Difference between revisions of "UKCA Chemistry and Aerosol Tutorial 10"

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==What you will learn in this Tutorial==
  
==What you will learn in this Tutorial==
   
−
In this tutorial you will learn how the wet deposition of chemical species is handelled in UKCA. You will then add-in the wet deposition of one of your new tracers.
 +
In this tutorial you will learn about the Aerosol Optical Depth and how the RADAER module diagnoses aerosol optical properties from the GLOMAP aerosol microphysics scheme included in UKCA.
   
  +
'''Note:''' The GLOMAP aerosol tutorials use a slightly different base job. Please take a copy of <code>'''xjrnk'''</code> and work from that for these tasks. Example output from this job can be found on ARCHER in the directory
−
==Task 10.1: Add wet deposition of a species==
  
   
  +
/work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Base_Aerosol
−
<span style="color:green">'''Task 10.1:''' Add in wet deposition for '''BOB''', using the following values:</span>
  
   
  +
==Task 10.1: What is the aerosol optical depth?==
−
{| border="1"
  
−
! <math>\ k(298)\ </math> || <math>\ -\left({\Delta H}/R\right)\ </math> || <math>\ k(298)</math> for the 1st dissociation || <math>\ -\left({\Delta H}/R\right)</math> for the 1st dissociation || <math>\ k(298)</math> for the 2nd dissociation || <math>\ -\left({\Delta H}/R\right)</math> for the 2nd dissociation
 
−
|-
  
−
| <math>\ 0.21 \times 10^{+06}\ </math> || <math>\ 0.87 \times 10^{+04}\ </math> || <math>\ 0.2 \times 10^{+02}\ </math> || <math>\ 0.0\ </math> || <math>\ 0.0\ </math> || <math>\ 0.0\ </math>
  
−
|}
  
   
  +
Aerosol particles affect the Earth's radiative balance by scattering and absorbing solar radiation and, where they are large enough, can also act similarly to a greenhouse gas by absorbing outgoing terrestrial long-wave radiation.
−
'''Note:''' If you were unable to successfully complete [[UKCA Chemistry and Aerosol Tutorial 9#Task 9.1: adding new dry deposition values|Task 9.1]], then please take a copy of the '''i''' job from the Tutorial experiment (''Tutorial: solution to Task 9.1 - add new dry deposition'') and work from there, as this will allow you to only make the changes required for this task.
  
  +
  +
The aerosol optical depth (AOD), sometimes referred to as aerosol optical thickness (AOT), is often used in atmospheric science to indicate the overall strength of aerosol-radiation interactions at a particular wavelength.
   
  +
The AOD is defined as the vertical integral of the monochromatic (single-wavelength) extinction (the sum of scattering plus absorption) through the atmospheric column.
−
==Adding Wet Deposition==
  
  +
It is common also to refer to an absorption AOD which represents the integral of just the single-wavelength absorption.
   
  +
The Unified Model (UM) radiation scheme divides the shortwave and longwave spectra into wavebands.
−
The formulation used in UKCA is described in Giannakopoulos (1999)[1]. This scheme uses the following formula to calculate the effective Henry's Law coefficient
  
  +
To enable UKCA simulated gases or aerosols to interact with the UM radiation scheme, their
  +
optical properties need to be integrated across each of these wavebands.
  +
For aerosols, the radiation scheme requires the specific scattering and
  +
absorption coefficients, which describe the strength of aerosol scattering and
  +
absorption processes per unit aerosol mass (in m<math>^{2}</math> kg<math>^{-1}</math>), and the
  +
asymmetry parameter, which describes in a simplified way the angular dependence
  +
of the scattering (dimensionless).
  +
The specific scattering and absorption coefficients, and the asymmetry
  +
parameter, are hereafter referred to as the ''aerosol optical properties''.
   
  +
==Task 10.2: Understand the principles behind GLOMAP and how aerosol optical properties are derived via RADAER==
−
<math>
  
−
H_{eff} = k\left(298\right) \exp \left(-\frac{\Delta H}{R}\left[\left(\frac{1}{T}\right) - \left(\frac{1}{298}\right)\right]\right)
  
−
</math>
  
   
  +
Mie theory describes the scattering and absorption of light by spherical particles.
−
where <math>k\left(298\right)</math> is the rate constant at 298K.
  
