geoschem_config.yml

Starting with GEOS-Chem 14.0.0, the input.geos configuration file (plain text) has been replaced with by the geoschem_config.yml file. This file is in YAML format, which is a text-based markup syntax used for representing dictionary-like data structures.

Note

The geoschem_config.yml file contains several sections. Only the sections relevant to a given type of simulation are present. For example, fullchem simulation options (such as aerosol settings and photolysis settings) are omitted from the geoschem_config.yml file for the CH4 simulation.

Simulation settings

#============================================================================
# Simulation settings
#============================================================================
simulation:
  name: fullchem
  start_date: [20190701, 000000]
  end_date: [20190801, 000000]
  root_data_dir: /path/to/ExtData
  met_field: MERRA2
  species_database_file: ./species_database.yml
  species_metadata_output_file: OutputDir/geoschem_species_metadata.yml
  verbose:
    activate: false
    on_cores: root       # Allowed values: root all
  use_gcclassic_timers: false

The simulation section contains general simulation options:

name

Specifies the type of GEOS-Chem simulation. Accepted values are

fullchem: Full-chemistry simulation.

aerosol: Aerosol-only simulation.

carbon

Coupled carbon gases simulation (CH4-CO-CO2-OCS), implemented as a KPP mechanism (cf Bukosa et al. [2023]).

You must configure your build with -DMECH=carbon in order to use this simulation.

CH4

Methane simulation.

This simulation will eventually be superseded by the carbon simulation.

CO2

Carbon dioxide simulation.

This simulation will eventually be superseded by the carbon simulation.

Hg

Mercury simulation.

You must configure your build with -DMECH=Hg in order to use this simulation.

POPs: Persistent organic pollutants (aka POPs) simulation.

Attention

The POPs simulation is currently stale. We look to members of the GEOS-Chem user community take the lead on updating this simulation.

tagCH4

Methane simulation with species tagged by geographic region or other criteria.

This simulation will eventually be superseded by the carbon simulation.

tagCO

Carbon dioxide simulation, with species tagged by geographic region and other criteria.

This simulation will eventually be superseded by the carbon simulation.

tagO3: Ozone simulation (using specified production and loss rates), with species tagged by geographical region.

TransportTracers: Transport Tracers simulation, with both radionuclide and passive_species. Useful for evaluating model transport.

metals: Trace metals simulation

start_date: Specifies the starting date and time of the simulation in list notation [YYYYMMDD, hhmmss].

end_date: Specifies the ending date and time of the simulation in list notation [YYYYMMDD, hhmmss].

root_data_dir: Path to the root data directory. All of the data that GEOS-Chem Classic reads must be located in subfolders of this directory.

met_field

Name of the meteorology product that will be used to drive GEOS-Chem Classic. Accepted values are:

MERRA2: The MERRA-2 meteorology product from NASA/GMAO. MERRA-2 is a stable reanalysis product, and extends from approximately 1980 to present. (Recommended option)

GEOS-FP: The GEOS-FP meteorology product from NASA/GMAO. GEOS-FP is an operational data product and, unlike MERRA-2, periodically receives science updates.

GCAP2: The GCAP-2 meteorology product, archived from the GISS-2 GCM. GCAP-2 has hundreds of years of data available, making it useful for simulations of historical climate.

species_database_file: Path to the GEOS-Chem Species Database file. This is stored in the run directory file ./species_database.yml. You should not have to edit this setting.

species_metadata_output_file: Path to the geoschem-species-metadata.yml file. This file contains echoback of information from species_database.yml, but only for species that are defined in this simulation (instead of all possible species). This facilitates interfacing GEOS-Chem with external models such as CESM.

verbose:

Menu controlling verbose printout. Starting with GEOS-Chem 14.2.0 and HEMCO 3.7.0, most informational printouts are now deactivated by default. You may choose to activate them (e.g. for debugging and/or testing) with the options below:

activate: Activates (true) or deactivates (false) printing extra informational printout to the screen and/or log file.

on_cores:

Specify on which computational cores informational printout should be done.

root: Print extra informational output only on the root core. Use this setting for GEOS-Chem Classic.

all: Print extra informational output on all cores. Consider using this when using GEOS-Chem as GCHP, or in MPI-based external models (NASA GEOS, CESM, etc.).

use_gcclassic_timers

Activates (true) or deactivates (false) the GEOS-Chem Classic timers. If activated, information about how long each component of GEOS-Chem took to execute will be printed to the screen and/or GEOS-Chem log file. The same information will also be written in JSON format to a file named gcclassic_timers.json.

