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 carbon gases 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
  read_restart_as_real8: true

The simulation section contains general simulation options:

name

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

fullchem: Full-chemistry simulation of Ox, NOx, VOCs, halogens, and aerosols.

aerosol: Aerosol-only simulation.

carbon

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:

Hg

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.

tagO3: Tagged O3 simulation (using specified production and loss rates), with species tagged by geographical region.

TransportTracers: TransportTracers simulation, with both radionuclide and passive_species. Useful for evaluating model transport, convection, and/or wet deposition.

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.

GEOS-IT: The GEOS-IT meteorology product from NASA/GMAO.

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

true: Activates writing extra informational printout to the screen and/or log file.

false: Deactivates writing extra informational printout. This is the default setting.

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.

false: Deactivates the GEOS-Chem Classic timers. This is the default setting.

true

Activates the GEOS-Chem Classic timers. 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 will only really need to activate the GEOS-Chem Classic timers if you are running a benchmark simulation or if you are doing performance testing.

read_restart_as_real8

Note

This setting is omitted for GCHP, as the MAPL library provides all disk I/O functionality and has the ability to read restart data as REAL*8.

Option controlling how the GEOS-Chem Classic restart file will be read.

false

The GEOS-Chem Classic restart file will be read by HEMCO (which reads all data as REAL*4). This is the default option.

Use this option if the resolution of the restart file does not match the simulation grid resolution (HEMCO will remap the initial initial species concentrations to the simulation grid).

true

The restart file will be read directly by GEOS-Chem Classic as REAL*8.

Use this option when the resolution of your restart file matches the simulation grid resolution (as this option bypasses HEMCO vertical regridding). Also use this option when conservation needs to be strictly enforced.

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 GEOS-Chem Classic 4° x 5° global grid.

2.0x2.5: The GEOS-Chem Classic 2° x 2.5° global grid.

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

0.25x0.3125: The GEOS-Chem Classic \(0.25^{\circ}{\times}0.3125^{\circ}\) grid. May be used for global or nested-grid simulations with GEOS-FP meteorology.

0.125x0.15625: The GEOS-Chem Classic global \(0.125^{\circ}{\times}0.15625^{\circ}\) grid. May be used for global or nested-grid simulations with GEOS-FP meteorology.

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, GEOS-FP, and GEOS-IT.

47: Use 47 vertical levels (for MERRA2, GEOS-FP, and GEOS-IT) in GEOS-Chem Classic simulations.

Important

If you select this option, you must also set read_restart_as_real8 to false, as reading the restart file as REAL*8 bypasses HEMCO vertical regridding. Otherwise your simulation will halt with an error.

40: Use 40 vertical levels (for GCAP2), in GEOS-Chem Classic simulations.

Important

If you select this option, you must also set read_restart_as_real8 to false, as reading the restart file as REAL*8 bypasses HEMCO vertical regridding. Otherwise your simulation will halt with an error.

longitude

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

center_at_180

true: Westernmost grid boxes are centered at \(-180^{\circ}\) longitude (the International Date Line). This is the default for MERRA2, GEOS-FP, and GEOS-IT meteorology.

false: Westernmost grid boxes have their western edges at \(-180^{\circ}\) longitude. This is the default setting for the GCAP2 grid.

latitude

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

use_halfpolar_boxes

true: Northernmost and southernmost grid boxes will be \(\frac{1}{2}\) the extent of other grid boxes. This the default for MERRA2, GEOS-FP, and GEOS-IT meteorology.

false: All grid boxes will have the same extent in latitude. This is the default for GCAP2 meteorology.

nested_grid_simulation

activate

true: Indicates this indicates that the simulation will use a sub-domain of the horizontal grid.

Important

We recommend that you run nested-grid fullchem simulations with the native 72 vertical levels. This will avoid a bias in tropospheric photolysis rates caused by the HEMCO vertical remapping from 72 to 47 levels.

false: 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 our Speeding up GEOS-Chem Classic simulations guide.

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.