  +
Essentially, the scattering/absorption efficiency can be parameterized in terms of two parameters: the (complex) refractive index of the particle and the Mie parameter, which describes the particle size dependence in relation to the wavelength of light under consideration.
   
  +
The Figure in the slide below shows the dependence on particle size of the extinction efficiency for mid-visible (550nm, green) light for two different types of particle (refractive index).
−
During this tutorial you will be tasked with adding the wet deposition of one of your new tracers.
  
   
  +
[[File:Slide_AOD_SizeDistribution_blankbackground.jpg]]
−
'''References'''
  
−
# Giannakopoulos, C., M. P. Chipperfield, K. S. Law, and J. A. Pyle (1999), Validation and intercomparison of wet and dry deposition schemes using 210Pb in a global three-dimensional off-line chemical transport model, J. Geophys. Res., 104(D19), 23761–23784, doi:10.1029/1999JD900392.
  
   
  +
The aerosol scheme used for UK climate model simulations in CMIP5
−
==Turning on Wet Deposition for a Species==
  
  +
was called the Coupled Large‐scale Aerosol Simulator for Studies In Climate
  +
(CLASSIC). CLASSIC is a simpler scheme than the microphysical GLOMAP scheme
  +
included in UKCA but has a comprehensive representation of the main aerosol
  +
sources, tracking up to eight tropospheric aerosol species: ammonium sulphate,
  +
mineral dust, sea salt, fossil fuel black carbon, fossil fuel
  +
organic carbon, biomass burning aerosols, secondary organic
  +
(also called biogenic), and ammonium nitrate aerosols.
   
  +
However, the size distribution and refractive index for each of the CLASSIC transported aerosol types
−
===Chemistry Scheme Specification===
  
  +
was prescribed to have globally and temporally uniform values. Some variation in aerosol
  +
properties was resolved by having fresh and aged sub-types for each aerosol type, which
  +
then allow size and refractive index to vary from values near-source (fresh) to remote
  +
(aged).
   
  +
With this approach, optical properties for each of the CLASSIC aerosol types is derived based on
−
Within the UKCA code, whether a species is wet deposited or not is controlled in the '''ukca_chem_<span style="color:blue">scheme</span>.F90''' file. In the '''chch_defs_<span style="color:blue">scheme</span>''' array there are lines like
  
  +
Mie calculations using the prescribed size distributions and refractive indices for each of the
  +
transported aerosol masses and assuming hygroscopic growth factors for the water associated
  +
with each.
   
  +
The GLOMAP-mode aerosol scheme in UKCA simulates the
−
chch_t( 10,'HONO2 ', 1,'TR ',' ', 1, <span style="color:red">'''1'''</span>, 0), & ! 10 DD: 7,WD: 4,
 
  +
evolution of size-resolved aerosol properties, including
−
chch_t( 11,'H2O2 ', 1,'TR ',' ', 1, <span style="color:red">'''1'''</span>, 0), & ! 11 DD: 8,WD: 5,
 
  +
microphysical processes such as new particle formation,
  +
coagulation, condensation (gas-to-particle-transfer) and
  +
cloud processing.
   
  +
Whereas CLASSIC simulated only the mass of several aerosol types,
−
Where the <span style="color:red">'''1'''</span> in the 7th column turns on wet deposition of that species (being 0 otherwise). You will need to change the 0 to a '''1''' for the species that you wish to now wet deposit.
  
  +
the transported tracers in GLOMAP are particle number and mass
  +
in different size classes spanning the particle
  +
size range from 3nm up to around 20 microns dry diameter.
   
  +
Processes such as condensation and aqueous
−
===Setting Henry's Law values===
  
  +
sulphate production grow particles
  +
by increasing the mass in a size class while conserving particle number.
   
  +
As was as microphysical processes, GLOMAP also includes size-resolved representations
−
In the '''ukca_chem_<span style="color:blue">scheme</span>.F90''' the parameters required to calculate <math>H_{eff}</math> are held in the '''henry_defs_<span style="color:blue">scheme</span>''' array, and has format
  
  +
of primary emissions (e.g. sea-salt, dust and carbonaceous particles) and of
  +
removal processes including particle dry deposition, sedimentation,
  +
nucleation scavenging (rainout) and impaction scavenging (washout).
   