You can set this option to false unless you are running benchmark or timing simulations.

Grid settings

#============================================================================
# Grid settings
#============================================================================
grid:
  resolution: 4.0x5.0
  number_of_levels: 72
  longitude:
    range: [-180.0, 180.0]
    center_at_180: true
  latitude:
    range: [-90.0, 90.0]
    half_size_polar_boxes: true
  nested_grid_simulation:
    activate: true
    buffer_zone_NSEW: [0, 0, 0, 0]

The grid section contains settings that define the grid used by GEOS-Chem Classic:

resolution

Specifies the horizontal resolution of the grid. Accepted values are:

4.0x5.0: The global \(4^{\circ}{\times}5^{\circ}\) GEOS-Chem Classic grid.

2.0x2.5: The global \(2.0{\circ}{\times}2.5^{\circ}\) GEOS-Chem Classic grid.

0.5x0.625: The global \(0.5^{\circ}{\times}0.625^{\circ}\) GEOS-Chem Classic grid (MERRA2 only). Can be used for global or nested simulations.

0.5x0.625: The global \(0.25^{\circ}{\times}0.3125^{\circ}\) GEOS-Chem Classic grid (GEOS-FP and MERRA2). Can be used for global or nested simulations.

number_of_levels

Number of vertical levels to use in the simulation. Accepted values are:

72: Use 72 vertical levels. This is the native vertical resolution of MERRA2 and GEOS-FP.

47: Use 47 vertical levels (for MERRA2 and GEOS-FP).

40: Use 40 vertical levels (for GCAP2).

longitude

Settings that define the longitude dimension of the grid. There are two sub-options:

range: The minimum and maximum longitude values (grid box centers), specified in list format.

center_at_180

If true, then westernmost grid boxes are centered at \(-180^{\circ}\) longitude (the International Date Line). This is true for both MERRA2 and GEOS-FP.

If false, then the westernmost grid boxes have their westernmost edges at \(-180^{\circ}\) longitude. This is true for the GCAP2 grid.

latitude

Settings to define the latitude dimension of the grid. There are two sub-options:

range: The minimum and maximum latitude values (grid box centers), specified in list format.

use_halfpolar_boxes

If true, then the northernmost and southernmost grid boxes will be \(\frac{1}{2}\) the extent of other grid boxes. This is true for both MERRA2 and GEOS-FP.

If false, then all grid boxes will have the same extent in latitude. This is true for the GCAP2 grid.

nested_grid_simulation

Settings for nested-grid simulations. There are two sub-options:

activate

If true, this indicates that the simulation will use a sub-window of the horizontal grid.

If false, this indicates that the simulation will use the entire global grid extent.

buffer_zone_NSEW: Specifies the nested grid latitude offsets (# of grid boxes) in list format [N-offset, S-offset, E-offset, W-offset]. These offsets are used to define an inner window region in which transport is actually done (aka the “transport window”). This “transport window” is always smaller than the actual size of the nested grid region in order to properly account for the boundary conditions.

For global simulations, use: [0, 0, 0, 0].
For nested-grid simulations, we recommend using: [3, 3, 3, 3].

Timesteps settings

#============================================================================
# Timesteps settings
#============================================================================
timesteps:
  transport_timestep_in_s: 600
  chemistry_timestep_in_s: 1200
  radiation_timestep_in_s: 10800

The timesteps section specifies the frequency at which various GEOS-Chem operations occur:

transport_timestep_in_s

Specifies the “heartbeat” timestep of GEOS-Chem.. This is the frequency at which transport, cloud convection, PBL mixing, and wet deposition will be done.

Recommended value for global simulations: 600
Recommended value for nested simluations: 300 or smaller

chemistry_timestep_in_s

Specifies the frequency at which chemistry and emissions will be done.

Recommended value for global simulations 1200
Recommended value for nested simulations 600 or smaller

radiation_timestep_in_s: Specifies the frequency at which the RRTMG radiative transfer model will be called (valid for fullchem simulations only).

Operations settings

This section of geoschem_config.yml is included for all simulations. However, some of the options listed below will be omitted for simulations that do not require them.

