diag_table_source.yaml

#######################################################################################################
# This yaml file is used by make_diag_table.py to create a diag_table file specifying MOM diagnostics.
# Latest version: https://github.com/COSIMA/make_diag_table
#
# Define the diagnostics you want in the diag_table section below.
#
# The MOM diag_table format is defined here:
# https://github.com/mom-ocean/MOM5/blob/master/src/shared/diag_manager/diag_table.F90
# https://mom6.readthedocs.io/en/main/api/generated/pages/Diagnostics.html
#######################################################################################################


# Define global default settings which will be applied to all diagnostics,
# unless overridden in diag_table section below, either in defaults or individual fields.
# You're unlikely to need to change any of the global_defaults.
global_defaults:
# global_section:
    title: ACCESS-OM2  # any string
    base_date: [ 1900, 1, 1, 0, 0, 0 ]  # reference time used for the time units. six integers: year, month, day, hour, minute, second
# file section:
    file_name:  # String, or list of components, for file name (without trailing ".nc").
    # If a list, its elements are a mixture of strings and dictionaries.
    # String list elements are concatenated, each preceded by file_name_separator.
    # Dictionary list elements must have one key-value pair; the value is a list
    # containing 1 or more strings to be concatenated, each preceded by the key
    # (a string) instead of file_name_separator. The key may be an empty string,
    # which is useful if file_name_date begins with %, since FMS prepends _ .
    # All filename list string elements (other than field_name) must exist as keys in global_defaults.
    # If file_name_date is used, it must be the last item.
    # Key values are looked up, converted to strings and then substituted using file_name_substitutions.
    # Empty strings (and their preceding separator) are ignored if file_name_omit_empty is true.
    # A separator is not used prior to the first item.
        - file_name_prefix
        - file_name_dimension
        - field_name  # substituted by field name in diag_table section below
        - output_freq
        - '':
            - output_freq_units
        - reduction_method
        - file_name_date
    output_freq: 1  # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run)
    output_freq_units: months  # time units for output: years, months, days, hours, minutes, or seconds
    file_format: 1  # integer, must be 1, specifying NetCDF (the only format currently supported)
    time_axis_units: days  # time units for the output file time axis: years, months, days, hours, minutes, or seconds
    time_axis_name: time  # must be "time" (case-insensitive)
    new_file_freq: 1  # optional integer: frequency (in new_file_freq_units) for closing the existing file, and creating a new file
    new_file_freq_units: years  # time units for new_file_freq: years, months, days, hours, minutes, or seconds (optional; required if and only if new_file_freq specified)
    start_time:  # Time to start the file for the first time. The format of this string is the same as base_date (optional; requires new_file_freq, new_file_freq_units)
    file_duration:  # integer: How long file should receive data after start time (optional; requires new_file_freq, new_file_freq_units, start_time)
    file_duration_units:  # units for file_duration: years, months, days, hours, minutes, or seconds (optional; required if and only if file_duration specified)
# field section:
    module_name: ocean_model
    field_name:  # set via keys in the fields section of the diag_table section below
    output_name:  # same as field_name unless overridden
    # file_name:  # same as file_name in file section above unless overridden in diag_table section below
    time_sampling: all  # Currently not used.  Please use the string "all".
    reduction_method: mean  # mean, snap, rms, pow##, min, max, or diurnal##
    # reduction_method options:
    #     mean or average or true: Average from the last time written to the current time. Becomes "average" in diag_table.
    #     snap or none or false: No reduction.  Write snapshot of current time step value only. Becomes "none" in diag_table.
