIO AFTER TSTEP
34 009 CH4 MASS MIXING RATIO AFTER TSTEP
34 010 CO MASS MIXING RATIO AFTER TSTEP
34 042 ClO MASS MIXING RATIO AFTER TSTEP
34 049 N2O MASS MIXING RATIO AFTER TIMESTEP
34 081 OH MASS MIXING RATIO AFTER TIMESTEP
34 150 AGE OF AIR IN SECONDS
34 992 HCl MASS MIXING RATIO AFTER TSTEP**
34 996 NO2 MASS MIXING RATIO AFTER TIMESTEP**
50 001 Ox PROD: HO2+NO
50 002 Ox PROD: MeOO+NO
50 003 Ox PROD: NO+RO2
50 004 Ox PROD: OH+INORGANIC ACID
50 005 Ox PROD: OH+ORGANIC NITRATE
50 006 Ox PROD: ORGANIC NITRATE PHOTOLYSIS
50 007 Ox PROD: OH + PAN-TYPE REACTIONS
50 011 Ox LOSS: O(1D)+H2O
50 012 Ox LOSS: MINOR LOSS REACTIONS
50 013 Ox LOSS: HO2+O3
50 014 Ox LOSS: OH+O3
50 015 Ox LOSS: O3+ALKENE
50 016 Ox LOSS: N2O5+H2O
50 017 Ox LOSS: NO3 CHEMICAL LOSS
50 021 Ox BUDGET: O3 DRY DEPOSITION (3D)
50 022 Ox BUDGET: NOy DRY DEPOSITION (3D)
50 031 Ox BUDGET: NOy WET DEPOSITION (3D)
50 041 RXN FLUX: OH+CH4 (CH4 LIFETIME) TROP
50 051 STE: O3
50 061 AIR MASS DIAGNOSTIC (TROP ONLY)
50 062 TROPOSPHERIC MASK
50 063 AIR MASS DIAGNOSTIC (WHOLE ATMOS)
50 081 Lightning NOx Emissions (3D)
50 219 Ozone column in Dobson Units

Notes:

* NO2 is not available in s34i004 in StratTrop/CheST
** HCl is only available in s34i992 in StratTrop/CheST
** NO2 is only available in s34i996 in StratTrop/CheST

If you are extracting these from MASS, you can use the following query file with the moo select command:

begin
   year=[1999..2008]
   stash=(10, 408, 16004, 30451, 30453, 34001, 34002, 34004, 34007, 34009, 34010, 34042, 34049, 34081, 34150, 34992, 
     34996, 50001, 50002, 50003, 50004, 50005, 50006, 50007, 50011, 50012, 50013, 50014, 50015, 50016, 50017, 50021, 
     50022, 50031, 50041, 50051, 50061, 50062, 50063, 50081, 50219)
end

Usage : moo select <query file> moose:crum/<suite-id>/apm.pp [output path or ./]

Note: If you copy the above and paste into you query file directly, align all the stashcodes in a single continuous line as line-breaks are not permitted for stash=. You might also need to run dos2unix <filename>.