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.

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.

Note

Settings that are not relevant to GCHP will be excluded from the geoschem_config.yml file that ships with the GCHP run directory. We will note these excluded settings below. All other settings in geoschem_config.yml will be treated in in the same way as in GEOS-Chem Classic.

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 with -DMECH=carbon in order to use this simulation. For more information, please see:

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This simulation will eventually be superseded by the carbon simulation.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This simulation will eventually be superseded by the carbon simulation.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 with -DMECH=Hg in order to use this simulation. For more information, please see:

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

Note

This option is omitted for GCHP. The simulation start date is specified in the CAP.rc and cap_restart files.

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

end_date

Note

This option is omitted for GCHP. Duration is specified in the cap_restart file.

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

root_data_dir

Note

This option is omitted for GCHP. All data paths (with the exception of the aerosol optics and photolysis paths) are specified in the ExtData.rc file.

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

Note

This option is omitted for GCHP. Met field source is described in file paths of the in the ExtData.rc file.

Name of the meteorology product that will be used to drive GEOS-Chem. 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

Note

This setting is omitted for GCHP, as the MAPL library provides all timer functionality.

Activates (true) or deactivates (false) the GEOS-Chem Classic timers. If activated, information about how long each component of GEOS-Chem Classic took to execute will be printed to the screen and/or the 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

Note

Grid settings are omitted for GCHP. Grid specifications are contained in the GCHP.rc file instead.

#============================================================================
# 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 edges), 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 edges), 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

Note

Timesteps settings are omitted for GCHP. Timesteps are specified in the CAP.rc file.

#============================================================================
# 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.

The table below contains our recommended GEOS-Chem Classic timestep settings.

GEOS-Chem Classic Resolution

Transport

Chemistry

\(4^{\circ}{\times}5^{\circ}\)

600s (10m)

1200s (20m)

\(2^{\circ}{\times}2.5^{\circ}\)

600s (10m)

1200s (20m)

\(0.5^{\circ}{\times}0.625^{\circ}\)

300s (5m)

600s (10m)

\(0.25^{\circ}{\times}0.3125^{\circ}\)

300s (5m)

600s (10m)

\(0.125^{\circ}{\times}0.15625^{\circ}\)

150s (2.5m)

300s (5m)

The Courant limit on the latitude-longitude grid constrains the choice of transport timestep for a given horizontal resolution. We choose a chemistry timestep that is double the transport timestep (i.e. Strang operator splitting).

Note

GCHP, which uses the FVdycore advection scheme on the cubed-sphere grid, does not have similar restrictions for timesteps.

See Philip et al. [2016] for a comprehensive study on GEOS-Chem timesteps. For some practical tips on speeding up your simulations, see:

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.

chemistry_timestep_in_s

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

radiation_timestep_in_s

Specifies the frequency at which the RRTMG radiative transfer model will be called (valid for fullchem simulations only). We recommend using a timestep of 10800s (3h), as the RRTMG calculations are computationally intensive.

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
    cloud-j:
      num_levs_with_cloud: 34
      cloud_scheme_flag: 3
      opt_depth_increase_factor: 1.050
      min_top_inserted_cloud_OD: 0.005
      cloud_overlap_correlation: 0.33
      num_cloud_overlap_blocks: 6
      sphere_correction: 1
      num_wavelength_bins: 18
      use_H2O_UV_absorption: true
    input_directories:
      fastjx_input_dir: /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2024-05/
      cloudj_input_dir: /path/to/ExtData/CHEM_INPUTS/CLOUD_J/v2024-09/
    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: 100.0
      NIT_Jscale: 100.0
      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.

cloud-j:

Specifies various options for the Cloud-J photolysis package.

Note

The Cloud-J settings have been preset to the recommended values. You should not need to modify these settings (unless you are investigating how aerosol and cloud interactions impact photolysis).

num_levs_with_cloud

Specifies the number of levels that can contain clouds, which is a required input for the Cloud-J photolysis module. This value is pre-set to the proper value for the vertical grid that your simulation will use.

GEOS-Chem variable:

Input_Opt%NLevs_Phot_Cloud

Cloud-J variable

LWEPAR

cloud_scheme_flag

Specifies the cloud option used in the computation of photolyis rates.

