import os
import shutil
from collections import OrderedDict
-from typing import List, Union
+from typing import Dict, List, Union
import numpy as np
import xarray as xr
@@ -175,6 +175,8 @@ Source code for polaris.model_step
Whether to create a yaml file with model config options and streams
instead of MPAS namelist and streams files
+ streams_section : str
+ The name of the streams section in yaml files
"""
[docs]
@@ -281,6 +283,7 @@ Source code for polaris.model_step
self.graph_filename = graph_filename
self.make_yaml = make_yaml
+ self.streams_section = 'streams'
self.add_input_file(filename='<<<model>>>')
@@ -398,7 +401,7 @@ Source code for polaris.model_step
[docs]
def map_yaml_options(self, options, config_model):
"""
- A mapping between model config options between different models. This
+ A mapping between model config options from different models. This
method should be overridden for situations in which yaml config
options have diverged in name or structure from their counterparts in
another model (e.g. when translating from MPAS-Ocean namelist options
@@ -427,7 +430,7 @@ Source code for polaris.model_step
[docs]
def map_yaml_configs(self, configs, config_model):
"""
- A mapping between model config options between different models. This
+ A mapping between model config options from different models. This
method should be overridden for situations in which yaml config
options have diverged in name or structure from their counterparts in
another model (e.g. when translating from MPAS-Ocean namelist options
@@ -452,6 +455,29 @@ Source code for polaris.model_step
return configs
+ def map_yaml_streams(self, streams, config_model):
+ """
+ A mapping between model streams from different models. This method
+ should be overridden for situations in which yaml streams have diverged
+ in name or structure from their counterparts in another model (e.g.
+ when translating from MPAS-Ocean streams to Omega IOStreams)
+
+ Parameters
+ ----------
+ streams : dict
+ A nested dictionary of streams data
+
+ config_model : str or None
+ If streams are available for multiple models, the model that the
+ streams are from
+
+ Returns
+ -------
+ configs : dict
+ A revised nested dictionary of streams data
+ """
+ return streams
+
[docs]
def map_yaml_to_namelist(self, options):
@@ -581,7 +607,7 @@ Source code for polaris.model_step
self.dynamic_model_config(at_setup=False)
if self.make_yaml:
- self._process_yaml(quiet=quiet)
+ self._process_yaml(quiet=quiet, remove_unrequested_streams=False)
else:
self._process_namelists(quiet=quiet)
self._process_streams(quiet=quiet, remove_unrequested=False)
@@ -625,7 +651,7 @@ Source code for polaris.model_step
self._create_model_config()
if self.make_yaml:
- self._process_yaml(quiet=quiet)
+ self._process_yaml(quiet=quiet, remove_unrequested_streams=True)
else:
self._process_namelists(quiet=quiet)
self._process_streams(quiet=quiet, remove_unrequested=True)
@@ -714,7 +740,8 @@ Source code for polaris.model_step
config = self.config
if self.make_yaml:
defaults_filename = config.get('model_config', 'defaults')
- self._yaml = PolarisYaml.read(defaults_filename)
+ self._yaml = PolarisYaml.read(defaults_filename,
+ streams_section=self.streams_section)
else:
defaults_filename = config.get('namelists', 'forward')
self._namelist = polaris.namelist.ingest(defaults_filename)
@@ -729,7 +756,8 @@ Source code for polaris.model_step
"""
if self.make_yaml:
filename = os.path.join(self.work_dir, self.yaml)
- self._yaml = PolarisYaml.read(filename)
+ self._yaml = PolarisYaml.read(filename,
+ streams_section=self.streams_section)
else:
filename = os.path.join(self.work_dir, self.namelist)
self._namelist = polaris.namelist.ingest(filename)
@@ -792,10 +820,10 @@ Source code for polaris.model_step
options = self.map_yaml_to_namelist(options)
replacements.update(options)
if 'yaml' in entry:
- yaml = PolarisYaml.read(filename=entry['yaml'],
- package=entry['package'],
- replacements=entry['replacements'],
- model=config_model)
+ yaml = PolarisYaml.read(
+ filename=entry['yaml'], package=entry['package'],
+ replacements=entry['replacements'], model=config_model,
+ streams_section=self.streams_section)
configs = self.map_yaml_configs(configs=yaml.configs,
config_model=config_model)
@@ -878,8 +906,7 @@ Source code for polaris.model_step
if not found:
defaults.remove(default)
- @staticmethod
- def _process_yaml_streams(yaml_filename, package, replacements,
+ def _process_yaml_streams(self, yaml_filename, package, replacements,
config_model, processed_registry_filename,
tree, quiet):
if not quiet:
@@ -888,14 +915,15 @@ Source code for polaris.model_step
yaml = PolarisYaml.read(filename=yaml_filename,
package=package,
replacements=replacements,
- model=config_model)
+ model=config_model,
+ streams_section=self.streams_section)
assert processed_registry_filename is not None
new_tree = yaml_to_mpas_streams(
processed_registry_filename, yaml)
tree = polaris.streams.update_tree(tree, new_tree)
return tree
- def _process_yaml(self, quiet):
+ def _process_yaml(self, quiet, remove_unrequested_streams):
"""
Processes changes to a yaml file from the files and dictionaries
in the step's ``model_config_data``.
@@ -910,6 +938,8 @@ Source code for polaris.model_step
if not quiet:
print(f'Warning: replacing yaml options in {self.yaml}')
+ streams: Dict[str, Dict[str, Union[str, float, int, List[str]]]] = {}
+
for entry in self.model_config_data:
if 'namelist' in entry:
raise ValueError('Cannot generate a yaml config from an MPAS '
@@ -924,14 +954,49 @@ Source code for polaris.model_step
config_model=config_model)
self._yaml.update(options=options, quiet=quiet)
if 'yaml' in entry:
- yaml = PolarisYaml.read(filename=entry['yaml'],
- package=entry['package'],
- replacements=entry['replacements'],
- model=config_model)
+ yaml = PolarisYaml.read(
+ filename=entry['yaml'], package=entry['package'],
+ replacements=entry['replacements'], model=config_model,
+ streams_section=self.streams_section)
configs = self.map_yaml_configs(configs=yaml.configs,
config_model=config_model)
- self._yaml.update(configs=configs, quiet=quiet)
+ new_streams = self.map_yaml_streams(
+ streams=yaml.streams, config_model=config_model)
+ self._update_yaml_streams(streams, new_streams,
+ quiet=quiet,
+ remove_unrequested=False)
+ self._yaml.update(configs=configs, quiet=quiet)
+ self._update_yaml_streams(
+ self._yaml.streams, streams, quiet=quiet,
+ remove_unrequested=remove_unrequested_streams)
+
+ @staticmethod
+ def _update_yaml_streams(streams, new_streams, quiet, remove_unrequested):
+ """
+ Update yaml streams, optionally removing any streams that aren't in
+ new_streams
+ """
+
+ for stream_name, new_stream in new_streams.items():
+ if stream_name in streams:
+ streams[stream_name].update(new_stream)
+ if not quiet:
+ print(f' updating: {stream_name}')
+ else:
+ if not quiet:
+ print(f' adding: {stream_name}')
+ streams[stream_name] = new_stream
+
+ if remove_unrequested:
+ # during setup, we remove any default streams that aren't requested
+ # but at runtime we don't want to do this because we would lose any
+ # streams added only during setup.
+ for stream_name in list(streams.keys()):
+ if stream_name not in new_streams:
+ if not quiet:
+ print(f' dropping: {stream_name}')
+ streams.pop(stream_name)
diff --git a/main/_modules/polaris/ocean/convergence/forward.html b/main/_modules/polaris/ocean/convergence/forward.html
index fcf33c6c3..23ce57b48 100644
--- a/main/_modules/polaris/ocean/convergence/forward.html
+++ b/main/_modules/polaris/ocean/convergence/forward.html
@@ -256,6 +256,9 @@ Source code for polaris.ocean.convergence.forward
output_interval_str = get_time_interval_string(
seconds=output_interval * s_per_hour)
+ # For Omega, we want the output interval as a number of seconds
+ output_freq = int(output_interval * s_per_hour)
+
time_integrator = section.get('time_integrator')
time_integrator_map = dict([('RK4', 'RungeKutta4')])
model = config.get('ocean', 'model')
@@ -273,6 +276,7 @@ Source code for polaris.ocean.convergence.forward
btr_dt=btr_dt_str,
run_duration=run_duration_str,
output_interval=output_interval_str,
+ output_freq=f'{output_freq}'
)
self.add_yaml_file(self.package, self.yaml_filename,
diff --git a/main/_modules/polaris/ocean/model/ocean_io_step.html b/main/_modules/polaris/ocean/model/ocean_io_step.html
index deddd68c8..45da5bb92 100644
--- a/main/_modules/polaris/ocean/model/ocean_io_step.html
+++ b/main/_modules/polaris/ocean/model/ocean_io_step.html
@@ -121,6 +121,13 @@ Source code for polaris.ocean.model.ocean_io_step
Attributes
----------
+ mpaso_to_omega_dim_map : dict
+ A map from MPAS-Ocean dimension names to their Omega equivalents
+
+ omega_to_mpaso_dim_map : dict
+ A map from Omega dimension names to their MPAS-Ocean equivalents, the
+ inverse of ``mpaso_to_omega_dim_map``
+
mpaso_to_omega_var_map : dict
A map from MPAS-Ocean variable names to their Omega equivalents
@@ -148,6 +155,8 @@ Source code for polaris.ocean.model.ocean_io_step
super().__init__(
component=component, name=name, **kwargs)
+ self.mpaso_to_omega_dim_map: Union[None, Dict[str, str]] = None
+ self.omega_to_mpaso_dim_map: Union[None, Dict[str, str]] = None
self.mpaso_to_omega_var_map: Union[None, Dict[str, str]] = None
self.omega_to_mpaso_var_map: Union[None, Dict[str, str]] = None
@@ -172,9 +181,9 @@ Source code for polaris.ocean.model.ocean_io_step
[docs]
def map_to_native_model_vars(self, ds):
"""
- If the model is Omega, rename variables in a dataset from their
- MPAS-Ocean names to the Omega equivalent (appropriate for input
- datasets like an initial condition)
+ If the model is Omega, rename dimensions and variables in a dataset
+ from their MPAS-Ocean names to the Omega equivalent (appropriate for
+ input datasets like an initial condition)
Parameters
----------
@@ -190,9 +199,13 @@ Source code for polaris.ocean.model.ocean_io_step
config = self.config
model = config.get('ocean', 'model')
if model == 'omega':
+ assert self.mpaso_to_omega_dim_map is not None
+ rename = {k: v for k, v in self.mpaso_to_omega_dim_map.items()
+ if k in ds.dims}
assert self.mpaso_to_omega_var_map is not None
- rename = {k: v for k, v in self.mpaso_to_omega_var_map.items()
- if k in ds}
+ rename_vars = {k: v for k, v in self.mpaso_to_omega_var_map.items()
+ if k in ds}
+ rename.update(rename_vars)
ds = ds.rename(rename)
return ds
@@ -201,8 +214,8 @@ Source code for polaris.ocean.model.ocean_io_step
[docs]
def write_model_dataset(self, ds, filename):
"""
- Write out the given dataset, mapping variable names from MPAS-Ocean
- to Omega names if appropriate
+ Write out the given dataset, mapping dimension and variable names from
+ MPAS-Ocean to Omega names if appropriate
Parameters
----------
@@ -220,9 +233,9 @@ Source code for polaris.ocean.model.ocean_io_step
[docs]
def map_from_native_model_vars(self, ds):
"""
- If the model is Omega, rename variables in a dataset from their
- Omega names to the MPAS-Ocean equivalent (appropriate for datasets
- that are output from the model)
+ If the model is Omega, rename dimensions and variables in a dataset
+ from their Omega names to the MPAS-Ocean equivalent (appropriate for
+ datasets that are output from the model)
Parameters
----------
@@ -237,9 +250,13 @@ Source code for polaris.ocean.model.ocean_io_step
config = self.config
model = config.get('ocean', 'model')
if model == 'omega':
+ assert self.omega_to_mpaso_dim_map is not None
+ rename = {k: v for k, v in self.omega_to_mpaso_dim_map.items()
+ if k in ds.dims}
assert self.omega_to_mpaso_var_map is not None
- rename = {k: v for k, v in self.omega_to_mpaso_var_map.items()
- if k in ds}
+ rename_vars = {k: v for k, v in self.omega_to_mpaso_var_map.items()
+ if k in ds}
+ rename.update(rename_vars)
ds = ds.rename(rename)
return ds
@@ -248,8 +265,8 @@ Source code for polaris.ocean.model.ocean_io_step
[docs]
def open_model_dataset(self, filename, **kwargs):
"""
- Open the given dataset, mapping variable names from Omega to MPAS-Ocean
- names if appropriate
+ Open the given dataset, mapping variable and dimension names from Omega
+ to MPAS-Ocean names if appropriate
Parameters
----------
@@ -271,7 +288,7 @@ Source code for polaris.ocean.model.ocean_io_step
def _read_var_map(self):
"""
- Read the map from MPAS-Ocean to Omega config options
+ Read the map from MPAS-Ocean to Omega dimension and variable names
"""
package = 'polaris.ocean.model'
filename = 'mpaso_to_omega.yaml'
@@ -279,7 +296,11 @@ Source code for polaris.ocean.model.ocean_io_step
yaml_data = YAML(typ='rt')
nested_dict = yaml_data.load(text)
+ self.mpaso_to_omega_dim_map = nested_dict['dimensions']
self.mpaso_to_omega_var_map = nested_dict['variables']
+ assert self.mpaso_to_omega_dim_map is not None
+ self.omega_to_mpaso_dim_map = {
+ v: k for k, v in self.mpaso_to_omega_dim_map.items()}
assert self.mpaso_to_omega_var_map is not None
self.omega_to_mpaso_var_map = {
v: k for k, v in self.mpaso_to_omega_var_map.items()}
diff --git a/main/_modules/polaris/ocean/model/ocean_model_step.html b/main/_modules/polaris/ocean/model/ocean_model_step.html
index 2330e0956..1eb6f4d7a 100644
--- a/main/_modules/polaris/ocean/model/ocean_model_step.html
+++ b/main/_modules/polaris/ocean/model/ocean_model_step.html
@@ -231,6 +231,7 @@ Source code for polaris.ocean.model.ocean_model_step
self.make_yaml = True
self.config_models = ['ocean', 'Omega']
self.yaml = 'omega.yml'
+ self.streams_section = 'IOStreams'
self._read_config_map()
self.partition_graph = False
elif model == 'mpas-ocean':
@@ -239,7 +240,7 @@ Source code for polaris.ocean.model.ocean_model_step
self.add_input_file(
filename='graph.info',
work_dir_target=self.graph_target)
-
+ self.streams_section = 'streams'
else:
raise ValueError(f'Unexpected ocean model: {model}')
diff --git a/main/_modules/polaris/ocean/tasks/manufactured_solution/forward.html b/main/_modules/polaris/ocean/tasks/manufactured_solution/forward.html
index 0def1536d..5b8c5e83d 100644
--- a/main/_modules/polaris/ocean/tasks/manufactured_solution/forward.html
+++ b/main/_modules/polaris/ocean/tasks/manufactured_solution/forward.html
@@ -176,7 +176,7 @@ Source code for polaris.ocean.tasks.manufactured_solution.forward
super().setup()
config = self.config
model = config.get('ocean', 'model')
- # TODO: remove as soon as Omega supports I/O streams
+ # TODO: remove as soon as Omega no longer hard-codes this file
if model == 'omega':
self.add_input_file(filename='OmegaMesh.nc', target='init.nc')
diff --git a/main/_modules/polaris/yaml.html b/main/_modules/polaris/yaml.html
index 6b32076f5..fcfb0bbaa 100644
--- a/main/_modules/polaris/yaml.html
+++ b/main/_modules/polaris/yaml.html
@@ -127,6 +127,9 @@ Source code for polaris.yaml
streams : dict
Nested dictionaries containing data about streams
+ streams_section : str
+ The name of the streams section
+
model : str
The name of the E3SM component
"""
@@ -138,6 +141,7 @@ Source code for polaris.yaml
Create a yaml config object
"""
self.configs = dict()
+ self.streams_section = 'streams'
self.streams = dict()
self.model = None
@@ -145,7 +149,8 @@ Source code for polaris.yaml
[docs]
@classmethod
- def read(cls, filename, package=None, replacements=None, model=None):
+ def read(cls, filename, package=None, replacements=None, model=None,
+ streams_section='streams'):
"""
Add config options from a yaml file
@@ -166,6 +171,9 @@ Source code for polaris.yaml
The name of the model to parse if the yaml file might have multiple
models
+ streams_section : str, optional
+ The name of the streams section
+
Returns
-------
yaml : polaris.yaml.PolarisYaml
@@ -185,6 +193,7 @@ Source code for polaris.yaml
text = template.render(**replacements)
yaml = cls()
+ yaml.streams_section = streams_section
yaml_data = YAML(typ='rt')
configs = yaml_data.load(text)
@@ -200,10 +209,10 @@ Source code for polaris.yaml
yaml.streams = {}
if model in configs:
configs = configs[model]
- if 'streams' in configs:
- yaml.streams = configs['streams']
+ if streams_section in configs:
+ yaml.streams = configs[streams_section]
configs = dict(configs)
- configs.pop('streams')
+ configs.pop(streams_section)
else:
configs = {}
@@ -253,20 +262,14 @@ Source code for polaris.yaml
yaml = YAML(typ='rt')
configs = dict(self.configs)
if self.streams:
- configs['streams'] = self.streams
+ configs[self.streams_section] = self.streams
model_configs = dict()
model_configs[self.model] = configs
with open(filename, 'w') as outfile:
yaml.dump(model_configs, outfile)
-
-
- def _add_stream(self, stream_name, stream):
- """
- Add stream from a dictionary
- """
- self.streams[stream_name] = stream
+
diff --git a/main/_sources/developers_guide/generated/polaris.ModelStep.rst.txt b/main/_sources/developers_guide/generated/polaris.ModelStep.rst.txt
index 0639ff569..861efebc7 100644
--- a/main/_sources/developers_guide/generated/polaris.ModelStep.rst.txt
+++ b/main/_sources/developers_guide/generated/polaris.ModelStep.rst.txt
@@ -25,6 +25,7 @@
~ModelStep.dynamic_model_config
~ModelStep.map_yaml_configs
~ModelStep.map_yaml_options
+ ~ModelStep.map_yaml_streams
~ModelStep.map_yaml_to_namelist
~ModelStep.partition
~ModelStep.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.convergence.forward.ConvergenceForward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.convergence.forward.ConvergenceForward.rst.txt
index 936be10c8..dba7b16dc 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.convergence.forward.ConvergenceForward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.convergence.forward.ConvergenceForward.rst.txt
@@ -26,6 +26,7 @@
~ConvergenceForward.dynamic_model_config
~ConvergenceForward.map_yaml_configs
~ConvergenceForward.map_yaml_options
+ ~ConvergenceForward.map_yaml_streams
~ConvergenceForward.map_yaml_to_namelist
~ConvergenceForward.partition
~ConvergenceForward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.convergence.spherical.SphericalConvergenceForward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.convergence.spherical.SphericalConvergenceForward.rst.txt
index c75c830ee..60f2a25c0 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.convergence.spherical.SphericalConvergenceForward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.convergence.spherical.SphericalConvergenceForward.rst.txt
@@ -26,6 +26,7 @@
~SphericalConvergenceForward.dynamic_model_config
~SphericalConvergenceForward.map_yaml_configs
~SphericalConvergenceForward.map_yaml_options
+ ~SphericalConvergenceForward.map_yaml_streams
~SphericalConvergenceForward.map_yaml_to_namelist
~SphericalConvergenceForward.partition
~SphericalConvergenceForward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.ice_shelf.SshForward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.ice_shelf.SshForward.rst.txt
index fdd271527..7ad67760b 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.ice_shelf.SshForward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.ice_shelf.SshForward.rst.txt
@@ -26,6 +26,7 @@
~SshForward.dynamic_model_config
~SshForward.map_yaml_configs
~SshForward.map_yaml_options
+ ~SshForward.map_yaml_streams
~SshForward.map_yaml_to_namelist
~SshForward.partition
~SshForward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.rst.txt
index b3d9fbca6..fa76cae96 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.rst.txt
@@ -26,6 +26,7 @@
~OceanModelStep.dynamic_model_config
~OceanModelStep.map_yaml_configs
~OceanModelStep.map_yaml_options
+ ~OceanModelStep.map_yaml_streams
~OceanModelStep.map_yaml_to_namelist
~OceanModelStep.partition
~OceanModelStep.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.forward.Forward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.forward.Forward.rst.txt
index 4730278cd..4c86a7adc 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.forward.Forward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.forward.Forward.rst.txt
@@ -26,6 +26,7 @@
~Forward.dynamic_model_config
~Forward.map_yaml_configs
~Forward.map_yaml_options
+ ~Forward.map_yaml_streams
~Forward.map_yaml_to_namelist
~Forward.partition
~Forward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep.rst.txt
index 2625715c2..877a5c63e 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep.rst.txt
@@ -26,6 +26,7 @@
~RestartStep.dynamic_model_config
~RestartStep.map_yaml_configs
~RestartStep.map_yaml_options
+ ~RestartStep.map_yaml_streams
~RestartStep.map_yaml_to_namelist
~RestartStep.partition
~RestartStep.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.barotropic_gyre.forward.Forward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.barotropic_gyre.forward.Forward.rst.txt
index 428e52252..312417499 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.barotropic_gyre.forward.Forward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.barotropic_gyre.forward.Forward.rst.txt
@@ -26,6 +26,7 @@
~Forward.dynamic_model_config
~Forward.map_yaml_configs
~Forward.map_yaml_options
+ ~Forward.map_yaml_streams
~Forward.map_yaml_to_namelist
~Forward.partition
~Forward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.forward.Forward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.forward.Forward.rst.txt
index 26c477028..eb8df7016 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.forward.Forward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.forward.Forward.rst.txt
@@ -26,6 +26,7 @@
~Forward.dynamic_model_config
~Forward.map_yaml_configs
~Forward.map_yaml_options
+ ~Forward.map_yaml_streams
~Forward.map_yaml_to_namelist
~Forward.partition
~Forward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.geostrophic.forward.Forward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.geostrophic.forward.Forward.rst.txt
index 55a77a0a1..2fb16faa5 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.geostrophic.forward.Forward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.geostrophic.forward.Forward.rst.txt
@@ -26,6 +26,7 @@
~Forward.dynamic_model_config
~Forward.map_yaml_configs
~Forward.map_yaml_options
+ ~Forward.map_yaml_streams
~Forward.map_yaml_to_namelist
~Forward.partition
~Forward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.forward.Forward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.forward.Forward.rst.txt
index 08450682e..69c03ad3a 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.forward.Forward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.forward.Forward.rst.txt
@@ -26,6 +26,7 @@
~Forward.dynamic_model_config
~Forward.map_yaml_configs
~Forward.map_yaml_options
+ ~Forward.map_yaml_streams
~Forward.map_yaml_to_namelist
~Forward.partition
~Forward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.forward.Forward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.forward.Forward.rst.txt
index e1b078fa1..cf1c11b1b 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.forward.Forward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.forward.Forward.rst.txt
@@ -26,6 +26,7 @@
~Forward.dynamic_model_config
~Forward.map_yaml_configs
~Forward.map_yaml_options
+ ~Forward.map_yaml_streams
~Forward.map_yaml_to_namelist
~Forward.partition
~Forward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.internal_wave.forward.Forward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.internal_wave.forward.Forward.rst.txt
index 769db098c..75ccfea2d 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.internal_wave.forward.Forward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.internal_wave.forward.Forward.rst.txt
@@ -26,6 +26,7 @@
~Forward.dynamic_model_config
~Forward.map_yaml_configs
~Forward.map_yaml_options
+ ~Forward.map_yaml_streams
~Forward.map_yaml_to_namelist
~Forward.partition
~Forward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.manufactured_solution.forward.Forward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.manufactured_solution.forward.Forward.rst.txt
index ce31420d7..0cfc9164e 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.manufactured_solution.forward.Forward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.manufactured_solution.forward.Forward.rst.txt
@@ -26,6 +26,7 @@
~Forward.dynamic_model_config
~Forward.map_yaml_configs
~Forward.map_yaml_options
+ ~Forward.map_yaml_streams
~Forward.map_yaml_to_namelist
~Forward.partition
~Forward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.single_column.forward.Forward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.single_column.forward.Forward.rst.txt
index 10f54feb9..0a3436b04 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.single_column.forward.Forward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.single_column.forward.Forward.rst.txt
@@ -26,6 +26,7 @@
~Forward.dynamic_model_config
~Forward.map_yaml_configs
~Forward.map_yaml_options
+ ~Forward.map_yaml_streams
~Forward.map_yaml_to_namelist
~Forward.partition
~Forward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.sphere_transport.forward.Forward.rst.txt b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.sphere_transport.forward.Forward.rst.txt
index a614b49c5..5181663fc 100644
--- a/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.sphere_transport.forward.Forward.rst.txt
+++ b/main/_sources/developers_guide/ocean/generated/polaris.ocean.tasks.sphere_transport.forward.Forward.rst.txt
@@ -26,6 +26,7 @@
~Forward.dynamic_model_config
~Forward.map_yaml_configs
~Forward.map_yaml_options
+ ~Forward.map_yaml_streams
~Forward.map_yaml_to_namelist
~Forward.partition
~Forward.process_inputs_and_outputs
diff --git a/main/_sources/developers_guide/seaice/generated/polaris.seaice.tasks.single_column.forward.Forward.rst.txt b/main/_sources/developers_guide/seaice/generated/polaris.seaice.tasks.single_column.forward.Forward.rst.txt
index 49e53c65f..8a5be2c52 100644
--- a/main/_sources/developers_guide/seaice/generated/polaris.seaice.tasks.single_column.forward.Forward.rst.txt
+++ b/main/_sources/developers_guide/seaice/generated/polaris.seaice.tasks.single_column.forward.Forward.rst.txt
@@ -25,6 +25,7 @@
~Forward.dynamic_model_config
~Forward.map_yaml_configs
~Forward.map_yaml_options
+ ~Forward.map_yaml_streams
~Forward.map_yaml_to_namelist
~Forward.partition
~Forward.process_inputs_and_outputs
diff --git a/main/developers_guide/api.html b/main/developers_guide/api.html
index acf3bdf5d..908309149 100644
--- a/main/developers_guide/api.html
+++ b/main/developers_guide/api.html
@@ -460,10 +460,10 @@ ModelStepModelStep.map_yaml_options(options, config_model)
A mapping between model config options between different models.
A mapping between model config options from different models.
ModelStep.map_yaml_configs(configs, config_model)
A mapping between model config options between different models.
A mapping between model config options from different models.
ModelStep.map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
plotting from lat/lon gridssymmetric log
colormap with a central linear region), or log (a logarithmic colormap).
The norm_args depend on the norm_typ and are the arguments to
-matplotlib.colors.Normalize, matplotlib.colors.SymLogNorm,
-and matplotlib.colors.LogNorm, respectively.
+matplotlib.colors.Normalize, matplotlib.colors.SymLogNorm,
+and matplotlib.colors.LogNorm, respectively.
The config option colorbar_ticks (if it is defined) specifies tick locations
along the colorbar. If it is not specified, they are determined automatically.
diff --git a/main/developers_guide/generated/polaris.ModelStep.html b/main/developers_guide/generated/polaris.ModelStep.html
index ade4fd501..7641c4c1f 100644
--- a/main/developers_guide/generated/polaris.ModelStep.html
+++ b/main/developers_guide/generated/polaris.ModelStep.html
@@ -170,6 +170,7 @@ polaris.ModelSteppolaris.ModelStep.add_streams_file()
make_yaml (bool) – Whether to create a yaml file with model config options and streams
instead of MPAS namelist and streams files
streams_section (str) – The name of the streams section in yaml files
polaris.ModelStepmap_yaml_configs(configs, config_model)
A mapping between model config options between different models.
A mapping between model config options from different models.
map_yaml_options(options, config_model)
A mapping between model config options between different models.
A mapping between model config options from different models.
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Setup the command-line arguments
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ModelStep.map_yaml_configs
ModelStep.map_yaml_configs(configs, config_model)[source]
-A mapping between model config options between different models. This
+
A mapping between model config options from different models. This
method should be overridden for situations in which yaml config
options have diverged in name or structure from their counterparts in
another model (e.g. when translating from MPAS-Ocean namelist options
diff --git a/main/developers_guide/generated/polaris.ModelStep.map_yaml_options.html b/main/developers_guide/generated/polaris.ModelStep.map_yaml_options.html
index 7363021a4..7a418f086 100644
--- a/main/developers_guide/generated/polaris.ModelStep.map_yaml_options.html
+++ b/main/developers_guide/generated/polaris.ModelStep.map_yaml_options.html
@@ -140,7 +140,7 @@
polaris.ModelStep.map_yaml_options
ModelStep.map_yaml_options(options, config_model)[source]
-A mapping between model config options between different models. This
+
A mapping between model config options from different models. This
method should be overridden for situations in which yaml config
options have diverged in name or structure from their counterparts in
another model (e.g. when translating from MPAS-Ocean namelist options
diff --git a/main/developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width.html b/main/developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width.html
index be502eb93..f358d040f 100644
--- a/main/developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width.html
+++ b/main/developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width.html
@@ -158,9 +158,9 @@
polaris.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width
Parameters:
-lon (numpy.ndarray) – longitude in degrees (length n and between -180 and 180)
lat (numpy.ndarray) – longitude in degrees (length m and between -90 and 90)
cell_width (numpy.ndarray) – m x n array of cell width in km
lon (numpy.ndarray) – longitude in degrees (length n and between -180 and 180)
lat (numpy.ndarray) – longitude in degrees (length m and between -90 and 90)
cell_width (numpy.ndarray) – m x n array of cell width in km
polaris.mpas.time_index_from_xtime
Parameters:
-xtime (numpy.ndarray of numpy.char) – Times in the dataset
xtime (numpy.ndarray of numpy.char) – Times in the dataset
dt_target (float) – Time in seconds since the first time in the list of xtime values
start_xtime (str, optional) – The start time, the first entry in xtime by default
diff --git a/main/developers_guide/generated/polaris.viz.plot_global_lat_lon_field.html b/main/developers_guide/generated/polaris.viz.plot_global_lat_lon_field.html
index 7a3fef3b0..6ae00df24 100644
--- a/main/developers_guide/generated/polaris.viz.plot_global_lat_lon_field.html
+++ b/main/developers_guide/generated/polaris.viz.plot_global_lat_lon_field.html
@@ -144,9 +144,9 @@ polaris.viz.plot_global_lat_lon_field
Parameters:
-lon (numpy.ndarray) – 1D longitude coordinate
lat (numpy.ndarray) – 1D latitude coordinate
data_array (numpy.ndarray) – 2D data array to plot
lon (numpy.ndarray) – 1D longitude coordinate
lat (numpy.ndarray) – 1D latitude coordinate
data_array (numpy.ndarray) – 2D data array to plot
out_filename (str) – The image file name to be written
config (polaris.config.PolarisConfigParser) – The config options to use for colormap settings
colormap_section (str) –
The name of a section in the config options. Options must include:
diff --git a/main/developers_guide/generated/polaris.viz.plot_horiz_field.html b/main/developers_guide/generated/polaris.viz.plot_horiz_field.html
index 4e3c8a3c0..55f416e82 100644
--- a/main/developers_guide/generated/polaris.viz.plot_horiz_field.html
+++ b/main/developers_guide/generated/polaris.viz.plot_horiz_field.html
@@ -149,7 +149,7 @@ polaris.viz.plot_horiz_fieldxarray.Dataset) – A data set containing horizontal mesh variables
field_name (str) – The name of the variable to plot, which must be present in ds
out_file_name (str, optional) – The path to which the plot image should be written
ax (matplotlib.axes.Axes) – Axes to plot to if making a multi-panel figure
ax (matplotlib.axes.Axes) – Axes to plot to if making a multi-panel figure
title (str, optional) – The title of the plot
vmin (float, optional) – The minimum values for the colorbar
vmax (float, optional) – The maximum values for the colorbar
polaris.viz.plot_horiz_fieldtuple, optional) – The width and height of the figure in inches. Default is determined
based on the aspect ratio of the domain.
vert_dim (str, optional) – Name of the vertical dimension
cell_mask (numpy.ndarray, optional) – A bool mask indicating where cells are valid, used to mask fields
+
cell_mask (numpy.ndarray, optional) – A bool mask indicating where cells are valid, used to mask fields
on both cells and edges. Not used if patches and patch_mask
are supplied
patches (list of numpy.ndarray, optional) – Patches from a previous call to plot_horiz_field()
patch_mask (numpy.ndarray, optional) – A mask of where the field has patches from a previous call to
+
patches (list of numpy.ndarray, optional) – Patches from a previous call to plot_horiz_field()
patch_mask (numpy.ndarray, optional) – A mask of where the field has patches from a previous call to
plot_horiz_field()
transect_x (numpy.ndarray or xarray.DataArray, optional) – The x coordinates of a transect to plot on the
transect_y (numpy.ndarray or xarray.DataArray, optional) – The y coordinates of a transect
transect_x (numpy.ndarray or xarray.DataArray, optional) – The x coordinates of a transect to plot on the
transect_y (numpy.ndarray or xarray.DataArray, optional) – The y coordinates of a transect
transect_color (str, optional) – The color of the transect line
transect_start (str or None, optional) – The color of a dot marking the start of the transect
transect_end (str or None, optional) – The color of a dot marking the end of the transect
polaris.yaml.PolarisYaml
polaris.yaml.PolarisYaml__init__()
Create a yaml config object
read(filename[, package, replacements, model])
read(filename[, package, replacements, ...])
Add config options from a yaml file
update([configs, options, quiet])
polaris.yaml.PolarisYaml.read
-
-classmethod PolarisYaml.read(filename, package=None, replacements=None, model=None)[source]
+classmethod PolarisYaml.read(filename, package=None, replacements=None, model=None, streams_section='streams')[source]
Add config options from a yaml file
- Parameters:
@@ -153,6 +153,7 @@ polaris.yaml.PolarisYaml.readstr, optional) – The name of the model to parse if the yaml file might have multiple
models
+
streams_section (str, optional) – The name of the streams section
- Returns:
diff --git a/main/developers_guide/ocean/api.html b/main/developers_guide/ocean/api.html
index 252811e75..4db7cdb72 100644
--- a/main/developers_guide/ocean/api.html
+++ b/main/developers_guide/ocean/api.html
@@ -690,16 +690,16 @@ Ocean ModelIf the model is Omega, rename variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
OceanIOStep.write_model_dataset(ds, filename)
Write out the given dataset, mapping variable names from MPAS-Ocean to Omega names if appropriate
Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
If the model is Omega, rename variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
OceanIOStep.open_model_dataset(filename, ...)
Open the given dataset, mapping variable names from Omega to MPAS-Ocean names if appropriate
Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
OceanModelStep(component, name[, subdir, ...])
An Omega or MPAS-Ocean step
polaris.ocean.convergence.analysis.ConvergenceAnalysisGet the model output field at the given time and z index
map_from_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
map_to_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
open_model_dataset(filename, **kwargs)
Open the given dataset, mapping variable names from Omega to MPAS-Ocean names if appropriate
Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
plot_convergence(variable_name, title, zidx)
Compute the error norm for each resolution and produce a convergence plot
polaris.ocean.convergence.analysis.ConvergenceAnalysisCompare variables between output files in this step and in the same step from a baseline run if one was provided.
write_model_dataset(ds, filename)
Write out the given dataset, mapping variable names from MPAS-Ocean to Omega names if appropriate
Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
polaris.ocean.convergence.forward.ConvergenceForwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.convergence.spherical.SphericalConvergenceForwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.ice_shelf.SshForwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.model.OceanIOStep
Variables:
+mpaso_to_omega_dim_map (dict) – A map from MPAS-Ocean dimension names to their Omega equivalents
omega_to_mpaso_dim_map (dict) – A map from Omega dimension names to their MPAS-Ocean equivalents, the
+inverse of mpaso_to_omega_dim_map
mpaso_to_omega_var_map (dict) – A map from MPAS-Ocean variable names to their Omega equivalents
omega_to_mpaso_var_map (dict) – A map from Omega variable names to their MPAS-Ocean equivalents, the
inverse of mpaso_to_omega_var_map
polaris.ocean.model.OceanIOStepcpus_per_task and ntasks based on the number of cores available to this step
If the model is Omega, rename variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
open_model_dataset(filename, **kwargs)
Open the given dataset, mapping variable names from Omega to MPAS-Ocean names if appropriate
Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
process_inputs_and_outputs()
Process the inputs to and outputs from a step added with polaris.Step.add_input_file() and polaris.Step.add_output_file().
polaris.ocean.model.OceanIOStepwrite_model_dataset(ds, filename)
Write out the given dataset, mapping variable names from MPAS-Ocean to Omega names if appropriate
Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
polaris.ocean.model.OceanIOStep.map_from_native_model_vars
-
OceanIOStep.map_from_native_model_vars(ds)[source]
-If the model is Omega, rename variables in a dataset from their
-Omega names to the MPAS-Ocean equivalent (appropriate for datasets
-that are output from the model)
+If the model is Omega, rename dimensions and variables in a dataset
+from their Omega names to the MPAS-Ocean equivalent (appropriate for
+datasets that are output from the model)
- Parameters:
ds (xarray.Dataset) – A dataset containing variable names native to either ocean model
diff --git a/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.map_to_native_model_vars.html b/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.map_to_native_model_vars.html
index 844001ded..5f8712d1a 100644
--- a/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.map_to_native_model_vars.html
+++ b/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.map_to_native_model_vars.html
@@ -124,9 +124,9 @@ polaris.ocean.model.OceanIOStep.map_to_native_model_vars
-
OceanIOStep.map_to_native_model_vars(ds)[source]
-If the model is Omega, rename variables in a dataset from their
-MPAS-Ocean names to the Omega equivalent (appropriate for input
-datasets like an initial condition)
+If the model is Omega, rename dimensions and variables in a dataset
+from their MPAS-Ocean names to the Omega equivalent (appropriate for
+input datasets like an initial condition)
- Parameters:
ds (xarray.Dataset) – A dataset containing MPAS-Ocean variable names
diff --git a/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.open_model_dataset.html b/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.open_model_dataset.html
index ad2ac2f84..afee85f5a 100644
--- a/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.open_model_dataset.html
+++ b/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.open_model_dataset.html
@@ -124,8 +124,8 @@ polaris.ocean.model.OceanIOStep.open_model_dataset
-
OceanIOStep.open_model_dataset(filename, **kwargs)[source]
-Open the given dataset, mapping variable names from Omega to MPAS-Ocean
-names if appropriate
+Open the given dataset, mapping variable and dimension names from Omega
+to MPAS-Ocean names if appropriate
- Parameters:
diff --git a/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.write_model_dataset.html b/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.write_model_dataset.html
index be9223046..d6b9d7a6d 100644
--- a/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.write_model_dataset.html
+++ b/main/developers_guide/ocean/generated/polaris.ocean.model.OceanIOStep.write_model_dataset.html
@@ -124,8 +124,8 @@ polaris.ocean.model.OceanIOStep.write_model_dataset
-
OceanIOStep.write_model_dataset(ds, filename)[source]
-Write out the given dataset, mapping variable names from MPAS-Ocean
-to Omega names if appropriate
+Write out the given dataset, mapping dimension and variable names from
+MPAS-Ocean to Omega names if appropriate
- Parameters:
diff --git a/main/developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.html b/main/developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.html
index 49f2f5505..93a6f818b 100644
--- a/main/developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.html
+++ b/main/developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.html
@@ -224,37 +224,40 @@ polaris.ocean.model.OceanModelStepmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.tasks.baroclinic_channel.forward.Forwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStepmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.tasks.barotropic_gyre.analysis.AnalysisExact solution to the sea surface height for the linearized Munk layer experiments.
map_from_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
map_to_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
open_model_dataset(filename, **kwargs)
Open the given dataset, mapping variable names from Omega to MPAS-Ocean names if appropriate
Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
process_inputs_and_outputs()
Process the inputs to and outputs from a step added with polaris.Step.add_input_file() and polaris.Step.add_output_file().
polaris.ocean.tasks.barotropic_gyre.analysis.AnalysisCompare variables between output files in this step and in the same step from a baseline run if one was provided.
write_model_dataset(ds, filename)
Write out the given dataset, mapping variable names from MPAS-Ocean to Omega names if appropriate
Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
polaris.ocean.tasks.barotropic_gyre.forward.Forwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.tasks.cosine_bell.analysis.AnalysisGet the model output field at the given time and z index
map_from_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
map_to_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
open_model_dataset(filename, **kwargs)
Open the given dataset, mapping variable names from Omega to MPAS-Ocean names if appropriate
Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
plot_convergence(variable_name, title, zidx)
Compute the error norm for each resolution and produce a convergence plot
polaris.ocean.tasks.cosine_bell.analysis.AnalysisCompare variables between output files in this step and in the same step from a baseline run if one was provided.
write_model_dataset(ds, filename)
Write out the given dataset, mapping variable names from MPAS-Ocean to Omega names if appropriate
Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
polaris.ocean.tasks.cosine_bell.forward.Forwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.tasks.geostrophic.analysis.AnalysisGet the model output field at the given time and z index
map_from_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
map_to_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
open_model_dataset(filename, **kwargs)
Open the given dataset, mapping variable names from Omega to MPAS-Ocean names if appropriate
Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
plot_convergence(variable_name, title, zidx)
Compute the error norm for each resolution and produce a convergence plot
polaris.ocean.tasks.geostrophic.analysis.AnalysisCompare variables between output files in this step and in the same step from a baseline run if one was provided.
write_model_dataset(ds, filename)
Write out the given dataset, mapping variable names from MPAS-Ocean to Omega names if appropriate
Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
polaris.ocean.tasks.geostrophic.forward.Forwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.tasks.ice_shelf_2d.forward.Forwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.tasks.inertial_gravity_wave.analysis.Analysismap_from_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
map_to_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
open_model_dataset(filename, **kwargs)
Open the given dataset, mapping variable names from Omega to MPAS-Ocean names if appropriate
Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
plot_convergence(variable_name, title, zidx)
Compute the error norm for each resolution and produce a convergence plot
polaris.ocean.tasks.inertial_gravity_wave.analysis.Analysiswrite_model_dataset(ds, filename)
Write out the given dataset, mapping variable names from MPAS-Ocean to Omega names if appropriate
Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
polaris.ocean.tasks.inertial_gravity_wave.forward.Forwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.tasks.internal_wave.forward.Forwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.tasks.manufactured_solution.analysis.Analysismap_from_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
map_to_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
open_model_dataset(filename, **kwargs)
Open the given dataset, mapping variable names from Omega to MPAS-Ocean names if appropriate
Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
plot_convergence(variable_name, title, zidx)
Compute the error norm for each resolution and produce a convergence plot
polaris.ocean.tasks.manufactured_solution.analysis.Analysiswrite_model_dataset(ds, filename)
Write out the given dataset, mapping variable names from MPAS-Ocean to Omega names if appropriate
Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
polaris.ocean.tasks.manufactured_solution.forward.Forwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
TEMP: symlink initial condition to name hard-coded in Omega
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.tasks.manufactured_solution.init.InitConstrain cpus_per_task and ntasks based on the number of cores available to this step
map_from_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
map_to_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
open_model_dataset(filename, **kwargs)
Open the given dataset, mapping variable names from Omega to MPAS-Ocean names if appropriate
Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
process_inputs_and_outputs()
Process the inputs to and outputs from a step added with polaris.Step.add_input_file() and polaris.Step.add_output_file().
polaris.ocean.tasks.manufactured_solution.init.InitCompare variables between output files in this step and in the same step from a baseline run if one was provided.
write_model_dataset(ds, filename)
Write out the given dataset, mapping variable names from MPAS-Ocean to Omega names if appropriate
Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
polaris.ocean.tasks.manufactured_solution.viz.VizConstrain cpus_per_task and ntasks based on the number of cores available to this step
map_from_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
map_to_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
open_model_dataset(filename, **kwargs)
Open the given dataset, mapping variable names from Omega to MPAS-Ocean names if appropriate
Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
process_inputs_and_outputs()
Process the inputs to and outputs from a step added with polaris.Step.add_input_file() and polaris.Step.add_output_file().
polaris.ocean.tasks.manufactured_solution.viz.VizCompare variables between output files in this step and in the same step from a baseline run if one was provided.
write_model_dataset(ds, filename)
Write out the given dataset, mapping variable names from MPAS-Ocean to Omega names if appropriate
Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
polaris.ocean.tasks.single_column.forward.Forwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.tasks.sphere_transport.analysis.AnalysisGet the model output field at the given time and z index
map_from_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
If the model is Omega, rename dimensions and variables in a dataset from their Omega names to the MPAS-Ocean equivalent (appropriate for datasets that are output from the model)
map_to_native_model_vars(ds)
If the model is Omega, rename variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
If the model is Omega, rename dimensions and variables in a dataset from their MPAS-Ocean names to the Omega equivalent (appropriate for input datasets like an initial condition)
open_model_dataset(filename, **kwargs)
Open the given dataset, mapping variable names from Omega to MPAS-Ocean names if appropriate
Open the given dataset, mapping variable and dimension names from Omega to MPAS-Ocean names if appropriate
plot_convergence(variable_name, title, zidx)
Compute the error norm for each resolution and produce a convergence plot
polaris.ocean.tasks.sphere_transport.analysis.AnalysisCompare variables between output files in this step and in the same step from a baseline run if one was provided.
write_model_dataset(ds, filename)
Write out the given dataset, mapping variable names from MPAS-Ocean to Omega names if appropriate
Write out the given dataset, mapping dimension and variable names from MPAS-Ocean to Omega names if appropriate
polaris.ocean.tasks.sphere_transport.forward.Forwardmap_yaml_options(options, config_model)
A mapping between model config options from MPAS-Ocean to Omega
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Determine if we will make yaml files or namelists and streams files, then, determine the number of MPI tasks to use based on the estimated mesh size
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
polaris.ocean.vertical.grid_1d.write_1d_grid
- Parameters:
-interfaces (numpy.ndarray) – A 1D array of positive depths for layer interfaces in meters
interfaces (numpy.ndarray) – A 1D array of positive depths for layer interfaces in meters
out_filename (str) – MPAS file name for output of vertical grid
polaris.ocean.viz.plot_transectpolaris.ocean.viz.compute_transect()
mpas_field (xarray.DataArray) – The MPAS-Ocean 3D field to plot
out_filename (str, optional) – The png file to write out to
ax (matplotlib.axes.Axes) – Axes to plot to if making a multi-panel figure
ax (matplotlib.axes.Axes) – Axes to plot to if making a multi-panel figure
title (str) – The title of the plot
vmin (float, optional) – The minimum values for the colorbar
vmax (float, optional) – The maximum values for the colorbar
polaris.seaice.tasks.single_column.forward.ForwardAdd model config options, namelist, streams and yaml files using config options or template replacements that need to be set both during step setup and at runtime
map_yaml_configs(configs, config_model)
A mapping between model config options between different models.
A mapping between model config options from different models.
map_yaml_options(options, config_model)
A mapping between model config options between different models.
A mapping between model config options from different models.
map_yaml_to_namelist(options)
map_yaml_streams(streams, config_model)
A mapping between model streams from different models.
map_yaml_to_namelist(options)
A mapping from yaml model config options to namelist options.
partition([graph_file])
partition([graph_file])
Partition the domain for the requested number of tasks
process_inputs_and_outputs()
process_inputs_and_outputs()
Process the model as an input, then call the parent class' version
run()
run()
Run the step.
runtime_setup()
runtime_setup()
Update PIO namelist options, make graph file, and partition graph file (if any of these are requested)
set_model_resources([ntasks, min_tasks, ...])
set_model_resources([ntasks, min_tasks, ...])
Update the resources for the step.
set_resources([cpus_per_task, ...])
set_resources([cpus_per_task, ...])
Update the resources for the subtask.
set_shared_config(config[, link])
set_shared_config(config[, link])
Replace the step's config parser with the shared config parser
setup()
setup()
Setup the command-line arguments
update_namelist_pio()
update_namelist_pio()
Modify the namelist so the number of PIO tasks and the stride between them consistent with the number of nodes and cores (one PIO task per node).
validate_baselines()
validate_baselines()
Compare variables between output files in this step and in the same step from a baseline run if one was provided.
": [[409, null], [414, null]], "A \u201cuser\u201d config file": [[382, "a-user-config-file"]], "API reference": [[3, null]], "Activating the environment": [[362, "activating-the-environment"]], "Adding E3SM component as an input": [[14, "adding-e3sm-component-as-an-input"]], "Adding a Machine Config File": [[141, "adding-a-machine-config-file"]], "Adding a New Supported Machine": [[141, "adding-a-new-supported-machine"]], "Adding a config file": [[381, "adding-a-config-file"]], "Adding a namelist file": [[14, "adding-a-namelist-file"]], "Adding a parameter study": [[381, "adding-a-parameter-study"]], "Adding a second task": [[381, "adding-a-second-task"]], "Adding a shared \u201csuperclass\u201d for tasks": [[381, "adding-a-shared-superclass-for-tasks"]], "Adding a streams file": [[14, "adding-a-streams-file"]], "Adding a template streams file": [[14, "adding-a-template-streams-file"]], "Adding a visualization step": [[381, "adding-a-visualization-step"]], "Adding a yaml file": [[14, "adding-a-yaml-file"]], "Adding a \u201cdefault\u201d task": [[381, "adding-a-default-task"]], "Adding dynamic model config options": [[381, "adding-dynamic-model-config-options"]], "Adding model config options": [[14, "adding-model-config-options"]], "Adding model config options in code": [[381, "adding-model-config-options-in-code"]], "Adding more validation": [[381, "adding-more-validation"]], "Adding other steps as dependencies": [[358, "adding-other-steps-as-dependencies"]], "Adding plots": [[381, "adding-plots"]], "Adding step outputs": [[381, "adding-step-outputs"]], "Adding the analysis step": [[381, "adding-the-analysis-step"]], "Adding the forward step": [[381, "adding-the-forward-step"]], "Adding the forward step to the task": [[381, "adding-the-forward-step-to-the-task"]], "Adding the init step": [[381, "adding-the-init-step"]], "Adding the step to the task": [[381, "adding-the-step-to-the-task"]], "Adding the steps to the task": [[381, "adding-the-steps-to-the-task"]], "Adding the viz step to the task": [[381, "adding-the-viz-step-to-the-task"]], "Adding validation": [[381, "adding-validation"], [381, "id1"]], "Adding yaml, namelist and streams files": [[14, "adding-yaml-namelist-and-streams-files"]], "Algorithm Design (optional)": [[2, "algorithm-design-optional"]], "Algorithm Design: name-of-topic-here (same as Requirement)": [[2, "algorithm-design-name-of-topic-here-same-as-requirement"]], "Anvil": [[136, null], [383, null]], "Area": [[15, "area"]], "Base Classes": [[3, "base-classes"]], "Boundary conditions": [[339, "boundary-conditions"]], "Building E3SM components": [[362, "building-e3sm-components"]], "Building supported E3SM components as standalone models": [[410, "building-supported-e3sm-components-as-standalone-models"]], "Building the Documentation": [[4, null]], "Building the Spack Environment": [[141, "building-the-spack-environment"]], "Cached output files": [[358, "cached-output-files"]], "Categories of tasks": [[354, null]], "Chicoma": [[137, null], [384, null]], "Chicoma-CPU": [[384, "chicoma-cpu"]], "Chrysalis": [[138, null], [385, null]], "Classes": [[361, "classes"]], "Code Style": [[361, "code-style"]], "Code sharing": [[361, "code-sharing"]], "Code style for polaris": [[362, "code-style-for-polaris"]], "Command-line interface": [[3, "command-line-interface"], [5, null]], "Comments in config files": [[9, "comments-in-config-files"]], "Compass": [[380, "compass"]], "Component": [[3, "component"]], "Components": [[3, "components"], [355, null]], "Computing the cell count": [[381, "computing-the-cell-count"]], "CompyMcNodeFace": [[139, null], [386, null]], "Conda": [[6, "conda"]], "Config Files": [[382, null]], "Config file": [[355, "config-file"]], "Config files": [[9, null]], "Config options describing E3SM machines": [[6, "config-options-describing-e3sm-machines"]], "Constructor": [[355, "constructor"]], "Convergence Tests": [[143, "convergence-tests"], [144, "convergence-tests"]], "Copying input files": [[358, "copying-input-files"]], "Creating a horizontal mesh": [[381, "creating-a-horizontal-mesh"]], "Creating a vertical coordinate": [[381, "creating-a-vertical-coordinate"]], "Creating an initial condition": [[381, "creating-an-initial-condition"]], "Creating spack environments": [[6, "creating-spack-environments"]], "Creating/updating only the polaris environment": [[362, "creating-updating-only-the-polaris-environment"]], "Defining model config options and streams": [[381, "defining-model-config-options-and-streams"]], "Deploy spack for polaris without Albany or PETSc": [[6, "deploy-spack-for-polaris-without-albany-or-petsc"]], "Deploying a new spack environment": [[6, null]], "Deploying shared spack environments": [[6, "deploying-shared-spack-environments"]], "Deploying spack with Albany": [[6, "deploying-spack-with-albany"]], "Deploying spack with PETSc (and Netlib LAPACK)": [[6, "deploying-spack-with-petsc-and-netlib-lapack"]], "Describing a Spack Environment": [[141, "describing-a-spack-environment"]], "Design Documents": [[0, null]], "Developer Tutorial: Adding a new test group": [[381, null]], "Developer's guide": [[380, null]], "Directory structure": [[356, null]], "Docstrings": [[7, "docstrings"]], "Documentation": [[7, null], [381, "documentation"]], "Download": [[11, "download"]], "Downloading and symlinking input files": [[358, "downloading-and-symlinking-input-files"]], "Dynamic model config options": [[14, "dynamic-model-config-options"]], "E3SM supported machines": [[410, "e3sm-supported-machines"]], "Enhancements": [[381, "enhancements"]], "Environments with Albany": [[362, "environments-with-albany"]], "Environments with PETSc and Netlib-LAPACK": [[362, "environments-with-petsc-and-netlib-lapack"]], "Forcing": [[339, "forcing"], [375, "forcing"]], "Framework": [[10, null], [391, null]], "Frontier": [[140, null], [387, null]], "General planar meshes": [[13, "general-planar-meshes"]], "Getting started": [[381, "getting-started"]], "Glossary": [[379, null], [380, null]], "How to (and how not to) pass data between steps": [[381, "how-to-and-how-not-to-pass-data-between-steps"]], "IO": [[11, null]], "Ice Shelf": [[143, "ice-shelf"]], "Ice Shelf Tasks": [[144, "ice-shelf-tasks"]], "Ice shelf": [[390, null]], "Identifying E3SM machines": [[6, "identifying-e3sm-machines"]], "Implementation": [[1, "implementation"], [2, "implementation"]], "Implementation: Shared steps are not daughters of a task": [[1, "implementation-shared-steps-are-not-daughters-of-a-task"]], "Implementation: Shared steps are run before steps that depend on their output.": [[1, "implementation-shared-steps-are-run-before-steps-that-depend-on-their-output"]], "Implementation: Shared steps are set up once.": [[1, "implementation-shared-steps-are-set-up-once"]], "Implementation: The output of shared steps may be used by multiple tasks.": [[1, "implementation-the-output-of-shared-steps-may-be-used-by-multiple-tasks"]], "Implementation: Working directory step paths are easily discoverable by users.": [[1, "implementation-working-directory-step-paths-are-easily-discoverable-by-users"]], "Implementation: Working directory structure is intuitive.": [[1, "implementation-working-directory-structure-is-intuitive"]], "Implementation: name-of-topic-here (same as Requirement)": [[2, "implementation-name-of-topic-here-same-as-requirement"]], "Implementation: tasks do not rely on outputs from steps in other tasks": [[1, "implementation-tasks-do-not-rely-on-outputs-from-steps-in-other-tasks"]], "Initial conditions": [[339, "initial-conditions"], [375, "initial-conditions"]], "Input and output from an E3SM component": [[144, "input-and-output-from-an-e3sm-component"]], "Input files": [[358, "input-files"]], "Jupyter notebook on remote data": [[389, "jupyter-notebook-on-remote-data"]], "Loading and running Polaris on Anvil": [[383, "loading-and-running-polaris-on-anvil"]], "Loading and running Polaris on Chicoma": [[384, "loading-and-running-polaris-on-chicoma"]], "Loading and running Polaris on Chrysalis": [[385, "loading-and-running-polaris-on-chrysalis"]], "Loading and running Polaris on CompyMcNodeFace": [[386, "loading-and-running-polaris-on-compymcnodeface"]], "Loading and running Polaris on Frontier": [[387, "loading-and-running-polaris-on-frontier"]], "Loading and running Polaris on Perlmutter": [[389, "loading-and-running-polaris-on-perlmutter"]], "Loading polaris conda and spack environments": [[410, "loading-polaris-conda-and-spack-environments"]], "Logging": [[12, null]], "MALI": [[362, "mali"]], "MPAS": [[15, null]], "MPAS-Ocean": [[339, null], [362, "mpas-ocean"]], "MPICH": [[388, "mpich"]], "Mache": [[6, "mache"], [6, "id1"]], "Machines": [[141, null], [388, null]], "Making a graph file": [[14, "making-a-graph-file"]], "Making a new test group": [[381, "making-a-new-test-group"]], "Mapping from MPAS-Ocean to Omega config options": [[144, "mapping-from-mpas-ocean-to-omega-config-options"]], "Mesh": [[13, null]], "Model": [[14, null], [144, "model"]], "Model config options and streams": [[144, "model-config-options-and-streams"]], "ModelStep": [[3, "modelstep"]], "Models": [[338, null]], "Modules": [[361, "modules"]], "Modules for polaris commands": [[8, null]], "Modules, env. variables, etc. for E3SM machines": [[6, "modules-env-variables-etc-for-e3sm-machines"]], "Nightly suite": [[359, "nightly-suite"]], "No MPI from conda-forge": [[388, "no-mpi-from-conda-forge"]], "Norms": [[18, "norms"]], "Ocean Framework": [[143, "ocean-framework"]], "Ocean Model": [[143, "ocean-model"]], "Ocean component": [[337, null], [393, null]], "Ocean framework": [[144, null]], "Omega": [[362, "omega"]], "OpenMPI": [[388, "openmpi"]], "Optional flags": [[362, "optional-flags"]], "Organization of Tasks": [[357, null]], "Other Machines": [[141, "other-machines"], [388, "other-machines"]], "Other machines": [[410, "other-machines"]], "Output files": [[358, "output-files"]], "Overview": [[361, null]], "Packages": [[361, "packages"]], "Packages and Modules": [[361, "packages-and-modules"]], "Partitioning the mesh": [[14, "partitioning-the-mesh"]], "Perlmutter": [[142, null], [389, null]], "Perlmutter-CPU": [[389, "perlmutter-cpu"]], "Permissions": [[11, "permissions"]], "Planar Meshes": [[13, "planar-meshes"]], "Polaris": [[380, null]], "Provenance": [[16, null]], "Proxy on LANL Macs": [[378, "proxy-on-lanl-macs"]], "Pull-Request (PR) suite": [[359, "pull-request-pr-suite"]], "Quasi-uniform and Icosahedral Spherical Meshes": [[144, "quasi-uniform-and-icosahedral-spherical-meshes"]], "Quick Start for Developers": [[362, null]], "Quick Start for Users": [[410, null]], "Quick Start for Users is not yet valid": [[410, null]], "RPE task": [[404, "rpe-task"]], "Reference Potential Energy (RPE)": [[143, "reference-potential-energy-rpe"]], "Remapping": [[17, null]], "Requirement: Shared steps are not daughters of a task": [[1, "requirement-shared-steps-are-not-daughters-of-a-task"]], "Requirement: Shared steps are run before steps that depend on their output.": [[1, "requirement-shared-steps-are-run-before-steps-that-depend-on-their-output"]], "Requirement: Shared steps are run once.": [[1, "requirement-shared-steps-are-run-once"]], "Requirement: The output of shared steps may be used by multiple tasks.": [[1, "requirement-the-output-of-shared-steps-may-be-used-by-multiple-tasks"]], "Requirement: Working directory step paths are easily discoverable by users.": [[1, "requirement-working-directory-step-paths-are-easily-discoverable-by-users"]], "Requirement: Working directory structure is intuitive.": [[1, "requirement-working-directory-structure-is-intuitive"]], "Requirement: name-of-topic-here": [[2, "requirement-name-of-topic-here"]], "Requirement: tasks do not rely on outputs from steps in other tasks": [[1, "requirement-tasks-do-not-rely-on-outputs-from-steps-in-other-tasks"]], "Requirements": [[1, "requirements"], [2, "requirements"]], "Running a task": [[410, "running-a-task"]], "Running an E3SM component": [[14, "running-an-e3sm-component"], [144, "running-an-e3sm-component"]], "Running polaris from the repo": [[362, "running-polaris-from-the-repo"]], "Running with a job script": [[410, "running-with-a-job-script"]], "SSH adjustment steps": [[390, "ssh-adjustment-steps"]], "Sea ice component": [[411, null]], "SeaIce component": [[374, null]], "SeaIce framework": [[364, null]], "Set up a polaris repository with worktrees: for advanced users": [[362, "set-up-a-polaris-repository-with-worktrees-for-advanced-users"]], "Set up a polaris repository: for beginners": [[362, "set-up-a-polaris-repository-for-beginners"]], "Setting MPI resources": [[144, "setting-mpi-resources"]], "Setting time intervals in model config options": [[144, "setting-time-intervals-in-model-config-options"]], "Setting up tasks": [[410, "setting-up-tasks"]], "Shared config files": [[9, "shared-config-files"]], "Shared steps": [[1, null]], "Slurm job queueing": [[388, "slurm-job-queueing"]], "Solver errors when configuring conda environment": [[378, "solver-errors-when-configuring-conda-environment"]], "Spack": [[6, "spack"]], "Spherical Base Mesh Step": [[143, "spherical-base-mesh-step"]], "Spherical Convergence Tests": [[143, "spherical-convergence-tests"]], "Spherical Meshes": [[13, "spherical-meshes"]], "Step": [[3, "step"]], "Step attributes": [[358, "step-attributes"]], "Steps": [[358, null]], "Suites": [[359, null], [394, null], [410, "suites"], [415, null]], "Summary": [[1, "summary"], [2, "summary"]], "Supported Machines": [[141, "supported-machines"], [388, "supported-machines"]], "Supported Model: MPAS-Seaice": [[375, null]], "Supported Models": [[338, "supported-models"]], "Supported machines": [[362, "supported-machines"]], "Switching between different polaris environments": [[362, "switching-between-different-polaris-environments"]], "Symlink to input files from polaris": [[358, 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"polaris.ocean.tasks.inertial_gravity_wave.InertialGravityWave", false]], "ingest() (in module polaris.namelist)": [[91, "polaris.namelist.ingest", false]], "init (class in polaris.ocean.tasks.baroclinic_channel.init)": [[187, "polaris.ocean.tasks.baroclinic_channel.init.Init", false]], "init (class in polaris.ocean.tasks.barotropic_gyre.init)": [[213, "polaris.ocean.tasks.barotropic_gyre.init.Init", false]], "init (class in polaris.ocean.tasks.cosine_bell.init)": [[224, "polaris.ocean.tasks.cosine_bell.init.Init", false]], "init (class in polaris.ocean.tasks.geostrophic.init)": [[236, "polaris.ocean.tasks.geostrophic.init.Init", false]], "init (class in polaris.ocean.tasks.ice_shelf_2d.init)": [[245, "polaris.ocean.tasks.ice_shelf_2d.init.Init", false]], "init (class in polaris.ocean.tasks.inertial_gravity_wave.init)": [[260, "polaris.ocean.tasks.inertial_gravity_wave.init.Init", false]], "init (class in polaris.ocean.tasks.internal_wave.init)": [[269, "polaris.ocean.tasks.internal_wave.init.Init", false]], "init (class in polaris.ocean.tasks.manufactured_solution.init)": [[286, "polaris.ocean.tasks.manufactured_solution.init.Init", false]], "init (class in polaris.ocean.tasks.single_column.init)": [[295, "polaris.ocean.tasks.single_column.init.Init", false]], "init (class in polaris.ocean.tasks.sphere_transport.init)": [[307, "polaris.ocean.tasks.sphere_transport.init.Init", false]], "init_sigma_vertical_coord() (in module polaris.ocean.vertical.sigma)": [[318, "polaris.ocean.vertical.sigma.init_sigma_vertical_coord", false]], "init_vertical_coord() (in module polaris.ocean.vertical)": [[315, "polaris.ocean.vertical.init_vertical_coord", false]], "init_z_level_vertical_coord() (in module polaris.ocean.vertical.zlevel)": [[324, "polaris.ocean.vertical.zlevel.init_z_level_vertical_coord", false]], "init_z_star_vertical_coord() (in module polaris.ocean.vertical.zstar)": [[326, "polaris.ocean.vertical.zstar.init_z_star_vertical_coord", false]], "interp_mpas_to_transect_cells() (in module polaris.ocean.viz.transect.vert)": [[335, "polaris.ocean.viz.transect.vert.interp_mpas_to_transect_cells", false]], "interp_mpas_to_transect_nodes() (in module polaris.ocean.viz.transect.vert)": [[336, "polaris.ocean.viz.transect.vert.interp_mpas_to_transect_nodes", false]], "list_cases() (in module polaris.list)": [[67, "polaris.list.list_cases", false]], "list_machines() (in module polaris.list)": [[68, "polaris.list.list_machines", false]], "list_suites() (in module polaris.list)": [[69, "polaris.list.list_suites", false]], "load_dependencies() (in module polaris.run)": [[112, "polaris.run.load_dependencies", false]], "log_method_call() (in module polaris.logging)": [[70, "polaris.logging.log_method_call", false]], "main() (in module polaris.__main__)": [[56, "polaris.__main__.main", false]], "main_mpas_to_yaml() (in module polaris.yaml)": [[133, "polaris.yaml.main_mpas_to_yaml", false]], "make_graph_file() (in module polaris.model_step)": [[88, "polaris.model_step.make_graph_file", false]], "make_jigsaw_mesh() (polaris.mesh.icosahedralmeshstep method)": [[75, "polaris.mesh.IcosahedralMeshStep.make_jigsaw_mesh", false]], "make_jigsaw_mesh() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[80, "polaris.mesh.QuasiUniformSphericalMeshStep.make_jigsaw_mesh", false]], "make_triangle_tree() (in module polaris.ocean.viz.transect.horiz)": [[332, "polaris.ocean.viz.transect.horiz.make_triangle_tree", false]], "manufacturedsolution (class in polaris.ocean.tasks.manufactured_solution)": [[277, "polaris.ocean.tasks.manufactured_solution.ManufacturedSolution", false]], "map_from_native_model_vars() (polaris.ocean.model.oceaniostep method)": [[168, "polaris.ocean.model.OceanIOStep.map_from_native_model_vars", false]], "map_to_native_model_vars() (polaris.ocean.model.oceaniostep method)": [[169, "polaris.ocean.model.OceanIOStep.map_to_native_model_vars", false]], "map_yaml_configs() (polaris.modelstep method)": [[31, "polaris.ModelStep.map_yaml_configs", false]], "map_yaml_configs() (polaris.ocean.model.oceanmodelstep method)": [[176, "polaris.ocean.model.OceanModelStep.map_yaml_configs", false]], "map_yaml_options() (polaris.modelstep method)": [[32, "polaris.ModelStep.map_yaml_options", false]], "map_yaml_options() (polaris.ocean.model.oceanmodelstep method)": [[177, "polaris.ocean.model.OceanModelStep.map_yaml_options", false]], "map_yaml_to_namelist() (polaris.modelstep method)": [[33, "polaris.ModelStep.map_yaml_to_namelist", false]], "mappingfilestep (class in polaris.remap)": [[100, "polaris.remap.MappingFileStep", false]], "mesh_to_triangles() (in module polaris.ocean.viz.transect.horiz)": [[333, "polaris.ocean.viz.transect.horiz.mesh_to_triangles", false]], "mixinganalysis (class in polaris.ocean.tasks.sphere_transport.mixing_analysis)": [[309, "polaris.ocean.tasks.sphere_transport.mixing_analysis.MixingAnalysis", false]], "modelstep (class in polaris)": [[25, "polaris.ModelStep", false]], "mpas_namelist_and_streams_to_yaml() (in module polaris.yaml)": [[134, "polaris.yaml.mpas_namelist_and_streams_to_yaml", false]], "normal_velocity() (polaris.ocean.tasks.inertial_gravity_wave.exact_solution.exactsolution method)": [[256, "polaris.ocean.tasks.inertial_gravity_wave.exact_solution.ExactSolution.normal_velocity", false]], "normal_velocity() (polaris.ocean.tasks.manufactured_solution.exact_solution.exactsolution method)": [[282, "polaris.ocean.tasks.manufactured_solution.exact_solution.ExactSolution.normal_velocity", false]], "ocean (class in polaris.ocean)": [[145, "polaris.ocean.Ocean", false]], "oceaniostep (class in polaris.ocean.model)": [[167, "polaris.ocean.model.OceanIOStep", false]], "oceanmodelstep (class in polaris.ocean.model)": [[173, "polaris.ocean.model.OceanModelStep", false]], "open_model_dataset() (polaris.ocean.model.oceaniostep method)": [[170, "polaris.ocean.model.OceanIOStep.open_model_dataset", false]], "parse_replacements() (in module polaris.namelist)": [[92, "polaris.namelist.parse_replacements", false]], "partition() (polaris.modelstep method)": [[34, "polaris.ModelStep.partition", false]], "plot_convergence() (polaris.ocean.convergence.analysis.convergenceanalysis method)": [[151, "polaris.ocean.convergence.analysis.ConvergenceAnalysis.plot_convergence", false]], "plot_global_lat_lon_field() (in module polaris.viz)": [[125, "polaris.viz.plot_global_lat_lon_field", false]], "plot_global_mpas_field() (in module polaris.viz)": [[126, "polaris.viz.plot_global_mpas_field", false]], "plot_horiz_field() (in module polaris.viz)": [[127, "polaris.viz.plot_horiz_field", false]], "plot_transect() (in module polaris.ocean.viz)": [[329, "polaris.ocean.viz.plot_transect", false]], "polarisconfigparser (class in polaris.config)": [[59, "polaris.config.PolarisConfigParser", false]], "polarisyaml (class in polaris.yaml)": [[129, "polaris.yaml.PolarisYaml", false]], "process_inputs_and_outputs() (polaris.modelstep method)": [[35, "polaris.ModelStep.process_inputs_and_outputs", false]], "quasiuniformsphericalmeshstep (class in polaris.mesh)": [[78, "polaris.mesh.QuasiUniformSphericalMeshStep", false]], "read() (in module polaris.streams)": [[119, "polaris.streams.read", false]], "read() (polaris.yaml.polarisyaml class method)": [[130, "polaris.yaml.PolarisYaml.read", false]], "remove_step() (polaris.component method)": [[24, "polaris.Component.remove_step", false]], "remove_step() (polaris.task method)": [[54, "polaris.Task.remove_step", false]], "replace() (in module polaris.namelist)": [[93, "polaris.namelist.replace", false]], "restart (class in polaris.ocean.tasks.baroclinic_channel.restart)": [[190, "polaris.ocean.tasks.baroclinic_channel.restart.Restart", false]], "restartstep (class in polaris.ocean.tasks.baroclinic_channel.restart.restart_step)": [[191, "polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep", false]], "rpe (class in polaris.ocean.tasks.baroclinic_channel.rpe)": [[193, "polaris.ocean.tasks.baroclinic_channel.rpe.Rpe", false]], "rpe (class in polaris.ocean.tasks.internal_wave.rpe)": [[271, "polaris.ocean.tasks.internal_wave.rpe.Rpe", false]], "run() (polaris.mesh.icosahedralmeshstep method)": [[76, "polaris.mesh.IcosahedralMeshStep.run", false]], "run() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[81, "polaris.mesh.QuasiUniformSphericalMeshStep.run", false]], "run() (polaris.mesh.spherical.sphericalbasestep method)": [[85, "polaris.mesh.spherical.SphericalBaseStep.run", false]], "run() (polaris.ocean.convergence.analysis.convergenceanalysis method)": [[152, "polaris.ocean.convergence.analysis.ConvergenceAnalysis.run", false]], "run() (polaris.ocean.ice_shelf.sshadjustment method)": [[162, "polaris.ocean.ice_shelf.SshAdjustment.run", false]], "run() (polaris.ocean.tasks.baroclinic_channel.init.init method)": [[188, "polaris.ocean.tasks.baroclinic_channel.init.Init.run", false]], "run() (polaris.ocean.tasks.baroclinic_channel.rpe.analysis.analysis method)": [[196, "polaris.ocean.tasks.baroclinic_channel.rpe.analysis.Analysis.run", false]], "run() (polaris.ocean.tasks.baroclinic_channel.validate.validate method)": [[200, "polaris.ocean.tasks.baroclinic_channel.validate.Validate.run", false]], "run() (polaris.ocean.tasks.baroclinic_channel.viz.viz method)": [[202, "polaris.ocean.tasks.baroclinic_channel.viz.Viz.run", false]], "run() (polaris.ocean.tasks.barotropic_gyre.analysis.analysis method)": [[208, "polaris.ocean.tasks.barotropic_gyre.analysis.Analysis.run", false]], "run() (polaris.ocean.tasks.barotropic_gyre.init.init method)": [[214, "polaris.ocean.tasks.barotropic_gyre.init.Init.run", false]], "run() (polaris.ocean.tasks.cosine_bell.init.init method)": [[225, "polaris.ocean.tasks.cosine_bell.init.Init.run", false]], "run() (polaris.ocean.tasks.cosine_bell.viz.viz method)": [[228, "polaris.ocean.tasks.cosine_bell.viz.Viz.run", false]], "run() 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"polaris.ocean.tasks.internal_wave.init.Init.run", false]], "run() (polaris.ocean.tasks.internal_wave.rpe.analysis.analysis method)": [[274, "polaris.ocean.tasks.internal_wave.rpe.analysis.Analysis.run", false]], "run() (polaris.ocean.tasks.internal_wave.viz.viz method)": [[276, "polaris.ocean.tasks.internal_wave.viz.Viz.run", false]], "run() (polaris.ocean.tasks.manufactured_solution.init.init method)": [[287, "polaris.ocean.tasks.manufactured_solution.init.Init.run", false]], "run() (polaris.ocean.tasks.manufactured_solution.viz.viz method)": [[290, "polaris.ocean.tasks.manufactured_solution.viz.Viz.run", false]], "run() (polaris.ocean.tasks.single_column.init.init method)": [[296, "polaris.ocean.tasks.single_column.init.Init.run", false]], "run() (polaris.ocean.tasks.single_column.viz.viz method)": [[298, "polaris.ocean.tasks.single_column.viz.Viz.run", false]], "run() (polaris.ocean.tasks.sphere_transport.filament_analysis.filamentanalysis method)": [[305, "polaris.ocean.tasks.sphere_transport.filament_analysis.FilamentAnalysis.run", false]], "run() (polaris.ocean.tasks.sphere_transport.init.init method)": [[308, "polaris.ocean.tasks.sphere_transport.init.Init.run", false]], "run() (polaris.ocean.tasks.sphere_transport.mixing_analysis.mixinganalysis method)": [[310, "polaris.ocean.tasks.sphere_transport.mixing_analysis.MixingAnalysis.run", false]], "run() (polaris.ocean.tasks.sphere_transport.viz.viz method)": [[312, "polaris.ocean.tasks.sphere_transport.viz.Viz.run", false]], "run() (polaris.seaice.tasks.single_column.exact_restart.validate.validate method)": [[369, "polaris.seaice.tasks.single_column.exact_restart.validate.Validate.run", false]], "run() (polaris.seaice.tasks.single_column.standard_physics.viz.viz method)": [[373, "polaris.seaice.tasks.single_column.standard_physics.viz.Viz.run", false]], "run() (polaris.step method)": [[45, "polaris.Step.run", false]], "run_command() (in module polaris.parallel)": [[97, "polaris.parallel.run_command", false]], "run_single_step() (in module polaris.run.serial)": [[113, "polaris.run.serial.run_single_step", false]], "run_tasks() (in module polaris.run.serial)": [[114, "polaris.run.serial.run_tasks", false]], "runtime_setup() (polaris.modelstep method)": [[36, "polaris.ModelStep.runtime_setup", false]], "runtime_setup() (polaris.remap.mappingfilestep method)": [[107, "polaris.remap.MappingFileStep.runtime_setup", false]], "runtime_setup() (polaris.step method)": [[46, "polaris.Step.runtime_setup", false]], "save_and_plot_cell_width() (polaris.mesh.spherical.sphericalbasestep method)": [[86, "polaris.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width", false]], "seaice (class in polaris.seaice)": [[365, "polaris.seaice.SeaIce", false]], "set_cores_per_node() (in module polaris.parallel)": [[98, "polaris.parallel.set_cores_per_node", false]], "set_model_resources() (polaris.modelstep method)": [[37, "polaris.ModelStep.set_model_resources", false]], "set_resources() (polaris.step method)": [[47, "polaris.Step.set_resources", false]], "set_shared_config() (polaris.step method)": [[48, "polaris.Step.set_shared_config", false]], "set_shared_config() (polaris.task method)": [[55, "polaris.Task.set_shared_config", false]], "setup() (polaris.config.polarisconfigparser method)": [[60, "polaris.config.PolarisConfigParser.setup", false]], "setup() (polaris.mesh.icosahedralmeshstep method)": [[77, "polaris.mesh.IcosahedralMeshStep.setup", false]], "setup() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[82, "polaris.mesh.QuasiUniformSphericalMeshStep.setup", false]], "setup() (polaris.mesh.spherical.sphericalbasestep method)": [[87, "polaris.mesh.spherical.SphericalBaseStep.setup", false]], "setup() (polaris.modelstep method)": [[38, "polaris.ModelStep.setup", false]], "setup() (polaris.ocean.convergence.analysis.convergenceanalysis method)": [[153, "polaris.ocean.convergence.analysis.ConvergenceAnalysis.setup", false]], "setup() (polaris.ocean.model.oceaniostep method)": [[171, "polaris.ocean.model.OceanIOStep.setup", false]], "setup() (polaris.ocean.model.oceanmodelstep method)": [[178, "polaris.ocean.model.OceanModelStep.setup", false]], "setup() (polaris.ocean.tasks.baroclinic_channel.init.init method)": [[189, "polaris.ocean.tasks.baroclinic_channel.init.Init.setup", false]], "setup() (polaris.ocean.tasks.baroclinic_channel.rpe.analysis.analysis method)": [[197, "polaris.ocean.tasks.baroclinic_channel.rpe.analysis.Analysis.setup", false]], "setup() (polaris.ocean.tasks.barotropic_gyre.init.init method)": [[215, "polaris.ocean.tasks.barotropic_gyre.init.Init.setup", false]], "setup() (polaris.ocean.tasks.manufactured_solution.init.init method)": [[288, "polaris.ocean.tasks.manufactured_solution.init.Init.setup", false]], "setup() (polaris.step method)": [[49, "polaris.Step.setup", false]], "setup_config() (in module polaris.run)": [[115, "polaris.run.setup_config", false]], "setup_ssh_adjustment_steps() (polaris.ocean.ice_shelf.iceshelftask method)": [[160, "polaris.ocean.ice_shelf.IceShelfTask.setup_ssh_adjustment_steps", false]], "setup_suite() (in module polaris.suite)": [[123, "polaris.suite.setup_suite", false]], "setup_task() (in module polaris.setup)": [[117, "polaris.setup.setup_task", false]], "setup_tasks() (in module polaris.setup)": [[118, "polaris.setup.setup_tasks", false]], "spheretransport (class in polaris.ocean.tasks.sphere_transport)": [[299, "polaris.ocean.tasks.sphere_transport.SphereTransport", false]], "sphericalbasestep (class in polaris.mesh.spherical)": [[84, "polaris.mesh.spherical.SphericalBaseStep", false]], "sphericalconvergenceforward (class in polaris.ocean.convergence.spherical)": [[157, "polaris.ocean.convergence.spherical.SphericalConvergenceForward", false]], "src_from_lon_lat() (polaris.remap.mappingfilestep method)": [[108, "polaris.remap.MappingFileStep.src_from_lon_lat", false]], "src_from_mpas() (polaris.remap.mappingfilestep method)": [[109, "polaris.remap.MappingFileStep.src_from_mpas", false]], "src_from_proj() (polaris.remap.mappingfilestep method)": [[110, "polaris.remap.MappingFileStep.src_from_proj", false]], "ssh() (polaris.ocean.tasks.inertial_gravity_wave.exact_solution.exactsolution method)": [[257, "polaris.ocean.tasks.inertial_gravity_wave.exact_solution.ExactSolution.ssh", false]], "ssh() (polaris.ocean.tasks.manufactured_solution.exact_solution.exactsolution method)": [[283, "polaris.ocean.tasks.manufactured_solution.exact_solution.ExactSolution.ssh", false]], "sshadjustment (class in polaris.ocean.ice_shelf)": [[161, "polaris.ocean.ice_shelf.SshAdjustment", false]], "sshforward (class in polaris.ocean.ice_shelf)": [[163, "polaris.ocean.ice_shelf.SshForward", false]], "standardphysics (class in polaris.seaice.tasks.single_column.standard_physics)": [[371, "polaris.seaice.tasks.single_column.standard_physics.StandardPhysics", false]], "step (class in polaris)": [[40, "polaris.Step", false]], "symlink() (in module polaris.io)": [[62, "polaris.io.symlink", false]], "task (class in polaris)": [[51, "polaris.Task", false]], "threads (class in polaris.ocean.tasks.baroclinic_channel.threads)": [[198, "polaris.ocean.tasks.baroclinic_channel.threads.Threads", false]], "time_index_from_xtime() (in module polaris.mpas)": [[90, "polaris.mpas.time_index_from_xtime", false]], "unpickle_suite() (in module polaris.run)": [[116, "polaris.run.unpickle_suite", false]], "update() (polaris.yaml.polarisyaml method)": [[131, "polaris.yaml.PolarisYaml.update", false]], "update_cache() (in module polaris.cache)": [[57, "polaris.cache.update_cache", false]], "update_defaults() (in module polaris.streams)": [[120, "polaris.streams.update_defaults", false]], "update_layer_thickness() (in module polaris.ocean.vertical)": [[320, "polaris.ocean.vertical.update_layer_thickness", false]], "update_namelist_pio() (polaris.modelstep method)": [[39, "polaris.ModelStep.update_namelist_pio", false]], "update_permissions() 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\ No newline at end of file
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"add_manufactured_solution_tasks() (in module polaris.ocean.tasks.manufactured_solution)": [[278, "polaris.ocean.tasks.manufactured_solution.add_manufactured_solution_tasks", false]], "add_model_config_options() (polaris.modelstep method)": [[26, "polaris.ModelStep.add_model_config_options", false]], "add_namelist_file() (polaris.modelstep method)": [[27, "polaris.ModelStep.add_namelist_file", false]], "add_output_file() (polaris.step method)": [[43, "polaris.Step.add_output_file", false]], "add_single_column_tasks() (in module polaris.ocean.tasks.single_column)": [[291, "polaris.ocean.tasks.single_column.add_single_column_tasks", false]], "add_single_column_tasks() (in module polaris.seaice.tasks.single_column)": [[366, "polaris.seaice.tasks.single_column.add_single_column_tasks", false]], "add_sphere_transport_tasks() (in module polaris.ocean.tasks.sphere_transport)": [[301, "polaris.ocean.tasks.sphere_transport.add_sphere_transport_tasks", false]], "add_spherical_base_mesh_step() (in module polaris.ocean.mesh.spherical)": [[166, "polaris.ocean.mesh.spherical.add_spherical_base_mesh_step", false]], "add_step() (polaris.component method)": [[22, "polaris.Component.add_step", false]], "add_step() (polaris.task method)": [[52, "polaris.Task.add_step", false]], "add_streams_file() (polaris.modelstep method)": [[28, "polaris.ModelStep.add_streams_file", false]], "add_task() (polaris.component method)": [[23, "polaris.Component.add_task", false]], "add_yaml_file() (polaris.modelstep method)": [[29, "polaris.ModelStep.add_yaml_file", false]], "alter_bottom_depth() (in module polaris.ocean.vertical.partial_cells)": [[316, "polaris.ocean.vertical.partial_cells.alter_bottom_depth", false]], "alter_ssh() (in module polaris.ocean.vertical.partial_cells)": [[317, "polaris.ocean.vertical.partial_cells.alter_ssh", false]], "analysis (class in polaris.ocean.tasks.baroclinic_channel.rpe.analysis)": [[195, "polaris.ocean.tasks.baroclinic_channel.rpe.analysis.Analysis", false]], "analysis (class in polaris.ocean.tasks.barotropic_gyre.analysis)": [[205, "polaris.ocean.tasks.barotropic_gyre.analysis.Analysis", false]], "analysis (class in polaris.ocean.tasks.cosine_bell.analysis)": [[219, "polaris.ocean.tasks.cosine_bell.analysis.Analysis", false]], "analysis (class in polaris.ocean.tasks.geostrophic.analysis)": [[232, "polaris.ocean.tasks.geostrophic.analysis.Analysis", false]], "analysis (class in polaris.ocean.tasks.inertial_gravity_wave.analysis)": [[253, "polaris.ocean.tasks.inertial_gravity_wave.analysis.Analysis", false]], "analysis (class in polaris.ocean.tasks.internal_wave.rpe.analysis)": [[273, "polaris.ocean.tasks.internal_wave.rpe.analysis.Analysis", false]], "analysis (class in polaris.ocean.tasks.manufactured_solution.analysis)": [[279, "polaris.ocean.tasks.manufactured_solution.analysis.Analysis", false]], "analysis (class in polaris.ocean.tasks.sphere_transport.analysis)": [[302, "polaris.ocean.tasks.sphere_transport.analysis.Analysis", false]], "area_for_field() (in module polaris.mpas)": [[89, "polaris.mpas.area_for_field", false]], "barotropicgyre (class in polaris.ocean.tasks.barotropic_gyre)": [[203, "polaris.ocean.tasks.barotropic_gyre.BarotropicGyre", false]], "build_cell_width_lat_lon() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[79, "polaris.mesh.QuasiUniformSphericalMeshStep.build_cell_width_lat_lon", false]], "build_subdivisions_cell_width_lat_lon() (polaris.mesh.icosahedralmeshstep method)": [[72, "polaris.mesh.IcosahedralMeshStep.build_subdivisions_cell_width_lat_lon", false]], "clean_up_whitespace() (in module polaris.job)": [[64, "polaris.job.clean_up_whitespace", false]], "compare_variables() (in module polaris.validate)": [[124, "polaris.validate.compare_variables", false]], "complete_step_run() (in module polaris.run)": [[111, "polaris.run.complete_step_run", false]], "component (class in polaris)": [[20, "polaris.Component", false]], "compute_cell_count() (polaris.ocean.convergence.forward.convergenceforward method)": [[155, "polaris.ocean.convergence.forward.ConvergenceForward.compute_cell_count", false]], "compute_cell_count() (polaris.ocean.convergence.spherical.sphericalconvergenceforward method)": [[158, "polaris.ocean.convergence.spherical.SphericalConvergenceForward.compute_cell_count", false]], "compute_cell_count() (polaris.ocean.ice_shelf.sshforward method)": [[164, "polaris.ocean.ice_shelf.SshForward.compute_cell_count", false]], "compute_cell_count() (polaris.ocean.model.oceanmodelstep method)": [[174, "polaris.ocean.model.OceanModelStep.compute_cell_count", false]], "compute_cell_count() (polaris.ocean.tasks.baroclinic_channel.forward.forward method)": [[185, "polaris.ocean.tasks.baroclinic_channel.forward.Forward.compute_cell_count", false]], "compute_cell_count() (polaris.ocean.tasks.barotropic_gyre.forward.forward method)": [[210, "polaris.ocean.tasks.barotropic_gyre.forward.Forward.compute_cell_count", false]], "compute_cell_count() (polaris.ocean.tasks.cosine_bell.forward.forward method)": [[222, "polaris.ocean.tasks.cosine_bell.forward.Forward.compute_cell_count", false]], "compute_cell_count() (polaris.ocean.tasks.ice_shelf_2d.forward.forward method)": [[243, "polaris.ocean.tasks.ice_shelf_2d.forward.Forward.compute_cell_count", false]], "compute_cell_count() (polaris.ocean.tasks.inertial_gravity_wave.forward.forward method)": [[259, "polaris.ocean.tasks.inertial_gravity_wave.forward.Forward.compute_cell_count", false]], "compute_cell_count() (polaris.ocean.tasks.internal_wave.forward.forward method)": [[267, "polaris.ocean.tasks.internal_wave.forward.Forward.compute_cell_count", false]], "compute_cell_count() (polaris.ocean.tasks.manufactured_solution.forward.forward method)": [[285, "polaris.ocean.tasks.manufactured_solution.forward.Forward.compute_cell_count", false]], "compute_error() (polaris.ocean.convergence.analysis.convergenceanalysis method)": [[147, "polaris.ocean.convergence.analysis.ConvergenceAnalysis.compute_error", false]], "compute_error() (polaris.ocean.tasks.barotropic_gyre.analysis.analysis method)": [[206, "polaris.ocean.tasks.barotropic_gyre.analysis.Analysis.compute_error", false]], "compute_max_time_step() (in module polaris.ocean.tasks.barotropic_gyre.forward)": [[212, "polaris.ocean.tasks.barotropic_gyre.forward.compute_max_time_step", false]], "compute_min_max_level_cell() (in module polaris.ocean.vertical.zlevel)": [[321, "polaris.ocean.vertical.zlevel.compute_min_max_level_cell", false]], "compute_planar_hex_nx_ny() (in module polaris.mesh.planar)": [[83, "polaris.mesh.planar.compute_planar_hex_nx_ny", false]], "compute_rpe() (in module polaris.ocean.rpe)": [[180, "polaris.ocean.rpe.compute_rpe", false]], "compute_transect() (in module polaris.ocean.viz)": [[328, "polaris.ocean.viz.compute_transect", false]], "compute_z_level_layer_thickness() (in module polaris.ocean.vertical.zlevel)": [[322, "polaris.ocean.vertical.zlevel.compute_z_level_layer_thickness", false]], "compute_z_level_resting_thickness() (in module polaris.ocean.vertical.zlevel)": [[323, "polaris.ocean.vertical.zlevel.compute_z_level_resting_thickness", false]], "configure() (polaris.ocean.tasks.baroclinic_channel.rpe.rpe method)": [[194, "polaris.ocean.tasks.baroclinic_channel.rpe.Rpe.configure", false]], "configure() (polaris.ocean.tasks.cosine_bell.cosinebell method)": [[217, "polaris.ocean.tasks.cosine_bell.CosineBell.configure", false]], "configure() (polaris.ocean.tasks.geostrophic.geostrophic method)": [[230, "polaris.ocean.tasks.geostrophic.Geostrophic.configure", false]], "configure() (polaris.ocean.tasks.internal_wave.rpe.rpe method)": [[272, "polaris.ocean.tasks.internal_wave.rpe.Rpe.configure", false]], "configure() (polaris.ocean.tasks.sphere_transport.spheretransport method)": [[300, "polaris.ocean.tasks.sphere_transport.SphereTransport.configure", false]], "configure() (polaris.task method)": [[53, "polaris.Task.configure", false]], "constrain_resources() (polaris.ocean.model.oceanmodelstep method)": [[175, "polaris.ocean.model.OceanModelStep.constrain_resources", false]], "constrain_resources() (polaris.step method)": [[44, "polaris.Step.constrain_resources", false]], "convergence_parameters() (polaris.ocean.convergence.analysis.convergenceanalysis method)": [[148, "polaris.ocean.convergence.analysis.ConvergenceAnalysis.convergence_parameters", false]], "convergence_parameters() (polaris.ocean.tasks.sphere_transport.analysis.analysis method)": [[303, "polaris.ocean.tasks.sphere_transport.analysis.Analysis.convergence_parameters", false]], "convergenceanalysis (class in polaris.ocean.convergence.analysis)": [[146, "polaris.ocean.convergence.analysis.ConvergenceAnalysis", false]], "convergenceforward (class in polaris.ocean.convergence.forward)": [[154, "polaris.ocean.convergence.forward.ConvergenceForward", false]], "cosine_bell() (in module polaris.ocean.tasks.cosine_bell.init)": [[226, "polaris.ocean.tasks.cosine_bell.init.cosine_bell", false]], "cosinebell (class in polaris.ocean.tasks.cosine_bell)": [[216, "polaris.ocean.tasks.cosine_bell.CosineBell", false]], "cvmix (class in polaris.ocean.tasks.single_column.cvmix)": [[292, "polaris.ocean.tasks.single_column.cvmix.CVMix", false]], "decomp (class in polaris.ocean.tasks.baroclinic_channel.decomp)": [[182, "polaris.ocean.tasks.baroclinic_channel.decomp.Decomp", false]], "default (class in polaris.ocean.tasks.baroclinic_channel.default)": [[183, "polaris.ocean.tasks.baroclinic_channel.default.Default", false]], "default (class in polaris.ocean.tasks.ice_shelf_2d.default)": [[241, "polaris.ocean.tasks.ice_shelf_2d.default.Default", false]], "default (class in polaris.ocean.tasks.internal_wave.default)": [[265, "polaris.ocean.tasks.internal_wave.default.Default", false]], "download() (in module polaris.io)": [[61, "polaris.io.download", false]], "dst_from_lon_lat() (polaris.remap.mappingfilestep method)": [[101, "polaris.remap.MappingFileStep.dst_from_lon_lat", false]], "dst_from_mpas() (polaris.remap.mappingfilestep method)": [[102, "polaris.remap.MappingFileStep.dst_from_mpas", false]], "dst_from_points() (polaris.remap.mappingfilestep method)": [[103, "polaris.remap.MappingFileStep.dst_from_points", false]], "dst_from_proj() (polaris.remap.mappingfilestep method)": [[104, "polaris.remap.MappingFileStep.dst_from_proj", false]], "dst_global_lon_lat() (polaris.remap.mappingfilestep method)": [[105, "polaris.remap.MappingFileStep.dst_global_lon_lat", false]], "dynamic_model_config() (polaris.modelstep method)": [[30, "polaris.ModelStep.dynamic_model_config", false]], "dynamic_model_config() (polaris.ocean.convergence.forward.convergenceforward method)": [[156, "polaris.ocean.convergence.forward.ConvergenceForward.dynamic_model_config", false]], "dynamic_model_config() (polaris.ocean.ice_shelf.sshforward method)": [[165, "polaris.ocean.ice_shelf.SshForward.dynamic_model_config", false]], "dynamic_model_config() (polaris.ocean.tasks.baroclinic_channel.forward.forward method)": [[186, "polaris.ocean.tasks.baroclinic_channel.forward.Forward.dynamic_model_config", false]], "dynamic_model_config() (polaris.ocean.tasks.baroclinic_channel.restart.restart_step.restartstep method)": [[192, "polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep.dynamic_model_config", false]], "dynamic_model_config() (polaris.ocean.tasks.barotropic_gyre.forward.forward method)": [[211, "polaris.ocean.tasks.barotropic_gyre.forward.Forward.dynamic_model_config", false]], "dynamic_model_config() (polaris.ocean.tasks.cosine_bell.forward.forward method)": [[223, "polaris.ocean.tasks.cosine_bell.forward.Forward.dynamic_model_config", false]], "dynamic_model_config() (polaris.ocean.tasks.ice_shelf_2d.forward.forward method)": [[244, "polaris.ocean.tasks.ice_shelf_2d.forward.Forward.dynamic_model_config", false]], "dynamic_model_config() (polaris.ocean.tasks.internal_wave.forward.forward method)": [[268, "polaris.ocean.tasks.internal_wave.forward.Forward.dynamic_model_config", false]], "exact_solution() (polaris.ocean.convergence.analysis.convergenceanalysis method)": [[149, "polaris.ocean.convergence.analysis.ConvergenceAnalysis.exact_solution", false]], "exact_solution() (polaris.ocean.tasks.barotropic_gyre.analysis.analysis method)": [[207, "polaris.ocean.tasks.barotropic_gyre.analysis.Analysis.exact_solution", false]], "exact_solution() (polaris.ocean.tasks.cosine_bell.analysis.analysis method)": [[220, "polaris.ocean.tasks.cosine_bell.analysis.Analysis.exact_solution", false]], "exact_solution() (polaris.ocean.tasks.geostrophic.analysis.analysis method)": [[233, "polaris.ocean.tasks.geostrophic.analysis.Analysis.exact_solution", false]], "exact_solution() (polaris.ocean.tasks.inertial_gravity_wave.analysis.analysis method)": [[254, "polaris.ocean.tasks.inertial_gravity_wave.analysis.Analysis.exact_solution", false]], "exact_solution() (polaris.ocean.tasks.manufactured_solution.analysis.analysis method)": [[280, "polaris.ocean.tasks.manufactured_solution.analysis.Analysis.exact_solution", false]], "exactrestart (class in polaris.seaice.tasks.single_column.exact_restart)": [[367, "polaris.seaice.tasks.single_column.exact_restart.ExactRestart", false]], "exactsolution (class in polaris.ocean.tasks.inertial_gravity_wave.exact_solution)": [[255, "polaris.ocean.tasks.inertial_gravity_wave.exact_solution.ExactSolution", false]], "exactsolution (class in polaris.ocean.tasks.manufactured_solution.exact_solution)": [[281, "polaris.ocean.tasks.manufactured_solution.exact_solution.ExactSolution", false]], "filamentanalysis (class in polaris.ocean.tasks.sphere_transport.filament_analysis)": [[304, "polaris.ocean.tasks.sphere_transport.filament_analysis.FilamentAnalysis", false]], "find_planar_transect_cells_and_weights() (in module polaris.ocean.viz.transect.horiz)": [[330, "polaris.ocean.viz.transect.horiz.find_planar_transect_cells_and_weights", false]], "find_spherical_transect_cells_and_weights() (in module polaris.ocean.viz.transect.horiz)": [[331, "polaris.ocean.viz.transect.horiz.find_spherical_transect_cells_and_weights", false]], "find_transect_levels_and_weights() (in module polaris.ocean.viz.transect.vert)": [[334, "polaris.ocean.viz.transect.vert.find_transect_levels_and_weights", false]], "forward (class in polaris.ocean.tasks.baroclinic_channel.forward)": [[184, "polaris.ocean.tasks.baroclinic_channel.forward.Forward", false]], "forward (class in polaris.ocean.tasks.barotropic_gyre.forward)": [[209, "polaris.ocean.tasks.barotropic_gyre.forward.Forward", false]], "forward (class in polaris.ocean.tasks.cosine_bell.forward)": [[221, "polaris.ocean.tasks.cosine_bell.forward.Forward", false]], "forward (class in polaris.ocean.tasks.geostrophic.forward)": [[235, "polaris.ocean.tasks.geostrophic.forward.Forward", false]], "forward (class in polaris.ocean.tasks.ice_shelf_2d.forward)": [[242, "polaris.ocean.tasks.ice_shelf_2d.forward.Forward", false]], "forward (class in polaris.ocean.tasks.inertial_gravity_wave.forward)": [[258, "polaris.ocean.tasks.inertial_gravity_wave.forward.Forward", false]], "forward (class in polaris.ocean.tasks.internal_wave.forward)": [[266, "polaris.ocean.tasks.internal_wave.forward.Forward", false]], "forward (class in polaris.ocean.tasks.manufactured_solution.forward)": [[284, "polaris.ocean.tasks.manufactured_solution.forward.Forward", false]], "forward (class in polaris.ocean.tasks.single_column.forward)": [[293, "polaris.ocean.tasks.single_column.forward.Forward", false]], "forward (class in polaris.ocean.tasks.sphere_transport.forward)": [[306, "polaris.ocean.tasks.sphere_transport.forward.Forward", false]], "forward (class in polaris.seaice.tasks.single_column.forward)": [[370, "polaris.seaice.tasks.single_column.forward.Forward", false]], "generate_1d_grid() (in module polaris.ocean.vertical.grid_1d)": [[313, "polaris.ocean.vertical.grid_1d.generate_1d_grid", false]], "geostrophic (class in polaris.ocean.tasks.geostrophic)": [[229, "polaris.ocean.tasks.geostrophic.Geostrophic", false]], "get_available_parallel_resources() (in module polaris.parallel)": [[95, "polaris.parallel.get_available_parallel_resources", false]], "get_cell_width() (polaris.mesh.icosahedralmeshstep static method)": [[73, "polaris.mesh.IcosahedralMeshStep.get_cell_width", false]], "get_components() (in module polaris.components)": [[58, "polaris.components.get_components", false]], "get_output_field() (polaris.ocean.convergence.analysis.convergenceanalysis method)": [[150, "polaris.ocean.convergence.analysis.ConvergenceAnalysis.get_output_field", false]], "get_output_field() (polaris.ocean.tasks.geostrophic.analysis.analysis method)": [[234, "polaris.ocean.tasks.geostrophic.analysis.Analysis.get_output_field", false]], "get_parallel_command() (in module polaris.parallel)": [[96, "polaris.parallel.get_parallel_command", false]], "get_remapper() (polaris.remap.mappingfilestep method)": [[106, "polaris.remap.MappingFileStep.get_remapper", false]], "get_slurm_options() (in module polaris.job)": [[65, "polaris.job.get_slurm_options", false]], "get_subdivisions() (polaris.mesh.icosahedralmeshstep static method)": [[74, "polaris.mesh.IcosahedralMeshStep.get_subdivisions", false]], "get_time_interval_string() (in module polaris.ocean.model)": [[179, "polaris.ocean.model.get_time_interval_string", false]], "iceshelftask (class in polaris.ocean.ice_shelf)": [[159, "polaris.ocean.ice_shelf.IceShelfTask", false]], "icosahedralmeshstep (class in polaris.mesh)": [[71, "polaris.mesh.IcosahedralMeshStep", false]], "idealage (class in polaris.ocean.tasks.single_column.ideal_age)": [[294, "polaris.ocean.tasks.single_column.ideal_age.IdealAge", false]], "inertialgravitywave (class in polaris.ocean.tasks.inertial_gravity_wave)": [[251, "polaris.ocean.tasks.inertial_gravity_wave.InertialGravityWave", false]], "ingest() (in module polaris.namelist)": [[91, "polaris.namelist.ingest", false]], "init (class in polaris.ocean.tasks.baroclinic_channel.init)": [[187, "polaris.ocean.tasks.baroclinic_channel.init.Init", false]], "init (class in polaris.ocean.tasks.barotropic_gyre.init)": [[213, "polaris.ocean.tasks.barotropic_gyre.init.Init", false]], "init (class in polaris.ocean.tasks.cosine_bell.init)": [[224, "polaris.ocean.tasks.cosine_bell.init.Init", false]], "init (class in polaris.ocean.tasks.geostrophic.init)": [[236, "polaris.ocean.tasks.geostrophic.init.Init", false]], "init (class in polaris.ocean.tasks.ice_shelf_2d.init)": [[245, "polaris.ocean.tasks.ice_shelf_2d.init.Init", false]], "init (class in polaris.ocean.tasks.inertial_gravity_wave.init)": [[260, "polaris.ocean.tasks.inertial_gravity_wave.init.Init", false]], "init (class in polaris.ocean.tasks.internal_wave.init)": [[269, "polaris.ocean.tasks.internal_wave.init.Init", false]], "init (class in polaris.ocean.tasks.manufactured_solution.init)": [[286, "polaris.ocean.tasks.manufactured_solution.init.Init", false]], "init (class in polaris.ocean.tasks.single_column.init)": [[295, "polaris.ocean.tasks.single_column.init.Init", false]], "init (class in polaris.ocean.tasks.sphere_transport.init)": [[307, "polaris.ocean.tasks.sphere_transport.init.Init", false]], "init_sigma_vertical_coord() (in module polaris.ocean.vertical.sigma)": [[318, "polaris.ocean.vertical.sigma.init_sigma_vertical_coord", false]], "init_vertical_coord() (in module polaris.ocean.vertical)": [[315, "polaris.ocean.vertical.init_vertical_coord", false]], "init_z_level_vertical_coord() (in module polaris.ocean.vertical.zlevel)": [[324, "polaris.ocean.vertical.zlevel.init_z_level_vertical_coord", false]], "init_z_star_vertical_coord() (in module polaris.ocean.vertical.zstar)": [[326, "polaris.ocean.vertical.zstar.init_z_star_vertical_coord", false]], "interp_mpas_to_transect_cells() (in module polaris.ocean.viz.transect.vert)": [[335, "polaris.ocean.viz.transect.vert.interp_mpas_to_transect_cells", false]], "interp_mpas_to_transect_nodes() (in module polaris.ocean.viz.transect.vert)": [[336, "polaris.ocean.viz.transect.vert.interp_mpas_to_transect_nodes", false]], "list_cases() (in module polaris.list)": [[67, "polaris.list.list_cases", false]], "list_machines() (in module polaris.list)": [[68, "polaris.list.list_machines", false]], "list_suites() (in module polaris.list)": [[69, "polaris.list.list_suites", false]], "load_dependencies() (in module polaris.run)": [[112, "polaris.run.load_dependencies", false]], "log_method_call() (in module polaris.logging)": [[70, "polaris.logging.log_method_call", false]], "main() (in module polaris.__main__)": [[56, "polaris.__main__.main", false]], "main_mpas_to_yaml() (in module polaris.yaml)": [[133, "polaris.yaml.main_mpas_to_yaml", false]], "make_graph_file() (in module polaris.model_step)": [[88, "polaris.model_step.make_graph_file", false]], "make_jigsaw_mesh() (polaris.mesh.icosahedralmeshstep method)": [[75, "polaris.mesh.IcosahedralMeshStep.make_jigsaw_mesh", false]], "make_jigsaw_mesh() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[80, "polaris.mesh.QuasiUniformSphericalMeshStep.make_jigsaw_mesh", false]], "make_triangle_tree() (in module polaris.ocean.viz.transect.horiz)": [[332, "polaris.ocean.viz.transect.horiz.make_triangle_tree", false]], "manufacturedsolution (class in polaris.ocean.tasks.manufactured_solution)": [[277, "polaris.ocean.tasks.manufactured_solution.ManufacturedSolution", false]], "map_from_native_model_vars() (polaris.ocean.model.oceaniostep method)": [[168, "polaris.ocean.model.OceanIOStep.map_from_native_model_vars", false]], "map_to_native_model_vars() (polaris.ocean.model.oceaniostep 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"polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep", false]], "rpe (class in polaris.ocean.tasks.baroclinic_channel.rpe)": [[193, "polaris.ocean.tasks.baroclinic_channel.rpe.Rpe", false]], "rpe (class in polaris.ocean.tasks.internal_wave.rpe)": [[271, "polaris.ocean.tasks.internal_wave.rpe.Rpe", false]], "run() (polaris.mesh.icosahedralmeshstep method)": [[76, "polaris.mesh.IcosahedralMeshStep.run", false]], "run() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[81, "polaris.mesh.QuasiUniformSphericalMeshStep.run", false]], "run() (polaris.mesh.spherical.sphericalbasestep method)": [[85, "polaris.mesh.spherical.SphericalBaseStep.run", false]], "run() (polaris.ocean.convergence.analysis.convergenceanalysis method)": [[152, "polaris.ocean.convergence.analysis.ConvergenceAnalysis.run", false]], "run() (polaris.ocean.ice_shelf.sshadjustment method)": [[162, "polaris.ocean.ice_shelf.SshAdjustment.run", false]], "run() 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\ No newline at end of file