geoschem_config.yml¶
Starting with GEOS-Chem 14.0.0, the input.geos
configuration
file (plain text) has been replaced with by the
geoschem_config.yml
file. This file is in YAML format, which is a text-based markup syntax used
for representing dictionary-like data structures.
Note
The geoschem_config.yml
file contains several sections. Only
the sections relevant to a given type of simulation are present.
For example, fullchem
simulation options (such as aerosol
settings and photolysis settings) are omitted from the
geoschem_config.yml
file for the CH4
simulation.
Simulation settings¶
#============================================================================
# Simulation settings
#============================================================================
simulation:
name: fullchem
start_date: [20190701, 000000]
end_date: [20190801, 000000]
root_data_dir: /path/to/ExtData
met_field: MERRA2
species_database_file: ./species_database.yml
debug_printout: false
use_gcclassic_timers: false
The simulation
section contains general simulation options:
-
name
¶
Specifies the type of GEOS-Chem simulation. Accepted values are
-
fullchem
¶
Full-chemistry simulation.
-
aerosol
¶
-
carbon
¶
Coupled carbon gases simulation (CH4-CO-CO2-OCS), implemented as a KPP mechanism (cf ).
You must configure your build with
-DMECH=carbon
in order to use this simulation.Attention
This simulation is still undergoing validation and testing. We therefore do not recommend using this simulation in the present version.
-
Hg
¶
-
You must configure your build with
-DMECH=Hg
in order to use this simulation.
-
POPs
¶
Persistent organic pollutants (aka POPs) simulation.
Attention
The POPs simulation is currently stale. We look to members of the GEOS-Chem user community take the lead on updating this simulation.
-
tagCH4
¶
Methane simulation with species tagged by geographic region or other criteria.
This simulation will eventually be superseded by the
carbon
simulation.
-
tagCO
¶
Carbon dioxide simulation, with species tagged by geographic region and other criteria.
This simulation will eventually be superseded by the
carbon
simulation.
-
tagO3
¶
Ozone simulation (using specified production and loss rates), with species tagged by geographical region.
-
TransportTracers
¶
Transport Tracers simulation, with both radionuclide and
passive_species
. Useful for evaluating model transport.
-
metals
¶
Trace metals simulation
-
-
start_date
¶
Specifies the starting date and time of the simulation in list notation
[YYYYMMDD, hhmmss]
.
-
end_date
¶
Specifies the ending date and time of the simulation in list notation
[YYYYMMDD, hhmmss]
.
-
root_data_dir
¶
Path to the root data directory. All of the data that GEOS-Chem Classic reads must be located in subfolders of this directory.
-
met_field
¶
Name of the meteorology product that will be used to drive GEOS-Chem Classic. Accepted values are:
-
MERRA2
¶
The MERRA-2 meteorology product from NASA/GMAO. MERRA-2 is a stable reanalysis product, and extends from approximately 1980 to present. (Recommended option)
-
GEOS-FP
¶
The GEOS-FP meteorology product from NASA/GMAO. GEOS-FP is an operational data product and, unlike MERRA-2, periodically receives science updates.
-
GCAP2
¶
The GCAP-2 meteorology product, archived from the GISS-2 GCM. GCAP-2 has hundreds of years of data available, making it useful for simulations of historical climate.
-
-
species_database_file
¶
Path to the GEOS-Chem Species Database file. This is stored in the run directory file
./species_database.yml
. You should not have to edit this setting.
-
debug_printout
¶
Activates (
true
) or deactivates (false
) debug print statements to the screen or log file.
-
use_gcclassic_timers
¶
Activates (
true
) or deactivates (false
) the GEOS-Chem Classic timers. If activated, information about how long each component of GEOS-Chem took to execute will be printed to the screen and/or GEOS-Chem log file. The same information will also be written in JSON format to a file named gcclassic_timers.json.You can set this option to
false
unless you are running benchmark or timing simulations.
Grid settings¶
#============================================================================
# Grid settings
#============================================================================
grid:
resolution: 4.0x5.0
number_of_levels: 72
longitude:
range: [-180.0, 180.0]
center_at_180: true
latitude:
range: [-90.0, 90.0]
half_size_polar_boxes: true
nested_grid_simulation:
activate: true
buffer_zone_NSEW: [0, 0, 0, 0]
The grid
section contains settings that define the grid used
by GEOS-Chem Classic:
-
resolution
¶
Specifies the horizontal resolution of the grid. Accepted values are:
-
4.0x5.0
¶
The global \(4^{\circ}{\times}5^{\circ}\) GEOS-Chem Classic grid.
