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.. _cfg-gc-yml: ################### geoschem_config.yml ################### Starting with GEOS-Chem 14.0.0, the :file:`input.geos` configuration file (plain text) has been replaced with by the :file:`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 :file:`geoschem_config.yml` file contains several sections. Only The sections relevant to a given type of simulation are present. For example, :option:`fullchem` simulation options (such as aerosol settings and photolysis settings) are omitted from the :file:`geoschem_config.yml` file for the :option:`CH4` simulation. .. note:: Settings that are not relevant to GCHP will be excluded from the :file:`geoschem_config.yml` file that ships with the GCHP run directory. We will note these excluded settings below. All other settings in :file:`geoschem_config.yml` will be treated in in the same way as in `GEOS-Chem Classic `_. .. _gc-yml-simulation: =================== Simulation settings =================== .. code-block:: yaml #============================================================================ # Simulation settings #============================================================================ simulation: name: fullchem start_date: [20190701, 000000] end_date: [20190801, 000000] root_data_dir: /path/to/ExtData met_field: MERRA2 species_database_file: ./species_database.yml species_metadata_output_file: OutputDir/geoschem_species_metadata.yml verbose: activate: false on_cores: root # Allowed values: root all use_gcclassic_timers: false The :literal:`simulation` section contains general simulation options: .. option:: name Specifies the type of GEOS-Chem simulation. Accepted values are .. option:: fullchem Full-chemistry simulation. .. option:: aerosol `Aerosol-only simulation `_. .. option:: carbon Coupled carbon gases simulation (CH4-CO-CO2-OCS), implemented as a KPP mechanism (cf :cite:t:`Bukosa_et_al._2023`). You must configure your build with with :literal:`-DMECH=carbon` in order to use this simulation. For more information, please see: - `GEOS-Chem Classic configuration instructions `_ or - `GCHP configuration instructions `_ .. option:: CH4 `Methane simulation `_. This simulation will eventually be superseded by the :option:`carbon` simulation. .. option:: CO2 `Carbon dioxide simulation `_. This simulation will eventually be superseded by the :option:`carbon` simulation. .. option:: Hg `Mercury simulation `_. You must configure your build with with :literal:`-DMECH=Hg` in order to use this simulation. For more information, please see: - `GEOS-Chem Classic configuration instructions `_ or - `GCHP configuration instructions `_ .. option:: 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. .. option:: tagCH4 `Methane simulation `_ with species tagged by geographic region or other criteria. This simulation will eventually be superseded by the :option:`carbon` simulation. .. option:: tagCO Carbon dioxide simulation, with species tagged by geographic region and other criteria. This simulation will eventually be superseded by the :option:`carbon` simulation. .. option:: tagO3 `Ozone simulation `_ (using specified production and loss rates), with species tagged by geographical region. .. option:: TransportTracers `Transport Tracers simulation `_, with both radionuclide and passive_species. Useful for evaluating model transport. .. option:: metals Trace metals simulation .. option:: start_date .. note:: This option is omitted for GCHP. The simulation start date is specified in the :file:`CAP.rc` and :file:`cap_restart` files. Specifies the starting date and time of the simulation in list notation :literal:`[YYYYMMDD, hhmmss]`. .. option:: end_date .. note:: This option is omitted for GCHP. Duration is specified in the :file:`cap_restart` file. Specifies the ending date and time of the simulation in list notation :literal:`[YYYYMMDD, hhmmss]`. .. option:: 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 :file:`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. .. option:: met_field .. note:: This option is omitted for GCHP. Met field source is described in file paths of the in the :file:`ExtData.rc` file. Name of the meteorology product that will be used to drive GEOS-Chem. Accepted values are: .. option:: 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)** .. 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. .. option:: 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. .. option:: species_database_file Path to the :ref:`GEOS-Chem Species Database ` file. This is stored in the run directory file :file:`./species_database.yml`. You should not have to edit this setting. .. option:: species_metadata_output_file Path to the :file:`geoschem-species-metadata.yml` file. This file contains echoback of information from :ref:`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. .. option:: 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: .