    #     rms: Calculate the root mean square from the last time written to the current time.
    #     pow##: Calculate the mean of the power ## from the last time written to the current time.
    #     min: Minimum value from last write to current time.
    #     max: Maximum value from last write to current time.
    #     diurnal##: ## diurnal averages
    regional_section: none  # string: bounds of the regional section to capture ("none" indicates a global region). String format: lat_min, lat_max, lon_min, lon_max, vert_min, vert_max. Use vert_min = -1 and vert_max = -1 to get the entire vertical axis.
    packing: 2
    # packing is the Fortran number KIND of the data written:
    #     1: double precision
    #     2: float (single precision)
    #     4: packed 16-bit integers
    #     8: packed 1-byte (not tested)
# extra things for constructing filename:
    file_name_dimension: 3d  # descriptor for filename, e.g. 3d, 2d, scalar
    file_name_prefix: ocean
    file_name_date: "ym%4yr%2mo"  # run date/time of file opening; format: %, 1 digit (#digits), one of (yr, mo, dy, hr, mi, sc); date/time components will be separated by _ in filename.
    file_name_separator: "-"  # used to separate filename components; best not to use "_" to avoid confusion with fields and dates
    file_name_omit_empty: true  # whether to omit empty filename components to avoid duplicate file_name_separator
    file_name_substitutions:  # string replacements for filename components
        years: yearly
        months: monthly
        days: daily
        hours: hourly
        none: snap  # careful! will apply to both reduction_method and regional_section
        'False': snap
        average: mean
        'True': mean
        None: ""  # for empty items


#######################################################################################################
# diag_table section - this defines the diagnostics that will appear in diag_table.
# 
# Top-level categories in diag_table have arbitrary names (they're just used for
# comments in the output diag_table). Make as many of these as you like to group
# similar diagnostics with shared defaults. Note that each of the top-level
# categories can have only have one instance of each field name, so if you need
# multiple outputs of the same field (e.g. as both averages and snapshots), you’ll
# need to make additional categories.
# 
# Within each top-level category there's an optional defaults section and a
# fields section. The defaults section overrides items in global_defaults for
# all fields in the category. The field section specifies diagnostic field
# names. To add a new diagnostic, all you need to do is add its name to the
# field section in the appropriate category. Each field name can be followed by
# a dictionary overriding the category and global defaults for that field only.
# 
# Some of the available MOM5 diagnostics are listed here:
# https://raw.githubusercontent.com/COSIMA/access-om2/master/MOM_diags.txt
# https://github.com/COSIMA/access-om2/wiki/Technical-documentation#MOM5-diagnostics-list
# MOM6 diagnostics are output in available_diags.* when you run the model - see
# https://mom6.readthedocs.io/en/main/api/generated/pages/Diagnostics.html
diag_table:
    'static 2d grid data':
        defaults:  # these can be overridden for individual fields below
            file_name_dimension: 2d  # descriptor for filename, e.g. 3d, 2d, scalar
            file_name:  # String, or list of components, for file name (without trailing ".nc").
