Difference between revisions of "UKCA Chemistry and Aerosol vn10.9 Tutorial 10"

From UKCA
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<span style="color:green">'''TASK 10.6:''' </span>
 
<span style="color:green">'''TASK 10.6:''' </span>
  +
  +
{| class="collapsible collapsed wikitable"
  +
|-
  +
! Hint
  +
|-
  +
| Remember to remove <code>Sec_Org</code> from the diagnostics as well as the reaction.
  +
|}
   
 
==Solution to Task 10.5 ==
 
==Solution to Task 10.5 ==

Revision as of 17:28, 12 December 2017

UKCA Chemistry and Aerosol Tutorials at vn10.9

What you will learn in this Tutorial

Task 10.1: Output aerosol diagnostics

TASK 10.1: Output the following aerosol and radiation diagnostics to the UPA output stream. 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.

STASH Section STASH Item STASH Name
1 207 INCOMING SW RAD FLUX (TOA): ALL TSS
1 208 OUTGOING SW RAD FLUX (TOA)
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
2 585 MINERAL DUST ABS. OPICAL DEPTH
2 240 AITKEN (SOLUBLE) ABS OPTICAL DEPTH
2 241 ACCUM (SOLUBLE) ABS OPTICAL DEPTH
2 242 COARSE (SOLUBLE) ABS OPTICAL DEPTH
2 243 AITKEN (INSOL) ABS OPTICAL DEPTH
2 244 ACCUM (INSOL) ABS OPTICAL DEPTH
2 245 COARSE (INSOL) ABS OPTICAL DEPTH
2 530 UKCA 3D AEROSOL EXTINCTION
2 540 CLASSIC 3D AEROSOL EXTINCTION

Solution to Task 10.1

You were given the task

  • Output the following aerosol and radiation diagnostics to the UPA output stream. 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.
STASH Section STASH Item STASH Name
1 207 INCOMING SW RAD FLUX (TOA): ALL TSS
1 208 OUTGOING SW RAD FLUX (TOA)
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
2 585 MINERAL DUST ABS. OPICAL DEPTH
2 240 AITKEN (SOLUBLE) ABS OPTICAL DEPTH
2 241 ACCUM (SOLUBLE) ABS OPTICAL DEPTH
2 242 COARSE (SOLUBLE) ABS OPTICAL DEPTH
2 243 AITKEN (INSOL) ABS OPTICAL DEPTH
2 244 ACCUM (INSOL) ABS OPTICAL DEPTH
2 245 COARSE (INSOL) ABS OPTICAL DEPTH
2 530 UKCA 3D AEROSOL EXTINCTION
2 540 CLASSIC 3D AEROSOL EXTINCTION

and were given the hint

  • You can find the number of radiation timesteps in a 24-hour period at: um namelist UM Science Settings Section 01 - 02 Radiation Shortwave.

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

  • ARCHER: u-as292@62651
  • vm: u-as297@62631

The specific Rose changes made are:

The specific Rose changes made are:

ARCHER:

Index: app/um/rose-app.conf
===================================================================
--- app/um/rose-app.conf       (revision 60289)
+++ app/um/rose-app.conf       (revision 62651)
@@ -2744,6 +2744,40 @@
 precip_segment_size=32
 ukca_mode_seg_size=4
 
+[namelist:umstash_domain(d3dar_72578706)]
+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=01
+!!levlst=0
+levt=85
+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
@@ -3025,6 +3059,22 @@
 tim_name='TALLTS'
 use_name='UPUKCA'
 
+[namelist:umstash_streq(01207_ed72c304)]
+dom_name='DIAG'
+isec=1
+item=207
+package=
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(01208_83140cd8)]
+dom_name='DIAG'
+isec=1
+item=208
+package=
+tim_name='TRAD'
+use_name='UPA'
+
 [namelist:umstash_streq(01235_3511dd9f)]
 dom_name='DIAG'
 isec=1
@@ -3033,14 +3083,142 @@
 tim_name='TALLTS'
 use_name='UPUKCA'
 