There are several sub-sections under operations:

Chemistry

#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:

chemistry:
  activate: true
  linear_chemistry_aloft:
    activate: true
    use_linoz_for_O3: true
  active_strat_H2O:
    activate: true
    use_static_bnd_cond: true
  gamma_HO2: 0.2
  autoreduce_solver:
    activate: false
    use_target_threshold:
      activate: true
      oh_tuning_factor: 0.00005
      no2_tuning_factor: 0.0001
    use_absolute_threshold:
      scale_by_pressure: true
      absolute_threshold: 100.0
    keep_halogens_active: false
    append_in_internal_timestep: false

    # ... following sub-sections omitted ...

The operations:chemistry section contains settings for chemistry:

activate: Activates (true) or deactivates (false) chemistry in GEOS-Chem.

linear_chemistry_aloft

Determines how linearized chemistry will be applied in the stratosphere and/or mesosphere. (Only valid for fullchem simulations).

There are two sub-options:

activate: Activates (true) or deactivates (false) linearized stratospheric chemistry in the stratosphere and/or mesosphere.

use_linoz_for_O3

If true, Linoz stratospheric ozone chemistry will be used.

If false, Synoz (i.e. a synthetic flux of ozone across the tropopause) will be used instead of Linoz.

active_strat_H2O

Determines if water vapor as modeled by GEOS-Chem will be allowed to influence humidity fields. (Only valid for fullchem simulations)

There are two sub-options:

activate: Allows (true) or disallows (false the H2O species in GEOS-Chem to influence specific humidity and relative humidity.

use_static_bnd_cond

Allows (true) or diasallows (false) a static boundary condition.

TODO Clarify this

gamma_HO2

Specifies \(\gamma\), the uptake coefficient for \(HO_2\) heterogeneous chemistry.

Recommended value: 0.2.

autoreduce_solver

Menu for controlling the adaptive mechanism auto-reduction feature, which is available in KPP 3.0.0. and later versions. See Lin et al. [2023] for details.

activate

If true, the mechanism will be integrated using the Rosenbrock method with the adaptive auto-reduction feature.

If false, the mechanism will be integrated using the traditional Rosenbrock method.

Default value: false.

use_target_threshold

Contains options for defining \(\partial\) (the partitioning threshold between “fast” and “slow” species”) by considering the production and loss of key species (OH for daytime, NO2 for nighttime).

activate

Activates (true) or deactivates (false) using OH and NO2 to determine \(\partial\).

Default value: true.

oh_tuning_factor: Specifies \({\alpha}_{OH}\), which is used to compute \(\partial\).

no2 tuning factor: Specifies \({\alpha}_{NO2}\), which is used to compute \(\partial\).

use_pressure_threshold

Contains options for setting an absolute threshold \(\partial\) that may be weighted by pressure.

scale_by_pressure: Activates (true) or deactivates (false) using a pressure-dependent method to determine \(\partial\).

absolute_threshold

The absolute partitioning threshold \(\partial\).

If scale_by_pressure is true, and use_target_threshold:activate is false , the value for \(\partial\) specified here will be scaled by the ratio \(P / P_{sfc}\). where \(P\) is the grid box pressure and \(P_{sfc}\) is the surface pressure for the column.

keep_halogens_active

If true, then all halogen species will be considered “fast”. This may be necessary in order to obtain realistic results for ozone and other important species.

If false, then halogen species will be determined as “slow” or “fast” depending on the partitioning threshold \(\partial\).

Default value: true

append_in_internal_timestep

If true, any “slow” species that later become “fast” will be appended to the list of “fast” species.

If false, any “slow” species that later become “fast” will NOT be appended to the list of “fast” species.

Default value: false

Convection

#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:

  # .. preceding sub-sections omitted ...

  convection:
    activate: true

  # ... following sub-sections omitted ...

The operations:convection section contains settings for cloud convection:

activate: Activates (true) or deactivates (false) cloud convection in GEOS-Chem.

Dry deposition

#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:

  # .. preceding sub-sections omitted ...

  dry_deposition:
    activate: true
    CO2_effect:
      activate: false
      CO2_level: 600.0
      reference_CO2_level: 380.0
    diag_alt_above_sfc_in_m: 10

  # ... following sub-sections omitted ...

The operations:dry_deposition section contains settings that for dry deposition:

activate: Activates (true) or deactivates (false) dry deposition.