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) printing extra informational printout to the screen and/or log file. .. option:: on_cores: Specify on which computational cores informational printout should be done. .. option:: root Print extra informational output only on the root core. Use this setting for GEOS-Chem Classic. .. option:: 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.). .. option:: use_gcclassic_timers .. note:: This setting is omitted for GCHP, as the MAPL library provides all timer functionality. Activates (:literal:`true`) or deactivates (:literal:`false`) the GEOS-Chem Classic timers. If activated, information about how long each component of GEOS-Chem Classic took to execute will be printed to the screen and/or the `log file `_ The same information will also be written in JSON format to a file named `gcclassic_timers.json `_. You can set this option to :literal:`false` unless you are running benchmark or timing simulations. .. _cfg-gc-yml-grid: ============= Grid settings ============= .. note:: Grid settings are omitted for GCHP. Grid specifications are contained in the :file:`GCHP.rc` file instead. .. code-block:: YAML #============================================================================ # 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 :literal:`grid` section contains settings that define the grid used by GEOS-Chem Classic: .. option:: resolution Specifies the horizontal resolution of the grid. Accepted values are: .. option:: 4.0x5.0 The global :math:`4^{\circ}{\times}5^{\circ}` GEOS-Chem Classic grid. .. option:: 2.0x2.5 The global :math:`2.0^{\circ}{\times}2.5^{\circ}` GEOS-Chem Classic grid. .. option:: 0.5x0.625 The global :math:`0.5^{\circ}{\times}0.625^{\circ}` GEOS-Chem Classic grid (:option:`MERRA2` only). Can be used for global or nested simulations. .. option:: 0.5x0.625 The global :math:`0.25^{\circ}{\times}0.3125^{\circ}` GEOS-Chem Classic grid (:option:`GEOS-FP` and :option:`MERRA2`). Can be used for global or nested simulations. .. option:: number_of_levels Number of vertical levels to use in the simulation. Accepted values are: .. option:: 72 Use 72 vertical levels. This is the native vertical resolution of :option:`MERRA2` and :option:`GEOS-FP`. .. option:: 47 Use 47 vertical levels (for :option:`MERRA2` and :option:`GEOS-FP`). .. option:: 40 Use 40 vertical levels (for :option:`GCAP2`). .. option:: longitude Settings that define the longitude dimension of the grid. There are two sub-options: .. option:: range The minimum and maximum longitude values (grid box edges), specified in list format. .. option:: center_at_180 If :literal:`true`, then westernmost grid boxes are centered at :math:`-180^{\circ}` longitude (the International Date Line). This is true for both :option:`MERRA2` and :option:`GEOS-FP`. If :literal:`false`, then the westernmost grid boxes have their westernmost edges at :math:`-180^{\circ}` longitude. This is true for the :option:`GCAP2` grid. .. option:: latitude Settings to define the latitude dimension of the grid. There are two sub-options: .. option:: range The minimum and maximum latitude values (grid box edges), specified in list format. .. option:: use_halfpolar_boxes If :literal:`true`, then the northernmost and southernmost grid boxes will be :math:`\frac{1}{2}` the extent of other grid boxes. This is true for both :option:`MERRA2` and :option:`GEOS-FP`. If :literal:`false`, then all grid boxes will have the same extent in latitude. This is true for the :option:`GCAP2` grid. .. option:: nested_grid_simulation Settings for nested-grid simulations. There are two sub-options: .. option:: activate If :literal:`true`, this indicates that the simulation will use a sub-window of the horizontal grid. If :literal:`false`, this indicates that the simulation will use the entire global grid extent. .. option:: buffer_zone_NSEW Specifies the nested grid latitude offsets (# of grid boxes) in list format :literal:`[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: :literal:`[0, 0, 0, 0]`. - For nested-grid simulations, we recommend using: :literal:`[3, 3, 3, 3]`. .. _cfg-gc-yml-timesteps: ================== Timesteps settings ================== .. note:: Timesteps settings are omitted for GCHP. Timesteps are specified in the :file:`CAP.rc` file. .. code-block:: YAML #============================================================================ # Timesteps settings #============================================================================ timesteps: transport_timestep_in_s: 600 chemistry_timestep_in_s: 1200 radiation_timestep_in_s: 10800 The :literal:`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 | +==============================================+=============+==============+ | :math:`4^{\circ}{\times}5^{\circ}` | 600s (10m) | 1200s (20m) | +----------------------------------------------+-------------+--------------+ | :math:`2^{\circ}{\times}2.5^{\circ}` | 600s (10m) | 1200s (20m) | +----------------------------------------------+-------------+--------------+ | :math:`0.5^{\circ}{\times}0.625^{\circ}` | 300s (5m) | 600s (10m) | +----------------------------------------------+-------------+--------------+ | :math:`0.25^{\circ}{\times}0.3125^{\circ}` | 300s (5m) | 600s (10m) | +----------------------------------------------+-------------+--------------+ | :math:`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 :cite:t:`Philip_et_al._2016` for a comprehensive study on GEOS-Chem timesteps. For some practical tips on speeding up your simulations, see: - `Speeding up GEOS-Chem Classic simulations `_ - .. option:: 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. .. option:: chemistry_timestep_in_s Specifies the frequency at which chemistry and emissions will be done. .. option:: radiation_timestep_in_s Specifies the frequency at which the `RRTMG `_ radiative transfer model will be called (valid for :option:`fullchem` simulations only). We recommend using a timestep of 10800s (3h), as the RRTMG calculations are computationally intensive. .. _cfg-gc-yml-operations: =================== Operations settings =================== This section of :file:`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 :literal:`operations`: .. _cfg-gc-yml-operations-chemistry: Chemistry ---------- .. code-block:: YAML #============================================================================ # 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 :literal:`operations:chemistry` section contains settings for chemistry: .