-[namelist:umstash_streq(02301_0f7c5f4a)]
+[namelist:umstash_streq(02205_357bf644)]
+dom_name='DIAG'
+isec=2
+item=205
+package=
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02240_d97aaab7)]
 dom_name='DIAGAOT'
 isec=2
+item=240
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02241_8cda3169)]
+dom_name='DIAGAOT'
+isec=2
+item=241
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02242_91e371db)]
+dom_name='DIAGAOT'
+isec=2
+item=242
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02243_21bc5f11)]
+dom_name='DIAGAOT'
+isec=2
+item=243
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02244_32fe0790)]
+dom_name='DIAGAOT'
+isec=2
+item=244
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02245_da00b6ef)]
+dom_name='DIAGAOT'
+isec=2
+item=245
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02285_1d9800f0)]
+dom_name='DIAGAOT'
+isec=2
+item=285
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02300_8b9907b5)]
+dom_name='DIAGAOT'
+isec=2
+item=300
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02301_b8711d23)]
+dom_name='DIAGAOT'
+isec=2
 item=301
-package='UKCA Testing'
-tim_name='T3HMN'
+package=' '
+tim_name='TRAD'
 use_name='UPA'
 
+[namelist:umstash_streq(02302_420d0ec7)]
+dom_name='DIAGAOT'
+isec=2
+item=302
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02303_ad5c3af4)]
+dom_name='DIAGAOT'
+isec=2
+item=303
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02304_8c1869b6)]
+dom_name='DIAGAOT'
+isec=2
+item=304
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02305_9ecd020a)]
+dom_name='DIAGAOT'
+isec=2
+item=305
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02530_7a218781)]
+dom_name='D3DAR'
+isec=2
+item=530
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02540_56484a28)]
+dom_name='D3DAR'
+isec=2
+item=540
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02585_38287367)]
+dom_name='DIAGAOT'
+isec=2
+item=585
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
 [namelist:umstash_streq(03025_c8768f77)]
 dom_name='DIAG'
 isec=3
@@ -3551,6 +3729,25 @@
 !!unt2=2
 unt3=1
 
+[namelist:umstash_time(trad_4c3a45a7)]
+!!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=2
+!!unt2=2
+unt3=1
+
 [namelist:umstash_use(upa_ffb3f00b)]
 file_id='pp0'
 locn=3 

These differences can be found in the file /home/ukca/Tutorial/vn10.9/worked_solutions/Task10.1/Task10.1_rose.patch on PUMA.

vm:

Index: app/um/rose-app.conf
===================================================================
--- app/um/rose-app.conf       (revision 60286)
+++ app/um/rose-app.conf       (revision 62631)
@@ -2849,6 +2849,40 @@
 !!ttlimr=0.0
 !!twlim=0
 
+[namelist:umstash_domain(d3dar_72578706)]
+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=01
+!!levlst=0
+levt=85
+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
@@ -3617,6 +3651,22 @@
 tim_name='TALLTS'
 use_name='UPUKCA'
 
+[namelist:umstash_streq(01207_ed72c304)]
+dom_name='DIAG'
+isec=1
+item=207
+package=
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(01208_83140cd8)]
+dom_name='DIAG'
+isec=1
+item=208
+package=
+tim_name='TRAD'
+use_name='UPA'
+
 [namelist:umstash_streq(01235_3511dd9f)]
 dom_name='DIAG'
 isec=1
@@ -3625,14 +3675,142 @@
 tim_name='TALLTS'
 use_name='UPUKCA'
 
-[namelist:umstash_streq(02301_0f7c5f4a)]
+[namelist:umstash_streq(02205_357bf644)]
+dom_name='DIAG'
+isec=2
+item=205
+package=
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02240_d97aaab7)]
 dom_name='DIAGAOT'
 isec=2
+item=240
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02241_8cda3169)]
+dom_name='DIAGAOT'
+isec=2
+item=241
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02242_91e371db)]
+dom_name='DIAGAOT'
+isec=2
+item=242
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02243_21bc5f11)]
+dom_name='DIAGAOT'
+isec=2
+item=243
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02244_32fe0790)]
+dom_name='DIAGAOT'
+isec=2
+item=244
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02245_da00b6ef)]
+dom_name='DIAGAOT'
+isec=2
+item=245
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02285_1d9800f0)]
+dom_name='DIAGAOT'
+isec=2
+item=285
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02300_8b9907b5)]
+dom_name='DIAGAOT'
+isec=2
+item=300
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02301_b8711d23)]
+dom_name='DIAGAOT'
+isec=2
 item=301
-package='UKCA Testing'
-tim_name='T3HMN'
+package=' '
+tim_name='TRAD'
 use_name='UPA'
 