            # If a list, its elements are a mixture of strings and dictionaries.
            # String list elements are concatenated, each preceded by file_name_separator.
            # Dictionary list elements must have one key-value pair; the value is a list
            # containing 1 or more strings to be concatenated, each preceded by the key
            # (a string) instead of file_name_separator. The key may be an empty string,
            # which is useful if file_name_date begins with %, since FMS prepends _ .
            # All filename list string elements (other than field_name) must exist as keys in global_defaults.
            # If file_name_date is used, it must be the last item.
            # Key values are looked up, converted to strings and then substituted using file_name_substitutions.
            # Empty strings (and their preceding separator) are ignored if file_name_omit_empty is true.
            # A separator is not used prior to the first item.
                - file_name_prefix
                - file_name_dimension
                - field_name  # substituted by field name in fields section below
            reduction_method: snap  # mean, snap, rms, pow##, min, max, or diurnal##
            output_freq: -1  # Output frequency in output_freq_units (0: every timestep; -1: only at end of run)
            new_file_freq:  # optional integer: frequency (in new_file_freq_units) for closing the existing file, and creating a new file
        fields:
            area_t:
            area_u:
            drag_coeff:
            dxt:
            dxu:
            dyt:
            dyu:
            geolat_c:
            geolat_t:
            geolon_c:
            geolon_t:
            ht:
            hu:
            kmt:
            kmu:
    'yearly 3d fields':
        defaults:  # these can be overridden for individual fields below
            file_name_dimension: 3d  # descriptor for filename, e.g. 3d, 2d, scalar
            output_freq: 1  # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run)
            output_freq_units: years  # time units for output: years, months, days, hours, minutes, or seconds
        fields:
            age_global:
            aiso_bih:
            buoyfreq2_wt:
            diff_cbt_t:
            pot_rho_0:
            pot_rho_2:
            pot_temp:
            salt:
            temp_xflux_adv:
            temp_yflux_adv:
            temp:
            tx_trans_rho:
            tx_trans:
            ty_trans_nrho_submeso:
            ty_trans_rho_gm:
            ty_trans_rho:
            ty_trans_submeso:
            ty_trans:
            u:
            v:
            vert_pv:
            wt:
    'yearly 3d squared fields':  # for calculating EKE etc
        defaults:  # these can be overridden for individual fields below
            file_name_dimension: 3d  # descriptor for filename, e.g. 3d, 2d, scalar
            output_freq: 1  # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run)
            output_freq_units: years  # time units for output: years, months, days, hours, minutes, or seconds
            reduction_method: pow02  # mean, snap, rms, pow##, min, max, or diurnal##
        fields:
            u:
            v:
    'monthly 3d fields':
        defaults:  # these can be overridden for individual fields below
            file_name_dimension: 3d  # descriptor for filename, e.g. 3d, 2d, scalar
            output_freq: 1  # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run)
            output_freq_units: months  # time units for output: years, months, days, hours, minutes, or seconds
        fields:
            dzt:
            # neutral_diffusion_temp:
            # neutral_gm_temp:
            # neutral_temp:
            # pot_temp:
            # salt:
            # temp_advection:
            # temp_eta_smooth:
            # temp_nonlocal_KPP:
            # temp_rivermix:
            # temp_sigma_diff:
            # temp_submeso:
            # temp_tendency_expl:
            # temp_tendency:
            # temp_vdiffuse_diff_cbt_conv:
            # temp_vdiffuse_diff_cbt:
            # temp_vdiffuse_impl:
            # temp_vdiffuse_k33:
            # temp_vdiffuse_sbc:
            # temp:
            # u:
            # v:
    'monthly 2d fields':
        defaults:  # these can be overridden for individual fields below
            file_name_dimension: 2d  # descriptor for filename, e.g. 3d, 2d, scalar
            output_freq: 1  # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run)
            output_freq_units: months  # time units for output: years, months, days, hours, minutes, or seconds
        fields:
            agm:
            aredi:
            bmf_u:
            bmf_v:
            eta_t:
            evap_heat:
            evap:
            fprec_melt_heat:
            fprec:
            frazil_3d_int_z:
            lprec:
            lw_heat:
            melt:
            mld:
            # net_sfc_heating:  # disabled - incorrect - see https://github.com/COSIMA/access-om2/issues/139
            pbot_t:
            pme_net:
            pme_river:
            river:
            runoff:
            sea_level_sq:
            sea_level:
            sens_heat:
            sfc_hflux_coupler:
            sfc_hflux_from_runoff:
            sfc_hflux_pme:
            sfc_salt_flux_coupler:
            sfc_salt_flux_ice:
            sfc_salt_flux_restore:
            surface_salt:
            surface_temp:
            sw_heat:
            swflx:
            tau_x:
            tau_y:
            temp_int_rhodz:
            temp_xflux_adv_int_z:
            temp_xflux_submeso_int_z:
            temp_yflux_adv_int_z:
            temp_yflux_submeso_int_z:
            tx_trans_int_z:
            ty_trans_int_z:
            wfiform:
            wfimelt:
    'monthly 2d fields with different reduction methods':
        defaults:  # these can be overridden for individual fields below
            file_name_dimension: 2d  # descriptor for filename, e.g. 3d, 2d, scalar
            output_freq: 1  # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run)
            output_freq_units: months  # time units for output: years, months, days, hours, minutes, or seconds
        fields:
            eta_t: {reduction_method: pow02}  # for calculating standard deviation
            mld: {reduction_method: max}  # max avoids spurious small values due to rainfall
            surface_temp: {reduction_method: min}  # min for comparison with foundation temperature
    'daily 2d fields':
        defaults:  # these can be overridden for individual fields below
            file_name_dimension: 2d  # descriptor for filename, e.g. 3d, 2d, scalar
            output_freq: 1  # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run)
            output_freq_units: days  # time units for output: years, months, days, hours, minutes, or seconds
        fields:
            eta_t:
            frazil_3d_int_z:
            mld:
            pme_river:
            sfc_hflux_coupler:
            sfc_hflux_from_runoff:
            sfc_hflux_pme:
            surface_salt:
            surface_temp:
            u_surf:
            v_surf:
    'monthly scalar timeseries':
        defaults:  # these can be overridden for individual fields below
            file_name_dimension: scalar  # descriptor for filename, e.g. 3d, 2d, scalar
            file_name:  # String, or list of components, for file name (without trailing ".nc").