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) chemistry in GEOS-Chem. .. option:: linear_chemistry_aloft Determines how linearized chemistry will be applied in the stratosphere and/or mesosphere. (Only valid for :option:`fullchem` simulations). There are two sub-options: .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) linearized stratospheric chemistry in the stratosphere and/or mesosphere. .. option:: use_linoz_for_O3 If :literal:`true`, `Linoz stratospheric ozone chemistry `_ will be used. If :literal:`false`, Synoz (i.e. a synthetic flux of ozone across the tropopause) will be used instead of Linoz. .. option:: active_strat_H2O Determines if water vapor as modeled by GEOS-Chem will be allowed to influence humidity fields. (Only valid for :option:`fullchem` simulations) There are two sub-options: .. option:: activate Allows (:literal:`true`) or disallows (:literal:`false` the H2O species in GEOS-Chem to influence specific humidity and relative humidity. .. option:: use_static_bnd_cond Allows (:literal:`true`) or diasallows (:literal:`false`) a static boundary condition. **TODO** Clarify this .. option:: gamma_HO2 Specifies :math:`\gamma`, the uptake coefficient for :math:`HO_2` heterogeneous chemistry. Recommended value: :literal:`0.2`. .. option:: autoreduce_solver Menu for controlling the adaptive mechanism auto-reduction feature, which is available in `KPP 3.0.0. `_ and later versions. See :cite:t:`Lin_et_al._2023` for details. .. option:: activate If :literal:`true`, the mechanism will be integrated using the Rosenbrock method with the adaptive auto-reduction feature. If :literal:`false`, the mechanism will be integrated using the traditional Rosenbrock method. Default value: :literal:`false`. .. option:: use_target_threshold Contains options for defining :math:`\partial` (the partitioning threshold between "fast" and "slow" species") by considering the production and loss of key species (OH for daytime, NO2 for nighttime). .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) using OH and NO2 to determine :math:`\partial`. Default value: :literal:`true`. .. option:: oh_tuning_factor Specifies :math:`{\alpha}_{OH}`, which is used to compute :math:`\partial`. .. option:: no2 tuning factor Specifies :math:`{\alpha}_{NO2}`, which is used to compute :math:`\partial`. .. option:: use_pressure_threshold Contains options for setting an absolute threshold :math:`\partial` that may be weighted by pressure. .. option:: scale_by_pressure Activates (:literal:`true`) or deactivates (:literal:`false`) using a pressure-dependent method to determine :math:`\partial`. .. option:: absolute_threshold The absolute partitioning threshold :math:`\partial`. If :option:`scale_by_pressure` is :literal:`true,` and :option:`use_target_threshold:activate` is :literal:`false` , the value for :math:`\partial` specified here will be scaled by the ratio :math:`P / P_{sfc}`. where :math:`P` is the grid box pressure and :math:`P_{sfc}` is the surface pressure for the column. .. option:: keep_halogens_active If :literal:`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 :literal:`false`, then halogen species will be determined as "slow" or "fast" depending on the partitioning threshold :math:`\partial`. Default value: :literal:`true` .. option:: append_in_internal_timestep If :literal:`true`, any "slow" species that later become "fast" will be appended to the list of "fast" species. If :literal:`false`, any "slow" species that later become "fast" will NOT be appended to the list of "fast" species. Default value: :literal:`false` .. _cfg-gc-yml-operations-convection: Convection ---------- .. code-block:: YAML #============================================================================ # Settings for GEOS-Chem operations #============================================================================ operations: # .. preceding sub-sections omitted ... convection: activate: true # ... following sub-sections omitted ... The :command:`operations:convection` section contains settings for `cloud convection `_: .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) cloud convection in GEOS-Chem. .. _cfg-gc-yml-operations-drydep: Dry deposition -------------- .. code-block:: YAML #============================================================================ # 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 :literal:`operations:dry_deposition` section contains settings that for `dry deposition `_: .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) dry deposition. .. option:: CO2_effect This sub-section contains options for applying the `simple parameterization for the CO2 effect on stomatal resistance `_. .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) the CO2 effect on stomatal resistance in dry deposition. Default value: :literal:`false`. .. option:: CO2_level Specifies the CO2 level (in ppb). .. option:: reference_CO2_level Specifies the reference CO2 level (in ppb). .. option:: diag_alt_above_sfc_in_m: Specifies the altitude above the surface (in m) to used with the `ConcAboveSfc diagnostic collection `_. .. _cfg-gc-yml-operations-pblmix: PBL mixing ---------- .. code-block:: YAML #============================================================================ # Settings for GEOS-Chem operations #============================================================================ operations: # .. preceding sub-sections omitted ... pbl_mixing: activate: true use_non_local_pbl: true # ... following sub-sections omitted ... The :literal:`operations:pbl_mixing` section contains settings that for `planetary boundary layer (PBL) mixing `_: .