-
2.0x2.5
¶
The global \(2.0{\circ}{\times}2.5^{\circ}\) GEOS-Chem Classic grid.
-
-
number_of_levels
¶
Number of vertical levels to use in the simulation. Accepted values are:
-
longitude
¶
Settings that define the longitude dimension of the grid. There are two sub-options:
-
range
¶
The minimum and maximum longitude values (grid box centers), specified in list format.
-
center_at_180
¶
If
true
, then westernmost grid boxes are centered at \(-180^{\circ}\) longitude (the International Date Line). This is true for bothMERRA2
andGEOS-FP
.If
false
, then the westernmost grid boxes have their westernmost edges at \(-180^{\circ}\) longitude. This is true for theGCAP2
grid.
-
-
latitude
¶
Settings to define the latitude dimension of the grid. There are two sub-options:
-
range
¶
The minimum and maximum latitude values (grid box centers), specified in list format.
-
-
nested_grid_simulation
¶
Settings for nested-grid simulations. There are two sub-options:
-
activate
¶
If
true
, this indicates that the simulation will use a sub-window of the horizontal grid.If
false
, this indicates that the simulation will use the entire global grid extent.
-
buffer_zone_NSEW
¶
Specifies the nested grid latitude offsets (# of grid boxes) in list format
[N-offset, S-offset, E-offset, W-offset]
. These offsets are used to define an inner window region in which transport is actually done (aka the “transport window”). This “transport window” is always smaller than the actual size of the nested grid region in order to properly account for the boundary conditions.
For global simulations, use:
[0, 0, 0, 0]
.For nested-grid simulations, we recommend using:
[3, 3, 3, 3]
.
-
Timesteps settings¶
#============================================================================
# Timesteps settings
#============================================================================
timesteps:
transport_timestep_in_s: 600
chemistry_timestep_in_s: 1200
radiation_timestep_in_s: 10800
The timesteps
section specifies the frequency at which
various GEOS-Chem operations occur:
-
transport_timestep_in_s
¶
Specifies the “heartbeat” timestep of GEOS-Chem.. This is the frequency at which transport, cloud convection, PBL mixing, and wet deposition will be done.
Recommended value for global simulations:
600
Recommended value for nested simluations:
300
or smaller
-
chemistry_timestep_in_s
¶
Specifies the frequency at which chemistry and emissions will be done.
Recommended value for global simulations
1200
Recommended value for nested simulations
600
or smaller
Operations settings¶
This section of geoschem_config.yml
is included for all
simulations. However, some of the options listed below will be omitted for
simulations that do not require them.
There are several sub-sections under operations
:
Chemistry¶
#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:
chemistry:
activate: true
linear_chemistry_aloft:
activate: true
use_linoz_for_O3: true
active_strat_H2O:
activate: true
use_static_bnd_cond: true
gamma_HO2: 0.2
autoreduce_solver:
activate: false
use_target_threshold:
activate: true
oh_tuning_factor: 0.00005
no2_tuning_factor: 0.0001
use_absolute_threshold:
scale_by_pressure: true
absolute_threshold: 100.0
keep_halogens_active: false
append_in_internal_timestep: false
# ... following sub-sections omitted ...
The operations:chemistry
section contains settings for chemistry:
-
activate
¶
Activates (
true
) or deactivates (false
) chemistry in GEOS-Chem.
-
linear_chemistry_aloft
¶
Determines how linearized chemistry will be applied in the stratosphere and/or mesosphere. (Only valid for
fullchem
simulations).There are two sub-options:
-
activate
¶
Activates (
true
) or deactivates (false
) linearized stratospheric chemistry in the stratosphere and/or mesosphere.
-
use_linoz_for_O3
¶
If
true
, Linoz stratospheric ozone chemistry will be used.If
false
, Synoz (i.e. a synthetic flux of ozone across the tropopause) will be used instead of Linoz.
