def test_configuration(shinnecock_mesh_directory):
output_directory = OUTPUT_DIRECTORY / 'test_configuration'
reference_directory = REFERENCE_DIRECTORY / 'test_configuration'
if not output_directory.exists():
output_directory.mkdir(parents=True, exist_ok=True)
mesh = AdcircMesh.open(shinnecock_mesh_directory / 'fort.14', crs=4326)
spinup_time = timedelta(days=2)
start_date = datetime(2015, 12, 14) + spinup_time
end_date = start_date + timedelta(days=3)
wind_forcing = AtmosphericMeshForcing(
filename='Wind_HWRF_SANDY_Nov2018_ExtendedSmoothT.nc', nws=17, interval_seconds=3600,
)
wave_forcing = WaveWatch3DataForcing(
filename='ww3.HWRF.NOV2018.2012_sxy.nc', nrs=5, interval_seconds=3600,
)
mesh.add_forcing(wind_forcing)
mesh.add_forcing(wave_forcing)
driver = AdcircRun(mesh, start_date, end_date, spinup_time,)
driver.write(output_directory, overwrite=True, nproc=2)
check_reference_directory(
output_directory, reference_directory, skip_lines={'fort.15': [0]},
)
def driver(self):
driver = AdcircRun(self.mesh,
self.start_date,
self.end_date,
self.spinup_time,
server_config=self.server_config)
self._enable_outputs(driver)
if self.args.timestep:
driver.timestep = self.args.timestep
driver.gwce_solution_scheme = self.args.gwce_solution_scheme
return driver
def main():
if not FORT14.is_file():
url = 'https://www.dropbox.com/s/1wk91r67cacf132/NetCDF_shinnecock_inlet.tar.bz2?dl=1'
g = urllib.request.urlopen(url)
tmpfile = tempfile.NamedTemporaryFile()
with open(tmpfile.name, 'b+w') as f:
f.write(g.read())
with tarfile.open(tmpfile.name, "r:bz2") as tar:
tar.extractall(PARENT / "data/NetCDF_Shinnecock_Inlet/")
mesh = AdcircMesh.open(FORT14, crs=4326)
tidal_forcing = Tides()
tidal_forcing.use_all()
wind_forcing = AtmosphericMeshForcing(
filename='Wind_HWRF_SANDY_Nov2018_ExtendedSmoothT.nc',
nws=17,
interval_seconds=3600,
)
wave_forcing = WaveWatch3DataForcing(
filename='ww3.HWRF.NOV2018.2012_sxy.nc',
nrs=5,
interval_seconds=3600,
)
mesh.add_forcing(tidal_forcing)
mesh.add_forcing(wind_forcing)
mesh.add_forcing(wave_forcing)
slurm = SlurmConfig(
account='account',
ntasks=1000,
run_name='AdcircPy/examples/example_3.py',
partition='partition',
walltime=timedelta(hours=8),
mail_type='all',
mail_user='******',
log_filename='example_3.log',
modules=['intel/2020', 'impi/2020', 'netcdf/4.7.2-parallel'],
path_prefix='$HOME/adcirc/build')
driver = AdcircRun(
mesh=mesh,
start_date=datetime.now(),
end_date=timedelta(days=7),
spinup_time=timedelta(days=5),
server_config=slurm,
)
driver.write(PARENT / "outputs/example_4", overwrite=True)
def test_slurm_driver(self):
output_directory = OUTPUT_DIRECTORY / 'test_slurm_driver'
reference_directory = REFERENCE_DIRECTORY / 'test_slurm_driver'
output_directory.mkdir(parents=True, exist_ok=True)
# open mesh file
mesh = AdcircMesh.open(FORT14_FILENAME, crs=4326)
