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Tagged CO is useful for tracing specific emissions in CAM-chem. Below describes how to set-up a tagged run, the process is similar to updating gas phase chemistry.


TAGGING CO

(1) Add to the chemical mechanism

Set-up and build model as usual to get the default chemical mechanism. After step (C) of building the executable, copy a version of the default chemical mechanism from CaseDocs/chem_mech.in to my_mech.in within the case directory and edit to add the CO tags.

> cp /glade/p/work/${USER}/cases/${case}/CaseDocs/chem_mech.in /glade/p/work/${USER}/cases/${case}/my_mech.in

  • Add CO, and tags (e.g. CO01 -> CO, CO02 -> CO etc.) under “Solution”. Note: CO tags must be numbered as in the example, a set of specific tag names are “expected” by CAM-chem.
  • Add CO and tags to “Solution Classes”, under “Implicit”

*** Be sure to add new reactions after the normal CO mechanism, otherwise a segmentation fault occurs ***

SPECIES
Solution
 CO01 -> CO
etc.
H2O
End Solution

...

[usr_CO_OH_b]    CO + OH -> CO2 + H    
[CO_OH_M]        CO + OH + M -> CO2 + HO2 + M  ; 5.90e-33, 1.4, 1.10e-12, -1.3, 0.6
Add in tagged reactions, e.g:
[usr_CO01_OH]  CO01 + OH -> OH
[CO01_OH_M]    CO01 + OH + M -> OH + M     ; 5.90e-33, 1.4, 1.10e-12, -1.3, 0.6

...

Add to drydep.

(2) Tell the model to read in the new mechanism file

Change in env_build.xml

> ./xmlchange CAM_CONFIG_OPTS='-phys cam4 -chem trop_bam -offline_dyn -nlev 56 -usr_mech_infile ${caseroot}/my_mech.in'

(3) Create tagged emission input files if required


(4) Describe tag sources

Define namelist variable in usr_nl_cam to define where tags will find sources of the emission:

Either from emission files

&cam_???_???
srf_emis_specifier = 'CO01 -> /glade/p/work/buchholz/emis/qfed_finn_2000_2014/qfed.emis_CO_1.9x2.5_mol_2000_2014_AUS.nc'
srf_emis_specifier = 'CO02 -> /glade/p/work/buchholz/emis/qfed_finn_2000_2014/qfed.emis_CO_1.9x2.5_mol_2000_2014_NAM.nc'
...
/

Or from biogenic emissions

&megan_emis_nl
megan_factors_file = '/glade/p/cesm/cseg/inputdata/atm/cam/chem/trop_mozart/emis/megan21_emis_factors_c20130304.nc'
megan_mapped_emisfctrs = .false.
megan_specifier = 'CO = carbon_monoxide', 'CO02 = carbon_monoxide'
/

Or alter the chemistry mechanism file, my_mech.in, to include a source from chemistry. For example methane oxidation results in CO approximately 86% or the time:

add in reaction

(5) Add a surface emission diagnostic to the history files


(6) Re-compile the setup and build

>./case.setup --clean
>./case.setup
>./case.build --clean
>qcmd -- ./case.build


Then you are ready to run (step D in running the model).


SETTING UP A SIMPLE TRACER RUN

Setting up a CAM-chem run with constant-year emissions and oxidants prescribed from a previous full chemistry run, to study the effect of variable dynamics.

(1) Create input

Save constant-year fields from a full-chemistry run: O3, OH, NO3, HO2. Also, save the chemically produced CO and MEGAN emissions from the full chemistry run. Create an oxidants file from the history files of a fullchem run by using netCDF operators.

> ncrcat -v date,datesec,P0,PS,hyam,hybm,hyai,hybi,OH,O3,HO2,NO3,CO_CHMP,MEG_CO *h0*2005* oxidants_2005.nc
> mv oxidants_2005.nc /glade/p/work/${USER}/emis/prescribed_fields

(2) Set up the model to run CAM with simple chemistry.

Required compset with specified dynamics: FSDBAM

Set-up and build model as usual to get the default chemical mechanism.

(3) Specify emissions and oxidant files

Emissions: Add emission files for CB1, CB2, CO, OC1, OC2, SO2 as per fullchem, (note can add two files for the same species and emissions will add) e.g.:

&chem_inparm

srf_emis_specifier     = 'CO -> /glade/p/work/buchholz/emis/qfed_finn_2000_2014/qfed.emis_CO_1.9x2.5_mol_2000_2014.nc'

...

Set emissions to be cyclic, so interannual concentration changes are only due to dynamics.

srf_emis_type          = 'CYCLICAL'

srf_emis_cycle_yr      = 2005

Prescribed fields: oxidants

tracer_cnst_cycle_yr   = 2005

tracer_cnst_datapath   = '/glade/p/work/${USER}/emis/prescribed_fields'

tracer_cnst_file       = 'oxidants_2005.nc'

tracer_cnst_specifier  = 'O3','OH','NO3','HO2'

tracer_cnst_type       = 'CYCLICAL'

Add prescribed fields: chemically produced CO:

tracer_srcs_cycle_yr   = 2005

tracer_srcs_datapath   = '/glade/p/work/${USER}/emis/prescribed_fields'\

tracer_srcs_file       = 'oxidants_2005.nc'

tracer_srcs_specifier  = 'CO:CO_CHMP', 'CO01:CO_CHMP'

tracer_srcs_type       = 'CYCLICAL'

/

Surface values - make sure same as full-chemistry simulation and cyclic for the year of interest.

&chem_surfvals_nl

flbc_file = '/glade/p/cesmdata/cseg/inputdata/atm/waccm/lb/LBC_1765-2500_1.9x2.5_CMIP5_RCP45_za_c120127.nc'

flbc_list              = 'CH4', 'CO2', 'N2O','CFC11', 'CFC12'

flbc_type              = 'CYCLICAL'

flbc_cycle_yr          =  2005

scenario_ghg           = 'CHEM_LBC_FILE'

/

Make sure MEGAN emissions are also the same as full-chemistry simulation (need to update this step)

&megan_emis_nl

megan_factors_file = '/glade/p/cesm/cseg/inputdata/atm/cam/chem/trop_mozart/emis/megan21_emis_factors_c20130304.nc'

megan_mapped_emisfctrs = .false.

megan_specifier = 'CO = carbon_monoxide', 'CO02 = carbon_monoxide'

/

(4) Re-compile the setup and build

>./case.setup --clean
>./case.setup
>./case.build --clean
>qcmd -- ./case.build


Then you are ready to run (step D in running the model)

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