Add a pre-industrial nitrogen example

CMIP7/esm1p6/atmosphere/nitrogen/cmip7_HI_nitrogen_generate.py

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+from argparse import ArgumentParser
+
+from cmip7_ancil_argparse import common_parser
+
+
+def parse_args():
+    parser = ArgumentParser(
+        parents=[common_parser()],
+        prog="cmip7_HI_nitrogen_generate",
+        description=(
+            "Generate input files from CMIP7 historical nitrogen forcings"
+        ),
+    )
+    parser.add_argument("--dataset-date-range-list")
+    parser.add_argument("--save-filename")
+    return parser.parse_args()
+
+
+if __name__ == "__main__":
+    args = parse_args()

CMIP7/esm1p6/atmosphere/nitrogen/cmip7_PI_nitrogen_generate.py

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+from argparse import ArgumentParser
+from pathlib import Path
+
+import iris
+from cmip7_ancil_argparse import common_parser
+from cmip7_ancil_common import (
+    INTERPOLATION_SCHEME,
+    esm_grid_mask_cube,
+    fix_coords,
+    save_ancil,
+)
+from cmip7_ancil_constants import ANCIL_TODAY
+from iris.util import equalise_attributes
+from nitrogen.cmip7_nitrogen import (
+    NITROGEN_SPECIES,
+    NITROGEN_STASH_ITEM,
+    cmip7_nitrogen_dirpath,
+)
+
+
+def parse_args():
+    parser = ArgumentParser(
+        parents=[common_parser()],
+        prog="cmip7_PI_nitrogen_generate",
+        description=(
+            "Generate input files from CMIP7 pre-industrial nitrogen forcings"
+        ),
+    )
+    parser.add_argument("--dataset-date-range")
+    parser.add_argument("--save-filename")
+    return parser.parse_args()
+
+
+def cmip7_pi_nitrogen_filepath(args, species):
+    dirpath = cmip7_nitrogen_dirpath(args, "monC", species)
+    filename = (
+        f"{species}_input4MIPs_surfaceFluxes_CMIP_"
+        f"{args.dataset_version}_gn_"
+        f"{args.dataset_date_range}-clim.nc"
+    )
+    return dirpath / filename
+
+
+def load_cmip7_pi_nitrogen_species(args, species):
+    species_filepath = cmip7_pi_nitrogen_filepath(args, species)
+    cube = iris.load_cube(species_filepath)
+    return cube
+
+
+def load_cmip7_pi_nitrogen(args):
+    # Load all of the PI nitrogen datasets into a CubeList
+    nitrogen_cubes = iris.cube.CubeList()
+    for species in NITROGEN_SPECIES:
+        species_cube = load_cmip7_pi_nitrogen_species(args, species)
+        nitrogen_cubes.append(species_cube)
+    # Remove all attributes that differ between cubes
+    equalise_attributes(nitrogen_cubes)
+    # Add the cubes together
+    cube_tot = nitrogen_cubes[0].copy()
+    for cube_nbr in range(1, 4):
+        iris.analysis.maths.add(
+            cube_tot, nitrogen_cubes[cube_nbr], in_place=True
+        )
+    # Change the units from kg m-2 s-1 to g m-2 day-1
+    cube_tot.convert_units("g m-2 day-1")
+    return cube_tot
+
+
+def regrid_cmip7_pi_nitrogen(args, cube):
+    # Make the coordinates comaptible with the ESM1.5 grid mask
+    fix_coords(args, cube)
+    # Regrid using the ESM1.5 grid mask
+    esm_cube = cube.regrid(esm_grid_mask_cube(args), INTERPOLATION_SCHEME)
+    esm_cube.data = esm_cube.data.filled(0.0)
+    return esm_cube
+
+
+def esm_pi_nitrogen_save_dirpath(args):
+    return (
+        Path(args.ancil_target_dirname)
+        / "modern"
+        / "pre-industrial"
+        / "atmosphere"
+        / "land"
+        / "biogeochemistry"
+        / args.esm_grid_rel_dirname
+        / ANCIL_TODAY
+    )
+
+
+def save_cmip7_pi_nitrogen(args, cube):
+    # Add STASH metadata
+    cube.attributes["STASH"] = iris.fileformats.pp.STASH(
+        model=1, section=0, item=NITROGEN_STASH_ITEM
+    )
+    # Save as an ancillary file
+    save_dirpath = esm_pi_nitrogen_save_dirpath(args)
+    save_ancil(cube, save_dirpath, args.save_filename)
+
+
+if __name__ == "__main__":
+    args = parse_args()
+
+    # Load the CMIP7 datasets
+    nitrogen_cube = load_cmip7_pi_nitrogen(args)
+    # Regrid to match the ESM1.5 mask
+    esm_cube = regrid_cmip7_pi_nitrogen(args, nitrogen_cube)
+    # Save the ancillary
+    save_cmip7_pi_nitrogen(args, esm_cube)

CMIP7/esm1p6/atmosphere/nitrogen/cmip7_nitrogen.py

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+from pathlib import Path
+
+NITROGEN_SPECIES = ("drynhx", "drynoy", "wetnhx", "wetnoy")
+"""
+The STASH code to use is m01s00i884 NITROGEN DEPOSITION as per
+https://github.com/ACCESS-NRI/access-esm1.6-configs/blob/dev-preindustrial%2Bconcentrations/atmosphere/prefix.PRESM_A#L711
+"""
+NITROGEN_STASH_ITEM = 884
+
+
+def cmip7_nitrogen_dirpath(args, period, species):
+    return (
+        Path(args.cmip7_source_data_dirname)
+        / "FZJ"
+        / args.dataset_version
+        / "atmos"
+        / period
+        / species
+        / "gn"
+        / args.dataset_vdate
+    )