+[namelist:umstash_streq(02302_420d0ec7)]
+dom_name='DIAGAOT'
+isec=2
+item=302
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02303_ad5c3af4)]
+dom_name='DIAGAOT'
+isec=2
+item=303
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02304_8c1869b6)]
+dom_name='DIAGAOT'
+isec=2
+item=304
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02305_9ecd020a)]
+dom_name='DIAGAOT'
+isec=2
+item=305
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02530_7a218781)]
+dom_name='D3DAR'
+isec=2
+item=530
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02540_56484a28)]
+dom_name='D3DAR'
+isec=2
+item=540
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
+[namelist:umstash_streq(02585_38287367)]
+dom_name='DIAGAOT'
+isec=2
+item=585
+package=' '
+tim_name='TRAD'
+use_name='UPA'
+
 [namelist:umstash_streq(03025_c8768f77)]
 dom_name='DIAG'
 isec=3
@@ -4504,6 +4682,25 @@
 unt2=2
 unt3=4
 
+[namelist:umstash_time(trad_4c3a45a7)]
+!!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=2
+!!unt2=2
+unt3=1
+
 [namelist:umstash_time(traddm_fa7c24ce)]
 !!iedt=0
 iend=-1 

If you open the .pa 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: Stash code = 2240      
4    : 96    72    6     2     unspecified: Stash code = 2241      
5    : 96    72    6     2     unspecified: Stash code = 2242      
6    : 96    72    6     2     unspecified: Stash code = 2243      
7    : 96    72    6     2     unspecified: Stash code = 2244      
8    : 96    72    6     2     unspecified: Stash code = 2245      
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: Stash code = 2530
17   : 96    72    38    2     unspecified: Stash code = 2530
18   : 96    72    38    2     unspecified: Stash code = 2530
19   : 96    72    38    2     unspecified: Stash code = 2530
20   : 96    72    38    2     unspecified: Stash code = 2530
21   : 96    72    38    2     unspecified: Stash code = 2530
22   : 96    72    38    2     unspecified: Stash code = 2540
23   : 96    72    38    2     unspecified: Stash code = 2540
24   : 96    72    38    2     unspecified: Stash code = 2540
25   : 96    72    38    2     unspecified: Stash code = 2540
26   : 96    72    38    2     unspecified: Stash code = 2540
27   : 96    72    38    2     unspecified: Stash code = 2540
28   : 96    72    6     2     unspecified: Stash code = 2585

Sample output from this task can be found at /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.1/atmosa.pa19810901_00 on ARCHER.

Task 10.2: Calculate aerosol optical depth

TASK 10.2: Calculate the aerosol optical depth at 0.55 microns.

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 script

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

On ARCHER, an example python script to do this has been provided at /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.2/write_AOD.py:

#!/usr/bin/env python

# This file is part of the UKCA Tutorials:
#  http://www.ukca.ac.uk/wiki/index.php/UKCA_Chemistry_and_Aerosol_Tutorials_at_vn10.9

# Copyright (C) 2017  University of Cambridge

# This is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option)
# any later version.

# It is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
# details.

# You find a copy of the GNU Lesser General Public License at <http://www.gnu.org/licenses/>.

# Written by N. Luke Abraham 2017-12-11 <nla27@cam.ac.uk> 

# preamble
import iris
import iris.time

fname='/work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.1/atmosa.pa19810901_00'

# constraint on time to get 2nd radiation timestep
tconstr=iris.Constraint(time=lambda cell: cell.point.hour == 2)

# load all AOD components at 0.55 micron
# must use this way of loading to account for constraint on time
with iris.FUTURE.context(cell_datetime_objects=True):
    aod=iris.load(fname,[
        iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i285') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i300') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i301') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i302') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i303') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i304') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i305') & tconstr])

# make cube to store total AOD
aodsum=aod[0].copy()

# add-up components
aodsum.data=aod[0].data+aod[1].data+aod[2].data+aod[3].data+aod[4].data+aod[5].data+aod[6].data

# rename
aodsum.rename('atmosphere_optical_thickness_due_to_aerosol')

# remove unlimited dimension when writing to netCDF
iris.FUTURE.netcdf_no_unlimited=True

# output to netCDF
iris.save(aodsum,'Task102_AOD.nc',netcdf_format='NETCDF3_CLASSIC')

You should edit this script to point to your UM output file, and will need to

module load anaconda/2.2.0-python2

before running it, e.g.

python -c 'execfile("write_AOD.py")'

Solution to Task 10.2

Sample output from this task can be found in the /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.2/ directory on ARCHER, containing the following:

Task102_AOD.nc
write_AOD.py

Task 10.3: Calculate the single-scattering albedo

TASK 10.3: Calculate the single-scattering albedo at 0.55 microns, defined as:

Python script

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.

