10. Chemistry specific modifications

Several standard chemistry mechanisms are supported for CAM, CAM-chem, and WACCM. Here, we describe details on how the chemical mechanism is compiled and how to perform modifications of chemistry in the model, including adding or removing chemical and aerosol species, which requires changing the chemical mechanism and if applicable changes to wet and dry deposition. Additional changes may be required in the namelist, e.g., adding or removing output, changing deposition species etc. Furthermore, code changes may be required, depending of the specifics of the changes.

10.1. Chemical mechanisms

Some supported chemical mechanism are listed in the table below. The chemical mechanism is a set used to calculate chemical reactions using the Chemical Preprocessor. For chemistry schemes that may be specified by using the -chem <scheme> argument to configure, the preprocessor has been used to generate the fortran routines required to run the model. This preprocessor output is located in directories $COMP_ROOT_DIR_ATM/src/chemistry/pp_scheme/, where scheme is the argument supplied to the -chem option.

Mechanism
(pre-processor code)
Model:
Chemistry Description
#Species
#Reactions
TSMLT1
(pp_waccm_tsmlt_mam4)
WACCM: Troposphere,
stratosphere, mesosphere,
and lower thermosphere
231 solution,
2 invariant
583
(433 kinetic,
150 photolysis)
TS1
(pp_trop_strat_mam4_vbs)
CAM-chem: Troposphere and
stratosphere
221 solution,
3 invariant
528
(405 kinetic,
123 photolysis)
MA
(pp_waccm_ma_mam4)
WACCM: Middle atmosphere
(stratosphere, mesosphere,
and lower thermosphere)
98 solution,
2 invariant
298
(207 kinetic,
91 photolysis)
MAD
(pp_waccm_mad_mam4)
WACCM: Middle atmosphere
plus D-region ion chemistry
135 solution,
2 invariant
593
(489 kinetic,
104 photolysis)
SC
(pp_waccm_sc_mam4)

WACCM: Specified chemistry
29 solution,
8 invariant
12
(11 kinetic,
1 photolysis)
CAM
(pp_ghg_mam4)
CAM: Aerosol chemistry,
simple GHG chemistry
31 solution,
8 invariant
15 (12 kinetic,
3 photolysis)

10.2. Modifications of the Chemical Mechanisms

To modify the chemical mechanism, including changing reaction rates requires the following steps:

  • Check out an existing compset that you would like to modify and compile and build your case

  • Copy the existing chemical mechanism in $CASEROOT/CaseDocs/chem_mech.in to a location (e.g., /my_dir/chem_mech_changed.in)

  • Alter your mechanism as desired (see details in CAMchem Wiki page)

  • Point to the new mechanism file by modifying CAM_CONFIG_OPTS, for example from the case directory issue the command:

    ./xmlchange --append CAM_CONFIG_OPTS='-usr_mech_infile /my_dir/chem_mech_changed.in'

  • Changing the chemical mechanism requires rebuilding the case, i.e.:

    ./case.build --clean
./case.build

10.3. Adding emissions and lower boundary conditions

Adding new chemical or aerosol species requires to include their sources (emissions) and sinks (deposition, see below). Sources can be either emissions (surface or vertical) or concentrations in form of lower boundary conditions. To add new emissions you have to copy the existing list of emisisons (set by ext_frc_specifier and srf_frc_specifier) to the user_nl_cam file and add the additional species.

To add new lower boundary conditions via namelist, you have to add the addition species to the flbc_list and modify the flbc_file:

flbc_file =
'$DIN_LOC_ROOT/atm/waccm/lb/LBC_17500116-20150116_CMIP6_0p5degLat_c180227.nc'
flbc_list =
'CCL4', 'CF2CLBR', 'CF3BR', 'CFC11', 'CFC113', 'CFC12', 'CH3BR',
'CH3CCL3', 'CH3CL', 'CH4', 'CO2', 'H2', 'HCFC22', 'N2O', 'CFC114',
'CFC115', 'HCFC141B', 'HCFC142B', 'CH2BR2', 'CHBR3', 'H2402',
'OCS', 'SF6', 'CFC11eq'

10.4. Adding species and changing the mechanism

The addition of species with dry and wet deposition requires code changes. This requires to add information of the Henry’s law coefficient:

  • Copy $CCSMROOT/cime/src/drivers/mct/shr/seq_drydep_mod.F90 in to your $CASEROOTSourceMods/src.share directory and modify the following. You can also map the new new species to deposit with the same rates as a species already undergoing wet deposition and therefore skip this step.

    • In this code, there are several arrays containing: 1) species names, 2) reactivity factors (f0), 3) henry’s law constants, and 4) molecular weights. Add your new species characteristics at the end of each of these arrays.

    • Update the variable “maxspc” to be the total number of species you are dry depositing.

    • Update the variable “n_species_table” to the total number of species listed in these arrays.

  • Additional routines may have to be modified:

    • $COMP_ROOT_DIR_ATM/src/chemistry/mozart/mo_neu_wetdep.F90

    • $COMP_ROOT_DIR_ATM/src/chemistry/mo_drydep.F90 (subroutine drydep_xactive)

    • $COMP_ROOT_DIR_LND/src/biogeochem/DryDepVelocity.F90

  • Add new species to the masterlist (to be automatically included in your namelists). If you don’t include your species to the mastlist you have to include those in your user_nl_cam namelist.

    • $COMP_ROOT_DIR_ATM/bld/namelist_files including master_drydep_list.xml, master_gas_wetdep_list.xml, master_aer_drydep_list.xml, master_aer_wetdep_list.xml

10.5. Running with interactive / prescribed biogenic emissions

Running with interactive biogenic emissions:

  • The default setting in CAM-chem and WACCM configuration is to run with interactive biogenic emissions, while CAM7 and WACCM SC do not use biogenic emissions. To run with interactive biogenic emissions, the following file needs to be specified:

    megan_factors_file =
'$DIN_LOC_ROOT/atm/cam/chem/trop_mozart/emis/megan21_emis_factors_78pft_c20161108.nc'

    This file contains the emission factors at standard temperature and pressure for each compound for each plant functional type, as well as the other model parameters. The compound names are given in the variable “Comp_Name”. The default file works with 78 plant functional types (PFTs).

  • CLM/MEGAN-v2.1 includes an option for using a map of emission factors for isoprene. The map in the current release is out of date and SHOULD NOT BE USED. Under megan_emis_nl, in drv_flds_on or user_nl_cam: megan_mapped_emisfctrs = .false.

Running with prescribed biogenic emissions:

To turn run with prescribed biogenic emissions requires including those emissions in the namelist for surface emission files that are not indluced in the namelist by default. Additionally, one needs to turn off interactive biogenic emissions, if using a CAMchem or WACCM TSML compset add the following in user_nl_cam:

megan_factors_file = ' '
megan_specifier = ' '

History output:

  • To save the MEGAN emissions in the CAM history files, include the desired MEG_{species} variables in the fincl* fields of user_nl_cam. The SF{species} variables are the total emissions fluxes for each species, so will include all sources if an emissions file was also read for other sources (such as bb).