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

true: Activates chemistry in GEOS-Chem. This is the default setting.

false: Deactivates chemistry in GEOS-Chem.

linear_chemistry_aloft

Determines how linearized chemistry will be applied in the stratosphere and/or mesosphere. These apply only to fullchem simulations.

activate

true: Activates linearized stratospheric chemistry in the stratosphere and/or mesosphere. This is the default setting.

false: Deactivates linearized stratospheric chemistry in the stratosphere and/or mesosphere.

use_linoz_for_O3

true: Activates Linoz stratospheric ozone chemistry will be used. This is the default setting.

false: Activates Synoz (i.e. a synthetic flux of ozone across the tropopause).

active_strat_H2O

Determines if water vapor as modeled by GEOS-Chem will be allowed to influence humidity fields. These apply only to fullchem simulations.

activate

true: Allows the H2O species in GEOS-Chem to influence specific humidity and relative humidity. This is the default setting.

false: Prevents the H2O species in GEOS-Chem to influence specific humidity and relative humidity.

use_static_bnd_cond

true: Uses a static boundary condition. This is the default setting.

false: Does not use a static boundary condition.

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

true: Integrates the chemistry mechanism using the Rosenbrock method with the adaptive auto-reduction feature.

false: Integrates the chemistry mechanism using the traditional Rosenbrock method. This is the default setting.

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

true: Uses OH and NO2 to determine \(\partial\). This is the default setting.

false: Skips computation of \(\partial\).

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_absolute_threshold

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

scale_by_pressure

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

false: Deactivates 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

true: All halogen species will be considered “fast”. This may be necessary in order to obtain realistic results for ozone and other important species. This is the default setting.

false: Halogen species will be determined as “slow” or “fast” depending on the partitioning threshold \(\partial\).

append_in_internal_timestep

true: Any “slow” species that later become “fast” will be appended to the list of “fast” species.

false: Any “slow” species that later become “fast” will NOT be appended to the list of “fast” species.

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

true: Activates cloud convection in GEOS-Chem

false: Deactivates 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

true: Activates dry deposition in GEOS-Chem.

false: Deactivates dry deposition in GEOS-Chem.

CO2_effect

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

activate

true: Activates the CO2 effect on stomatal resistance in dry deposition.

false: DeActivates the CO2 effect on stomatal resistance in dry deposition. This is the default setting.

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

true: Activates planetary boundary layer mixing in GEOS-Chem.

false: Deactivates planetary boundary layer mixing in GEOS-Chem.

use_non_local_pbl

true: Uses the non-local PBL mixing scheme (VDIFF). This is the default setting.

false: Uses the full PBL mixing scheme (TURBDAY).

Photolysis

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

  # .. preceding sub-sections omitted ...

  photolysis:
    activate: true
    cloud-j:
      cloudj_input_dir: ${RUNDIR_DATA_ROOT}/CHEM_INPUTS/CLOUD_J/v2025-01/
      verbose: false
      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
    fast-jx:
      fastjx_input_dir: /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2024-05/
    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: 100.0
      NIT_Jscale: 100.0
      percent_channel_A_HONO: 66.667
      percent_channel_B_NO2: 33.333

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

The operations:photolysis section contains settings for photolysis. This section only applies to fullchem and Hg simulations.

activate

true: Activates photolysis in GEOS-Chem. This is the default setting.

false: Deactivates photolysis in GEOS-Chem.

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).

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

verbose

false: Disables verbose printout from Cloud-J. This is the default setting.

true: Enables verbose printout from Cloud-J. Use this option for debugging.

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	Cloud-J variable
`Input_Opt%NLevs_Phot_Cloud`	`LWEPAR`

cloud_scheme_flag

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

GEOS-Chem variable	Cloud-J variable
`Input_Opt%CLDFLAG`	`LWEPAR`

opt_depth_increase_factor

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

GEOS-Chem variable	Cloud-J variable
`Input_Opt%OD_Increase_Factor`	`ATAU`

min_top_inserted_cloud_OD

Specifies the minimum cloud OD in the uppermost inserted layer.