On ARCHER, an example python script to do this has been provided at /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.3/write_SSA.py:

#!/usr/bin/env python

# This file is part of the UKCA Tutorials:
#  http://www.ukca.ac.uk/wiki/index.php/UKCA_Chemistry_and_Aerosol_Tutorials_at_vn10.9

# Copyright (C) 2017  University of Cambridge

# This is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option)
# any later version.

# It is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
# details.

# You find a copy of the GNU Lesser General Public License at <http://www.gnu.org/licenses/>.

# Written by N. Luke Abraham 2017-12-11 <nla27@cam.ac.uk> 

# preamble
import iris
import iris.time

fname='/work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.1/atmosa.pa19810901_00'

# constraint on time to get 2nd radiation timestep
tconstr=iris.Constraint(time=lambda cell: cell.point.hour == 2)

# load all AOD & AAOD components at 0.55 micron
# must use this way of loading to account for constraint on time
with iris.FUTURE.context(cell_datetime_objects=True):
    aod=iris.load(fname,[
        iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i285') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i300') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i301') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i302') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i303') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i304') & tconstr,
       iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i305') & tconstr])
    aaod=iris.load(fname,[
         iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i585') & tconstr,
        iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i240') & tconstr,
        iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i241') & tconstr,
        iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i242') & tconstr,
        iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i243') & tconstr,
        iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i244') & tconstr,
        iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i245') & tconstr])

# make cube to store total AOD
aodsum=aod[0].copy()
# add-up components
aodsum.data=aod[0].data+aod[1].data+aod[2].data+aod[3].data+aod[4].data+aod[5].data+aod[6].data

# make cube to store total AAOD
aaodsum=aaod[0].copy()
# add-up components
aaodsum.data=aaod[0].data+aaod[1].data+aaod[2].data+aaod[3].data+aaod[4].data+aaod[5].data+aaod[6].data

# calculate single-scattering albedo
ssa=aodsum.copy()
ssa.data = 1.0 - (aaodsum.data/aodsum.data)

# rename
ssa.rename('single_scattering_albedo_in_air_due_to_ambient_aerosol_particles')

# remove unlimited dimension when writing to netCDF
iris.FUTURE.netcdf_no_unlimited=True

# output to netCDF
iris.save(ssa,'Task103_SSA.nc',netcdf_format='NETCDF3_CLASSIC')

Solution to Task 10.3

Sample output from this task can be found in the /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.3/ directory on ARCHER, containing the following:

Task103_SSA.nc
write_SSA.py

Task 10.4: Calculate the top of the atmosphere net downward radiative flux

TASK 10.4: Calculate the net downward top of the atmosphere radiative flux.

Python script

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.

On ARCHER, an example python script to do this has been provided at /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.4/write_TOA.py:

#!/usr/bin/env python

# This file is part of the UKCA Tutorials:
#  http://www.ukca.ac.uk/wiki/index.php/UKCA_Chemistry_and_Aerosol_Tutorials_at_vn10.9

# Copyright (C) 2017  University of Cambridge

# This is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option)
# any later version.

# It is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
# details.

# You find a copy of the GNU Lesser General Public License at <http://www.gnu.org/licenses/>.

# Written by N. Luke Abraham 2017-12-11 <nla27@cam.ac.uk> 

# preamble
import iris
import iris.time

fname='/work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.1/atmosa.pa19810901_00'

# constraint on time to get 2nd radiation timestep
tconstr=iris.Constraint(time=lambda cell: cell.point.hour == 2)

# load all TOA components at 0.55 micron
# must use this way of loading to account for constraint on time
with iris.FUTURE.context(cell_datetime_objects=True):
    isw=iris.load_cube(fname,[iris.AttributeConstraint(STASH='m01s01i207') & tconstr])
    osw=iris.load_cube(fname,[iris.AttributeConstraint(STASH='m01s01i208') & tconstr])
    olw=iris.load_cube(fname,[iris.AttributeConstraint(STASH='m01s02i205') & tconstr])

# make cube to store net downward TOA flux
toa=isw.copy()
# add-up components
toa.data=isw.data - (osw.data + olw.data)

toa.rename('toa_net_downward_radiative_flux')

# remove unlimited dimension when writing to netCDF
iris.FUTURE.netcdf_no_unlimited=True

# output to netCDF
iris.save(toa,'Task104_TOA.nc',netcdf_format='NETCDF3_CLASSIC')

Solution to Task 10.4

Sample output from this task can be found in the /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.4/ directory on ARCHER, containing the following:

Task104_TOA.nc
write_TOA.py

Task 10.5: Calculate aerosol optical depth from the 3D aerosol extinction

TASK 10.5: Using the 3D aerosol extinction, calculate the 0.55 micron aerosol optical depth, and compare this to your AOD from Task10.2.