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) planetary boundary layer mixing in GEOS-Chem Classic. .. option:: use_non_local_pbl If :literal:`true`, then the `non-local PBL mixing scheme (VDIFF) `_ will be used. (Default option) If :literal:`false`, then the `full PBL mixing scheme (TURBDAY) `_ will be used. .. _cfg-gc-yml-operations-photolysis: Photolysis ---------- .. code-block:: YAML #============================================================================ # Settings for GEOS-Chem operations #============================================================================ operations: # .. preceding sub-sections omitted ... photolysis: activate: true cloud-j: num_levs_with_cloud: 34 cloud_scheme_flag: 3 opt_depth_increase_factor: 1.050 min_top_inserted_cloud_OD: 0.005 cloud_overlap_correlation: 0.33 num_cloud_overlap_blocks: 6 sphere_correction: 1 num_wavelength_bins: 18 use_H2O_UV_absorption: true input_directories: fastjx_input_dir: /path/to/ExtData/CHEM_INPUTS/FAST_JX/v2024-05/ cloudj_input_dir: /path/to/ExtData/CHEM_INPUTS/CLOUD_J/v2024-09/ overhead_O3: use_online_O3_from_model: true use_column_O3_from_met: true use_TOMS_SBUV_O3: false photolyze_nitrate_aerosol: activate: true NITs_Jscale: 100.0 NIT_Jscale: 100.0 percent_channel_A_HONO: 66.667 percent_channel_B_NO2: 33.333 # ... following sub-sections omitted ... The :literal:`operation:photolysis` section contains settings for photolysis. This section only applies to fullchem, Hg, and aerosol-only simulations. .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) photolysis. .. attention:: You should always keep photolysis turned on in your simulations. Disabling photolysis should only be done when debugging. .. option:: 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). .. option:: num_levs_with_cloud Specifies the number of levels that can contain clouds, which is a required input for the Cloud-J photolysis module. This value is pre-set to the proper value for the vertical grid that your simulation will use. +--------------------------+------------------------------------+ | **GEOS-Chem variable:** | ``Input_Opt%NLevs_Phot_Cloud`` | +--------------------------+------------------------------------+ | **Cloud-J variable** | ``LWEPAR`` | +--------------------------+------------------------------------+ .. option:: cloud_scheme_flag Specifies the `cloud option `_ used in the computation of photolyis rates. +--------------------------+------------------------------------+ | **GEOS-Chem variable:** | ``Input_Opt%CLDFLAG`` | +--------------------------+------------------------------------+ | **Cloud-J variable** | ``LWEPAR`` | +--------------------------+------------------------------------+ .. option:: opt_depth_increase_factor Specifies the factor increase in cloud optical depth from a given layer to the layer below. +--------------------------+------------------------------------+ | **GEOS-Chem variable:** | ``Input_Opt%OD_Increase_Factor`` | +--------------------------+------------------------------------+ | **Cloud-J variable** | ``ATAU`` | +--------------------------+------------------------------------+ .. option:: min_top_inserted_cloud_OD Specifies the minimum cloud OD in the uppermost inserted layer. +--------------------------+------------------------------------+ | **GEOS-Chem variable:** | ``Input_Opt%Min_Cloud_OD`` | +--------------------------+------------------------------------+ | **Cloud-J variable** | ``ATAU0`` | +--------------------------+------------------------------------+ .. option:: cloud_overlap_correlation Specifies the cloud de-corellation between max-overlap blocks, where 0.00 is random overlap. This option is only used when :option:`cloud_scheme_flag` is set to 5 or higher. +--------------------------+------------------------------------+ | **GEOS-Chem variable:** | ``Input_Opt%Cloud_Corr`` | +--------------------------+------------------------------------+ | **Cloud-J variable** | ``CLDCOR`` | +--------------------------+------------------------------------+ .. option:: num_cloud_overlap_blocks Specifies the number of `maximum-overlap blocks `_. +--------------------------+------------------------------------+ | **GEOS-Chem variable:** | ``Input_Opt%Num_Max_Overlap`` | +--------------------------+------------------------------------+ | **Cloud-J variable** | ``LNRG`` | +--------------------------+------------------------------------+ .. option:: sphere_correction Specifies the type of `spherical correction `_ to be applied. +--------------------------+------------------------------------+ | **GEOS-Chem variable:** | ``Input_Opt%OD_Increase_Factor`` | +--------------------------+------------------------------------+ | **Cloud-J variable** | ``ATM0`` | +--------------------------+------------------------------------+ .. option:: num_wavelength_bins Specifies the `number of wavelength bins `_ to use in the computation of photolysis reaction rates. +--------------------------+------------------------------------+ | **GEOS-Chem variable:** | ``Input_Opt%Num_WV_Bins`` | +--------------------------+------------------------------------+ | **Cloud-J variable** | ``ATM0`` | +--------------------------+------------------------------------+ .. option:: use_H2O_UV_absorption Specifies whether to enable (:literal:`true`) or disable (:literal:`false`) UV absorption of water vapor in the computations for photolysis rates. Default value: :literal:`true`. +--------------------------+------------------------------------+ | **GEOS-Chem variable:** | ``Input_Opt%Use_H2O_UV_Abs`` | +--------------------------+------------------------------------+ | **Cloud-J variable** | ``USEH2OUV`` | +--------------------------+------------------------------------+ .. option:: input_directories Specifies the location of directories containing photolysis configuration files. .. option:: 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 :literal:`-DFASTJX=y` during build. .. option:: cloudj_input_dir Specifies the path to the Cloud-J configuration files containing information about species cross sections and quantum yields. .. option:: overhead_O3 This section contains settings that control which overhead ozone sources are used for photolysis .. option:: use_online_O3_from_model Activates (:literal:`true`) or deactivates (:literal:`false`) using online O3 from GEOS-Chem in the extinction calculations for photolysis. Recommended value: :literal:`true` .. option:: use_column_O3_from_met Activates (:literal:`true`) or deactivates (:literal:`false`) using ozone columns (e.g. TO3) from the meteorology fields. Recommended value: :literal:`true`. .. option:: use_TOMS_SBUV_O3 Activates (:literal:`true`) or deactivates (:literal:`false`) using ozone columns from the TOMS-SBUV archive will be used. Recommended value: :literal:`false`. .. option:: photolyze_nitrate_aerosol This section contains settings that control options for nitrate aerosol photolysis. .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) nitrate aerosol photolysis. Recommended value: :literal:`true`. .. option:: NITs_Jscale Scale factor (percent) for JNO3 that photolyzes NITs aerosol. .. option:: NIT_Jscale Scale factor (percent) for JHNO2 that photolyzes NIT aerosol. .. option:: percent_channel_A_HONO Fraction of JNITs/JNIT in channel A (HNO2) for NITs photolysis. .. option:: percent_channel_B_HO2 Fraction of JNITs/JNIT in channel B (NO2) for NITs photolysis. .. _cfg-gc-yml-rrtmg: RRTMG radiative transfer model ------------------------------ .. code-block:: YAML #============================================================================ # 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 :literal:`operations:rrtmg_rad_transfer_model` section contains settings for the `RRTMG radiative transfer model `_: This section only applies to :option:`fullchem` simultions. .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) the RRTMG radiative transfer model. Default value: :literal:`false`. .. option:: 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. .. option:: longwave_fluxes Activates (:literal:`true`) or deactivates (:literal:`false`) RRTMG longwave flux calculations. Default value: :literal:`false`. .. option:: shortwave_fluxes Activates (:literal:`true`) or deactivates (:literal:`false`) RRTMG shortwave calculations. Default value: :literal:`false`. .. option:: clear_sky_flux Activates (:literal:`true`) or deactivates (:literal:`false`) RRTMG clear-sky flux calculations. Default value: :literal:`false`. .. option:: all_sky_flux Activates (:literal:`true`) or deactivates (:literal:`false`) RRTMG all-sky flux calculations. Default value: :literal:`false`. .. option:: fixed_dyn_heating Activates (:literal:`true`) or deactivates (:literal:`false`) fixed dynamic heating (FDH) approximation as described by Forster *et al.* [`1997 `_]. Default value: :literal:`false`. .. option:: seasonal_fdh Activates (:literal:`true`) or deactivates (:literal:`false`) seasonally-evolving fixed dynamic heating (SEFDH) approzimation as described by Kiehl *et al.* [`1999 `_]. .. attention:: This option has not been extensively tested, and is considered experimental. Default value: :literal:`false`. .. option:: read_dyn_heating Activates (:literal:`true`) or deactivates (:literal:`false`) reading previously-archived dynamical heating outputs from disk. Default value: :literal:`false`. .. option:: co2_ppmv Specify the value of CO2 [in parts per million by volume] to be used in radiative forcing calculations. Default value: :literal:`390.0`. .. _cfg-gc-yml-transport: Transport --------- .. code-block:: YAML #============================================================================ # 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 :literal:`operations:transport` section contains settings for `species transport `_: .. option:: gcclassic_tpcore .. note:: These settings are omitted for GCHP, which uses the FVdycore advection package instead. Contains options that control species transport in GEOS-Chem Classic with the `TPCORE advection scheme `_: .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) species transport in GEOS-Chem Classic. Default value: :literal:`true`. .. option:: fill_negative_values If :literal:`true`, negative species concentrations will be replaced with zeros. If :literal:`false`, no change will be made to species concentrations. Default value: :literal:`true`. .. option:: 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: :literal:`[3, 3, 7]` .. option:: transported_species A list of species names (in `YAML sequence format `_) that will be transported by the TPCORE advection scheme. .. _cfg-gc-yml-wetdep: Wet deposition -------------- .. code-block:: YAML #============================================================================ # Settings for GEOS-Chem operations #============================================================================ operations: # .. preceding sub-sections omitted ... wet_deposition: activate: true The :literal:`operations:wet_deposition` section contains settings for `wet deposition `_. .