GEOS-Chem variable	Cloud-J variable
`Input_Opt%Min_Cloud_OD`	`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	Cloud-J variable
`Input_Opt%Cloud_Corr`	`CLDCOR`

num_cloud_overlap_blocks

Specifies the number of maximum-overlap blocks.

GEOS-Chem variable	Cloud-J variable
`Input_Opt%Num_Max_Overlap`	`LNRG`

sphere_correction

Specifies the type of spherical correction to be applied.

GEOS-Chem variable	Cloud-J variable
`Input_Opt%OD_Increase_Factor`	`ATM0`

num_wavelength_bins

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

GEOS-Chem variable	Cloud-J variable
`Input_Opt%Num_WV_Bins`	`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	Cloud-J variable
`Input_Opt%Use_H2O_UV_Abs`	`USEH2OUV`

fast-jx

Specifies various options for the Fast-JX photolysis package.

Attention

FAST-JX is currently used only by the Hg (mercury) simulation, In the near future, the Hg simulation will be updated to use Cloud-J, and FAST_JX will be retired from GEOS-Chem.

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.

overhead_O3

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

use_online_O3_from_model

true: Uses the advected O3 species from GEOS-Chem in the extinction calculations for photolysis. This is the recommended setting.

false: Does not use the advected O3 species from GEOS-Chem in the extinction calculations for photolysis.

use_column_O3_from_met

true: Uses ozone columns (e.g. TO3) from the meteorology fields. This is the recommended setting.

false: Does not not use ozone columns from the meteorology fields.

use_TOMS_SBUV_O3

true: Uses ozone columms from the TOMS-SBUV archive.

false: Does not use ozone columsn from the TOMS-SBUV archive. This is the recommended setting.

photolyze_nitrate_aerosol

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

activate

true: Activates nitrate aerosol photolysis. This is the recommended setting.

false: Deactivates nitrate aerosol photolysis.

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 (which only applies to fullchem simultions).

activate

true: Activates the RRTMG radiative transfer model.

false: Deactivates the RRTMG radiative transfer model. This is the default setting.

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

true: Activates RRTMG longwave flux calculations.

false: Dectivates RRTMG longwave flux calculations. This is the default setting.

shortwave_fluxes

true: Activates RRTMG shortwave flux calculations.

false: Dectivates RRTMG shortwave flux calculations. This is the default setting.

clear_sky_flux

true: Activates RRTMG clear-sky flux calculations.

false: Dectivates RRTMG clear-sky flux calculations. This is the default setting.

all_sky_flux

true: Activates RRTMG all-sky flux calculations.

false: Dectivates RRTMG clear-sky flux calculations. This is the default setting.

fixed_dyn_heating

true: Activates fixed dynamic heating (FDH) approximation as described by de F. Forster and Shine [1997].

false: Deactivates fixed dynamic heating (FDH) approximation. This is the default setting.

seasonal_fdh

true: Activates seasonally-evolving fixed dynamic heating (SEFDH) approximation as described by Kiehl et al. [1999].

Attention

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

false: Deactivates seasonally-evolving fixed dynamic heating (SEFDH) approximation. This is the default setting.

read_dyn_heating

true: Activates reading previously-archived dynamical heating outputs from disk.

false: Dectivates reading previously-archived dynamical heating outputs from disk. This is the default setting.

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.

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

activate

true: Activates species transport in GEOS-Chem Classic. This is the default setting.

false: Deactivates species transport in GEOS-Chem Classic.

fill_negative_values

true: Will replace negative species concentrations with zeros. This is the default setting.

false: Will not replace negative species concentrations with zeros.

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

true: Activates wet deposition of soluble species in GEOS-Chem. This is the default setting for simulations containing soluble species.

false: Deactivates wet deposition of soluble species in GEOS-Chem. This is the default setting for simulations that do not have soluble species.

There are several sub-sections under aerosols:

Aerosol optics

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

  optics:
    input_dir: /path/to/ExtData/CHEM_INPUTS/Aerosol_Optics/v2025-03/

  # .. following sub-sections omitted ...

The aerosols:optics section contains settings for aerosol optics data. This section only applies to fullchem and aerosol-only simulations.

