Qusetion about source code

[pengyf]

I wanna add some external forcing in pp_waccm_mozart_mam3 by modifying mo_extfrc.F90 and other files.
However, something confused me when I read the source code in chemistry/pp_waccm_mozart_mam3/mo_nln_matrix.F90 file. In this file, array of mat contain 527 index(species) that is correspond to nzcnt(number of non-zero matrix entries) in chem_mods.F90, but I don't get any message about these 527 speceis.Is there any document or file that shows what species correspond to these 527 indexes?

 

[mmills]

I wanna add some external forcing in pp_waccm_mozart_mam3 by modifying mo_extfrc.F90 and other files.
However, something confused me when I read the source code in chemistry/pp_waccm_mozart_mam3/mo_nln_matrix.F90 file. In this file, array of mat contain 527 index(species) that is correspond to nzcnt(number of non-zero matrix entries) in chem_mods.F90, but I don't get any message about these 527 speceis.Is there any document or file that shows what species correspond to these 527 indexes?

Yes, look in the chem_mech.doc file that is in the same directory.

The chemistry pre-processor reads the chem_mech.in file, and generates the chem_mech.doc file, as well as all of the source code in that directory. The correct way to modify chemistry is to copy the chem_mech.in file, modify it, and feed it back into the chemistry pre-processor with a -user_mech_infile flag in your CAM_CONFIG_OPTS line in your env_build.xml file.

 

[pengyf]

Thanks for your reply. I will try to add a -user_mech_infile flag in the env_build.xml file. The file chem_mech.doc really provides many useful messages. However, I don't get the 527 species refers to in the mo_nln_matrix.F90 file. Could you please give me more details about these 527 species refers to . Thanks so much.
Additionally, I read one of your paper in 2017 JGR (Effects of Different Stratospheric SO2 Injection Altitudes on Stratospheric Chemistry and Dynamics). Something confused me. What the Ox, NOx, HOx, CLOx and BROx refers to in fig.15. I found d(O3)/dt is calculated by CL+O3, BR+O3 and other reactions in chem_mech.doc file not CLOX and BROx as fig.15 shows. If these question is not appropriate here, can I send you an email for this question.
Looking forward to your reply.