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recipe_ocean_bgc.yml
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recipe_ocean_bgc.yml
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# ESMValTool
# recipe_ocean_bcg.yml
---
documentation:
description: |
Recipe to evaluate the marine biogeochemistry models of CMIP5.
There are also some physical evaluation metrics here too.
This work based on the BGC-val toolkit GMD-2018-103.
DOI: https://doi.org/10.5194/gmd-11-4215-2018
Written by Lee de Mora, Plymouth Marine Laboratory, ledm@pml.ac.uk
authors:
- demora_lee
maintainer:
- demora_lee
references:
- demora2018gmd
projects:
- ukesm
datasets:
- {dataset: HadGEM2-ES, project: CMIP5, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# working datasets
# - {dataset: CanESM2, project: CMIP5, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# - {dataset: CanCM4, project: CMIP5, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# - {dataset: CSIRO-Mk3-6-0, project: CMIP5, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# - {dataset: GISS-E2-H, project: CMIP5, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# - {dataset: HadGEM2-AO, project: CMIP5, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# - {dataset: HadGEM2-CC, project: CMIP5, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# - {dataset: HadCM3, project: CMIP5, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
###
# Problem with times
# - {dataset: MIROC-ESM, project: CMIP5, mip: Oyr, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# - {dataset: MIROC-ESM-CHEM, project: CMIP5, mip: Oyr, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# Unstructured grids
# - {dataset: MPI-ESM-LR, project: CMIP5, mip: Oyr, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2003}
# - {dataset: MPI-ESM-MR, project: CMIP5, mip: Oyr, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# - {dataset: ACCESS1-0, project: CMIP5, mip: Oyr, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# - {dataset: ACCESS1-3, project: CMIP5, mip: Oyr, exp: historical, ensemble: r1i1p1, start_year: 2001, end_year: 2004}
# --------------------------------------------------
# Preprocessors
# --------------------------------------------------
preprocessors:
# Global 3D Volume-weighted Average
prep_timeseries_global_volume_average:
custom_order: true
volume_statistics:
operator: mean
multi_model_statistics:
span: overlap
statistics: [mean ]
# Global area-weighted Average from 2D field
prep_global_Surface_average_timeseries_2D:
custom_order: true
area_statistics:
operator: mean
multi_model_statistics:
span: overlap
statistics: [mean ]
# Global area -weighted surface Average from 3D field
prep_global_Surface_average_timeseries_3D:
custom_order: true
extract_levels:
levels: [0., ]
scheme: linear_horizontal_extrapolate_vertical
area_statistics:
operator: mean
multi_model_statistics:
span: overlap
statistics: [mean ]
prep_timeseries_scalar: # Load file as is.
custom_order: true
# For a 2D global surface map
prep_surface_map_2D:
climate_statistics:
operator: mean
# For a 3D global surface map
prep_surface_map_3D:
extract_levels:
levels: [0., ]
scheme: linear_horizontal_extrapolate_vertical
climate_statistics:
operator: mean
prep_surface_map_regrid_3D:
custom_order: true
extract_levels:
levels: [0., ]
scheme: linear_horizontal_extrapolate_vertical
climate_statistics:
operator: mean
regrid:
target_grid: 1x1
scheme: linear
prep_global_profile:
annual_statistics:
operator: mean
area_statistics:
operator: mean
prep_global_profile_decadal:
decadal_statistics:
operator: mean
area_statistics:
operator: mean
prep_transect_AMT: # Atlantic Meridional Transect (28W)
custom_order: true
climate_statistics:
operator: mean
extract_region:
start_longitude: 320.
end_longitude: 345.
start_latitude: -81.
end_latitude: 89.9
regrid:
target_grid: 1x1
scheme: linear
extract_transect:
longitude: 332.
# # 2D map global depth integration
# prep_depth_integration:
# depth_integration:
# # new_units: kg m-2 # need to specify in advance, as cf_units has strange behaviour.
# climate_statistics:
# operator: mean
#
# # 2D map global depth integration time series maps
# prep_depth_integration_timeseries:
# custom_order: true
# depth_integration:
# area_statistics:
# operator: mean
# --------------------------------------------------
# Diagnostics
# --------------------------------------------------
diagnostics:
# Need to add:
# Global Air sea flux of CO2
# Added:
# Global volume average Temperature time series
# Global volumne average salinity time series
# Drake passge/AMOC (if exists as scalar field)
# Global net integrated primary production timeseries
# Global surface mean chlorophyll timeseries
# Global surface mean nutrients timeseries
# Global surface mean chlorophyll map
# Global surface mean nutrients map
# Global net integrated primary production map
# --------------------------------------------------
# Volume average time series vs WOA
# --------------------------------------------------
diag_timeseries_volume_average_vs_WOA:
description: Global volume average time series (WOA observations)
variables:
thetao: # Temperature 3D
preprocessor: prep_timeseries_global_volume_average
mip: Omon
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
so: # Salinity 3D
preprocessor: prep_timeseries_global_volume_average
mip: Omon
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
no3: # nitrate
preprocessor: prep_timeseries_global_volume_average
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
o2: # oxygen
preprocessor: prep_timeseries_global_volume_average
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
si: # Silicate
preprocessor: prep_timeseries_global_volume_average
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
volcello:
mip: fx
# po4: # phosphate # No HadGEM2-ES phosphate.
# preprocessor: prep_timeseries_global_volume_average
# mip: Oyr
# additional_datasets:
# - {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
scripts:
Global_Volume_Average_timeseries:
script: ocean/diagnostic_timeseries.py
# --------------------------------------------------
# Volume average time series - no data
# --------------------------------------------------
diag_timeseries_volume_average_no_obs:
description: Global volume average time series (No observations)
variables:
# This can't run on jasmin until issue #773 is resolved.
# gtfgco2: # Global Total flux co2
# preprocessor: prep_timeseries_scalar
# mip: Omon
# derive: true
# force_derivation: false
chl: # chlorophyll
preprocessor: prep_timeseries_global_volume_average
mip: Oyr
dfe: # iron
preprocessor: prep_timeseries_global_volume_average
mip: Oyr
talk: # alkalinity
preprocessor: prep_timeseries_global_volume_average
mip: Oyr
volcello:
mip: fx
# dic: # Dissolved inorganic carbon
# preprocessor: prep_timeseries_global_volume_average
# mip: Oyr
scripts:
Global_Volume_verage_timeseries:
script: ocean/diagnostic_timeseries.py
# --------------------------------------------------
# Surface and 2D fields time series
# --------------------------------------------------
diag_timeseries_surface_average_no_obs:
description: Global volume average time series - no data
variables:
talk: # alkalinity
preprocessor: prep_global_Surface_average_timeseries_3D
mip: Oyr
intpp:
preprocessor: prep_global_Surface_average_timeseries_2D
mip: Omon
chl:
preprocessor: prep_global_Surface_average_timeseries_3D
mip: Oyr
thresholds: [0.1, 0.2, 0.5]
areacello:
mip: fx
# dfe: # iron
# preprocessor: prep_global_Surface_average_timeseries_3D
# mip: Oyr
# dic: # Dissolved inorganic carbon
# preprocessor: prep_global_Surface_average_timeseries_3D
# mip: Oyr
scripts:
Global_Volume_Average_timeseries:
script: ocean/diagnostic_timeseries.py
# --------------------------------------------------
# Surface time series vs WOA
# --------------------------------------------------
diag_timeseries_surface_average_vs_WOA:
description: Global surface time series (WOA observations)
variables:
thetao: # Temperature ocean surface
preprocessor: prep_global_Surface_average_timeseries_3D
mip: Omon
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
so: # Salinity ocean surface
preprocessor: prep_global_Surface_average_timeseries_3D
mip: Omon
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
no3: # Nitrate ocean surface
preprocessor: prep_global_Surface_average_timeseries_3D
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
o2: # oxygen
preprocessor: prep_global_Surface_average_timeseries_3D
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
si: # Silicate
preprocessor: prep_global_Surface_average_timeseries_3D
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
areacello:
mip: fx
# po4: # Phosphate
# preprocessor: prep_global_Surface_average_timeseries_3D
# mip: Oyr
# additional_datasets:
# - {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
scripts:
Global_Volume_Average_timeseries:
script: ocean/diagnostic_timeseries.py
observational_dataset: {dataset: WOA, project: OBS}
# --------------------------------------------------
# Scalar time series
# --------------------------------------------------
diag_timeseries_scalars:
description: Scalar time series
variables:
mfo: # Marine currents flux
preprocessor: prep_timeseries_scalar
mip: Omon
scripts:
Scalar_timeseries:
script: ocean/diagnostic_timeseries.py
# --------------------------------------------------
# Profile diagnostics - vs WOA
# --------------------------------------------------
diag_profile_vs_WOA:
description: Global profile (WOA observations)
variables:
thetao: # Temperature ocean surface
preprocessor: prep_global_profile
mip: Omon
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
so: # Salinity ocean surface
preprocessor: prep_global_profile
mip: Omon
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
no3: # Nitrate ocean surface
preprocessor: prep_global_profile
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
o2: # oxygen
preprocessor: prep_global_profile
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
si: # Silicate
preprocessor: prep_global_profile
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
volcello:
mip: fx