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 carbonaceous aerosols. This section only apply to fullchem and aerosol-only simulations.

activate

true: Activates carbon aerosols in GEOS-Chem. This is the default setting.

true: Deactivates carbon aerosols in GEOS-Chem

brown_carbon

true: Activates brown carbon aerosols in GEOS-Chem.

true: Deactivates brown carbon aerosols in GEOS-Chem. This is the default setting.

enhance_black_carbon_absorption

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

activate

true: Activates black carbon absorption enhancement. This is the default setting.

false: Deactivates black carbon absorption enhancement.

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

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

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

  complex_SOA:
    activate:  true
    semivolatile_POA: false

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

The aerosols:complex_SOA section contains settings for the complex SOA scheme used in GEOS-Chem. This section only applies to fullchem and aerosol simulations.

activate

true: Activates the complex SOA scheme. This is the default setting for the for the fullchem benchmark simulation.

false: Deactivates the complex SOA scheme. This is the default setting for all other fullchem simulations.

semivolatile_POA

true: Activates the semi-volatile primary organic aerosol (POA) option.

false: Deactivates the semi-volatile primary organic aerosol (POA) option. This is the default setting.

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 ...

The aerosols:dust section contains settings for mineral dust aerosols. This section only applies to arvard.edu/geos-chem/index.php/Mineral_dust_aerosols>`_. This section only apply to fullchem and aerosol-only simulations.

activate

true: Activates the mineral dust aerosols in GEOS-Chem. This is the default setting.

false: Deactivates the mineral dust aerosols in GEOS-Chem.

acid_uptake_on_dust

true: Activates the acid uptake on dust option, which includes 12 additional species

false: Deactivates the acid uptake on dust option. This is the default setting.

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 ...

The aerosols:sea_salt section contains settings for sea salt aerosols. This section only apply to fullchem and aerosol-only simulations.

activate

true: Activates sea salt aerosols in GEOS-Chem. This is the default setting.

false: Deactivates sea salt aerosols.

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, 0.5]

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, 8.0]

marine_organic_aerosols

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

false: Deactivates emission of marine primary organic aerosols. This is the default setting.

Stratospheric 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 ...

The aerosols:stratosphere section contains settings for stratopsheric aerosols. This section only applies to fullchem simulations.

settle_strat_aerosol

true: Activates gravitational settling of stratospheric solid particulate aerosols (SPA, trapezoidal scheme) and stratospheric liquid aerosols (SLA, corrected Stokes’ Law). This is the default setting.

false: Dectivates gravitational settling of stratospheric solid particulate aerosols and stratopsheric liquid aerosols.

polar_strat_clouds

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

activate

true: Activates formation of polar stratospheric clouds. This is the default setting.

false: Dectivates formation of polar stratospheric clouds.

het_chem

true: Activates heterogeneous chemistry within polar stratospheric clouds. This is the default setting.

false: Dectivates heterogeneous chemistry within polar stratospheric clouds.

allow_homogeneous_NAT

true: Activates heterogeneous formation of NAT from freezing of HNO3.

false: Deactivates heterogeneous formation of NAT from freezing of HNO3. This is the default setting.

..option:: 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

true: Includes online stratospheric aerosols in extinction calculations for photolysis. This is the default setting.

false: Excludes online stratospheric aerosols in extinction calculations for photolysis.

Sulfate aerosols

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

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

  sulfate:
    activate: true
    metal_cat_SO2_oxidation: true

The aerosols:sulfate section contains settings for sulfur and nitrogen aerosols. This section only applies to fullchem and aerosol-only simulations.

activate

true: Activates sulfate aerosols in GEOS-Chem. This is the default setting.

false: Deactivates sulfate aerosols in GEOS-Chem.

metal_cat_SO2_oxidation

true: Activates metal catalyzed oxidation of SO2 This is the default setting.

false: Deactivates metal-catalyzed oxidation of SO2.

CH₄ settings

This section contains options pertaining to the CH₄ species in the carbon gases simulation.