  +
GLOMAP therefore simulates the evolution of particle number and composition across the
−
{| border="1"
  
  +
size spectrum over several different components as determined by the aerosol
−
| <math>\ k(298)\ </math> || <math>\ -\left({\Delta H}/R\right)\ </math> || <math>\ k(298)</math> for the 1st dissociation || <math>\ -\left({\Delta H}/R\right)</math> for the 1st dissociation || <math>\ k(298)</math> for the 2nd dissociation || <math>\ -\left({\Delta H}/R\right)</math> for the 2nd dissociation
 
  +
processes included.
−
|}
 
   
  +
The original version of GLOMAP (known as GLOMAP-bin) uses a
−
Columns 3 and 4 are used if the species dissociates in the aqueous phase. In this case, <math>H_{eff}</math> is further multiplied by a factor of
  
  +
two-moment sectional aerosol dynamics approach, with typically 20 bins
  +
spanning the size spectrum, but when tracking several aerosol types,
  +
becomes too expensive for running multi-decadal integrations as
  +
required in a climate model. For UKCA, a new computationally cheaper
  +
version of GLOMAP was developed (GLOMAP-mode), which has the same
  +
process representations, but using log-normal modes as its size classes.
  +
Each size mode in GLOMAP-mode covers one of four size ranges, with additional
  +
separation among soluble and insoluble modes.
   
  +
GLOMAP has been developed to follow a flexible multi-component approach, with the
−
<math>
  
  +
same code able to be run with different levels of composition/size sophistication
−
1+\frac{k(aq)}{H^{+}}
  
  +
with FORTRAN-90 modules providing alternative aerosol ''mode set-up'' arrays.
−
</math>
  
  +
The GLOMAP-mode aerosol scheme in UKCA not only simulates the dry aerosol mass, but also
  +
the mass of water attached to the aerosol, and the aerosol number concentrations.
   
  +
The calculation of aerosol optical properties from GLOMAP is carried out via the RADAER module within UKCA.
−
where
  
   
  +
Compared to CLASSIC, the GLOMAP-mode scheme introduces three important changes
−
<math>
  
  +
which are relevant for simulated aerosol-radiation interactions:
−
k(aq) = k\left(298\right) \exp \left(-\frac{\Delta H}{R}\left[\left(\frac{1}{T}\right) - \left(\frac{1}{298}\right)\right]\right)
  
−
</math>
  
   
  +
* The mean radius of each size class (mode) varies in time and space as determined by transport and aerosol processes.
−
and column 3 contains the values of <math>k(298)</math> and column 4 contains the value of <math>-{\Delta H}/R</math>. Similarly, if the species dissociates a second time then a further factor of <math>1+k(aq)/H^{+}</math> is applied, where this value of <math>k(aq)</math> is calculated from the values of <math>k(298)</math> and <math>-{\Delta H}/R</math> in columns 5 and 6.
  
   
  +
* There is a refractive index for each size class (mode) which varies according to its internally-mixed composition.
−
'''Note:''' As with the 2D dry deposition values in '''depvel_defs_<span style="color:blue">scheme</span>''', the order of '''henry_defs_<span style="color:blue">scheme</span>''' also assumes that the values are in the same order as the species (that wet deposit) in the '''chch_defs_<span style="color:blue">scheme</span>''' array.
  
   
  +
* The amount of aerosol water in each soluble mode varies interactively consistent with its composition.
−
Examples for this array are
  
   
  +
RADAER relies on pre-computed look-up tables of monochromatic optical properties, covering all realistic combinations of modal radii and refractive indices. At runtime, remaining tasks are:
−
0.2100E+06, 0.8700E+04, 0.2000E+02, 0.0000E+00, 0.0000E+00, 0.0000E+00,& ! 4 HONO2
  
−
0.8300E+05, 0.7400E+04, 0.2400E-11,-0.3730E+04, 0.0000E+00, 0.0000E+00,& ! 5 H2O2
  
   
  +
* To compute the modal refractive index out of the simulated chemical composition of each mode.
−
===Increase the value of JPDW===
  
   
  +
* To obtain the monochromatic properties from the look-up tables at selected wavelengths within each shortwave and longwave waveband.
−
Similar to when adding dry deposition of a species you will need to increase the size of the '''JPDW''' counter. This is done with a hand-edit, the value of '''JPDW''' being set in the '''CNTLATM''' file in your <tt>$HOME/umui_jobs/<span style="color:blue">jobid</span></tt> directory.
  