# po4: # Phosphate
# preprocessor: prep_global_profile
# mip: Oyr
# additional_datasets:
# - {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
scripts:
Global_profile_vs_WOA:
script: ocean/diagnostic_profiles.py
observational_dataset: {dataset: WOA, project: OBS}
# --------------------------------------------------
# Profile diagnostics - no data
# --------------------------------------------------
diag_profile_no_obs:
description: Global profile (No observations)
variables:
chl: # chlorophyll
preprocessor: prep_global_profile
mip: Oyr
dfe: # iron
preprocessor: prep_global_profile
mip: Oyr
talk: # alkalinity
preprocessor: prep_global_profile
mip: Oyr
volcello:
mip: fx
# dic: # Dissolved inorganic carbon
# preprocessor: prep_global_profile
# mip: Oyr
scripts:
Global_profile_no_obs:
script: ocean/diagnostic_profiles.py
# --------------------------------------------------
# Map diagnostics - vs WOA
# --------------------------------------------------
diag_surface_maps_vs_WOA:
description: Global Ocean Surface maps vs WOA
variables:
thetao:
preprocessor: prep_surface_map_regrid_3D
mip: Omon
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
so:
preprocessor: prep_surface_map_regrid_3D
mip: Omon
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
no3:
preprocessor: prep_surface_map_regrid_3D
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
si: # Silicate
preprocessor: prep_surface_map_regrid_3D
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
o2: # Oxygen
preprocessor: prep_surface_map_regrid_3D
mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
areacello:
mip: fx
# po4:
# preprocessor: prep_surface_map_3D
# mip: Oyr
# additional_datasets:
# - {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
scripts:
Global_Ocean_surface_map:
script: ocean/diagnostic_maps.py
Global_Ocean_model_vs_obs:
script: ocean/diagnostic_model_vs_obs.py
observational_dataset: {dataset: WOA, project: OBS}
# --------------------------------------------------
# Map diagnostics - no data
# --------------------------------------------------
diag_surface_maps_no_data:
description: Global Ocean Surface maps - no data
variables:
intpp:
preprocessor: prep_surface_map_2D
mip: Omon
fgco2:
preprocessor: prep_surface_map_2D
mip: Omon
chl:
preprocessor: prep_surface_map_3D
mip: Oyr
# thresholds: [0.1, 0.2, 0.5]
dfe:
preprocessor: prep_surface_map_3D
mip: Oyr
areacello:
mip: fx
# dic:
# preprocessor: prep_surface_map_3D
# mip: Oyr
scripts:
Global_Ocean_surface_map:
script: ocean/diagnostic_maps.py
# --------------------------------------------------
# Transects diagnostics - vs WOA
# --------------------------------------------------
diag_transect_vs_WOA:
description: Transect maps vs WOA
variables:
thetao:
preprocessor: prep_transect_AMT
mip: Omon
thresholds: [0., 5., 10., 15., 20., 25., 30.]
so:
preprocessor: prep_transect_AMT
mip: Omon
no3:
preprocessor: prep_transect_AMT
mip: Oyr
thresholds: [10., 20., 30.]
si: # Silicate
preprocessor: prep_transect_AMT
mip: Oyr
o2: # Oxygen
preprocessor: prep_transect_AMT
mip: Oyr
thresholds: [0.03, ]
# po4:
# preprocessor: prep_transect_AMT
# mip: Oyr
additional_datasets:
- {dataset: WOA, project: OBS, type: clim, version: 2013v2, start_year: 2000, end_year: 2000, tier: 2}
scripts:
Transects_vs_WOA:
script: ocean/diagnostic_transects.py
# observational_dataset: {dataset: WOA, project: OBS}
# # --------------------------------------------------
# # Map diagnostics - no data
# # --------------------------------------------------
diag_transect_no_data:
description: Transects - no data
variables:
chl:
preprocessor: prep_transect_AMT
mip: Oyr
dfe:
preprocessor: prep_transect_AMT
mip: Oyr
# dic:
# preprocessor: prep_transect_AMT
# mip: Oyr
scripts:
Transects_no_data:
script: ocean/diagnostic_transects.py
# # # Depth integrated maps
# # diag_depth_int_maps:
# # description: Global Ocean Depth Integrated maps
# # variables:
# # chl:
# # preprocessor: prep_depth_integration
# # mip: Oyr
# # # intpp:
# # # preprocessor: prep_depth_integration
# # # mip: Oyr
# # scripts:
# # Global_Ocean_DepthIntegration_map:
# # script: ocean/diagnostic_maps.py
#
# diag_depth_int_timeseries:
# description: Global Ocean Depth Integrated time series
# variables:
# chl:
# preprocessor: prep_depth_integration_timeseries
# mip: Oyr
# # intpp:
# # preprocessor: prep_depth_integration_timeseries
# # mip: Oyr
# scripts:
# Global_Ocean_DepthIntegration_timeseries:
# script: ocean/diagnostic_timeseries.py
# flags: area_total