Source code for compass.ocean.tests.global_ocean.dynamic_adjustment

import glob
import importlib.resources
import os
import platform
from datetime import datetime, timedelta

import xarray as xr
from ruamel.yaml import YAML

from compass.ocean.tests.global_ocean.forward import (
from compass.validate import compare_variables

[docs] class DynamicAdjustment(ForwardTestCase): """ A parent test case for performing dynamic adjustment (dissipating fast-moving waves) from an MPAS-Ocean initial condition. The final stage of the dynamic adjustment is assumed to be called ``simulation``, and is expected to have a file ```` that can be compared against a baseline. Attributes ---------- restart_filenames : list of str A list of restart files from each dynamic-adjustment step """
[docs] def __init__(self, test_group, mesh, init, time_integrator): """ Create the test case Parameters ---------- test_group : compass.ocean.tests.global_ocean.GlobalOcean The global ocean test group that this test case belongs to mesh : compass.ocean.tests.global_ocean.mesh.Mesh The test case that produces the mesh for this run init : compass.ocean.tests.global_ocean.init.Init The test case that produces the initial condition for this run time_integrator : {'split_explicit_ab2', 'RK4'} The time integrator to use for the forward run """ super().__init__(test_group=test_group, mesh=mesh, init=init, time_integrator=time_integrator, name='dynamic_adjustment') if time_integrator == 'split_explicit_ab2': yaml_filename = 'dynamic_adjustment.yaml' else: yaml_filename = f'dynamic_adjustment_{time_integrator}.yaml' yaml_filename = str( importlib.resources.files(mesh.package) / yaml_filename) text = importlib.resources.files(mesh.package).joinpath( yaml_filename).read_text() yaml_data = YAML(typ='rt') options_dict = yaml_data.load(text) if 'dynamic_adjustment' not in options_dict: raise ValueError(f'{yaml_filename} in {mesh.package} does not ' f'start with "dynamic_adjustment:" as expected.') options_dict = options_dict['dynamic_adjustment'] if 'land_ice_flux_mode' in options_dict: land_ice_flux_mode = options_dict['land_ice_flux_mode'] else: land_ice_flux_mode = 'pressure_only' if 'get_dt_from_min_res' not in options_dict: raise ValueError(f'{yaml_filename} in {mesh.package} does not ' f'have a "get_dt_from_min_res:" option as ' f'expected.') get_dt_from_min_res = options_dict['get_dt_from_min_res'] shared_options = { 'config_AM_globalStats_enable': '.true.', 'config_AM_globalStats_compute_on_startup': '.true.', 'config_AM_globalStats_write_on_startup': '.true.', 'config_use_activeTracers_surface_restoring': '.true.' } if 'shared' in options_dict: # replace the defaults with values from shared options shared_options.update(options_dict['shared']) if 'steps' not in options_dict: raise ValueError(f'{yaml_filename} in {mesh.package} does not ' f'have a "steps:" item as expected.') start_time = '0001-01-01_00:00:00' previous_restart_filename = None restart_filenames = list() for step_name in options_dict['steps']: options = options_dict['steps'][step_name] restart_time, restart_filename = self._add_step( step_name, options, get_dt_from_min_res, time_integrator, yaml_filename, start_time, previous_restart_filename, mesh, init, land_ice_flux_mode, shared_options) start_time = restart_time previous_restart_filename = restart_filename restart_filenames.append(restart_filename) self.restart_filenames = restart_filenames