-
-
active_strat_H2O
¶
Determines if water vapor as modeled by GEOS-Chem will be allowed to influence humidity fields. (Only valid for
fullchem
simulations)There are two sub-options:
-
activate
¶
Allows (
true
) or disallows (false
the H2O species in GEOS-Chem to influence specific humidity and relative humidity.
-
use_static_bnd_cond
¶
Allows (
true
) or diasallows (false
) a static boundary condition.TODO Clarify this
-
-
gamma_HO2
¶
Specifies \(\gamma\), the uptake coefficient for \(HO_2\) heterogeneous chemistry.
Recommended value:
0.2
.
-
autoreduce_solver
¶
Menu for controlling the adaptive mechanism auto-reduction feature, which is available in KPP 3.0.0. and later versions. See Lin et al. [2023] for details.
-
activate
¶
If
true
, the mechanism will be integrated using the Rosenbrock method with the adaptive auto-reduction feature.If
false
, the mechanism will be integrated using the traditional Rosenbrock method.Default value:
false
.
-
use_target_threshold
¶
Contains options for defining \(\partial\) (the partitioning threshold between “fast” and “slow” species”) by considering the production and loss of key species (OH for daytime, NO2 for nighttime).
-
activate
¶
Activates (
true
) or deactivates (false
) using OH and NO2 to determine \(\partial\).Default value:
true
.
-
oh_tuning_factor
¶
Specifies \({\alpha}_{OH}\), which is used to compute \(\partial\).
-
no2
tuning factor
¶ Specifies \({\alpha}_{NO2}\), which is used to compute \(\partial\).
-
-
use_pressure_threshold
¶
Contains options for setting an absolute threshold \(\partial\) that may be weighted by pressure.
-
scale_by_pressure
¶
Activates (
true
) or deactivates (false
) using a pressure-dependent method to determine \(\partial\).
-
absolute_threshold
¶
The absolute partitioning threshold \(\partial\).
If
scale_by_pressure
istrue,
anduse_target_threshold:activate
isfalse
, the value for \(\partial\) specified here will be scaled by the ratio \(P / P_{sfc}\). where \(P\) is the grid box pressure and \(P_{sfc}\) is the surface pressure for the column.
-
-
keep_halogens_active
¶
If
true
, then all halogen species will be considered “fast”. This may be necessary in order to obtain realistic results for ozone and other important species.If
false
, then halogen species will be determined as “slow” or “fast” depending on the partitioning threshold \(\partial\).Default value:
true
-
append_in_internal_timestep
¶
If
true
, any “slow” species that later become “fast” will be appended to the list of “fast” species.If
false
, any “slow” species that later become “fast” will NOT be appended to the list of “fast” species.Default value:
false
-
Convection¶
#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:
# .. preceding sub-sections omitted ...
convection:
activate: true
# ... following sub-sections omitted ...
The operations:convection section contains settings for cloud convection:
-
activate
¶
Activates (
true
) or deactivates (false
) cloud convection in GEOS-Chem.
Dry deposition¶
#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:
# .. preceding sub-sections omitted ...
dry_deposition:
activate: true
CO2_effect:
activate: false
CO2_level: 600.0
reference_CO2_level: 380.0
diag_alt_above_sfc_in_m: 10
# ... following sub-sections omitted ...
The operations:dry_deposition
section contains settings that
for dry deposition:
-
activate
¶
Activates (
true
) or deactivates (false
) dry deposition.
-
CO2_effect
¶
This sub-section contains options for applying the simple parameterization for the CO2 effect on stomatal resistance.
-
activate
¶
Activates (
true
) or deactivates (false
) the CO2 effect on stomatal resistance in dry deposition.Default value:
false
.
-
CO2_level
¶
Specifies the CO2 level (in ppb).
-
reference_CO2_level
¶
Specifies the reference CO2 level (in ppb).
-
-
diag_alt_above_sfc_in_m:
¶
Specifies the altitude above the surface (in m) to used with the ConcAboveSfc diagnostic collection.
PBL mixing¶
#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:
# .. preceding sub-sections omitted ...
pbl_mixing:
activate: true
use_non_local_pbl: true
# ... following sub-sections omitted ...
The operations:pbl_mixing
section contains settings that
for planetary boundary layer (PBL) mixing:
-
activate
¶
Activates (
true
) or deactivates (false
) planetary boundary layer mixing in GEOS-Chem Classic.
