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Running CAM5.3 with trop_mam7 chemistry

L

liurj04@gmail_com

Member
Hello,I am running CESM1.2.0, and I want to run CAM with trop_mam7 chemistry package.  As I know if the physics package is CAM5, the chemistry package default is trop_mam3. so if I want change the chemistry package to trop_mam7, how should I set the model ? Any suggestions would be great!Thank you !liurj 
 
T

tilmes

Member
Hi Liurj,a trop_mam7 chemistry package is not available. You have two options, either use the trop_strat_mam7 package, which also include the calculation of stratospheric chemistry, which is available as compset: FSTRATMAM7.
Your other option is to start from trop_mam3 chemistry compset and replace the mam3 chemistry to the mam7 chemistry in your mechanism file.  If you want to change the mechanism file, you need to change your CaseDocs/chem_mech.in file,  to replace the mam3 reactions to the mam7 reactions, and point to the new chem_mech.in file in your CAM_CONFIG_OPTS in env_build.xmlSimone
 
F

fwang26@wisc_edu

New Member
Dear Simone,I checked the configure file in directory cesm1_2_2/models/atm/cam/bld/, and the there is a trop_mam7 option in the available chemistry package list. My question is can I just add -chem trop_mam7 in CAM_CONFIG_OPTS if I wanna replace mam3 chemistry to mam7?I am not quite understand why you say trop_mam7 is not available, and if I my way doesn't work and I wanna follow your instruction, should I just change mam3 reactions to mam7 or the whole chem_mech.in file to mam7's?Thanks a lot.Olivia
 
T

tilmes

Member
Dear Olivia,it depends what you mean by running with chemistry. There are different options CAM5 can be setup. The default option is that there is only very basic chemistry in the model that uses climatological fields to describe chemistry  including ozone and OH. The required simple chemistry in the CAM5 version is called trop_mam3 for MAM3 or trop_mam7 for MAM7. You can certainly run with MAM7, and substitute -trop_mam3 with trop_mam7 in your env_build file. You will have to make sure to also change your atm_in file (user_nl_cam) to add the emissions required for MAM7 species (which are different from MAM3). I don't think there is a compset that is setup for MAM7, so, you would also have to evaluate your run and potentially retune it.If you would like to run your simulation with extended tropospheric and maybe stratospheric chemistry, you can start with the FSTRATMAM7 compset, but again, this compset is not scientifically validated and results have to be carefully evaluated before being used for scientific studies.
Hope that is helpful? Simone
 
F

fwang26@wisc_edu

New Member
Thanks Simone,It is really helpful. Are the emissions required for MAM7 species defined by srf_emis_specifier under &chem_inparm in atm_in? My atm_in looks like this: srf_emis_cycle_yr              = 2000 srf_emis_specifier             = 'DMS       -> /global/project/projectdirs/m2067/EXPERIMENT/inputdata/atm/cam/chem/trop_mozart_aero/emis/aerocom_mam3_dms_surf_2000_c120315.nc',         'NH3       -> /global/project/projectdirs/m2067/EXPERIMENT/inputdata/atm/cam/chem/trop_mozart_aero/emis/emis_NH3_2000_c111014.nc',         'SO2       -> /global/project/projectdirs/m2067/EXPERIMENT/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_so2_surf_2000_c120315.nc',         'SOAG      -> /global/project/projectdirs/m2067/EXPERIMENT/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_soag_1.5_surf_2000_c120315.nc',         'bc_a3     -> /global/project/projectdirs/m2067/EXPERIMENT/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_bc_surf_2000_c120315.nc',         'num_a1    -> /global/project/projectdirs/m2067/EXPERIMENT/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam7_num_a1_surf_2000_c120716.nc',         'num_a2    -> /global/project/projectdirs/m2067/EXPERIMENT/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_num_a2_surf_2000_c120315.nc',         'num_a3    -> /global/project/projectdirs/m2067/EXPERIMENT/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam7_num_a3_surf_2000_c120716.nc',         'pom_a3    -> /global/project/projectdirs/m2067/EXPERIMENT/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_oc_surf_2000_c120315.nc',         'so4_a1    -> /global/project/projectdirs/m2067/EXPERIMENT/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_so4_a1_surf_2000_c120315.nc',         'so4_a2    -> /global/project/projectdirs/m2067/EXPERIMENT/inputdata/atm/cam/chem/trop_mozart_aero/emis/ar5_mam3_so4_a2_surf_2000_c120315.nc'  srf_emis_type          = 'CYCLICAL'Could you help me to check whether this is right? Thanks.Olivia  
 
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