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) wet deposition in GEOS-Chem Classic. .. _gc-yml-aerosols: ================= Aerosols settings ================= This section of :file:`geoschem_config.yml` is included for :option:`fullchem` and :option:`aerosol` simulations. There are several sub-sections under :literal:`aerosols`: .. _cfg-gc-yml-aerosol-optics: Optics ------ .. code-block:: YAML #============================================================================ # Settings for GEOS-Chem aerosols #============================================================================ aerosols: optics: input_dir: /path/to/ExtData/CHEM_INPUTS/Aerosol_Optics/v2024-08/ # .. following sub-sections omitted ... .. option:: optics .. option:: input_dir Specifies the path to files used containing aerosol optical properties for computing aerosol optical depth. .. _cfg-gc-yml-aerosol-carbon: Carbon aerosols --------------- .. code-block:: YAML #============================================================================ # 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 :literal:`aerosols:carbon` section contains settings for `carbon aerosols `_: .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) carbon aerosols in GEOS-Chem. Default value: :literal:`true`. .. option:: brown_carbon Activates (:literal:`true`) or deactivates (:literal:`false`) brown carbon aerosols in GEOS-Chem. Default value: :literal:`false`. .. option:: enhance_black_carbon_absorption Options for enhancing the absorption of black carbon aerosols due to external coating. .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) black carbon absorption enhancement. Default value: :literal:`true`. .. option:: hydrophilic Absorption enhancement factor for hydrophilic black carbon aerosol (species name **BCPI**). Default value: :literal:`1.5` .. option:: hydrophobic Absorption enhancement factor for hydrophilic black carbon aerosol (species name **BCPO**). Default value: :literal:`1.0` .. _cfg-gc-yml-aerosols-soa: Complex SOA ----------- The :code:`aerosols:complex_SOA` section contains settings for `the complex SOA scheme used in GEOS-Chem `_. .. code-block:: YAML #============================================================================ # Settings for GEOS-Chem aerosols #============================================================================ aerosols: # ... preceding sub-sections omitted ... complex_SOA: activate: true semivolatile_POA: false # ... following sub-sections omitted ... .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) the complex SOA scheme. Default value: - :literal:`true` for the :option:`fullchem` benchmark simulation - :literal:`false` for all other :option:`fullchem` simulations .. option:: semivolatile_POA Activates (:literal:`true`) or deactivates (:literal:`false`) the semi-volatile primary organic aerosol (POA) option. Default value: :literal:`false` .. _gc-yml-aerosols-dust: Mineral dust aerosols --------------------- The :literal:`aerosols:dust` section contains settings for `mineral dust aerosols `_. .. code-block:: YAML #============================================================================ # Settings for GEOS-Chem aerosols #============================================================================ aerosols: # ... preceding sub-sections omitted ... dust: activate: true acid_uptake_on_dust: false # ... following sub-sections omitted ... .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) mineral dust aerosols in GEOS-Chem. Default value: :literal:`true` .. option:: acid_uptake_on_dust Activates (:literal:`true`) or deactivates (:literal:`false`) the `acid uptake on dust option `_, which includes 12 additional species. Default value: :literal:`false` .. _cfg-gc-yml-aerosols-seasalt: Sea salt aerosols ----------------- The :literal:`aerosols:sea_salt` section contains settings for `sea salt aerosols `_: .. code-block:: YAML #============================================================================ # 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 ... .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) sea salt aerosols. Default value: :literal:`true` .. option:: SALA_radius_bin_in_um Specifies the upper and lower boundaries (in nm) for accumulation-mode sea salt aerosol (aka **SALA**). Default value: :literal:`0.01 nm - 0.5 nm` .. option:: SALC_radius_bin_in_um Specifies the upper and lower boundaries (in nm) for coarse-mode sea salt aerosol (aka **SALC**). Default value: :literal:`0.5 nm - 8.0 nm` .. option:: marine_organic_aerosols Activates (:literal:`true`) or deactivates (:literal:`false`) `emission of marine primary organic aerosols `_. This option includes two extra species (**MOPO** and **MOPI**). Default value: :literal:`false` .. _cfg-gc-yml-aerosols-strat: Stratospheric aerosols ---------------------- The :literal:`aerosols:sulfate` section contains settings for stratopsheric aerosols. .. code-block:: YAML #============================================================================ # 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 ... .. option:: settle_strat_aerosol Activates (:literal:`true`) or deactivates (:literal:`false`) gravitational settling of stratospheric solid particulate aerosols (SPA, trapezoidal scheme) and stratospheric liquid aerosols (SLA, corrected Stokes' Law). Default value: :literal:`true` .. option:: polar_strat_clouds Contains settings for how aerosols are handled in polar stratospheric clouds (PSC): .