-
use_non_local_pbl
¶
If
true
, then the non-local PBL mixing scheme (VDIFF) will be used. (Default option)If
false
, then the full PBL mixing scheme (TURBDAY) will be used.
Photolysis¶
#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:
# .. preceding sub-sections omitted ...
photolysis:
input_dir: /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2021-10/
overhead_O3:
use_online_O3_from_model: true
use_column_O3_from_met: true
use_TOMS_SBUV_O3: false
photolyze_nitrate_aerosol:
activate: false
NITs_Jscale_JHNO3: 0.0
NIT_Jscale_JHNO2: 0.0
percent_channel_A_HONO: 66.667
percent_channel_B_NO2: 33.333
# ... following sub-sections omitted ...
The operation:photolysis
section contains settings for
photolysis.
This section only applies to fullchem
and Hg
simultions.
-
input_dir
¶
Specifies the path to the FAST_JX configuration file that contain information about species cross sections and quantum yields.
-
overhead_O3
¶
This section contains settings that control which overhead ozone sources are used for photolysis
-
use_online_O3_from_model
¶
Activates (
true
) or deactivates (false
) using online O3 from GEOS-Chem in the extinction calculations for FAST-JX photolysis.Recommended value:
true
-
use_column_O3_from_met
¶
Activates (
true
) or deactivates (false
) using ozone columns (e.g. TO3) from the meteorology fields.Recommended value:
true
.
-
use_TOMS_SBUV_O3
¶
Activates (
true
) or deactivates (false
) using ozone columns from the TOMS-SBUV archive will be used.Recommended value:
false
.
-
RRTMG radiative transfer model¶
#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:
# .. preceding sub-sections omitted ...
rrtmg_rad_transfer_model:
activate: false
aod_wavelengths_in_nm:
- 550
longwave_fluxes: false
shortwave_fluxes: false
clear_sky_flux: false
all_sky_flux: false
# .. following sub-sections omitted ...
The operations:rrtmg_rad_transfer_model
section contains
settings for the RRTMG radiative transfer model:
This section only applies to fullchem
simultions.
-
activate
¶
Activates (
true
) or deactivates (false
) the RRTMG radiative transfer model.Default value:
false
.
-
aod_wavelengths_in_nm
¶
Specify wavelength(s) for the aerosol optical properties in nm (in YAML sequence format) Up to three wavelengths can be selected. The specified wavelengths are used for the FAST-JX photolysis mechanism regardless of whether the RRTMG radiative transfer model is used.
-
longwave_fluxes
¶
Activates (
true
) or deactivates (false
) RRTMG longwave flux calculations.Default value:
false
.
-
shortwave_fluxes
¶
Activates (
true
) or deactivates (false
) RRTMG shortwave calculations.Default value:
false
.
-
clear_sky_flux
¶
Activates (
true
) or deactivates (false
) RRTMG clear-sky flux calculations.Default value:
false
.
-
all_sky_flux
¶
Activates (
true
) or deactivates (false
) RRTMG all-sky flux calculations.Default value:
false
.
Transport¶
#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:
# .. preceding sub-sections omitted ...
transport:
gcclassic_tpcore: # GEOS-Chem Classic only
activate: true # GEOS-Chem Classic only
fill_negative_values: true # GEOS-Chem Classic only
iord_jord_kord: [3, 3, 7] # GEOS-Chem Classic only
transported_species:
- ACET
- ACTA
- AERI
# ... etc more transported species ...
passive_species:
PassiveTracer:
long_name: Passive_tracer_for_mass_conservation_evaluation
mol_wt_in_g: 1.0
lifetime_in_s: -1
default_bkg_conc_in_vv: 1.0e-7
# ... etc more passive species ...
# .. following sub-sections omitted ...
The operations:transport
section contains
settings for species transport:
-
gcclassic_tpcore
¶
Contains options that control species transport in GEOS-Chem Classic with the TPCORE advection scheme:
-
activate
¶
Activates (
true
) or deactivates (false
) species transport in GEOS-Chem Classic.Default value:
true
.
-
fill_negative_values
¶
If
true
, negative species concentrations will be replaced with zeros.If
false
, no change will be made to species concentrations.Default value:
true
.
