Difference between revisions of "UKCA Chemistry and Aerosol vn11.8 Tutorial 6"
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− | * ''You should now add in the bimolecular reaction of '''ALICE''' with '''OH''' to form '''BOB''' and a |
+ | * ''You should now add in the bimolecular reaction of '''ALICE''' with '''OH''' to form '''BOB''' and a '''secondary organic compound''' (labelled in UKCA as '''Sec_Org'''). You should use version '''111'''. This reaction is given by:'' |
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Revision as of 17:37, 7 January 2021
UKCA Chemistry and Aerosol Tutorials at vn11.8
What you will learn in this tutorial
During this tutorial you will learn how UKCA specifies different chemical reactions. You will then add a new reaction involving the new tracers that you have added.
Task 6.1: Add a bimolecular reaction
TASK 6.1: You should now add in the bimolecular reaction of ALICE with OH to form BOB and a secondary organic compound (labelled in UKCA as Sec_Org). You should use version 111. This reaction is given by:
Parameter | Value |
---|---|
2.70E-11 | |
0.00 | |
-390.00 |
Hint |
---|
Remember that as Sec_Org is part of the aerosol chemistry, this reaction should be given the a qualifier. You should increment the value of nr_therm accordingly. |
Adding new Chemical Reactions
UKCA currently uses two different methods of defining the chemical reactions solved in the model. The first is a backward Euler solver, and is used for the RAQ and StdTrop chemistry schemes where the solver itself is created by a code-writer. The second makes use of the ASAD chemical integration software package, and is used for the CheT/TropIsop, CheS/Strat, and CheST/StratTrop chemistry schemes. ASAD can use many different solvers, although currently it uses a symbolic Newton-Raphson solver. In this tutorial we will only consider the ASAD framework, as this is easily extended by a user.
ASAD considers four different types of chemical reactions: bimolecular reactions, termolecular reactions, heterogeneous reactions, and photolysis reactions. To make changes and add reactions you will need to make changes to the UKCA source code which can be found in
vn10.9_your_branch_name/src/atmosphere/UKCA
During this tutorial you will be tasked with adding a new reaction into your branch.
Biomolecular Reactions
For most bimolecular reactions, it is sufficient to provide the , , and coefficients that are used to compute the rate coefficient from the Arrhenius expression
Bimolecular Reaction Definition
The bimolecular reactions are defined in the ukca_chem_master.F90
module using the ratb_t1
Fortran type specification, and are held in arrays. At the end of this routine the ratb_defs_master
array is created from these, and if that scheme is selected in UKCA these reactions are copied across into the master ratb_defs
array.
The format of this ratb_t1
type (defined in ukca_chem_defs_mod.F90
) is
ratb_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, 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 N
, SCHEME
, QUALIFIER
, DISQUALIFIER
, and VN
are the same as in the adding new tracers tutorial, although here N
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), & 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),& ! 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), & 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), &
- The first reaction above takes its kinetic data from 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 JPL2011 document.
- The second reaction in these examples takes its kinetic data from IUPAC. Going to this website, this reaction is defined here.
- The third reaction shows the use of fractional products.
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 ratb_t1 type (n_bimol_master). 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 asad_bimol.F90
routine, which is held in the UKCA/ 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, , of a termolecular reaction is given by
where the low pressure rate constant is given by
and the high pressure rate constant is given by
Termolecular Reaction Definition
The termolecular reactions are defined in the ukca_chem_master.F90
module using the ratt_t1
Fortran type specification and are held in the ratt_defs_master
array.
To format of this ratt_t1
type is
ratt_t(N,'Reactant 1','Reactant 2','Product 1 ','Product 2 ', , & , , , , , , Fraction of Product 1 produced, Fraction of Product 2 produced,SCHEME,QUALIFIER, DISQUALIFIER,VN), &
and as in rabt_t1
, where the fraction of a product should be set to 0.0 if this functionality does not need to be used.
The settings for N
, SCHEME
, QUALIFIER
, DISQUALIFIER
, and VN
are the same as in the adding new tracers tutorial, although here N
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 value is used to define the value by
If then
else
as 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), & ! 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) , & ! T005 JPL 2011 ratt_t1(5,'BrO ','NO2 ','BrONO2 ','m ', 0.6, & 5.20e-31, -3.20, 0.00, 6.90e-12, 0.0, 0.0, 0.0, 0.0, st+cs,0,0,107), & ratt_t1(5,'BrO ','NO2 ','BrONO2 ','m ', 327.0, & 4.70e-31, -3.10, 0.00, 1.40e-11, -1.2, 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 ratt_defs_master
array (increasing the array size n_ratt_master accordingly). If there is any special code that needs to be added, this should be placed in the asad_trimol.F90
routine, which is held in the UKCA/ 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 ukca_chem_master.F90
module using the rath_t1
Fortran type specification, usually in one array (rath_defs_master
).
To format of this rath_t1
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 ukca_hetero_mod.F90
, and for other reactions there is code in asad_hetero.F90
.
The settings for N
, SCHEME
, QUALIFIER
, DISQUALIFIER
, and VN
are the same as in the adding new tracers tutorial, although here N
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 rath_defs_master array (increasing the array size n_het_master accordingly), before adding code to either ukca_hetero_mod.F90
(for stratospheric reactions) or asad_hetero.F90
(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)[1] and Law et al (1998)[2].