GEOS-Chem variable:

Input_Opt%CLDFLAG

Cloud-J variable

LWEPAR

opt_depth_increase_factor

Specifies the factor increase in cloud optical depth from a given layer to the layer below.

GEOS-Chem variable:

Input_Opt%OD_Increase_Factor

Cloud-J variable

ATAU

min_top_inserted_cloud_OD

Specifies the minimum cloud OD in the uppermost inserted layer.

GEOS-Chem variable:

Input_Opt%Min_Cloud_OD

Cloud-J variable

ATAU0

cloud_overlap_correlation

Specifies the cloud de-corellation between max-overlap blocks, where 0.00 is random overlap. This option is only used when cloud_scheme_flag is set to 5 or higher.

GEOS-Chem variable:

Input_Opt%Cloud_Corr

Cloud-J variable

CLDCOR

num_cloud_overlap_blocks

Specifies the number of maximum-overlap blocks.

GEOS-Chem variable:

Input_Opt%Num_Max_Overlap

Cloud-J variable

LNRG

sphere_correction

Specifies the type of spherical correction to be applied.

GEOS-Chem variable:

Input_Opt%OD_Increase_Factor

Cloud-J variable

ATM0

num_wavelength_bins

Specifies the number of wavelength bins to use in the computation of photolysis reaction rates.

GEOS-Chem variable:

Input_Opt%Num_WV_Bins

Cloud-J variable

ATM0

use_H2O_UV_absorption

Specifies whether to enable (true) or disable (false) UV absorption of water vapor in the computations for photolysis rates. Default value: true.

GEOS-Chem variable:

Input_Opt%Use_H2O_UV_Abs

Cloud-J variable

USEH2OUV

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. These are used to define several aerosol optical properties even when FAST-JX is not used.

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

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

NIT_Jscale

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_HO2

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
    fixed_dyn_heating: false
    seasonal_fdh: false
    read_dyn_heating: false
    co2_ppmv: 390.0

  # .. 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.

fixed_dyn_heating

Activates (true) or deactivates (false) fixed dynamic heating (FDH) approximation as described by Forster et al. [1997].

Default value: false.

seasonal_fdh

Activates (true) or deactivates (false) seasonally-evolving fixed dynamic heating (SEFDH) approzimation as described by Kiehl et al. [1999].

Attention

This option has not been extensively tested, and is considered experimental.

Default value: false.

read_dyn_heating

Activates (true) or deactivates (false) reading previously-archived dynamical heating outputs from disk.

Default value: false.

co2_ppmv

Specify the value of CO2 [in parts per million by volume] to be used in radiative forcing calculations.

Default value: 390.0.

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

Note

These settings are omitted for GCHP, which uses the FVdycore advection package instead.

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:

  1. 1st order upstream scheme (use for debugging only)

  2. 2nd order van Leer (full monotonicity constraint)

  3. Monotonic PPM

  4. Semi-monotonic PPM (same as 3, but overshoots are allowed)

  5. Positive-definite PPM

  6. Un-constrained PPM (use when fields & winds are very smooth) this option only when the fields and winds are very smooth.

  7. 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:

Optics

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

  optics:
    input_dir: /path/to/ExtData/CHEM_INPUTS/Aerosol_Optics/v2024-08/

  # .. following sub-sections omitted ...
optics
input_dir

Specifies the path to files used containing aerosol optical properties for computing aerosol optical depth.

Carbon aerosols

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

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

  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 diagnostics or HEMCO.

Obspack diagnostic

Note

These settings are omitted for GCHP, as ObsPack diagnostics can only be used with GEOS-Chem Classic.

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

Note

These settings are omitted for GCHP, as the Planeflight diagnostics can only be used with GEOS-Chem Classic.

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:
    perturb_OH_boundary_conditions: false
    CH4_boundary_condition_ppb_increase_NSEW: [0.0, 0.0, 0.0, 0.0]
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:
    3D_chemical_oxidation_source: true

  # ... following sub-sections omitted ...
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:
    tag_bio_and_ocean_CO2: false
    tag_land_fossil_fuel_CO2: false

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

tag_land_fossil_fuel_CO2:

Activates (true) or deactivates (false) tagging of land and ocean fossil fuel regions.

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