   
  +
* To integrate across each waveband to obtain the waveband-averaged optical properties, which can be used by the radiation code.
−
==Solution to Task 10.1: Add wet deposition of a species==
  
   
  +
As well as providing the waveband-averaged scattering, extinction and asymmetry parameters from GLOMAP, RADAER also diagnoses monochromatic Aerosol Optical Depth (AOD) for each of the GLOMAP modes.
−
Please see [[Solution to UKCA Chemistry and Aerosol Tutorial 10 Task 10.1 |this page]] for a solution of [[#Task 10.1: Add wet deposition of a species|Task 10.1]].
  
   
  +
==Task 10.3: Output daily-mean Aerosol Optical Depths from your UKCA model run==
−
----
  
  +
−
''Written by [[User:Nla27 | Luke Abraham]] 2014''
  
  +
In this task you will update your copy of the UKCA tutorial job (<code>'''xjrnk'''</code>) adding extra STASH requests to output daily-mean AODs from GLOMAP.
  +
  +
UM-UKCA diagnoses the AOD from each of the GLOMAP modes as a separate STASH item.
  +
  +
All of the GLOMAP AOD diagnostics are contained with STASH section 2 (long-wave radiation) in items numbers near to those used for the AOD diagnostics from CLASSIC.
  +
  +
Section 2 items 300-305 contain the AOD for the Aitken-soluble, accumulation-soluble, coarse-soluble, Aitken-insoluble, accumulation-insoluble and coarse-insoluble modes respectively.
  +
  +
The dimensions for each of these STASH items is 2D global in longitude and latitude but there is also a third dimension containing 6 pseudo levels for the 6 monochromatic AODs stored by the model (at 0.38, 0.44, 0.55, 0.67, 0.87, 1.02 micron wavelengths).
  +
  +
Note that there is no nucleation mode AOD as those particles are too small to significantly scatter or absorb radiation at these wavelenghts.
  +
  +
Note that although the absorption AOD in these 6 modes can usually be requested via STASH section 2 items 240 to 245, in the job here these are not available.
  +
  +
There are also separate "stratospheric AOD" diagnostics in section 2 items 251 to 256 which can also be requested to store the AOD in levels above the tropopause.
  +
  +
To output AODs from GLOMAP, you need to add in some extra STASH requests for the section 2 items 300 to 305.
  +
  +
To output as a daily-mean select the usage profile "UPA" to output to the .pa files and the time profile "TDAYM" for daily-means.
  +
For AOD STASH requests, you need to select the domain profile DIAGAOT to output over the longitude, latitude and 6 wavelength pseudo-levels.
  +
  +
Section 34 items 106, 110, 116, 121 and 126 contain the OM mmr's in the Aitken-soluble, accumulation-soluble, coarse-soluble, Aitken-insoluble and nucleation-soluble modes respectively.
  +
  +
When requesting the OM mmr's you should use the DALLTH domain profile to request the variable on the full 3D model grid.
  +
  +
So now you should have an equivalent version of the UKCA tutorial job with extra daily-mean fields requested.
  +
  +
Since you specified the UPA usage profile in the job, these fields will be output to the so-called ''.pa files''.
  +
  +
These can be found in your /work/n02/n02/ directory on ARCHER.
  +
You should have a file like '''jobid'''a.pa19991201 for the daily-mean fields for the 1 day that the job was set to run for.
  +
  +
In the first instance you should use xconv to open the file although you can use convsh or other tools to extract required fields from the .pa file and then manipulate them in IDL or python.
  +
  +
As an example I have put below a jpeg showing a global map produced in IDL of the daily-mean AOD at 550nm (total over all modes) for 1st December 1999 from the UKCA tutorial job (worked solution <code>'''xjrnl'''</code>).
  +
  +
In preparation for the next task, you should also re-run the job adding also daily-mean STASH requests for the following mass mixing ratios (mmr's) for the Organic Matter (OM) in each mode (34106, 34110, 34116, 34121 and 34126).
  +
  +
Once you have re-run the job with these extra fields available in the .pa file, you can use the cdo operator ''cdo add'' to sum up each of the OM mmrs to give a total OM mmr in a separate netCDF file.
  +
  +
[[File:idl_dailyAOD550_xkwhg.jpg]]
  +
  +
===Worked Solution===
  +
  +
A worked soltion to '''Task 10.3''' is job <code>'''xjrnl'''</code>.
  +
  +
You can use '''cdo''' as so to add the 5 separate netCDF files containing the OC mass-mixing ratios:
  +
  +
$ cdo add xkvxm_aitken_sol_OCmmr.nc -add xkvxm_accum_sol_OCmmr.nc -add xkvxm_coarse_sol_OCmmr.nc -add xkvxm_aitken_insol_OCmmr.nc
  +
xkvxm_nuc_sol_OCmmr.nc xkvxm_OCmmr.nc
  +
cdo add: Started child process "add xkvxm_accum_sol_OCmmr.nc -add xkvxm_coarse_sol_OCmmr.nc -add xkvxm_aitken_insol_OCmmr.nc
  +
xkvxm_nuc_sol_OCmmr.nc (pipe1.1)".
  +
cdo(2) add: Started child process "add xkvxm_coarse_sol_OCmmr.nc -add xkvxm_aitken_insol_OCmmr.nc xkvxm_nuc_sol_OCmmr.nc (pipe2.1)".
  +
cdo(3) add: Started child process "add xkvxm_aitken_insol_OCmmr.nc xkvxm_nuc_sol_OCmmr.nc (pipe3.1)".
  +
cdo(4) add: Processed 4732800 values from 2 variables over 2 timesteps ( 0.23s )
  +
cdo(3) add: Processed 4732800 values from 2 variables over 2 timesteps ( 0.25s )
  +
cdo(2) add: Processed 4732800 values from 2 variables over 2 timesteps ( 0.27s )
  +
cdo add: Processed 4732800 values from 2 variables over 2 timesteps ( 0.28s )
  +
  +
When opening the output file (<code>xkvxm_OCmmr.nc</code> in the example above) the variable name is taken from the first file in the list.
  +
  +
Example output can be found on ARCHER in the directory
  +
  +
/work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Task10.3
  +
  +
  +
''Written by [[User:Gmann | Graham Mann]] 2014''

