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:

• GEOS-Chem Classic configuration instructions, or

• GCHP configuration instructions

Hg

Hg (mercury) simulation.

You must configure your build with with -DMECH=Hg in order to use this simulation. For more information, please see:

• GEOS-Chem Classic configuration instructions, or

• GCHP configuration instructions

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. You must use this option if the resolution of the restart file does not match the simulation grid resolution.

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, and when mass 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 gcc-hgrids-global-4x5.

2.0x2.5

The GEOS-Chem Classic gcc-hgrids-global-2x25.

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).

40

Use 40 vertical levels (for GCAP2).

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.

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/
      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.

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:

This section 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 Forster et al. [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:

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

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 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 carbon aerosols. This section only applies to fullchem and aerosol 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 fullchem and aerosol 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 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 applies to fullchem and aerosol 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:sulfate 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 sulfate aerosols. This section only applies to the fullchem and aerosol 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.

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.

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 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 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.

CH4 observational operators

#============================================================================
# Settings specific to the CH4 simulation / Integrated Methane Inversion
#============================================================================
CH4_options:

  use_observational_operators:
    AIRS: false
    GOSAT: false
    TCCON: false

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

The CH4_simulation_options:use_observational_operators section contains options for using satellite observational operators for CH4. This section only applies to simulations with carbon gases (carbon).

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.

CH4 analytical inversion options

#============================================================================
# Settings specific to the CH4 simulation / Integrated Methane Inversion
#============================================================================
CH4_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]

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.

This section only applies to the Carbon gases simulation.

perturb_CH4_boundary_conditions

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

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

#============================================================================
# Settings specific to the CO2 simulation
#============================================================================
CO2_options:

  sources:
    3D_chemical_oxidation_source: true

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

The CO2_simulation_options:sources section contains toggles for activating sources of \(CO_2\). This section only applies to simulations the Carbon gases simulation.

3D_chemical_oxidation_source

true

Activates \(CO_2\) production by archived chemical oxidation, as read by HEMCO. This is the default setting.

false

Deactivates \(CO_2\) production by archived chemical oxidation.

CO2 tagged species

#============================================================================
# Settings specific to the CO2 simulation
#============================================================================
CO2_options:

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

  tagged_species:
    tag_bio_and_ocean_CO2: false
    tag_land_fossil_fuel_CO2: false

  # .. following sub-sections omitted ...

The CO2_simulation_options:tagged_species section contains toggles for activating tagged \(CO_2\) species. This section only applies to the Carbon gases simulation.

Attention

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

tag_bio_and_ocean_CO2

true

Activates 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.

false

DeActivates tagging of regions. This is the default setting.

tag_land_fossil_fuel_CO2

true

Activates tagging of land and ocean fossil fuel regions.

false

Deactivates tagging of land and ocean fossil fuel regions. This is the default setting.

CO chemical sources

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

CO_options:
  use_fullchem_PCO_from_CH4: true
  use_fullchem_PCO_from_NMVOC: true

The tagged_CO_simulation_options section contains settings for sources of CO used in the Carbon gases simulation.

use_fullchem_PCO_from_CH4

true

Activates 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. This is the default setting.

false

DeActivates applying the production of \(CO\) from \(CH_4\).

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 full-chemistry benchmark simulation and is read from disk via HEMCO. This is the default setting.

false

Deactivates applying the production of \(CO\) from NMVOCs.