# instantiate AdcircRun object.
slurm = SlurmConfig(
account='account',
ntasks=1000,
run_name='AdcircPy/examples/example_3.py',
partition='partition',
walltime=timedelta(hours=8),
mail_type='all',
mail_user='******',
log_filename='example_3.log',
modules=['intel/2020', 'impi/2020', 'netcdf/4.7.2-parallel'],
path_prefix='$HOME/adcirc/build')
driver = AdcircRun(mesh=mesh,
start_date=datetime.now(),
end_date=timedelta(days=7),
spinup_time=timedelta(days=5),
server_config=slurm)
DriverFile(driver).write(output_directory / 'slurm.job',
overwrite=True)
with open(output_directory / 'slurm.job') as generated_file:
with open(reference_directory / 'slurm.job') as reference_file:
assert generated_file.read() == reference_file.read()
def test_slurm_driver(shinnecock_mesh_directory):
output_directory = OUTPUT_DIRECTORY / 'test_slurm_driver'
reference_directory = REFERENCE_DIRECTORY / 'test_slurm_driver'
if not output_directory.exists():
output_directory.mkdir(parents=True, exist_ok=True)
mesh = AdcircMesh.open(shinnecock_mesh_directory / 'fort.14', crs=4326)
slurm = SlurmConfig(
account='account',
ntasks=1000,
run_name='adcircpy/tests/test_configuration.py',
partition='partition',
walltime=timedelta(hours=8),
mail_type='all',
mail_user='******',
log_filename='test_configuration.log',
modules=['intel/2020', 'impi/2020', 'netcdf/4.7.2-parallel'],
path_prefix='$HOME/adcirc/build',
)
driver = AdcircRun(
mesh=mesh,
start_date=datetime.now(),
end_date=timedelta(days=7),
spinup_time=timedelta(days=5),
server_config=slurm,
)
DriverFile(driver).write(output_directory / 'slurm.job', overwrite=True)
check_reference_directory(output_directory, reference_directory)
def test_configuration(self):
output_directory = OUTPUT_DIRECTORY / 'test_configuration'
reference_directory = REFERENCE_DIRECTORY / 'test_configuration'
output_directory.mkdir(parents=True, exist_ok=True)
# open mesh file
mesh = AdcircMesh.open(FORT14_FILENAME, crs=4326)
# set simulation dates
spinup_time = timedelta(days=2)
start_date = datetime(2015, 12, 14) + spinup_time
end_date = start_date + timedelta(days=3)
wind_forcing = AtmosphericMeshForcing(
filename='Wind_HWRF_SANDY_Nov2018_ExtendedSmoothT.nc',
nws=17,
interval_seconds=3600,
)
wave_forcing = WaveWatch3DataForcing(
filename='ww3.HWRF.NOV2018.2012_sxy.nc',
nrs=5,
interval_seconds=3600,
)
mesh.add_forcing(wind_forcing)
mesh.add_forcing(wave_forcing)
# instantiate AdcircRun object.
driver = AdcircRun(
mesh,
start_date,
end_date,
spinup_time,
)
driver.write(output_directory, overwrite=True)
for reference_filename in reference_directory.iterdir():
generated_filename = output_directory / reference_filename.name
with open(generated_filename) as generated_file, \
open(reference_filename) as reference_file:
self.assertMultiLineEqual(
''.join(generated_file.readlines()[1:]),
''.join(reference_file.readlines()[1:]))
def main():
# fetch shinnecock inlet test data
if not FORT14.is_file():
url = "https://www.dropbox.com/s/1wk91r67cacf132/"
url += "NetCDF_shinnecock_inlet.tar.bz2?dl=1"
g = urllib.request.urlopen(url)
tmpfile = tempfile.NamedTemporaryFile()
with open(tmpfile.name, 'b+w') as f:
f.write(g.read())
with tarfile.open(tmpfile.name, "r:bz2") as tar:
tar.extractall(PARENT / "data/NetCDF_Shinnecock_Inlet/")
# open mesh file
mesh = AdcircMesh.open(FORT14, crs=4326)
# init tidal forcing and setup requests
tidal_forcing = Tides()
tidal_forcing.use_all()
mesh.add_forcing(tidal_forcing)
# Add wind forcing to model
wind_forcing = BestTrackForcing('Sandy2012')
mesh.add_forcing(wind_forcing)
# instantiate AdcircRun object.
slurm = SlurmConfig(
account='account',
ntasks=1000,
run_name='AdcircPy/examples/example_3.py',
partition='partition',
walltime=timedelta(hours=8),
mail_type='all',
mail_user='******',
log_filename='example_3.log',
modules=['intel/2020', 'impi/2020', 'netcdf/4.7.2-parallel'],
path_prefix='$HOME/adcirc/build')
driver = AdcircRun(mesh,
spinup_time=timedelta(days=15),
server_config=slurm)