[docs] def validate(self): """ Test cases can override this method to perform validation of variables and timers """ config = self.config variables = ['temperature', 'salinity', 'layerThickness', 'normalVelocity'] compare_variables(test_case=self, variables=variables, filename1='simulation/') temp_max = config.getfloat('dynamic_adjustment', 'temperature_max') max_values = {'temperatureMax': temp_max} for step_name in self.steps_to_run: step = self.steps[step_name] step_path = os.path.join(self.work_dir, step.subdir) global_stats_path = os.path.join(step_path, 'analysis_members', 'globalStats.*.nc') global_stats_path = glob.glob(global_stats_path) for filename in global_stats_path: ds = xr.open_dataset(filename) for var, max_value in max_values.items(): max_in_global_stats = ds[var].max().values if max_in_global_stats > max_value: raise ValueError( f'Max of {var} > allowed threshold: ' f'{max_in_global_stats} > {max_value} ' f'in {filename}')
def _add_step(self, step_name, options, get_dt_from_min_res, time_integrator, yaml_filename, start_time, previous_restart_filename, mesh, init, land_ice_flux_mode, shared_options): required = ['run_duration', 'output_interval', 'restart_interval'] if not get_dt_from_min_res: required.append('dt') if time_integrator == 'split_explicit_ab2': required.append('btr_dt') for option in required: if option not in options: raise ValueError( f'In {yaml_filename} in {mesh.package}, step ' f'{step_name} does not have required option {option}.') if get_dt_from_min_res: omit = ['dt', 'btr_dt'] for option in omit: if option in options: raise ValueError( f'In {yaml_filename} in {mesh.package}, step ' f'{step_name} is getting dt from the minimum ' f'resolution of the mesh but dt and/or btr_dt ' f'are also specified.') run_duration = options['run_duration'] restart_time = _get_restart_time(start_time, run_duration) step = ForwardStep(test_case=self, mesh=mesh, init=init, time_integrator=time_integrator, name=step_name, subdir=step_name, land_ice_flux_mode=land_ice_flux_mode, get_dt_from_min_res=get_dt_from_min_res) namelist_options = dict(shared_options) if previous_restart_filename is None: namelist_options['config_do_restart'] = '.false.' else: namelist_options['config_do_restart'] = '.true.' namelist_options['config_start_time'] = f"'{start_time}'" for option in ['run_duration', 'dt', 'btr_dt']: if option in options: namelist_options[f'config_{option}'] = \ f"'{options[option]}'" if ('Rayleigh_damping_coeff' in options and options['Rayleigh_damping_coeff'] != 'None'): namelist_options['config_implicit_bottom_drag_type'] = \ "'constant_and_rayleigh'" namelist_options['config_Rayleigh_damping_coeff'] = \ f"{options['Rayleigh_damping_coeff']}" else: namelist_options['config_implicit_bottom_drag_type'] = \ "'constant'" step.add_namelist_options(namelist_options) stream_replacements = { 'output_interval': options['output_interval'], 'restart_interval': options['restart_interval']} package = 'compass.ocean.tests.global_ocean.dynamic_adjustment' step.add_streams_file(package, 'streams.template', template_replacements=stream_replacements) restart_filename = \ f'restarts/rst.{restart_time.replace(":", ".")}.nc' if previous_restart_filename is not None: step.add_input_file(filename=f'../{previous_restart_filename}') step.add_output_file(filename=f'../{restart_filename}') step.add_output_file(filename='') self.add_step(step) return restart_time, restart_filename
def _get_restart_time(start_time, run_duration): start = datetime.strptime(start_time, '%Y-%m-%d_%H:%M:%S') duration = _parse_duration(run_duration) restart = start + duration if platform.system() == 'Darwin': restart_time = restart.strftime('%Y-%m-%d_%H:%M:%S') else: restart_time = restart.strftime('%4Y-%m-%d_%H:%M:%S') return restart_time def _parse_duration(duration_str): days = 0 hours = 0 minutes = 0 split = duration_str.split('_') hms = split[-1] if len(split) > 1: days = int(split[-2]) split = hms.split(':') seconds = int(split[-1]) if len(split) > 1: minutes = int(split[-2]) if len(split) > 2: hours = int(split[-3]) return timedelta(days=days, hours=hours, minutes=minutes, seconds=seconds)