Latest revision as of 17:43, 7 January 2016

Back to UKCA Chemistry and Aerosol Tutorials

What you will learn in this Tutorial

In this tutorial you will learn about the Aerosol Optical Depth and how the RADAER module diagnoses aerosol optical properties from the GLOMAP aerosol microphysics scheme included in UKCA.

Note: The GLOMAP aerosol tutorials use a slightly different base job. Please take a copy of xjrnk and work from that for these tasks. Example output from this job can be found on ARCHER in the directory 

/work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Base_Aerosol

Task 10.1: What is the aerosol optical depth?

Aerosol particles affect the Earth's radiative balance by scattering and absorbing solar radiation and, where they are large enough, can also act similarly to a greenhouse gas by absorbing outgoing terrestrial long-wave radiation.

The aerosol optical depth (AOD), sometimes referred to as aerosol optical thickness (AOT), is often used in atmospheric science to indicate the overall strength of aerosol-radiation interactions at a particular wavelength.

The AOD is defined as the vertical integral of the monochromatic (single-wavelength) extinction (the sum of scattering plus absorption) through the atmospheric column. It is common also to refer to an absorption AOD which represents the integral of just the single-wavelength absorption.

The Unified Model (UM) radiation scheme divides the shortwave and longwave spectra into wavebands. To enable UKCA simulated gases or aerosols to interact with the UM radiation scheme, their optical properties need to be integrated across each of these wavebands. For aerosols, the radiation scheme requires the specific scattering and absorption coefficients, which describe the strength of aerosol scattering and absorption processes per unit aerosol mass (in m kg), and the asymmetry parameter, which describes in a simplified way the angular dependence of the scattering (dimensionless). The specific scattering and absorption coefficients, and the asymmetry parameter, are hereafter referred to as the aerosol optical properties.

Task 10.2: Understand the principles behind GLOMAP and how aerosol optical properties are derived via RADAER

Mie theory describes the scattering and absorption of light by spherical particles. Essentially, the scattering/absorption efficiency can be parameterized in terms of two parameters: the (complex) refractive index of the particle and the Mie parameter, which describes the particle size dependence in relation to the wavelength of light under consideration.

The Figure in the slide below shows the dependence on particle size of the extinction efficiency for mid-visible (550nm, green) light for two different types of particle (refractive index).