# Write driver state to file.
driver.write(PARENT / "outputs/example_3", overwrite=True)
def test_configuration(self):
output_directory = OUTPUT_DIRECTORY / 'test_configuration'
reference_directory = REFERENCE_DIRECTORY / 'test_configuration'
output_directory.mkdir(parents=True, exist_ok=True)
# open mesh file
mesh = AdcircMesh.open(FORT14_FILENAME, crs=4326)
# let's generate the tau0 factor
mesh.generate_tau0()
# let's also add a mannings to the domain (constant for this example)
mesh.mannings_n_at_sea_floor = numpy.full(mesh.values.shape, 0.025)
# set simulation dates
spinup_time = timedelta(days=2)
start_date = datetime(2015, 12, 14) + spinup_time
end_date = start_date + timedelta(days=3)
wind_forcing = AtmosphericMeshForcing(17, 3600)
wave_forcing = WaveWatch3DataForcing(5, 3600)
mesh.add_forcing(wind_forcing)
mesh.add_forcing(wave_forcing)
# instantiate AdcircRun object.
driver = AdcircRun(
mesh,
start_date,
end_date,
spinup_time,
)
driver.write(output_directory, overwrite=True)
for reference_filename in reference_directory.iterdir():
generated_filename = output_directory / reference_filename.name
with open(generated_filename) as generated_file, \
open(reference_filename) as reference_file:
assert generated_file.readlines()[1:] == \
reference_file.readlines()[1:]
def main():
# fetch shinnecock inlet test data
if not FORT14.is_file():
url = "https://www.dropbox.com/s/1wk91r67cacf132/"
url += "NetCDF_shinnecock_inlet.tar.bz2?dl=1"
g = urllib.request.urlopen(url)
tmpfile = tempfile.NamedTemporaryFile()
with open(tmpfile.name, 'b+w') as f:
f.write(g.read())
with tarfile.open(tmpfile.name, "r:bz2") as tar:
tar.extractall(PARENT / "data/NetCDF_Shinnecock_Inlet/")
# open mesh file
mesh = AdcircMesh.open(FORT14, crs=4326)
# init tidal forcing and setup requests
tidal_forcing = Tides()
tidal_forcing.use_constituent('M2')
tidal_forcing.use_constituent('N2')
tidal_forcing.use_constituent('S2')
tidal_forcing.use_constituent('K1')
tidal_forcing.use_constituent('O1')
mesh.add_forcing(tidal_forcing)
# set simulation dates
start_date = datetime(2015, 12, 14)
end_date = start_date + timedelta(days=5)
# instantiate AdcircRun object.
driver = AdcircRun(mesh, start_date, end_date)
# request outputs
driver.set_elevation_surface_output(sampling_rate=timedelta(minutes=30))
driver.set_velocity_surface_output(sampling_rate=timedelta(minutes=30))
# override the AdcircPy defaults so that the fort.15
# matches the original Shinnecock test case options
driver.timestep = 6.
driver.DRAMP = 2.
driver.smagorinsky = False
driver.horizontal_mixing_coefficient = 5.
driver.TOUTGE = 3.8
driver.TOUTGV = 3.8
# run parallel ADCIRC if binary is installed
if shutil.which('padcirc') is not None:
driver.run(PARENT / "outputs/example_1", overwrite=True)
# run serial ADCIRC if binary is installed
elif shutil.which('adcirc') is not None:
driver.run(PARENT / "outputs/example_1", overwrite=True, nproc=1)
# binaries are not installed, write to disk and exit
else:
msg = 'ADCIRC binaries were not found in PATH. ADCIRC will not run. '
msg += "Writing files to disk..."