-
iord_jord_kord
¶
Specifies advection options (in list format) for TPCORE in the longitude, latitude, and vertical dimensions. The options are listed below:
1st order upstream scheme (use for debugging only)
2nd order van Leer (full monotonicity constraint)
Monotonic PPM
Semi-monotonic PPM (same as 3, but overshoots are allowed)
Positive-definite PPM
Un-constrained PPM (use when fields & winds are very smooth) this option only when the fields and winds are very smooth.
Huynh/Van Leer/Lin full monotonicity constraint (KORD only)
Default (and recommended) value:
[3, 3, 7]
-
-
transported_species
¶
A list of species names (in YAML sequence format) that will be transported by the TPCORE advection scheme.
-
passive_species
¶
Optional menu that allows you to specify passive species, which are excluded from undergoing chemical reactions.
Define passive species by providing the name of the species along with associated metadata fields. For example:
PassiveTracer: long_name: Passive_tracer_for_mass_conservation_evaluation mol_wt_in_g: 1.0 lifetime_in_s: -1 # -1 indicates infinite lifetime! default_bkg_conc_in_vv: 1.0e-7
Each passive species must also be listed under
transported_species
.
Wet deposition¶
#============================================================================
# Settings for GEOS-Chem operations
#============================================================================
operations:
# .. preceding sub-sections omitted ...
wet_deposition:
activate: true
The operations:wet_deposition
section contains settings
for wet deposition.
-
activate
¶
Activates (
true
) or deactivates (false
) wet deposition in GEOS-Chem Classic.
Aerosols settings¶
This section of geoschem_config.yml
is included for
fullchem
and aerosol
simulations.
There are several sub-sections under aerosols
:
Carbon aerosols¶
#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:
carbon:
activate: true
brown_carbon: false
enhance_black_carbon_absorption:
activate: true
hydrophilic: 1.5
hydrophobic: 1.0
# .. following sub-sections omitted ...
The aerosols:carbon
section contains settings for
carbon aerosols:
-
activate
¶
Activates (
true
) or deactivates (false
) carbon aerosols in GEOS-Chem.Default value:
true
.
-
brown_carbon
¶
Activates (
true
) or deactivates (false
) brown carbon aerosols in GEOS-Chem.Default value:
false
.
-
enhance_black_carbon_absorption
¶
Options for enhancing the absorption of black carbon aerosols due to external coating.
-
activate
¶
Activates (
true
) or deactivates (false
) black carbon absorption enhancement.Default value:
true
.
-
hydrophilic
¶
Absorption enhancement factor for hydrophilic black carbon aerosol (species name BCPI).
Default value:
1.5
-
hydrophobic
¶
Absorption enhancement factor for hydrophilic black carbon aerosol (species name BCPO).
Default value:
1.0
-
Complex SOA¶
The aerosols:complex_SOA
section contains settings for
the complex SOA scheme used in GEOS-Chem.
#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:
# ... preceding sub-sections omitted ...
complex_SOA:
activate: true
semivolatile_POA: false
# ... following sub-sections omitted ...
-
activate
¶
Activates (
true
) or deactivates (false
) the complex SOA scheme.Default value:
-
semivolatile_POA
¶
Activates (
true
) or deactivates (false
) the semi-volatile primary organic aerosol (POA) option.Default value:
false
Mineral dust aerosols¶
The aerosols:dust
section contains settings for
mineral dust aerosols.
#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:
# ... preceding sub-sections omitted ...
dust:
activate: true
acid_uptake_on_dust: false
# ... following sub-sections omitted ...
-
activate
¶
Activates (
true
) or deactivates (false
) mineral dust aerosols in GEOS-Chem.Default value:
true
-
acid_uptake_on_dust
¶
Activates (
true
) or deactivates (false
) the acid uptake on dust option, which includes 12 additional species.Default value:
false
Sea salt aerosols¶
The aerosols:sea_salt
section contains settings for sea salt
aerosols:
#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:
# ... preceding sub-sections omitted ...
sea_salt:
activate: true
SALA_radius_bin_in_um: [0.01, 0.5]
SALC_radius_bin_in_um: [0.5, 8.0]
marine_organic_aerosols: false
# ... following sub-sections omitted ...
-
activate
¶
Activates (
true
) or deactivates (false
) sea salt aerosols.Default value:
true
-
SALA_radius_bin_in_um
¶
Specifies the upper and lower boundaries (in nm) for accumulation-mode sea salt aerosol (aka SALA).