CO2_effect

This sub-section contains options for applying the simple parameterization for the CO2 effect on stomatal resistance.

activate

Activates (true) or deactivates (false) the CO2 effect on stomatal resistance in dry deposition.

Default value: false.

CO2_level: Specifies the CO2 level (in ppb).

reference_CO2_level: Specifies the reference CO2 level (in ppb).

diag_alt_above_sfc_in_m:: Specifies the altitude above the surface (in m) to used with the ConcAboveSfc diagnostic collection.

PBL mixing

#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:

  # .. preceding sub-sections omitted ...

  pbl_mixing:
    activate: true
    use_non_local_pbl: true

  # ... following sub-sections omitted ...

The operations:pbl_mixing section contains settings that for planetary boundary layer (PBL) mixing:

activate: Activates (true) or deactivates (false) planetary boundary layer mixing in GEOS-Chem Classic.

use_non_local_pbl

If true, then the non-local PBL mixing scheme (VDIFF) will be used. (Default option)

If false, then the full PBL mixing scheme (TURBDAY) will be used.

Photolysis

#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:

  # .. preceding sub-sections omitted ...

  photolysis:
    activate: true
    input_directories:
      fastjx_input_dir: /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2021-10/
      cloudj_input_dir: /path/to/ExtData/CHEM_INPUTS/CLOUD_J/v2023-05/
    overhead_O3:
      use_online_O3_from_model: true
      use_column_O3_from_met: true
      use_TOMS_SBUV_O3: false
    photolyze_nitrate_aerosol:
      activate: true
      NITs_Jscale_JHNO3: 0.0
      NIT_Jscale_JHNO2: 0.0
      percent_channel_A_HONO: 66.667
      percent_channel_B_NO2: 33.333

  # ... following sub-sections omitted ...

The operation:photolysis section contains settings for photolysis. This section only applies to fullchem, Hg, and aerosol-only simulations.

activate: Activates (true) or deactivates (false) photolysis.

Attention

You should always keep photolysis turned on in your simulations. Disabling photolysis should only be done when debugging.

input_directories

Specifies the location of directories containing photolysis configuration files.

fastjx_input_dir: Specifies the path to the legacy FAST_JX configuration files containing information about species cross sections and quantum yields. Note that FAST-JX is off by default and Cloud-J is used instead. You can use legacy FAST-JX instead of Cloud-J by configuring with -DFASTJX=y during build.

cloudj_input_dir: Specifies the path to the Cloud-J configuration files containing information about species cross sections and quantum yields.

overhead_O3

This section contains settings that control which overhead ozone sources are used for photolysis

use_online_O3_from_model

Activates (true) or deactivates (false) using online O3 from GEOS-Chem in the extinction calculations for photolysis.

Recommended value: true

use_column_O3_from_met

Activates (true) or deactivates (false) using ozone columns (e.g. TO3) from the meteorology fields.

Recommended value: true.

use_TOMS_SBUV_O3

Activates (true) or deactivates (false) using ozone columns from the TOMS-SBUV archive will be used.

Recommended value: false.

photolyze_nitrate_aerosol:

This section contains settings that control options for nitrate aerosol photolysis.

activate

Activates (true) or deactivates (false) nitrate aerosol photolysis.

Recommended value: true.

NITs_Jscale_JHNO3: Scale factor (percent) for JNO3 that photolyzes NITs aerosol.

NIT_Jscale_JHNO2: Scale factor (percent) for JHNO2 that photolyzes NIT aerosol.

percent_channel_A_HONO: Fraction of JNITs/JNIT in channel A (HNO2) for NITs photolysis.

percent_channel_B_NO2: Fraction of JNITs/JNIT in channel B (NO2) for NITs photolysis.

RRTMG radiative transfer model

#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:

  # .. preceding sub-sections omitted ...

  rrtmg_rad_transfer_model:
    activate: false
    aod_wavelengths_in_nm:
      - 550
    longwave_fluxes: false
    shortwave_fluxes: false
    clear_sky_flux: false
    all_sky_flux: false

  # .. following sub-sections omitted ...

The operations:rrtmg_rad_transfer_model section contains settings for the RRTMG radiative transfer model:

This section only applies to fullchem simultions.

activate

Activates (true) or deactivates (false) the RRTMG radiative transfer model.