warnings.warn(msg)
driver.write(PARENT / "outputs/example_1", overwrite=True)
# initialize tidal forcing and constituents
tidal_forcing = Tides()
tidal_forcing.use_constituent('M2')
tidal_forcing.use_constituent('N2')
tidal_forcing.use_constituent('S2')
tidal_forcing.use_constituent('K1')
tidal_forcing.use_constituent('O1')
mesh.add_forcing(tidal_forcing)
# set simulation dates
duration = timedelta(days=5)
start_date = datetime(2015, 12, 14)
end_date = start_date + duration
# instantiate driver object
driver = AdcircRun(mesh, start_date, end_date)
# request outputs
driver.set_elevation_surface_output(sampling_rate=timedelta(minutes=30))
driver.set_velocity_surface_output(sampling_rate=timedelta(minutes=30))
# override default options so the resulting `fort.15` matches the original Shinnecock test case options
driver.timestep = 6.0
driver.DRAMP = 2.0
driver.TOUTGE = 3.8
driver.TOUTGV = 3.8
driver.smagorinsky = False
driver.horizontal_mixing_coefficient = 5.0
driver.gwce_solution_scheme = 'semi-implicit-legacy'
if shutil.which('padcirc') is not None:
def test_import_stations(shinnecock_mesh_directory):
input_directory = INPUT_DIRECTORY / 'test_import_stations'
mesh = AdcircMesh.open(shinnecock_mesh_directory / 'fort.14', crs=4326)
spinup_time = timedelta(days=2)
start_date = datetime(2015, 12, 14) + spinup_time
end_date = start_date + timedelta(days=3)
driver_1 = AdcircRun(copy(mesh), start_date, end_date, spinup_time)
driver_1.import_stations(input_directory / 'stations_1.txt')
driver_2 = AdcircRun(copy(mesh), start_date, end_date, spinup_time)
driver_2.import_stations(input_directory / 'stations_2.txt')
driver_3 = AdcircRun(copy(mesh), start_date, end_date, spinup_time)
driver_3.import_stations(input_directory / 'stations_3.txt')
driver_4 = AdcircRun(copy(mesh), start_date, end_date, spinup_time)
driver_4.import_stations(
input_directory / 'stations_3.txt',
station_types=['elevation', 'NSTAC', StationType.METEOROLOGICAL],
)
assert driver_1.elevation_stations == {'8512769': (-72.5772, 40.823)}
assert driver_1.velocity_stations == {}
assert driver_1.concentration_stations == {}
assert driver_1.meteorological_stations == {}
assert driver_2.elevation_stations == {'8512769': (-72.5772, 40.823)}
assert driver_2.velocity_stations == {'8512769': (-72.5772, 40.823)}
assert driver_2.concentration_stations == {}
assert driver_2.meteorological_stations == {}
assert driver_3.elevation_stations == {'8512769': (-72.5772, 40.823)}
assert driver_3.velocity_stations == {'8512769': (-72.5772, 40.823)}
assert driver_3.concentration_stations == {}
assert driver_3.meteorological_stations == {}
assert driver_4.elevation_stations == {'8512769': (-72.5772, 40.823)}
assert driver_4.velocity_stations == {}
assert driver_4.concentration_stations == {'8512769': (-72.5772, 40.823)}
assert driver_4.meteorological_stations == {}
# initialize Slurm configuration
slurm = SlurmConfig(
account='account',
ntasks=1000,
run_name='adcircpy/examples/example_3.py',
partition='partition',
walltime=timedelta(hours=8),
mail_type='all',
mail_user='******',
log_filename='example_3.log',
modules=['intel/2020', 'impi/2020', 'netcdf/4.7.2-parallel'],
path_prefix='$HOME/adcirc/build',
)
# set simulation dates
spinup_time = timedelta(days=15)
duration = timedelta(days=3)
start_date = datetime(2012, 10, 21, 18)
end_date = start_date + duration
# instantiate driver object
driver = AdcircRun(mesh,
start_date,
end_date,
spinup_time,
server_config=slurm)
# write driver state to disk
driver.write(OUTPUT_DIRECTORY, overwrite=True)
def main():
# fetch shinnecock inlet test data
if not FORT14.is_file():
url = "https://www.dropbox.com/s/1wk91r67cacf132/"
url += "NetCDF_shinnecock_inlet.tar.bz2?dl=1"
g = urllib.request.urlopen(url)
tmpfile = tempfile.NamedTemporaryFile()
with open(tmpfile.name, 'b+w') as f:
f.write(g.read())
with tarfile.open(tmpfile.name, "r:bz2") as tar:
tar.extractall(PARENT / "data/NetCDF_Shinnecock_Inlet/")
# open mesh file
mesh = AdcircMesh.open(FORT14, crs=4326)
# let's generate the tau0 factor
mesh.generate_tau0()
# let's also add a mannings to the domain (constant for this example)
mesh.mannings_n_at_sea_floor = np.full(mesh.values.shape, 0.025)
# init tidal forcing and setup requests
tidal_forcing = Tides()
tidal_forcing.use_constituent('M2')
tidal_forcing.use_constituent('N2')
tidal_forcing.use_constituent('S2')
tidal_forcing.use_constituent('K1')
tidal_forcing.use_constituent('O1')
mesh.add_forcing(tidal_forcing)
# set simulation dates
spinup_time = timedelta(days=2)
start_date = datetime(2015, 12, 14) + spinup_time
end_date = start_date + timedelta(days=3)
