Solution to UKCA Chemistry and Aerosol Tutorial 6 Task 6.1

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Task

You were asked to

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). This reaction is given by:

${\textrm {ALICE}}+{\textrm {OH}}\longrightarrow {\textrm {BOB}}+{\textrm {Sec\_Org}}$

Parameter	Value
$k_{0}$	2.70E-11
$\alpha$	0.00
$\beta$	-390.00

Solution

Changes to ukca_chem_strattrop.F90

The only UKCA code changes that are required, are in ukca_chem_strattrop.F90. You should add the following line at the end of the ratb_defs_strattrop05 array

ratb_t('ALICE     ','OH        ','BOB       ','Sec_Org   ','          ',& 
'          ',  2.70E-11,  0.00,   -390.00, 0.000, 0.000, 0.000, 0.000)  & 

(remembering to add a comma at the end of the line above) and increase the size of the ratb_defs_strattrop05 array to 21 and the size of the ratb_defs_strattrop_chem master array to 201.

Hand-edit to increase JPBK and JPNR

You will now need to make a hand-edit to increase the size of JPBK and JPNR, which are set in CNTLATM. This should look like

ed CNTLATM<<\EOF
/JPBK/
d
i
 JPBK=216,
.
/JPNR/
d
i
 JPNR=309,
.
w
q
EOF

Figure 1: Surface plot of the BOB tracer after bimolecular reaction has been applied.

You should make this script executable (chmod a+rx script.ed) and add it to the UMUI in the Model Selection → Input/Output Control and Resource → User hand edit files by placing it in the table and putting a Y in the Include Y/N column.

An example hand-edit can be found at

/home/ukca/hand_edits/VN8.4/Tutorial/Task6.1_incr_JPvals.ed

on PUMA.

Output

Now that we are forming BOB, this tracer field will be non-zero. If you open the pb file (located in your archive directory) in Xconv and plot the surface of 34065, you should see a field similar to that in Figure 1.

Sample output from this job can be found in

/work/n02/n02/ukca/Tutorial/vn8.4/sample_output/Task6.1/

on ARCHER, and in

/projects/ukca/Tutorial/vn8.4/sample_ouput/Task6.1/

on MONSooN.

Worked Solution

There is a worked solution to this problem in the UMUI Tutorial experiment. This is job g: Tutorial: solution to Task 6.1 - add a new bimolecular reaction.

The code changes can be viewed by using the following FCM command

fcm diff fcm:um_br/dev/luke/vn8.4_UKCA_Tutorial_Solns@14697 fcm:um_br/dev/luke/vn8.4_UKCA_Tutorial_Solns@14703

This gives the following output:

Index: src/atmosphere/UKCA/ukca_chem_strattrop.F90
===================================================================
--- src/atmosphere/UKCA/ukca_chem_strattrop.F90	(revision 14697)
+++ src/atmosphere/UKCA/ukca_chem_strattrop.F90	(revision 14703)
@@ -399,7 +399,7 @@
 chch_t( 90,'BOB       ',  1,'TR        ','          ',  0,  0,  0)   & 
   /)
 
-TYPE(RATB_T) :: ratb_defs_strattrop_chem(200)
+TYPE(RATB_T) :: ratb_defs_strattrop_chem(201)
 
 ! reactions found in either Trop or Strat but not both 
 TYPE(RATB_T), PARAMETER :: ratb_defs_strattrop_aer(1:15)=(/              &
@@ -1011,7 +1011,7 @@
 TYPE(RATB_T) :: ratb_defs_strattrop02(45)
 TYPE(RATB_T) :: ratb_defs_strattrop03(45)
 TYPE(RATB_T) :: ratb_defs_strattrop04(45)
-TYPE(RATB_T) :: ratb_defs_strattrop05(20)
+TYPE(RATB_T) :: ratb_defs_strattrop05(21)
 
 REAL :: depvel_defs_strattrop01(360)
 REAL :: depvel_defs_strattrop02(360)
@@ -1649,7 +1649,9 @@
 ratb_t('ISO2      ','O2        ','OH        ','HCHO      ','MACR      ',& ! B198
 '          ',  4.00E-03,  0.00,      0.00, 0.000, 0.000, 0.000, 0.000) ,& ! B198  ATA HOx recyc - added by hand
 ratb_t('ISO2      ','N2        ','HO2       ','MGLY      ','HACET     ',& ! B199
-'OH        ',  8.00E-02,  0.00,      0.00, 1.000, 1.000, 0.650, 0.600) &  ! B199  ATA HOx recyc - added by hand
+'OH        ',  8.00E-02,  0.00,      0.00, 1.000, 1.000, 0.650, 0.600) ,& ! B199  ATA HOx recyc - added by hand
+ratb_t('ALICE     ','OH        ','BOB       ','Sec_Org   ','          ',& ! UKCA TUTORIAL RXN 01
+'          ',  2.70E-11,  0.00,   -390.00, 0.000, 0.000, 0.000, 0.000)  & ! UKCA TUTORIAL RXN 01
   /) 
   
 !---------------------------------------------------------------------- 

---

Written by Luke Abraham 2014