Python script

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.

On ARCHER, an example python script to do this has been provided at /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.5/calc_AOD.py:

#!/usr/bin/env python

# This file is part of the UKCA Tutorials:
#  http://www.ukca.ac.uk/wiki/index.php/UKCA_Chemistry_and_Aerosol_Tutorials_at_vn10.9

# Copyright (C) 2017  University of Cambridge

# This is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option)
# any later version.

# It is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
# details.

# You find a copy of the GNU Lesser General Public License at <http://www.gnu.org/licenses/>.

# Written by N. Luke Abraham 2017-12-11 <nla27@cam.ac.uk> 

# preamble
import iris
import iris.time
import iris.analysis
import numpy as np

fname='/work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.1/atmosa.pa19810901_00'

# constraint on time to get 2nd radiation timestep
tconstr=iris.Constraint(time=lambda cell: cell.point.hour == 2)

# load orography to enable correct calculation of level heights
orog=iris.load_cube(
     '/work/n02/n02/hum/ancil/atmos/n48e/orography/globe30/v1/qrparm.orog',
     iris.AttributeConstraint(STASH='m01s00i033'))

# load all extinction components at 0.55 micron
# must use this way of loading to account for constraint on time
with iris.FUTURE.context(cell_datetime_objects=True):
    ukca=iris.load_cube(fname,[
         iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i530') & tconstr])
    classic=iris.load_cube(fname,[
            iris.Constraint(pseudo_level=3) & iris.AttributeConstraint(STASH='m01s02i540') & tconstr])

# Calculate the correct height of each cell
# add the orography as an auxillary coordinate
auxcoord=iris.coords.AuxCoord(orog.data,standard_name=str(orog.standard_name),long_name="orography",var_name="orog",units=orog.units)
# added in to lat/lon (ht=0,lat=1,lon=2)
ukca.add_aux_coord(auxcoord,(1,2,))
# now calculate the correct altitude above sea-level
factory=iris.aux_factory.HybridHeightFactory(delta=ukca.coord("level_height"),sigma=ukca.coord("sigma"),orography=ukca.coord("surface_altitude"))
# now create the 'altitude' derrived coordinate
ukca.add_aux_factory(factory)
# now calculate the height from the bounds
bounds = ukca.coord('altitude').bounds[:,:,:,1] - ukca.coord('altitude').bounds[:,:,:,0]
    
# mutliply by the height of each cell
ukca.data = ukca.data * bounds
classic.data = classic.data * bounds

# now sum up the column
ukca_int=ukca.collapsed('model_level_number',iris.analysis.SUM)
classic_int=classic.collapsed('model_level_number',iris.analysis.SUM)

# add together
aod=ukca_int.copy()
aod.data = ukca_int.data + classic_int.data
# rename
aod.rename('atmosphere_optical_thickness_due_to_aerosol')

# remove unlimited dimension when writing to netCDF
iris.FUTURE.netcdf_no_unlimited=True

# output to netCDF
iris.save(aod,'Task105_AOD.nc',netcdf_format='NETCDF3_CLASSIC')

On ARCHER, an example python script to calculate the difference from this AOD and the AOD calculated in Task10.2 is also provided at /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.5/diff_AOD_methods.py:

#!/usr/bin/env python

# This file is part of the UKCA Tutorials:
#  http://www.ukca.ac.uk/wiki/index.php/UKCA_Chemistry_and_Aerosol_Tutorials_at_vn10.9

# Copyright (C) 2017  University of Cambridge

# This is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option)
# any later version.

# It is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
# details.

# You find a copy of the GNU Lesser General Public License at <http://www.gnu.org/licenses/>.

# Written by N. Luke Abraham 2017-12-11 <nla27@cam.ac.uk> 

# preamble
import iris

dname='./Task102_AOD.nc'
cname='./Task105_AOD.nc'

diag=iris.load_cube(dname)
calc=iris.load_cube(cname)

# difference the fields
calc.data=calc.data - diag.data

# remove unlimited dimension when writing to netCDF
iris.FUTURE.netcdf_no_unlimited=True

# output to netCDF
iris.save(calc,'Task105_AOD_diff.nc',netcdf_format='NETCDF3_CLASSIC')

Solution to Task 10.5

Note that there will be some small differences between these two fields, especially around coastlines.

