modify the chemistry code

[ljdiao@gmail_com]

I am trying to delete some species from the default pp_waccm_mozart chemical shcheme. At first I just tried to delete CL2. I deleted all the CL2 related things from chem_mech.in file and run the chemical preprocessor. The other changes I made are: (1)change the $chem_nadv = 57 from $chem_nadv = 58 in the ../models/atm/cam/bld/configure file. (2)deleted all the CL2 things in the atm_in file. I run the cesm but it stopped at the beginning of the execution. I think it is before the execution of “QNEG3 from vertical diffusion/HORZ”. The error messages are related to the memory leakage as “*** glibc detected *** /tng4/users/ldiao/CESM/cesm1_2_0/exe/cesm.exe: corrupted double-linked list: 0x0000000036372c10 ***” Apprecaited for your help!

 

[fvitt]

 Lijun,

Removal of some of the het reactions is causing a problem.  mo_usrrxt is
expecting het1 reaction rate constant to be defined.  Since you removed
some of the het reactions from the mechanism file het1 is not defined.
You need to have all het1 through het17 reactions in the mech file.

Removal of CL2 from the mechanism requires removal of only the the photo
reaction:

[jcl2]    CL2 + hv -> 2*CL

You don't need to remove reactions where CL2 is produced.

You need to include these het reactions in your chem_mech.in file:

290,291d289
<  [het4] CLONO2 + HCL -> CL2 + HNO3
<  [het5] HOCL + HCL -> CL2 + H2O
298,299d295
<  [het9] CLONO2 + HCL -> CL2 + HNO3
<  [het10] HOCL + HCL -> CL2 + H2O
307,308d302
<  [het15] CLONO2 + HCL -> CL2 + HNO3
<  [het16] HOCL + HCL -> CL2 + H2O