Slide AOD SizeDistribution blankbackground.jpg

The aerosol scheme used for UK climate model simulations in CMIP5 was called the Coupled Large‐scale Aerosol Simulator for Studies In Climate (CLASSIC). CLASSIC is a simpler scheme than the microphysical GLOMAP scheme included in UKCA but has a comprehensive representation of the main aerosol sources, tracking up to eight tropospheric aerosol species: ammonium sulphate, mineral dust, sea salt, fossil fuel black carbon, fossil fuel organic carbon, biomass burning aerosols, secondary organic (also called biogenic), and ammonium nitrate aerosols.

However, the size distribution and refractive index for each of the CLASSIC transported aerosol types was prescribed to have globally and temporally uniform values. Some variation in aerosol properties was resolved by having fresh and aged sub-types for each aerosol type, which then allow size and refractive index to vary from values near-source (fresh) to remote (aged).

With this approach, optical properties for each of the CLASSIC aerosol types is derived based on Mie calculations using the prescribed size distributions and refractive indices for each of the transported aerosol masses and assuming hygroscopic growth factors for the water associated with each.

The GLOMAP-mode aerosol scheme in UKCA simulates the evolution of size-resolved aerosol properties, including microphysical processes such as new particle formation, coagulation, condensation (gas-to-particle-transfer) and cloud processing.

Whereas CLASSIC simulated only the mass of several aerosol types, the transported tracers in GLOMAP are particle number and mass in different size classes spanning the particle size range from 3nm up to around 20 microns dry diameter.

Processes such as condensation and aqueous sulphate production grow particles by increasing the mass in a size class while conserving particle number.

As was as microphysical processes, GLOMAP also includes size-resolved representations of primary emissions (e.g. sea-salt, dust and carbonaceous particles) and of removal processes including particle dry deposition, sedimentation, nucleation scavenging (rainout) and impaction scavenging (washout).

GLOMAP therefore simulates the evolution of particle number and composition across the size spectrum over several different components as determined by the aerosol processes included.

The original version of GLOMAP (known as GLOMAP-bin) uses a two-moment sectional aerosol dynamics approach, with typically 20 bins spanning the size spectrum, but when tracking several aerosol types, becomes too expensive for running multi-decadal integrations as required in a climate model. For UKCA, a new computationally cheaper version of GLOMAP was developed (GLOMAP-mode), which has the same process representations, but using log-normal modes as its size classes. Each size mode in GLOMAP-mode covers one of four size ranges, with additional separation among soluble and insoluble modes.

GLOMAP has been developed to follow a flexible multi-component approach, with the same code able to be run with different levels of composition/size sophistication with FORTRAN-90 modules providing alternative aerosol mode set-up arrays. The GLOMAP-mode aerosol scheme in UKCA not only simulates the dry aerosol mass, but also the mass of water attached to the aerosol, and the aerosol number concentrations.

The calculation of aerosol optical properties from GLOMAP is carried out via the RADAER module within UKCA.

Compared to CLASSIC, the GLOMAP-mode scheme introduces three important changes which are relevant for simulated aerosol-radiation interactions:

  • The mean radius of each size class (mode) varies in time and space as determined by transport and aerosol processes.
  • There is a refractive index for each size class (mode) which varies according to its internally-mixed composition.
  • The amount of aerosol water in each soluble mode varies interactively consistent with its composition.

RADAER relies on pre-computed look-up tables of monochromatic optical properties, covering all realistic combinations of modal radii and refractive indices. At runtime, remaining tasks are:

  • To compute the modal refractive index out of the simulated chemical composition of each mode.
  • To obtain the monochromatic properties from the look-up tables at selected wavelengths within each shortwave and longwave waveband.
  • To integrate across each waveband to obtain the waveband-averaged optical properties, which can be used by the radiation code.

As well as providing the waveband-averaged scattering, extinction and asymmetry parameters from GLOMAP, RADAER also diagnoses monochromatic Aerosol Optical Depth (AOD) for each of the GLOMAP modes.

Task 10.3: Output daily-mean Aerosol Optical Depths from your UKCA model run

In this task you will update your copy of the UKCA tutorial job (xjrnk) adding extra STASH requests to output daily-mean AODs from GLOMAP.

UM-UKCA diagnoses the AOD from each of the GLOMAP modes as a separate STASH item.

All of the GLOMAP AOD diagnostics are contained with STASH section 2 (long-wave radiation) in items numbers near to those used for the AOD diagnostics from CLASSIC.