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 i_ukca_photol
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 ukca_phot2d.F90
.
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)[3] is used (below 300hPa the tropospheric scheme described above is used). To use this scheme set the value of i_ukca_photol
by clicking 2D Photolysis Scheme. The code for this scheme is held in ukca_strat_update.F90
.
References
- Lary, D. and Pyle, J.: Diffuse-radiation, twilight, and photochemistry, J. Atmos. Chem., 13, 393–406, 1991.
Interactive Photolysis
The original Fast-J scheme (Wild et al, 2000)[4] uses 7 different wavelength bins appropriate for the troposphere, and the updated Fast-JX scheme (Neu et al, 2007)[5] adds up to an extra 11 bins allowing use in the stratosphere. At vn10.4 only Fast-JX is available, although previous UM version used Fast-J as well.
To use this scheme set the value of i_ukca_photol
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 Telford et al (2013)[6].
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
- 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 ukca_chem_master.F90
module using the ratj_t1
Fortran type specification and held in the ratj_defs_master
array.
To format of this ratj_t1
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 N
, SCHEME
, QUALIFIER
, DISQUALIFIER
, and VN
are the same as in the adding new tracers tutorial, although here N
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),& 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),&
To add new heterogeneous reactions you will need to append equivalent lines for the new reactions to the end of the ratj_defs_master array (increasing the array size n_ratj_master accordingly), adding new files/code as necessary as described above.
Solution to Task 6.1: Add a bimolecular reaction
You were given the task
- You should now add in the bimolecular reaction of ALICE with OH to form BOB and a secondary organic compound (labelled in UKCA as Sec_Org). You should use version 111. This reaction is given by:
Parameter | Value |
---|---|
2.70E-11 | |
0.00 | |
-390.00 |
For a working Rose suite that has completed this task, please see
- ARCHER:
u-as292@60067
- vm:
u-as297@59986
The specific Rose changes made are:
- ARCHER: https://code.metoffice.gov.uk/trac/roses-u/changeset/60067/a/s/2/9/2/trunk
- vm: https://code.metoffice.gov.uk/trac/roses-u/changeset/59986/a/s/2/9/7/trunk
The specific Rose changes made are:
ARCHER:
Index: app/fcm_make/rose-app.conf =================================================================== --- app/fcm_make/rose-app.conf (revision 59937) +++ app/fcm_make/rose-app.conf (revision 60067) @@ -42,4 +42,4 @@ stash_version=1A timer_version=3A um_rev=vn10.9 -um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46574 +um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46619
These differences can be found in the file /home/ukca/Tutorial/vn10.9/worked_solutions/Task6.1/Task6.1_rose.patch
on PUMA.
vm:
Index: app/fcm_make/rose-app.conf =================================================================== --- app/fcm_make/rose-app.conf (revision 59931) +++ app/fcm_make/rose-app.conf (revision 59986) @@ -42,4 +42,4 @@ stash_version=1A timer_version=3A um_rev=vn10.9 -um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46574 +um_sources=branches/dev/lukeabraham/vn10.9_UKCA_Tutorial_Solns@46619
The specific UM changes made are:
Index: src/atmosphere/UKCA/ukca_chem_master.F90 =================================================================== --- src/atmosphere/UKCA/ukca_chem_master.F90 (revision 46574) +++ src/atmosphere/UKCA/ukca_chem_master.F90 (revision 46619) @@ -83,7 +83,7 @@ INTEGER, PARAMETER :: n_het_master = 10 ! number of heterogeneous reactions INTEGER, PARAMETER :: n_dry_master = 57 ! number of dry deposition reactions INTEGER, PARAMETER :: n_wet_master = 49 ! number of wet deposition reactions -INTEGER, PARAMETER :: n_bimol_master= 400 ! number of bimolecular reactions +INTEGER, PARAMETER :: n_bimol_master= 401 ! number of bimolecular reactions INTEGER, PARAMETER :: n_ratj_master = 76 ! number of photolysis reactions INTEGER, PARAMETER :: n_ratt_master = 49 ! number of termolecular reactions @@ -2152,7 +2152,9 @@ ratb_t1(276,'MACRO2 ','MeOO ','MGLY ','HACET ','MeCO3 ',& '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) /) +' ',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 ',' ',& +' ',2.70E-11, 0.00, -390.00, 0.00, 0.00, 0.00, 0.00, ST,0,0,107) /) !---------------------------------------------------------------------- ! NOTES: CheST Bimolecular Reactions
These differences can be found in the file /home/ukca/Tutorial/vn10.9/worked_solutions/Task6.1/Task6.1_code.patch
on PUMA.
Sample output from this task can be found at /work/n02/n02/ukca/Tutorial/vn10.9/sample_output/Task6.1/atmosa.pa19810901_00
on ARCHER.
Checklist
- ☐ Add the new reaction into the correct reaction type array in
ukca_chem_master.F90
, incrementing the size of the array accordingly. - ☐ If required, add special code to the
asad_bimol.F90
,asad_trimol.F90
,ukca_hetero_mod.F90
, orasad_hetero.F90
routines. - ☐ For photolysis reactions, further work is required to calculate new cross sections. Code will also need to be added to
ukca_strat_update.F90
.
Written by Luke Abraham 2021