Default value: false.

aod_wavelengths_in_nm: Specify wavelength(s) for the aerosol optical properties in nm (in YAML sequence format) Up to three wavelengths can be selected. The specified wavelengths are used for the photolysis mechanism (either legacy FAST-JX or Cloud-J) regardless of whether the RRTMG radiative transfer model is used.

longwave_fluxes

Activates (true) or deactivates (false) RRTMG longwave flux calculations.

Default value: false.

shortwave_fluxes

Activates (true) or deactivates (false) RRTMG shortwave calculations.

Default value: false.

clear_sky_flux

Activates (true) or deactivates (false) RRTMG clear-sky flux calculations.

Default value: false.

all_sky_flux

Activates (true) or deactivates (false) RRTMG all-sky flux calculations.

Default value: false.

Transport

#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:

  # .. preceding sub-sections omitted ...

  transport:
    gcclassic_tpcore:                 # GEOS-Chem Classic only
      activate: true                  # GEOS-Chem Classic only
      fill_negative_values: true      # GEOS-Chem Classic only
      iord_jord_kord: [3, 3, 7]       # GEOS-Chem Classic only
    transported_species:
      - ACET
      - ACTA
      - AERI
      # ... etc more transported species ...

# .. following sub-sections omitted ...

The operations:transport section contains settings for species transport:

gcclassic_tpcore

Contains options that control species transport in GEOS-Chem Classic with the TPCORE advection scheme:

activate

Activates (true) or deactivates (false) species transport in GEOS-Chem Classic.

Default value: true.

fill_negative_values

If true, negative species concentrations will be replaced with zeros.

If false, no change will be made to species concentrations.

Default value: true.

iord_jord_kord

Specifies advection options (in list format) for TPCORE in the longitude, latitude, and vertical dimensions. The options are listed below:

1st order upstream scheme (use for debugging only)
2nd order van Leer (full monotonicity constraint)
Monotonic PPM
Semi-monotonic PPM (same as 3, but overshoots are allowed)
Positive-definite PPM
Un-constrained PPM (use when fields & winds are very smooth) this option only when the fields and winds are very smooth.
Huynh/Van Leer/Lin full monotonicity constraint (KORD only)

Default (and recommended) value: [3, 3, 7]

transported_species: A list of species names (in YAML sequence format) that will be transported by the TPCORE advection scheme.

Wet deposition

#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:

  # .. preceding sub-sections omitted ...

  wet_deposition:
    activate: true

The operations:wet_deposition section contains settings for wet deposition.

activate: Activates (true) or deactivates (false) wet deposition in GEOS-Chem Classic.

Aerosols settings

This section of geoschem_config.yml is included for fullchem and aerosol simulations.

There are several sub-sections under aerosols:

Carbon aerosols

#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:

  carbon:
    activate: true
    brown_carbon: false
    enhance_black_carbon_absorption:
      activate: true
      hydrophilic: 1.5
      hydrophobic: 1.0

  # .. following sub-sections omitted ...

The aerosols:carbon section contains settings for carbon aerosols:

activate

Activates (true) or deactivates (false) carbon aerosols in GEOS-Chem.

Default value: true.

brown_carbon

Activates (true) or deactivates (false) brown carbon aerosols in GEOS-Chem.

Default value: false.

enhance_black_carbon_absorption

Options for enhancing the absorption of black carbon aerosols due to external coating.

activate

Activates (true) or deactivates (false) black carbon absorption enhancement.

Default value: true.

hydrophilic

Absorption enhancement factor for hydrophilic black carbon aerosol (species name BCPI).

Default value: 1.5

hydrophobic

Absorption enhancement factor for hydrophilic black carbon aerosol (species name BCPO).

Default value: 1.0

Complex SOA

The aerosols:complex_SOA section contains settings for the complex SOA scheme used in GEOS-Chem.

#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:

  # ... preceding sub-sections omitted ...

  complex_SOA:
    activate:  true
    semivolatile_POA: false

  # ... following sub-sections omitted ...

activate

Activates (true) or deactivates (false) the complex SOA scheme.

Default value:

true for the fullchem benchmark simulation
false for all other fullchem simulations

semivolatile_POA

Activates (true) or deactivates (false) the semi-volatile primary organic aerosol (POA) option.

Default value: false

Mineral dust aerosols

The aerosols:dust section contains settings for mineral dust aerosols.