# instantiate AdcircRun object.
driver = AdcircRun(
mesh,
start_date,
end_date,
spinup_time,
)
# request outputs
driver.set_elevation_surface_output(sampling_rate=timedelta(minutes=30))
driver.set_velocity_surface_output(sampling_rate=timedelta(minutes=30))
# override defaults options
driver.timestep = 4.0
# run parallel ADCIRC if binary is installed
if shutil.which('padcirc') is not None:
driver.run(PARENT / "outputs/example_2", overwrite=True)
# run serial ADCIRC if binary is installed
elif shutil.which('adcirc') is not None:
driver.run(PARENT / "outputs/example_2", overwrite=True, nproc=1)
# binaries are not installed, write to disk and exit
else:
msg = 'ADCIRC binaries were not found in PATH. ADCIRC will not run. '
msg += "Writing files to disk..."
warnings.warn(msg)
driver.write(PARENT / "outputs/example_2", overwrite=True)
nrs=5,
interval_seconds=3600,
)
mesh.add_forcing(wave_forcing)
# initialize Slurm configuration
slurm = SlurmConfig(
account='account',
ntasks=1000,
run_name='adcircpy/examples/example_4.py',
partition='partition',
walltime=timedelta(hours=8),
mail_type='all',
mail_user='******',
log_filename='example_4.log',
modules=['intel/2020', 'impi/2020', 'netcdf/4.7.2-parallel'],
path_prefix='$HOME/adcirc/build',
)
# instantiate driver object
driver = AdcircRun(
mesh=mesh,
start_date=datetime.now(),
end_date=timedelta(days=7),
spinup_time=timedelta(days=5),
server_config=slurm,
)
# write driver state to disk
driver.write(OUTPUT_DIRECTORY, overwrite=True)
tidal_forcing = Tides()
tidal_forcing.use_constituent('M2')
tidal_forcing.use_constituent('N2')
tidal_forcing.use_constituent('S2')
tidal_forcing.use_constituent('K1')
tidal_forcing.use_constituent('O1')
mesh.add_forcing(tidal_forcing)
# set simulation dates
spinup_time = timedelta(days=2)
duration = timedelta(days=3)
start_date = datetime(2015, 12, 14) + spinup_time
end_date = start_date + duration
# instantiate driver object
driver = AdcircRun(mesh, start_date, end_date, spinup_time)
# request outputs
driver.set_elevation_surface_output(sampling_rate=timedelta(minutes=30))
driver.set_velocity_surface_output(sampling_rate=timedelta(minutes=30))
# override default options
driver.timestep = 4.0
if shutil.which('padcirc') is not None:
driver.run(OUTPUT_DIRECTORY, overwrite=True)
elif shutil.which('adcirc') is not None:
driver.run(OUTPUT_DIRECTORY, overwrite=True, nproc=1)
else:
logging.warning('ADCIRC binaries were not found in PATH. '
'ADCIRC will not run. Writing files to disk...')
tidal_forcing.use_all()
mesh.add_forcing(tidal_forcing)
# initialize wind forcing
wind_forcing = BestTrackForcing('Sandy2012')
mesh.add_forcing(wind_forcing)
# initialize Slurm configuration
slurm = SlurmConfig(
account='account',
ntasks=1000,
run_name='adcircpy/examples/example_3.py',
partition='partition',
walltime=timedelta(hours=8),
mail_type='all',
mail_user='******',
log_filename='example_3.log',
modules=['intel/2020', 'impi/2020', 'netcdf/4.7.2-parallel'],
path_prefix='$HOME/adcirc/build',
)
# instantiate driver object
driver = AdcircRun(
mesh,
spinup_time=timedelta(days=15),
server_config=slurm,
)
# write driver state to disk
driver.write(OUTPUT_DIRECTORY, overwrite=True)