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) formation of polar stratospheric clouds. Default value: :literal:`true` .. option:: het_chem Activates (:literal:`true`) or deactivates (:literal:`false`) heterogeneous chemistry within polar stratospheric clouds. Default value: :literal:`true` .. option:: allow_homogeneous_NAT Activates (:literal:`true`) or deactivates (:literal:`false`) heterogeneous formation of NAT from freezing of HNO3. Default value: :literal:`false` .. option:: NAT_supercooling_req_in_K Specifies the cooling (in K) required for homogeneous NAT nucleation. Default value: :literal:`3.0` .. option:: supersat_factor_req_for_ice_nucl Specifies the supersaturation factor required for ice nucleation. Recommended values: :literal:`1.2` for coarse grids; :literal:`1.5` for fine grids. .. option:: calc_strat_aod Includes (:literal:`true`) or excludes (:literal:`false`) online stratospheric aerosols in extinction calculations for photolysis. Default value: :literal:`true` .. _cfg-gc-yml-aerosols-sulfate: Sulfate aerosols ---------------- The :literal:`aerosols:sulfate` section contains settings for `sulfate aerosols `_: .. code-block:: YAML #============================================================================ # Settings for GEOS-Chem aerosols #============================================================================ aerosols: # ... preceding sub-sections omitted ... sulfate: activate: true metal_cat_SO2_oxidation: true .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) sulfate aerosols. Default value: :literal:`true` .. option:: metal_cat_SO2_oxidation Activates (:literal:`true`) or deactivates (:literal:`false`) the `metal catalyzed oxidation of SO2 `_. Default value: :literal:`true` .. _cfg-gc-yml-xdiag: ================= Extra diagnostics ================= The :literal:`extra_diagnostics` section contains settings for GEOS-Chem Classic diagnostics that are not archived by `History diagnostics `_ or `HEMCO `_. .. _gc-yml-xdiag-obspack: Obspack diagnostic ------------------ .. note:: These settings are omitted for GCHP, as ObsPack diagnostics can only be used with GEOS-Chem Classic. The :literal:`extra_diagnostics:obspack` section contains settings for the `Obspack diagnostic `_: .. code-block:: YAML #============================================================================ # 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 ... .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) ObsPack diagnostic output. Default value: :literal:`true` .. option:: quiet_logfile_output Deactivates (:literal:`true`) or activates (:literal:`false`) printing informational output to :literal:`stdout` (i.e. the screen or log file). Default value: :literal:`false` .. option:: input_file Specifies the path to an ObsPack data file (in netCDF format). .. option:: 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 :option:`input_file`. .. option:: output_species A list of GEOS-Chem species (as a YAML sequence) to archive to the output file. .. _gc-yml-xdiag-plane: Planeflight diagnostic ----------------------- .. note:: These settings are omitted for GCHP, as the Planeflight diagnostics can only be used with GEOS-Chem Classic. The :literal:`extra_diagnostics:planeflight` section contains settings for the `GEOS-Chem planeflight diagnostic `_: .. code-block:: YAML #============================================================================ # 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 ... .. option:: activate Activates (:literal:`true`) or deactivates (:literal:`false`) the Planeflight diagnostic output. Default value: :literal:`false` .. option:: 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. .. option:: output_file Specifies the path to the Planeflight output file. Requested quantities will be archived from GEOS-Chem along the flight track specified in :option:`flight_track_file`. .. _cfg-gc-yml-hg: ===================== Hg simulation options ===================== This section of :file:`geoschem_config.yml` is included for the `mercury (Hg) simulation `_: .. _cfg-gc-yml-hg-src: Hg sources ---------- The :literal:`Hg_simulation_options:sources` section contains settings for various mercury sources. .. code-block:: YAML #============================================================================ # 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 ... .. option:: use_dynamic_ocean_Hg Activates (:literal:`true`) or deactivates (:literal:`false`) the online slab ocean mercury model. Default value: :literal:`false` .. option:: use_preindustrial_Hg Activates (:literal:`true`) or deactivates (:literal:`false`) the preindustrial mercury simulation. This will turn off all anthropogenic emissions. Default value: :literal:`false` .. option:: use_arctic_river_Hg Activates (:literal:`true`) or deactivates (:literal:`false`) the source of mercury from arctic rivers. Default value: :literal:`true` .. _cfg-gc-yml-hg-chem: Hg chemistry ------------ The :literal:`Hg_simulation_options:chemistry` section contains settings for mercury chemistry: .. code-block:: YAML #============================================================================ # Settings specific to the Hg simulation #============================================================================ Hg_simulation_options: # ... preceding sub-sections omitted ... chemistry: tie_HgIIaq_reduction_to_UVB: true # ... following sub-sections omitted ... .. option:: tie_HgIIaq_reduction_to_UVB Activates (:literal:`true`) or deactivates (:literal:`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: :literal:`true` .. _cfg-gc-yml-carbon: ========================================= Options for simulations with carbon gases ========================================= These sections of :file:`geoschem_config.yml` are included for simulations with carbon gases (:option:`carbon`, :option:`CH4`, :option:`CO2`, :option:`tagCO`, :option:`tagCH4`). .. _gc-yml-ch4_obsopt: CH4 observational operators ---------------------------- The :literal:`CH4_simulation_options:use_observational_operators` section contains options for using satellite observational operators for CH4: .. code-block:: YAML #============================================================================ # 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 ... .. option:: AIRS Activates (:literal:`true`) or deactivates (:literal:`false`) the AIRS observational operator. Default value: :literal:`false` .. option:: GOSAT Activates (:literal:`true`) or deactivates (:literal:`false`) the GOSAT observational operator. Default value: :literal:`false` .. option:: TCCON Activates (:literal:`true`) or deactivates (:literal:`false`) the GOSAT observational operator. Default value: :literal:`false` .. _gc-yml-ch4_anopt: CH4 analytical inversion options --------------------------------- The :literal:`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. .. code-block:: YAML #============================================================================ # Settings specific to the CH4 simulation / Integrated Methane Inversion #============================================================================ CH4_simulation_options: # ... preceding sub-sections omitted ... analytical_inversion: perturb_OH_boundary_conditions: false CH4_boundary_condition_ppb_increase_NSEW: [0.0, 0.0, 0.0, 0.0] .. option:: perturb_CH4_boundary_conditions Activates (:literal:`true`) or deactivatees (:literal:`false`) perturbation of CH4 nested-grid boundary conditions in analytical inversions. Default value: :literal:`false` .. option:: 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 :option:`perturb_CH4_boundary_conditions` option. Default value: :literal:`[0.0, 0.0, 0.0, 0.0]` (no perturbation) .. _cfg-gc-yml-co2: CO2 Sources ----------- The :literal:`CO2_simulation_options:sources` section contains toggles for activating sources of :math:`CO_2`: .. code-block:: YAML #============================================================================ # Settings specific to the CO2 simulation #============================================================================ CO2_simulation_options: sources: 3D_chemical_oxidation_source: true # ... following sub-sections omitted ... .. option:: 3D_chemical_oxidation_source Activates (:literal:`true`) or deactivates (:literal:`false`) :math:`CO_2` production by archived chemical oxidation, as read by HEMCO. Default value: :literal:`true` .. _cfg-gc-yml-co2-tagspc: CO2 tagged species ------------------ The :literal:`CO2_simulation_options:tagged_species` section contains toggles for activating tagged :math:`CO_2` species: .. attention:: Tagged :math:`CO_2` tracers should be customized by each user and the present configuration will not work for resolutions other than :math:`2.0^{\circ} {\times} 2.5^{\circ}`. .. code-block:: YAML #============================================================================ # Settings specific to the CO2 simulation #============================================================================ CO2_simulation_options: # ... preceding sub-sections omitted ... tagged_species: tag_bio_and_ocean_CO2: false tag_land_fossil_fuel_CO2: false # .. following sub-sections omitted ... .. option:: tag_bio_and_ocean_CO2 Activates (:literal:`true`) or deactivates (:literal:`false`) tagging of biosphere regions (28), ocean regions (11), and the rest of the world (ROW) as specified in :file:`Regions_land.dat` and :file:`Regions_ocean.dat` files. .. option:: tag_land_fossil_fuel_CO2: Activates (:literal:`true`) or deactivates (:literal:`false`) tagging of land and ocean fossil fuel regions. .. _cfg-gc-yml-co: CO chemical sources ------------------- The :literal:`tagged_CO_simulation_options` section contains settings for the :option:`carbon` simulation and `tagged CO simulation `_. .. code-block:: YAML #============================================================================ # Settings specific to the tagged CO simulation #============================================================================ tagged_CO_simulation_options: use_fullchem_PCO_from_CH4: true use_fullchem_PCO_from_NMVOC: true .. option:: use_fullchem_PCO_from_CH4 Activates (:literal:`true`) or deactivates (:literal:`false`) applying the production of :math:`CO` from :math:`CH_4`. This field is archived from a 1-year or 10-year :option:`fullchem` benchmark simulation and is read from disk via HEMCO. Default value: :literal:`true` .. option:: use_fullchem_PCO_from_NMVOC Activates (:literal:`true`) or deactivates (:literal:`false`) applying the production of :math:`CO` from non-methane volatile organic compounds (VOCs). This field is archived from a 1-year or 10-year :option:`fullchem` benchmark simulation and is read from disk via HEMCO. Default value: :literal:`true`