#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:

  # ... preceding sub-sections omitted ...

  dust:
    activate: true
    acid_uptake_on_dust: false

  # ... following sub-sections omitted ...

activate

Activates (true) or deactivates (false) mineral dust aerosols in GEOS-Chem.

Default value: true

acid_uptake_on_dust

Activates (true) or deactivates (false) the acid uptake on dust option, which includes 12 additional species.

Default value: false

Sea salt aerosols

The aerosols:sea_salt section contains settings for sea salt aerosols:

#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:

  # ... preceding sub-sections omitted ...

  sea_salt:
    activate: true
    SALA_radius_bin_in_um: [0.01, 0.5]
    SALC_radius_bin_in_um: [0.5,  8.0]
    marine_organic_aerosols: false

  # ... following sub-sections omitted ...

activate

Activates (true) or deactivates (false) sea salt aerosols.

Default value: true

SALA_radius_bin_in_um

Specifies the upper and lower boundaries (in nm) for accumulation-mode sea salt aerosol (aka SALA).

Default value: 0.01 nm - 0.5 nm

SALC_radius_bin_in_um

Specifies the upper and lower boundaries (in nm) for coarse-mode sea salt aerosol (aka SALC).

Default value: 0.5 nm - 8.0 nm

marine_organic_aerosols

Activates (true) or deactivates (false) emission of marine primary organic aerosols. This option includes two extra species (MOPO and MOPI).

Default value: false

Stratospheric aerosols

The aerosols:sulfate section contains settings for stratopsheric aerosols.

#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:

  # ... preceding sub-sections omitted ...

  stratosphere:
    settle_strat_aerosol: true
    polar_strat_clouds:
      activate: true
      het_chem: true
    allow_homogeneous_NAT: false
    NAT_supercooling_req_in_K: 3.0
    supersat_factor_req_for_ice_nucl: 1.2
    calc_strat_aod: true

  # ... following sub-sections omitted ...

settle_strat_aerosol

Activates (true) or deactivates (false) gravitational settling of stratospheric solid particulate aerosols (SPA, trapezoidal scheme) and stratospheric liquid aerosols (SLA, corrected Stokes’ Law).

Default value: true

polar_strat_clouds

Contains settings for how aerosols are handled in polar stratospheric clouds (PSC):

activate

Activates (true) or deactivates (false) formation of polar stratospheric clouds.

Default value: true

het_chem

Activates (true) or deactivates (false) heterogeneous chemistry within polar stratospheric clouds.

Default value: true

allow_homogeneous_NAT

Activates (true) or deactivates (false) heterogeneous formation of NAT from freezing of HNO3.

Default value: false

NAT_supercooling_req_in_K

Specifies the cooling (in K) required for homogeneous NAT nucleation.

Default value: 3.0

supersat_factor_req_for_ice_nucl

Specifies the supersaturation factor required for ice nucleation.

Recommended values: 1.2 for coarse grids; 1.5 for fine grids.

calc_strat_aod

Includes (true) or excludes (false) online stratospheric aerosols in extinction calculations for photolysis.

Default value: true

Sulfate aerosols

The aerosols:sulfate section contains settings for sulfate aerosols:

#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:

  # ... preceding sub-sections omitted ...

  sulfate:
    activate: true
    metal_cat_SO2_oxidation: true

activate

Activates (true) or deactivates (false) sulfate aerosols.

Default value: true

metal_cat_SO2_oxidation

Activates (true) or deactivates (false) the metal catalyzed oxidation of SO2.

Default value: true

Extra diagnostics

The extra_diagnostics section contains settings for GEOS-Chem Classic diagnostics that are not archived by History or HEMCO:

Obspack diagnostic

The extra_diagnostics:obspack section contains settings for the Obspack diagnostic:

#============================================================================
# Settings for diagnostics (other than HISTORY and HEMCO)
#============================================================================
extra_diagnostics:

  obspack:
    activate: false
    quiet_logfile_output: false
    input_file: ./obspack_co2_1_OCO2MIP_2018-11-28.YYYYMMDD.nc
    output_file: ./OutputDir/GEOSChem.ObsPack.YYYYMMDD_hhmmz.nc4
    output_species:
      - CO
      - 'NO'
      - O3

  # ... following sub-sections omitted ...

activate

Activates (true) or deactivates (false) ObsPack diagnostic output.

Default value: true

quiet_logfile_output

Deactivates (true) or activates (false) printing informational output to stdout (i.e. the screen or log file).