Sample output from this task can be found in the /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.5/ directory on ARCHER, containing the following:

Task105_AOD.nc
Task105_AOD_diff.nc
calc_AOD.py
diff_AOD_methods.py

Task 10.6: Calculate the difference in aerosol impacts when Sec_Org is no longer formed from ALICE

TASK 10.6:

Solution to Task 10.5

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

  • ARCHER: u-as292@62669
  • vm: u-as297@62632

The specific Rose changes made are:

The specific Rose changes made are:

ARCHER:

Index: app/fcm_make/rose-app.conf
===================================================================
--- app/fcm_make/rose-app.conf (revision 62651)
+++ app/fcm_make/rose-app.conf (revision 62669)
@@ -42,4 +42,4 @@
 stash_version=1A
 timer_version=3A
 um_rev=vn10.9
-um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46718
+um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@47380

These differences can be found in the file /home/ukca/Tutorial/vn10.9/worked_solutions/Task10.6/Task10.6_rose.patch on PUMA.

vm:

Index: app/fcm_make/rose-app.conf
===================================================================
--- app/fcm_make/rose-app.conf (revision 62631)
+++ app/fcm_make/rose-app.conf (revision 62632)
@@ -42,4 +42,4 @@
 stash_version=1A
 timer_version=3A
 um_rev=vn10.9
-um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46718
+um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@47380

The specific UM changes made are:

Index: src/atmosphere/UKCA/asad_flux_dat.F90
===================================================================
--- src/atmosphere/UKCA/asad_flux_dat.F90      (revision 46718)
+++ src/atmosphere/UKCA/asad_flux_dat.F90      (revision 47380)
@@ -1287,9 +1287,9 @@
 
 TYPE(asad_flux_defn), PARAMETER, PUBLIC ::                       &
                                     ukca_tutorial_fluxes(3) = (/ &
-asad_flux_defn('RXN',50134,'B',.FALSE.,0,4,                      &
+asad_flux_defn('RXN',50134,'B',.FALSE.,0,3,                      &
 (/'ALICE     ','OH        '/),                                   &
-(/'BOB       ','Sec_Org   ','          ','          '/)),        &
+(/'BOB       ','          ','          ','          '/)),        &
 asad_flux_defn('DEP',50135,'D',.FALSE.,0,1,                      &
 (/'ALICE     ','          '/),                                   &
 (/'          ','          ','          ','          '/)),        &
Index: src/atmosphere/UKCA/ukca_chem_master.F90
===================================================================
--- src/atmosphere/UKCA/ukca_chem_master.F90   (revision 46718)
+++ src/atmosphere/UKCA/ukca_chem_master.F90   (revision 47380)
@@ -2156,7 +2156,7 @@
 'HCHO      ',1.00e-12,  0.00,    0.00, 1.00, 0.75, 0.25, 2.75, TI,0,0,107),&
 ratb_t1(277,'MACRO2    ','MeOO      ','HO2       ','CO        ','          ',& 
 '          ',1.00e-12,  0.00,    0.00, 1.17, 0.25, 0.00, 0.00, TI,0,0,107),&
-ratb_t1(278,'ALICE     ','OH        ','BOB       ','Sec_Org   ','          ',& 
+ratb_t1(278,'ALICE     ','OH        ','BOB       ','          ','          ',& 
 '          ',2.70E-11,  0.00, -390.00, 0.00, 0.00, 0.00, 0.00, ST,0,0,107) /)
 
 !----------------------------------------------------------------------

These differences can be found in the file /home/ukca/Tutorial/vn10.9/worked_solutions/Task10.6/Task10.6_code.patch on PUMA.

Sample output from this task can be found in the /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task10.6/ directory on ARCHER, containing the following:

Task106_AOD.nc
Task106_AOD_diff.nc
Task106_SSA.nc
Task106_SSA_diff.nc
Task106_TOA.nc
Task106_TOA_diff.nc
atmosa.pa19810901_00
diff_AOD_rxn.py
diff_SSA_rxn.py
diff_TOA_rxn.py

Checklist

Tutorial 11


Written by Luke Abraham, Nicolas Bellouin, & Anja Schmidt 2017