Default value:
0.01 nm - 0.5 nm
-
SALC_radius_bin_in_um
¶
Specifies the upper and lower boundaries (in nm) for coarse-mode sea salt aerosol (aka SALC).
Default value:
0.5 nm - 8.0 nm
-
marine_organic_aerosols
¶
Activates (
true
) or deactivates (false
) emission of marine primary organic aerosols. This option includes two extra species (MOPO and MOPI).Default value:
false
Stratospheric aerosols¶
The aerosols:sulfate
section contains settings for
stratopsheric aerosols.
#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:
# ... preceding sub-sections omitted ...
stratosphere:
settle_strat_aerosol: true
polar_strat_clouds:
activate: true
het_chem: true
allow_homogeneous_NAT: false
NAT_supercooling_req_in_K: 3.0
supersat_factor_req_for_ice_nucl: 1.2
calc_strat_aod: true
# ... following sub-sections omitted ...
-
settle_strat_aerosol
¶
Activates (
true
) or deactivates (false
) gravitational settling of stratospheric solid particulate aerosols (SPA, trapezoidal scheme) and stratospheric liquid aerosols (SLA, corrected Stokes’ Law).Default value:
true
-
polar_strat_clouds
¶
Contains settings for how aerosols are handled in polar stratospheric clouds (PSC):
-
activate
¶
Activates (
true
) or deactivates (false
) formation of polar stratospheric clouds.Default value:
true
-
het_chem
¶
Activates (
true
) or deactivates (false
) heterogeneous chemistry within polar stratospheric clouds.Default value:
true
-
-
allow_homogeneous_NAT
¶
Activates (
true
) or deactivates (false
) heterogeneous formation of NAT from freezing of HNO3.Default value:
false
-
NAT_supercooling_req_in_K
¶
Specifies the cooling (in K) required for homogeneous NAT nucleation.
Default value:
3.0
-
supersat_factor_req_for_ice_nucl
¶
Specifies the supersaturation factor required for ice nucleation.
Recommended values:
1.2
for coarse grids;1.5
for fine grids.
-
calc_strat_aod
¶
Includes (
true
) or excludes (false
) online stratospheric aerosols in extinction calculations for photolysis.Default value:
true
Sulfate aerosols¶
The aerosols:sulfate
section contains settings for sulfate
aerosols:
#============================================================================
# Settings for GEOS-Chem aerosols
#============================================================================
aerosols:
# ... preceding sub-sections omitted ...
sulfate:
activate: true
metal_cat_SO2_oxidation: true
-
activate
¶
Activates (
true
) or deactivates (false
) sulfate aerosols.Default value:
true
-
metal_cat_SO2_oxidation
¶
Activates (
true
) or deactivates (false
) the metal catalyzed oxidation of SO2.Default value:
true
Extra diagnostics¶
The extra_diagnostics
section contains settings for GEOS-Chem Classic
diagnostics that are not archived by History or HEMCO:
Obspack diagnostic¶
The extra_diagnostics:obspack
section contains settings for
the Obspack diagnostic:
#============================================================================
# Settings for diagnostics (other than HISTORY and HEMCO)
#============================================================================
extra_diagnostics:
obspack:
activate: false
quiet_logfile_output: false
input_file: ./obspack_co2_1_OCO2MIP_2018-11-28.YYYYMMDD.nc
output_file: ./OutputDir/GEOSChem.ObsPack.YYYYMMDD_hhmmz.nc4
output_species:
- CO
- 'NO'
- O3
# ... following sub-sections omitted ...
-
activate
¶
Activates (
true
) or deactivates (false
) ObsPack diagnostic output.Default value:
true
-
quiet_logfile_output
¶
Deactivates (
true
) or activates (false
) printing informational output tostdout
(i.e. the screen or log file).Default value:
false
-
input_file
¶
Specifies the path to an ObsPack data file (in netCDF format).
-
output_file
¶
Specifies the path to the ObsPack diagnostic output file. This will be a file that contains data at the same locations as specified in
input_file
.
-
output_species
¶
A list of GEOS-Chem species (as a YAML sequence) to archive to the output file.