Default value: false

input_file: Specifies the path to an ObsPack data file (in netCDF format).

output_file: Specifies the path to the ObsPack diagnostic output file. This will be a file that contains data at the same locations as specified in input_file.

output_species: A list of GEOS-Chem species (as a YAML sequence) to archive to the output file.

Planeflight diagnostic

The extra_diagnostics:planeflight section contains settings for the GEOS-Chem planeflight diagnostic:

#============================================================================
# Settings for diagnostics (other than HISTORY and HEMCO)
#============================================================================
extra_diagnostics:

  # ... preceding sub-sections omitted ...

  planeflight:
    activate: false
    flight_track_file: Planeflight.dat.YYYYMMDD
    output_file: plane.log.YYYYMMDD

  # ... following sub-sections omitted ...

activate

Activates (true) or deactivates (false) the Planeflight diagnostic output.

Default value: false

flight_track_file: Specifies the path to a flight track file. This file contains the coordinates of the plane as a function of time, as well as the requested quantities to archive.

output_file: Specifies the path to the Planeflight output file. Requested quantities will be archived from GEOS-Chem along the flight track specified in flight_track_file.

Hg simulation options

This section of geoschem_config.yml is included for the mercury (Hg) simulation:

Hg sources

The Hg_simulation_options:sources section contains settings for various mercury sources.

#============================================================================
# Settings specific to the Hg simulation
#============================================================================
Hg_simulation_options:

  sources:
    use_dynamic_ocean_Hg: false
    use_preindustrial_Hg: false
    use_arctic_river_Hg: true

  # ... following sub-sections omitted ...

use_dynamic_ocean_Hg

Activates (true) or deactivates (false) the online slab ocean mercury model.

Default value: false

use_preindustrial_Hg

Activates (true) or deactivates (false) the preindustrial mercury simulation. This will turn off all anthropogenic emissions.

Default value: false

use_arctic_river_Hg

Activates (true) or deactivates (false) the source of mercury from arctic rivers.

Default value: true

Hg chemistry

The Hg_simulation_options:chemistry section contains settings for mercury chemistry:

#============================================================================
# Settings specific to the Hg simulation
#============================================================================
Hg_simulation_options:

  # ... preceding sub-sections omitted ...

  chemistry:
    tie_HgIIaq_reduction_to_UVB: true

  # ... following sub-sections omitted ...

tie_HgIIaq_reduction_to_UVB

Activates (true) or deactivates (false) linking the reduction of aqueous oxidized mercury to UVB radiation. A lifetime of -1 seconds indicates the species has an infinite lifetime.

Default value: true

Options for simulations with carbon gases

These sections of geoschem_config.yml are included for simulations with carbon gases (carbon, CH4, CO2, tagCO, tagCH4).

CH4 observational operators

The CH4_simulation_options:use_observational_operators section contains options for using satellite observational operators for CH4:

#============================================================================
# Settings specific to the CH4 simulation / Integrated Methane Inversion
#============================================================================
CH4_simulation_options:

  use_observational_operators:
    AIRS: false
    GOSAT: false
    TCCON: false

  # ... following sub-sections omitted ...

AIRS

Activates (true) or deactivates (false) the AIRS observational operator.

Default value: false

GOSAT

Activates (true) or deactivates (false) the GOSAT observational operator.

Default value: false

TCCON

Activates (true) or deactivates (false) the GOSAT observational operator.

Default value: false

CH4 analytical inversion options

The ch4_simulation_options:analytical_inversion section contains options for analytical inversions with the Integrated Methane Inversion workflow (aka IMI). The IMI will automatically modify several of these options based on the inversion parameters that you specify.

#============================================================================
# Settings specific to the CH4 simulation / Integrated Methane Inversion
#============================================================================
CH4_simulation_options:

  # ... preceding sub-sections omitted ...

  analytical_inversion:
    activate: false
    emission_perturbation: 1.0
    state_vector_element_number: 0
    use_emission_scale_factor: false
    use_OH_scale_factors: false
    perturb_OH_boundary_conditions: false
    CH4_boundary_condition_ppb_increase_NSEW: [0.0, 0.0, 0.0, 0.0]

activate

Activates (true) or deactivates (false) the analytical inversion.

Default value: false

emission perturbation

Specifies a unitless factor by which emissions for this state vector element will be perturbed.

