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Add CABLE model driver (#314)
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Co-authored-by: @SeanBryan51  <[email protected]>

This change adds a model driver for running CABLE spatially in the offline
configuration (forced atmosphere).

A template for CABLE experiments can be found [here][cable_example].

Fixes #313

[cable_example]: https://github.com/CABLE-LSM/cable_example
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aidanheerdegen authored Dec 21, 2023
1 parent 8089edb commit d738c9f
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2 changes: 2 additions & 0 deletions payu/models/__init__.py
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from payu.models.access import Access
from payu.models.accessom2 import AccessOm2
from payu.models.cesm_cmeps import AccessOm3
from payu.models.cable import Cable
from payu.models.cice import Cice
from payu.models.cice5 import Cice5
from payu.models.gold import Gold
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'ww3': WW3,
'mom6': Mom6,
'qgcm': Qgcm,
'cable': Cable,

# Default
'default': Model,
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182 changes: 182 additions & 0 deletions payu/models/cable.py
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"""payu.models.cable
================
Driver interface to CABLE
:copyright: Copyright 2021 Marshall Ward, see AUTHORS for details
:license: Apache License, Version 2.0, see LICENSE for details
"""

# Standard Library
import glob
import os
import shutil

# Extensions
import f90nml
import yaml

# Local
from payu.fsops import mkdir_p
from payu.models.model import Model


def _get_forcing_path(variable, year, input_dir, offset=None, repeat=None):
"""Return the met forcing file path for a given variable and year.
Parameters
----------
variable : str
Variable name.
year : int
Year value.
input_dir : str
Path to work input directory.
offset : list of int, optional
Offset the current simulation year from `offset[0]` to `offset[1]`
before inferring the met forcing path.
repeat : list of int, optional
Constrain the current simulation year between `repeat[0]` and
`repeat[1]` (inclusive) before inferring the met forcing path. If the
year is outside the interval, the constrained year repeats over the
interval.
Returns
-------
path : str
Path (relative to control directory) to the inferred met forcing file.
Raises
------
FileNotFoundError
If unable to infer met forcing path.
"""
if offset:
year += offset[1] - offset[0]
if repeat:
year = repeat[0] + ((year - repeat[0]) % (repeat[1] - repeat[0] + 1))
pattern = os.path.join(input_dir, f"*{variable}*{year}*.nc")
for path in glob.glob(pattern):
return path
msg = f"Unable to infer met forcing path for variable {variable} for year {year}."
raise FileNotFoundError(msg)


class Cable(Model):

def __init__(self, expt, name, config):
super(Cable, self).__init__(expt, name, config)

self.model_type = 'cable'
self.default_exec = 'cable'

self.cable_nml_fname = 'cable.nml'

self.config_files = [
self.cable_nml_fname,
'cable_soilparm.nml',
'pft_params.nml',
]

self.forcing_year_config = 'cable.forcing_year.yaml'
self.optional_config_files = [self.forcing_year_config]

self.met_forcing_vars = [
"Rainf",
"Snowf",
"LWdown",
"SWdown",
"PSurf",
"Qair",
"Tair",
"Wind",
]

def set_model_pathnames(self):
super(Cable, self).set_model_pathnames()

# TODO: Check for path in filename%type
self.work_input_path = os.path.join(self.work_path, 'INPUT')
self.work_init_path = self.work_input_path
# TODO: Check for path in filename%restart_out
self.work_restart_path = os.path.join(self.work_path, 'RESTART')

self.restart_calendar_file = self.model_type + '.res.yaml'
self.restart_calendar_path = os.path.join(self.work_init_path,
self.restart_calendar_file)

self.cable_nml_path = os.path.join(self.work_path,
self.cable_nml_fname)

def setup(self):
super(Cable, self).setup()

self.cable_nml = f90nml.read(self.cable_nml_path)
if self.prior_restart_path:
with open(self.restart_calendar_path, 'r') as restart_file:
self.restart_info = yaml.safe_load(restart_file)
else:
self.restart_info = {'year': self.cable_nml['cable']['ncciy']}