Planeflight diagnostic¶
The extra_diagnostics:planeflight
section contains settings for
the GEOS-Chem planeflight diagnostic:
#============================================================================
# Settings for diagnostics (other than HISTORY and HEMCO)
#============================================================================
extra_diagnostics:
# ... preceding sub-sections omitted ...
planeflight:
activate: false
flight_track_file: Planeflight.dat.YYYYMMDD
output_file: plane.log.YYYYMMDD
# ... following sub-sections omitted ...
-
activate
¶
Activates (
true
) or deactivates (false
) the Planeflight diagnostic output.Default value:
false
-
flight_track_file
¶
Specifies the path to a flight track file. This file contains the coordinates of the plane as a function of time, as well as the requested quantities to archive.
-
output_file
¶
Specifies the path to the Planeflight output file. Requested quantities will be archived from GEOS-Chem along the flight track specified in
flight_track_file
.
Legacy diagnostics¶
Attention
These diagnostics (in the older binary data format) are slated to be replaced by netCDF output in an upcoming version.
#============================================================================
# Settings for diagnostics (other than HISTORY and HEMCO)
#============================================================================
extra_diagnostics:
# ... preceding sub-sections omitted ...
gamap:
diaginfo_dat_file: ./diaginfo.dat
tracerinfo_dat_file: ./tracerinfo.dat
ND51_satellite:
activate: false
output_file: ts_satellite.YYYYMMDD.bpch
tracers:
- 1
- 2
- 501
UTC_hour_for_write: 0
averaging_period_in_LT: [9, 11]
IMIN_and_IMAX_of_region: [1, 72]
JMIN_and_JMAX_of_region: [1, 46]
LMIN_and_LMAX_of_region: [1, 1]
ND51b_satellite:
# same format as ND51_satellite
The extra_diagnostics:gamap
specify the paths where GEOS-Chem
will create the diaginfo.dat
and tracerinfo.dat
files
used by GAMAP.
The extra_diagnostics:ND51_satellite
and
extra_diagnostics:ND51b_satellite
contain settings for the
GEOS-Chem satellite timeseries
diagnostics..
These will be replaced by GEOS-Chem History diagnostics (in netCDF format) in an
upcoming version.
Hg simulation options¶
This section of geoschem_config.yml
is included for
the mercury (Hg) simulation:
Hg sources¶
The Hg_simulation_options:sources
section contains settings
for various mercury sources.
#============================================================================
# Settings specific to the Hg simulation
#============================================================================
Hg_simulation_options:
sources:
use_dynamic_ocean_Hg: false
use_preindustrial_Hg: false
use_arctic_river_Hg: true
# ... following sub-sections omitted ...
-
use_dynamic_ocean_Hg
¶
Activates (
true
) or deactivates (false
) the online slab ocean mercury model.Default value:
false
-
use_preindustrial_Hg
¶
Activates (
true
) or deactivates (false
) the preindustrial mercury simulation. This will turn off all anthropogenic emissions.Default value:
false
-
use_arctic_river_Hg
¶
Activates (
true
) or deactivates (false
) the source of mercury from arctic rivers.Default value:
true
Hg chemistry¶
The Hg_simulation_options:chemistry
section contains settings
for mercury chemistry:
#============================================================================
# Settings specific to the Hg simulation
#============================================================================
Hg_simulation_options:
# ... preceding sub-sections omitted ...
chemistry:
tie_HgIIaq_reduction_to_UVB: true
# ... following sub-sections omitted ...
-
tie_HgIIaq_reduction_to_UVB
¶
Activates (
true
) or deactivates (false
) linking the reduction of aqueous oxidized mercury to UVB radiation. A lifetime of -1 seconds indicates the species has an infinite lifetime.Default value:
true
Options for simulations with carbon gases¶
These sections of geoschem_config.yml
are included for
simulations with carbon gases (carbon
, CH4
,
CO2
, tagCO
, tagCH4
).
CH4 observational operators¶
The CH4_simulation_options:use_observational_operators
section
contains options for using satellite observational operators for CH4:
#============================================================================
# Settings specific to the CH4 simulation / Integrated Methane Inversion
#============================================================================
CH4_simulation_options:
use_observational_operators:
AIRS: false
GOSAT: false
TCCON: false
# ... following sub-sections omitted ...
-
AIRS
¶
Activates (
true
) or deactivates (false
) the AIRS observational operator.Default value:
false
-
GOSAT
¶
Activates (
true
) or deactivates (false
) the GOSAT observational operator.Default value:
false
-
TCCON
¶
Activates (
true
) or deactivates (false
) the GOSAT observational operator.Default value:
false
CH4 analytical inversion options¶
The ch4_simulation_options:analytical_inversion
section
contains options for analytical inversions (cf. the
Integrated Methane Inversion).