            # If a list, its elements are a mixture of strings and dictionaries.
            # String list elements are concatenated, each preceded by file_name_separator.
            # Dictionary list elements must have one key-value pair; the value is a list
            # containing 1 or more strings to be concatenated, each preceded by the key
            # (a string) instead of file_name_separator. The key may be an empty string,
            # which is useful if file_name_date begins with %, since FMS prepends _ .
            # All filename list string elements (other than field_name) must exist as keys in global_defaults.
            # If file_name_date is used, it must be the last item.
            # Key values are looked up, converted to strings and then substituted using file_name_substitutions.
            # Empty strings (and their preceding separator) are ignored if file_name_omit_empty is true.
            # A separator is not used prior to the first item.
                - file_name_prefix
                - file_name_dimension
                - output_freq
                - output_freq_units
                - file_name_date
            output_freq: 1  # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run)
            output_freq_units: months  # time units for output: years, months, days, hours, minutes, or seconds
            packing: 1  # double precision
        fields:
            eta_global:
            ke_tot:
            pe_tot:
            rhoave:
            salt_global_ave:
            salt_surface_ave:
            temp_global_ave:
            temp_surface_ave:
            # total_net_sfc_heating:  # disabled - incorrect - see https://github.com/COSIMA/access-om2/issues/139
            total_ocean_calving_heat:
            total_ocean_calving_melt_heat:
            total_ocean_calving:
            total_ocean_evap_heat:
            total_ocean_evap:
            total_ocean_fprec_melt_heat:
            total_ocean_fprec:
            total_ocean_heat:
            total_ocean_hflux_coupler:
            total_ocean_hflux_evap:
            total_ocean_hflux_prec:
            total_ocean_lprec:
            total_ocean_lw_heat:
            total_ocean_melt:
            total_ocean_pme_river:
            total_ocean_river_heat:
            total_ocean_river:
            total_ocean_runoff_heat:
            total_ocean_runoff:
            total_ocean_salt:
            total_ocean_sens_heat:
            total_ocean_sfc_salt_flux_coupler:
            total_ocean_swflx_vis:
            total_ocean_swflx:
    'monthly 2d snapshots':
        defaults:  # these can be overridden for individual fields below
            file_name_dimension: 2d  # descriptor for filename, e.g. 3d, 2d, scalar
            output_freq: 1  # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run)
            output_freq_units: months  # time units for output: years, months, days, hours, minutes, or seconds
            reduction_method: snap  # mean, snap, rms, pow##, min, max, or diurnal##
        fields:
            # eta_t:
    'monthly 3d snapshots':
        defaults:  # these can be overridden for individual fields below
            file_name_dimension: 3d  # descriptor for filename, e.g. 3d, 2d, scalar
            output_freq: 1  # integer: output sampling frequency in output_freq_units (0: every timestep; -1: only at end of run)
            output_freq_units: months  # time units for output: years, months, days, hours, minutes, or seconds
            reduction_method: snap  # mean, snap, rms, pow##, min, max, or diurnal##
        fields:
            # u:
            # v: