Merge pull request #66 from noaa-ocs-modeling/develop

move functions from NEMS ADCIRC into ADCIRC submodule

coupledmodeldriver/configure/__init__.py

@@ -1 +1,3 @@
-from .base import ModelDriverJSON, SlurmJSON
+from .base import ModelDriverJSON, NEMSJSON, SlurmJSON
+from .forcings import *
+from .models import *

coupledmodeldriver/configure/base.py

@@ -1,11 +1,12 @@
 from abc import ABC, abstractmethod
-from datetime import timedelta
+from datetime import datetime, timedelta
 import json
 from os import PathLike
 from pathlib import Path
 from typing import Any
 
 from adcircpy.server import SlurmConfig
+from nemspy import ModelingSystem
 from nemspy.model import ModelEntry
 
 from ..platforms import Platform
@@ -161,6 +162,82 @@ def to_file(self, filename: PathLike = None, overwrite: bool = False):
             LOGGER.debug(f'skipping existing file "{filename}"')
 
 
+class NEMSJSON(ConfigurationJSON):
+    name = 'nems'
+    default_filename = f'configure_nems.json'
+    field_types = {
+        'executable_path': Path,
+        'modeled_start_time': datetime,
+        'modeled_end_time': datetime,
+        'interval': timedelta,
+        'models': [ModelEntry],
+        'connections': [[str]],
+        'mediations': [str],
+        'sequence': [str],
+    }
+
+    def __init__(
+        self,
+        executable_path: PathLike,
+        modeled_start_time: datetime,
+        modeled_end_time: datetime,
+        interval: timedelta = None,
+        models: [ModelEntry] = None,
+        connections: [[str]] = None,
+        mediations: [[str]] = None,
+        sequence: [str] = None,
+        **kwargs,
+    ):
+        if 'fields' not in kwargs:
+            kwargs['fields'] = {}
+        kwargs['fields'].update(NEMSJSON.field_types)
+
+        ConfigurationJSON.__init__(self, **kwargs)
+
+        self['executable_path'] = executable_path
+        self['modeled_start_time'] = modeled_start_time
+        self['modeled_end_time'] = modeled_end_time
+        self['interval'] = interval
+        self['models'] = models
+        self['connections'] = connections
+        self['mediations'] = mediations
+        self['sequence'] = sequence
+
+    @property
+    def nemspy_modeling_system(self) -> ModelingSystem:
+        modeling_system = ModelingSystem(
+            start_time=self['modeled_start_time'],
+            end_time=self['modeled_end_time'],
+            interval=self['interval'],
+            **{model.model_type.value.lower(): model for model in self['models']},
+        )
+        for connection in self['connections']:
+            modeling_system.connect(*connection)
+        for mediation in self['mediations']:
+            modeling_system.mediate(*mediation)
+
+        modeling_system.sequence = self['sequence']
+
+        return modeling_system
+
+    def to_nemspy(self) -> ModelingSystem:
+        return self.nemspy_modeling_system
+
+    @classmethod
+    def from_nemspy(cls, modeling_system: ModelingSystem, executable_path: PathLike = None):
+        if executable_path is None:
+            executable_path = 'NEMS.x'
+        return cls(
+            executable_path=executable_path,
+            modeled_start_time=modeling_system.start_time,
+            modeled_end_time=modeling_system.end_time,
+            interval=modeling_system.interval,
+            models=modeling_system.models,
+            connections=modeling_system.connections,
+            sequence=modeling_system.sequence,
+        )
+
+
 class NEMSCapJSON(ConfigurationJSON, ABC):
     field_types = {
         'processors': int,

coupledmodeldriver/configure/run.py → coupledmodeldriver/configure/configure.py

@@ -6,8 +6,8 @@
 from adcircpy.forcing.base import Forcing
 from nemspy.model import ModelEntry
 
-from coupledmodeldriver.configure.forcings.base import ForcingJSON
 from .base import ConfigurationJSON, NEMSCapJSON
+from .forcings.base import ForcingJSON
 
 
 class RunConfiguration(ABC):

coupledmodeldriver/configure/forcings/base.py

@@ -13,8 +13,7 @@
 from adcircpy.forcing.winds.owi import OwiForcing
 from nemspy.model import AtmosphericMeshEntry, WaveMeshEntry
 
-from coupledmodeldriver.configure.base import ConfigurationJSON, \
-    NEMSCapJSON
+from ..base import ConfigurationJSON, NEMSCapJSON
 
 
 class ForcingJSON(ConfigurationJSON, ABC):

coupledmodeldriver/configure/models.py

@@ -9,8 +9,8 @@
 from adcircpy.server import SlurmConfig
 from nemspy.model import ADCIRCEntry
 
-from coupledmodeldriver.configure.forcings.base import ForcingJSON
 from .base import ConfigurationJSON, NEMSCapJSON, SlurmJSON
+from .forcings.base import ForcingJSON
 from ..utilities import LOGGER
 
 

coupledmodeldriver/generate/__init__.py

@@ -1,2 +1 @@
 from .adcirc import *
-from .nems import *

coupledmodeldriver/generate/adcirc/__init__.py

@@ -1,3 +1,3 @@
-from .configure import ADCIRCRunConfiguration
-from .generate import generate_adcirc_configuration
-from .script import ADCIRCGenerationScript
+from .configure import ADCIRCRunConfiguration, NEMSADCIRCRunConfiguration
+from .generate import generate_adcirc_configuration, generate_nems_adcirc_configuration
+from .script import ADCIRCGenerationScript, NEMSADCIRCGenerationScript

coupledmodeldriver/generate/adcirc/configure.py

@@ -3,19 +3,21 @@
 from pathlib import Path
 
 from adcircpy import AdcircMesh, AdcircRun, Tides
+from adcircpy.forcing.base import Forcing
 from adcircpy.forcing.waves.ww3 import WaveWatch3DataForcing
 from adcircpy.forcing.winds.atmesh import AtmosphericMeshForcing
+from nemspy import ModelingSystem
 
-from coupledmodeldriver.configure.base import ModelDriverJSON, SlurmJSON
-from coupledmodeldriver.configure.forcings import (
+from ...configure.base import ModelDriverJSON, NEMSJSON, SlurmJSON
+from ...configure.configure import RunConfiguration
+from ...configure.forcings.base import (
     ATMESHForcingJSON,
+    ForcingJSON,
     TidalForcingJSON,
     WW3DATAForcingJSON,
 )
-from coupledmodeldriver.configure.forcings.base import ForcingJSON
-from coupledmodeldriver.configure.models import ADCIRCJSON
-from coupledmodeldriver.configure.run import RunConfiguration
-from coupledmodeldriver.platforms import Platform
+from ...configure.models import ADCIRCJSON
+from ...platforms import Platform
 
 
 class ADCIRCRunConfiguration(RunConfiguration):
@@ -180,3 +182,144 @@ def read_directory(cls, directory: PathLike) -> 'ADCIRCRunConfiguration':
             adcirc=configurations[2],
             forcings=forcings,
         )
+
+
+class NEMSADCIRCRunConfiguration(ADCIRCRunConfiguration):
+    required = [
+        ModelDriverJSON,
+        NEMSJSON,
+        SlurmJSON,
+        ADCIRCJSON,
+    ]
+
+    def __init__(
+        self,
+        fort13: PathLike,
+        fort14: PathLike,
+        modeled_start_time: datetime,
+        modeled_end_time: datetime,
+        modeled_timestep: timedelta,
+        nems_interval: timedelta,
+        nems_connections: [str],
+        nems_mediations: [str],
+        nems_sequence: [str],
+        tidal_spinup_duration: timedelta = None,
+        platform: Platform = None,
+        runs: {str: (float, str)} = None,
+        forcings: [ForcingJSON] = None,
+        adcirc_processors: int = None,
+        slurm_job_duration: timedelta = None,
+        slurm_partition: str = None,
+        slurm_email_address: str = None,
+        nems_executable: PathLike = None,
+        adcprep_executable: PathLike = None,
+        source_filename: PathLike = None,
+    ):
+        self.__nems = None
+
+        super().__init__(
+            fort13=fort13,
+            fort14=fort14,
+            modeled_start_time=modeled_start_time,
+            modeled_end_time=modeled_end_time,
+            modeled_timestep=modeled_timestep,
+            tidal_spinup_duration=tidal_spinup_duration,
+            platform=platform,
+            runs=runs,
+            forcings=None,
+            adcirc_processors=adcirc_processors,
+            slurm_job_duration=slurm_job_duration,
+            slurm_partition=slurm_partition,
+            slurm_email_address=slurm_email_address,
+            adcprep_executable=adcprep_executable,
+            source_filename=source_filename,
+        )
+
+        nems = NEMSJSON(
+            executable_path=nems_executable,
+            modeled_start_time=modeled_start_time,
+            modeled_end_time=modeled_end_time,
+            interval=nems_interval,
+            models=self.nemspy_entries,
+            connections=nems_connections,
+            mediations=nems_mediations,
+            sequence=nems_sequence,
+        )
+
+        self.configurations[nems.name] = nems
+
+        for forcing in forcings:
+            self.add_forcing(forcing)
+
+        self['slurm']['tasks'] = self['nems'].nemspy_modeling_system.processors
+
+    @property
+    def nemspy_modeling_system(self) -> ModelingSystem:
+        return self['nems'].nemspy_modeling_system
+
+    def add_forcing(self, forcing: Forcing):
+        if not isinstance(forcing, ForcingJSON):
+            if isinstance(forcing, AtmosphericMeshForcing):
+                forcing = ATMESHForcingJSON.from_adcircpy(forcing)
+                self['nems']['models'].append(forcing.nemspy_entry)
+            elif isinstance(forcing, WaveWatch3DataForcing):
+                forcing = WW3DATAForcingJSON.from_adcircpy(forcing)
+                self['nems']['models'].append(forcing.nemspy_entry)
+            elif isinstance(forcing, Tides):
+                forcing = TidalForcingJSON.from_adcircpy(forcing)
+            else:
+                raise NotImplementedError(f'unable to parse object of type {type(forcing)}')
+
+        if forcing not in self:
+            self[forcing.name] = forcing
+            self['adcirc'].forcings.append(forcing)
+
+    @classmethod
+    def from_configurations(
+        cls,
+        driver: ModelDriverJSON,
+        nems: NEMSJSON,
+        slurm: SlurmJSON,
+        adcirc: ADCIRCJSON,
+        forcings: [ForcingJSON] = None,
+    ) -> 'NEMSADCIRCRunConfiguration':
+        instance = super().from_configurations(
+            driver=driver, slurm=slurm, adcirc=adcirc, forcings=None,
+        )
+        instance.__class__ = cls
+        instance.configurations['nems'] = nems
+
+        if forcings is not None:
+            for forcing in forcings:
+                instance.add_forcing(forcing)
+
+        return instance
+
+    @classmethod
+    def read_directory(cls, directory: PathLike) -> 'NEMSADCIRCRunConfiguration':
+        if not isinstance(directory, Path):
+            directory = Path(directory)
+        if directory.is_file():
+            directory = directory.parent
+
+        configurations = []
+        for configuration_class in cls.required:
+            filename = directory / configuration_class.default_filename
+            if filename.exists():
+                configurations.append(configuration_class.from_file(filename))
+            else:
+                raise FileNotFoundError(f'missing required configuration file "{filename}"')
+
+        forcings = []
+        for configuration_class in cls.forcings:
+            filename = directory / configuration_class.default_filename
+            if filename.exists():
+                forcings.append(configuration_class.from_file(filename))
+
+        return cls.from_configurations(
+            driver=configurations[0],
+            nems=configurations[1],
+            slurm=configurations[2],
+            adcirc=configurations[3],
+            forcings=forcings,
+        )