year = self.cable_nml['cable']['ncciy'] = self.restart_info['year']

self.cable_nml['cable']['filename']['restart_in'] = (
os.path.join('INPUT', 'restart.nc')
)
self.cable_nml['cable']['filename']['restart_out'] = (
os.path.join('RESTART', 'restart.nc')
)
self.cable_nml['cable']['output']['restart'] = True

forcing_year_config_path = os.path.join(self.work_path, self.forcing_year_config)
if os.path.exists(forcing_year_config_path):
with open(forcing_year_config_path, 'r') as file:
conf = yaml.safe_load(file)
forcing_year_config = conf if conf else {}
for var in self.met_forcing_vars:
path = _get_forcing_path(
var, year, self.work_input_path, **forcing_year_config
)
self.cable_nml["cable"]["gswpfile"][var] = (
os.path.relpath(path, start=self.work_path)
)

# Write modified namelist file to work dir
self.cable_nml.write(
os.path.join(self.work_path, self.cable_nml_fname),
force=True
)

def archive(self, **kwargs):

# Save model time to restart next run
with open(os.path.join(self.restart_path,
self.restart_calendar_file), 'w') as restart_file:
restart = {'year': self.restart_info['year'] + 1}
restart_file.write(yaml.dump(restart, default_flow_style=False))

super(Cable, self).archive()

# Archive the restart files
mkdir_p(self.restart_path)

restart_files = [f for f in os.listdir(self.work_restart_path)
if f.endswith('restart.nc')]

for f in restart_files:
f_src = os.path.join(self.work_restart_path, f)
shutil.move(f_src, self.restart_path)

os.rmdir(self.work_restart_path)

# Move all logs into a logs subdir
log_path = os.path.join(self.work_path, 'logs')
mkdir_p(log_path)
log_files = [f for f in os.listdir(self.work_path)
if f.startswith('cable_log')]
for f in log_files:
f_src = os.path.join(self.work_path, f)
shutil.move(f_src, log_path)

def collate(self):
pass
52 changes: 52 additions & 0 deletions test/models/test_cable.py
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import os
import shutil
import tempfile

import pytest

import payu.models.cable as cable

from test.common import make_random_file


class TestGetForcingPath:
"""Tests for `payu.models.cable._get_forcing_path()`."""

@pytest.fixture()
def input_dir(self):
"""Create a temporary input directory and return its path."""
_input_dir = tempfile.mkdtemp(prefix="payu_test_get_forcing_path")
yield _input_dir
shutil.rmtree(_input_dir)

@pytest.fixture(autouse=True)
def _make_forcing_inputs(self, input_dir):
"""Create forcing inputs from 1900 to 1903."""
for year in [1900, 1901, 1903]:
make_random_file(os.path.join(input_dir, f"crujra_LWdown_{year}.nc"))

def test_get_forcing_path(self, input_dir):
"""Success case: test correct path can be inferred."""
assert cable._get_forcing_path("LWdown", 1900, input_dir) == os.path.join(
input_dir, "crujra_LWdown_1900.nc"
)

def test_year_offset(self, input_dir):
"""Success case: test correct path can be inferred with offset."""
assert cable._get_forcing_path(
"LWdown", 2000, input_dir, offset=[2000, 1900]
) == os.path.join(input_dir, "crujra_LWdown_1900.nc")

def test_year_repeat(self, input_dir):
"""Success case: test correct path can be inferred with repeat."""
assert cable._get_forcing_path(
"LWdown", 1904, input_dir, repeat=[1900, 1903]
) == os.path.join(input_dir, "crujra_LWdown_1900.nc")

def test_file_not_found_exception(self, input_dir):
"""Failure case: test exception is raised if path cannot be inferred."""
with pytest.raises(
FileNotFoundError,
match="Unable to infer met forcing path for variable LWdown for year 1904.",
):
_ = cable._get_forcing_path("LWdown", 1904, input_dir)

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