#============================================================================
# Options for CH4
#============================================================================
CH4_options:

  use_observational_operators:
    AIRS: false
    GOSAT: false
    TCCON: false

  analytical_inversion:
    perturb_CH4_boundary_conditions: false
    CH4_boundary_condition_ppb_increase_NSEW: [0.0, 0.0, 0.0, 0.0]

AIRS

true: Activates the AIRS observational operator.

false: Deactivates the AIRS observational operator. This is the default setting.

GOSAT

true: Activates the GOSAT observational operator.

false: Deactivates the GOSAT observational operator. This is the default setting.

TCCON

true: Activates the TCCON observational operator.

false: Deactivates the TCCON observational operator. This is the default setting.

perturb_CH4_boundary_conditions

Note

This setting only applies to carbon gases simulations done within the Integrated Methane Inversion workflow (aka IMI).

true: Activates perturbation of CH4 nested-grid boundary conditions in analytical inversions.

false: Deactivates perturbation of CH4 nested-grid boundary conditions in analytical inversions. This is the default setting.

CH4_boundary_condition_ppb_increase_NSEW

Note

This setting only applies to <carbon gases simulations done within the Integrated Methane Inversion workflow (aka IMI).

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)

CO settings

#============================================================================
# Options for CO
#============================================================================
CO_options:
  use_archived_PCO_from_CH4: true
  use_archived_PCO_from_NMVOC: true

The CO_options section contains settings for chemical sources of CO in the carbon gases simulation.

use_fullchem_PCO_from_CH4

true: Activates applying the production of CO from CH₄. This field is archived from a 1-year or 10-year fullchem benchmark simulation and is read from disk via HEMCO. This is the default setting.

false: Deactivates applying the production of CO from CH₄.

use_fullchem_PCO_from_NMVOC

true: Activates applying the production of CO from non-methane volatile organic compounds (NMVOCs). This field is archived from a 1-year or 10-year fullchem benchmark simulation and is read from disk via HEMCO. This is the default setting.

false: Deactivates applying the production of CO from NMVOCs.

CO₂ settings

#============================================================================
# Options for CO2
#============================================================================
CO2_options:

  sources:
    use_archived_PCO2_from_CO: true

This section contains settings for chemical sources of CO₂ in the carbon gases simulation.

use_archived_PCO2_from_CO

true: Activates CO₂ production by archived chemical oxidation, as read by HEMCO. This is the default setting.

false: Deactivates CO₂ production by archived chemical oxidation.

Hg 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 ...

The Hg_simulation_options:sources section contains settings for various mercury sources. This section only applies to the mercury (Hg) simulation.

use_dynamic_ocean_Hg

true: Activates the online slab ocean mercury model.

false: Deactivates the online slab ocean mercury model. This is the default setting.

use_preindustrial_Hg

true: Activates the preindustrial mercury simulation. This will turn off all anthropogenic emissions.

false: Deactivates the preindustrial mercury simulation. This is the default setting.

use_arctic_river_Hg

true: Activates the source of mercury from arctic rivers. This is the default setting.

false: Deactivates the source of mercury from arctic rivers.

Hg 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 ...

The Hg_simulation_options:chemistry section contains settings for mercury chemistry. This section only applies to the mercury (Hg) simulation.

tie_HgIIaq_reduction_to_UVB

true: Activates linking the reduction of aqueous oxidized mercury to UVB radiation. (A lifetime of -1 seconds indicates the species has an infinite lifetime.) This is the default setting.

false: Deactivates linking the reduction of aqueous oxidized mercury to UVB radiation.

Obspack diagnostic

Note

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

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

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

activate

true: Activates ObsPack diagnostic output in GEOS-Chem Classic.

false: Activates ObsPack diagnostic output in GEOS-Chem Classic. This is the default setting.

quiet_logfile_output

true: Suppresses printing extra informational output from ObsPack to stdout (i.e. the screen or log file).

false: Activates printing extra informational output from ObsPack to stdout (i.e. the screen or log file). This is the default setting.

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.

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

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

activate

true: Activates the Planeflight diagnostic output in GEOS-Chem Classic.

false: Deactivates (false) the Planeflight diagnostic output in GEOS-Chem Classic. This is the default setting.

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.