#============================================================================
# Settings specific to the CH4 simulation / Integrated Methane Inversion
#============================================================================
CH4_simulation_options:
# ... preceding sub-sections omitted ...
analytical_inversion:
activate: true
emission_perturbation: 1.0
state_vector_element_number: 0
use_emission_scale_factor: false
use_OH_scale_factors: false
-
activate
¶
Activates (
true
) or deactivates (false
) the analytical inversion.Default value:
true
-
activate
¶
Specifies a factor by which emissions at a grid box will be perturbed.
Default value:
1.0
-
state_vector_element_number
¶
Specifies the element of the state vector used for the inversion.
Default value:
0
-
use_emission_scale_factor
¶
Activates (
true
) or deactivates (false
) scaling methane emissions by a fixed factor.Default value:
false
-
use_emission_scale_factor
¶
Activates (
true
) or deactivates (false
) scaling OH by a fixed factor.Default value:
false
CO2 Sources¶
The CO2_simulation_options:sources
section contains toggles
for activating sources of \(CO_2\):
#============================================================================
# Settings specific to the CO2 simulation
#============================================================================
CO2_simulation_options:
sources:
fossil_fuel_emissions: true
ocean_exchange: true
balanced_biosphere_exchange: true
net_terrestrial_exchange: true
ship_emissions: true
aviation_emissions: true
3D_chemical_oxidation_source: true
# ... following sub-sections omitted ...
-
fossil_fuel_emissions
¶
Activates (
true
) or deactivates (false
) using \(CO_2\) fossil fuel emissions as computed by HEMCO.Default value:
true
-
ocean_exchange
¶
Activates (
true
) or deactivates (false
) \(CO_2\) ocean-air exchange.Default value:
true
-
balanced_biosphere_exchange
¶
Activates (
true
) or deactivates (false
) \(CO_2\) balanced-biosphere exchange.Default value:
true
-
net_terrestrial_exchange
¶
Activates (
true
) or deactivates (false
) \(CO_2\) net terrestrial exchange.Default value:
true
-
ship_emissions
¶
Activates (
true
) or deactivates (false
) \(CO_2\) ship emissions as computed by HEMCO.Default value:
true
-
aviation_emissions
¶
Activates (
true
) or deactivates (false
) \(CO_2\) aviation emissions as computed by HEMCO.Default value:
true
-
3D_chemical_oxidation_source
¶
Activates (
true
) or deactivates (false
) \(CO_2\) production by archived chemical oxidation, as read by HEMCO.Default value:
true
CO2 tagged species¶
The CO2_simulation_options:tagged_species
section contains toggles
for activating tagged \(CO_2\) species:
Attention
Tagged \(CO_2\) tracers should be customized by each user and the present configuration will not work for resolutions other than \(2.0^{\circ} {\times} 2.5^{\circ}\).
#============================================================================
# Settings specific to the CO2 simulation
#============================================================================
CO2_simulation_options:
# ... preceding sub-sections omitted ...
tagged_species:
save_fossil_fuel_in_background: false
tag_bio_and_ocean_CO2: false
tag_land_fossil_fuel_CO2:
tag_global_ship_CO2: false
tag_global_aircraft_CO2: false
-
save_fossil_fuel_in_background
¶
Activates (
true
) or deactivates (false
) saving the \(CO_2\) background.Default value:
false
-
tag_bio_and_ocean_CO2
¶
Activates (
true
) or deactivates (false
) tagging of biosphere regions (28), ocean regions (11), and the rest of the world (ROW) as specified inRegions_land.dat
andRegions_ocean.dat
files.# .. following sub-sections omitted …
CO chemical sources¶
The tagged_CO_simulation_options
section contains settings
for the carbon
simulation and tagged CO simulation.
#============================================================================
# Settings specific to the tagged CO simulation
#============================================================================
tagged_CO_simulation_options:
use_fullchem_PCO_from_CH4: true
use_fullchem_PCO_from_NMVOC: true