Section 2 items 300-305 contain the AOD for the Aitken-soluble, accumulation-soluble, coarse-soluble, Aitken-insoluble, accumulation-insoluble and coarse-insoluble modes respectively.

The dimensions for each of these STASH items is 2D global in longitude and latitude but there is also a third dimension containing 6 pseudo levels for the 6 monochromatic AODs stored by the model (at 0.38, 0.44, 0.55, 0.67, 0.87, 1.02 micron wavelengths).

Note that there is no nucleation mode AOD as those particles are too small to significantly scatter or absorb radiation at these wavelenghts.

Note that although the absorption AOD in these 6 modes can usually be requested via STASH section 2 items 240 to 245, in the job here these are not available.

There are also separate "stratospheric AOD" diagnostics in section 2 items 251 to 256 which can also be requested to store the AOD in levels above the tropopause.

To output AODs from GLOMAP, you need to add in some extra STASH requests for the section 2 items 300 to 305.

To output as a daily-mean select the usage profile "UPA" to output to the .pa files and the time profile "TDAYM" for daily-means. For AOD STASH requests, you need to select the domain profile DIAGAOT to output over the longitude, latitude and 6 wavelength pseudo-levels.

Section 34 items 106, 110, 116, 121 and 126 contain the OM mmr's in the Aitken-soluble, accumulation-soluble, coarse-soluble, Aitken-insoluble and nucleation-soluble modes respectively.

When requesting the OM mmr's you should use the DALLTH domain profile to request the variable on the full 3D model grid.

So now you should have an equivalent version of the UKCA tutorial job with extra daily-mean fields requested.

Since you specified the UPA usage profile in the job, these fields will be output to the so-called .pa files.

These can be found in your /work/n02/n02/ directory on ARCHER. You should have a file like jobida.pa19991201 for the daily-mean fields for the 1 day that the job was set to run for.

In the first instance you should use xconv to open the file although you can use convsh or other tools to extract required fields from the .pa file and then manipulate them in IDL or python.

As an example I have put below a jpeg showing a global map produced in IDL of the daily-mean AOD at 550nm (total over all modes) for 1st December 1999 from the UKCA tutorial job (worked solution xjrnl).

In preparation for the next task, you should also re-run the job adding also daily-mean STASH requests for the following mass mixing ratios (mmr's) for the Organic Matter (OM) in each mode (34106, 34110, 34116, 34121 and 34126).

Once you have re-run the job with these extra fields available in the .pa file, you can use the cdo operator cdo add to sum up each of the OM mmrs to give a total OM mmr in a separate netCDF file.

Idl dailyAOD550 xkwhg.jpg

Worked Solution

A worked soltion to Task 10.3 is job xjrnl.

You can use cdo as so to add the 5 separate netCDF files containing the OC mass-mixing ratios: 

$ cdo add xkvxm_aitken_sol_OCmmr.nc -add xkvxm_accum_sol_OCmmr.nc -add xkvxm_coarse_sol_OCmmr.nc -add xkvxm_aitken_insol_OCmmr.nc 
xkvxm_nuc_sol_OCmmr.nc xkvxm_OCmmr.nc
cdo add: Started child process "add xkvxm_accum_sol_OCmmr.nc -add xkvxm_coarse_sol_OCmmr.nc -add xkvxm_aitken_insol_OCmmr.nc 
xkvxm_nuc_sol_OCmmr.nc (pipe1.1)".
cdo(2) add: Started child process "add xkvxm_coarse_sol_OCmmr.nc -add xkvxm_aitken_insol_OCmmr.nc xkvxm_nuc_sol_OCmmr.nc (pipe2.1)".
cdo(3) add: Started child process "add xkvxm_aitken_insol_OCmmr.nc xkvxm_nuc_sol_OCmmr.nc (pipe3.1)".
cdo(4) add: Processed 4732800 values from 2 variables over 2 timesteps ( 0.23s )
cdo(3) add: Processed 4732800 values from 2 variables over 2 timesteps ( 0.25s )
cdo(2) add: Processed 4732800 values from 2 variables over 2 timesteps ( 0.27s )
cdo add: Processed 4732800 values from 2 variables over 2 timesteps ( 0.28s )

When opening the output file (xkvxm_OCmmr.nc in the example above) the variable name is taken from the first file in the list.

Example output can be found on ARCHER in the directory 

/work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Task10.3


Written by Graham Mann 2014

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