Default value: 1.0 (no perturbation)

state_vector_element_number

Specifies the element of the state vector corresponding to this simulation.

Default value: 0

use_emission_scale_factor

Activates (true) or deactivates (false) scaling methane emissions by a fixed factor. This scale factor is specified in the HEMCO_Config.rc file.

Default value: false

use_oh_scale_factors

Activates (true) or deactivates (false) perturbation of OH in analytical inversions of methane. The OH scale factors are specified in the OH_SF entry of HEMCO_Config.rc file.

Default value: false

perturb_CH4_boundary_conditions

Activates (true) or deactivatees (false) perturbation of CH4 nested-grid boundary conditions in analytical inversions.

Default value: false

CH4_boundary_condition_ppb_increase_NSEW

Specifies the perturbation amount (in ppbv) to apply to the north, south, east and west CH4 nested-grid boundary conditions. Used in conjunction with the perturb_CH4_boundary_conditions option.

Default value: [0.0, 0.0, 0.0, 0.0] (no perturbation)

CO2 Sources

The CO2_simulation_options:sources section contains toggles for activating sources of \(CO_2\):

#============================================================================
# Settings specific to the CO2 simulation
#============================================================================
CO2_simulation_options:

  sources:
    fossil_fuel_emissions: true
    ocean_exchange: true
    balanced_biosphere_exchange: true
    net_terrestrial_exchange: true
    ship_emissions: true
    aviation_emissions: true
    3D_chemical_oxidation_source: true

  # ... following sub-sections omitted ...

fossil_fuel_emissions

Activates (true) or deactivates (false) using \(CO_2\) fossil fuel emissions as computed by HEMCO.

Default value: true

ocean_exchange

Activates (true) or deactivates (false) \(CO_2\) ocean-air exchange.

Default value: true

balanced_biosphere_exchange

Activates (true) or deactivates (false) \(CO_2\) balanced-biosphere exchange.

Default value: true

net_terrestrial_exchange

Activates (true) or deactivates (false) \(CO_2\) net terrestrial exchange.

Default value: true

ship_emissions

Activates (true) or deactivates (false) \(CO_2\) ship emissions as computed by HEMCO.

Default value: true

aviation_emissions

Activates (true) or deactivates (false) \(CO_2\) aviation emissions as computed by HEMCO.

Default value: true

3D_chemical_oxidation_source

Activates (true) or deactivates (false) \(CO_2\) production by archived chemical oxidation, as read by HEMCO.

Default value: true

CO2 tagged species

The CO2_simulation_options:tagged_species section contains toggles for activating tagged \(CO_2\) species:

Attention

Tagged \(CO_2\) tracers should be customized by each user and the present configuration will not work for resolutions other than \(2.0^{\circ} {\times} 2.5^{\circ}\).

#============================================================================
# Settings specific to the CO2 simulation
#============================================================================
CO2_simulation_options:

  # ... preceding sub-sections omitted ...

  tagged_species:
    save_fossil_fuel_in_background: false
    tag_bio_and_ocean_CO2: false
    tag_land_fossil_fuel_CO2:
    tag_global_ship_CO2: false
    tag_global_aircraft_CO2: false

save_fossil_fuel_in_background

Activates (true) or deactivates (false) saving the \(CO_2\) background.

Default value: false

tag_bio_and_ocean_CO2: Activates (true) or deactivates (false) tagging of biosphere regions (28), ocean regions (11), and the rest of the world (ROW) as specified in Regions_land.dat and Regions_ocean.dat files.

# .. following sub-sections omitted …

CO chemical sources

The tagged_CO_simulation_options section contains settings for the carbon simulation and tagged CO simulation.

#============================================================================
# Settings specific to the tagged CO simulation
#============================================================================

tagged_CO_simulation_options:
  use_fullchem_PCO_from_CH4: true
  use_fullchem_PCO_from_NMVOC: true

use_fullchem_PCO_from_CH4

Activates (true) or deactivates (false) applying the production of \(CO\) from \(CH_4\). This field is archived from a 1-year or 10-year fullchem benchmark simulation and is read from disk via HEMCO.

Default value: true

use_fullchem_PCO_from_NMVOC

Activates (true) or deactivates (false) applying the production of \(CO\) from non-methane volatile organic compounds (VOCs). This field is archived from a 1-year or 10-year fullchem benchmark simulation and is read from disk via HEMCO.

Default value: true