def test_dissolution(oil, temp, num_elems, on):
'''
Fuel Oil #6 does not exist...
'''
et = floating(substance=oil)
diss = Dissolution(waves)
(sc, time_step) = weathering_data_arrays(diss.array_types,
water,
element_type=et,
num_elements=num_elems)[:2]
print 'num spills:', len(sc.spills)
print 'spill[0] amount:', sc.spills[0].amount
model_time = (sc.spills[0].get('release_time') +
timedelta(seconds=time_step))
diss.on = on
diss.prepare_for_model_run(sc)
diss.initialize_data(sc, sc.num_released)
diss.prepare_for_model_step(sc, time_step, model_time)
diss.weather_elements(sc, time_step, model_time)
if on:
print sc._data_arrays
assert all(np.isclose(sc._data_arrays['partition_coeff'], 511.445))
assert sc.mass_balance['dissolution'] > 0
print "sc.mass_balance['dissolution']"
print sc.mass_balance['dissolution']
else:
assert 'dissolution' not in sc.mass_balance
def test_dissolution_k_ow(oil, temp, num_elems, k_ow, on):
'''
Here we are testing that the molar averaged oil/water partition
coefficient (K_ow) is getting calculated with reasonable values
'''
et = floating(substance=oil)
diss = Dissolution(waves)
(sc, time_step) = weathering_data_arrays(diss.array_types,
water,
element_type=et,
num_elements=num_elems)[:2]
print 'num spills:', len(sc.spills)
print 'spill[0] amount:', sc.spills[0].amount
# we don't want to query the oil database, but get the sample oil
assert sc.spills[0].element_type.substance.record.id is None
model_time = (sc.spills[0].release_time +
timedelta(seconds=time_step))
diss.on = on
diss.prepare_for_model_run(sc)
diss.initialize_data(sc, sc.num_released)
diss.prepare_for_model_step(sc, time_step, model_time)
diss.weather_elements(sc, time_step, model_time)
assert all(np.isclose(sc._data_arrays['partition_coeff'], k_ow))
def test_prepare_for_model_run():
'test sort order for Dissolution weatherer'
diss = Dissolution(waves, wind)
(sc, _time_step) = weathering_data_arrays(diss.array_types,
water)[:2]
assert 'partition_coeff' in sc.data_arrays
assert 'dissolution' not in sc.mass_balance
diss.prepare_for_model_run(sc)
assert 'dissolution' in sc.mass_balance
def test_prepare_for_model_run():
'test sort order for Dissolution weatherer'
et = floating(substance='ABU SAFAH')
diss = Dissolution(waves)
(sc, time_step) = weathering_data_arrays(diss.array_types,
water,
element_type=et)[:2]
assert 'partition_coeff' in sc.data_arrays
assert 'dissolution' not in sc.mass_balance
diss.prepare_for_model_run(sc)
assert 'dissolution' in sc.mass_balance
def test_prepare_for_model_run():
'test sort order for Dissolution weatherer'
et = floating(substance='ABU SAFAH')
diss = Dissolution(waves)
(sc, time_step) = weathering_data_arrays(diss.array_types,
water,
element_type=et)[:2]
assert 'partition_coeff' in sc.data_arrays
assert 'dissolution' not in sc.mass_balance
diss.prepare_for_model_run(sc)
assert 'dissolution' in sc.mass_balance
def test_sort_order():
'test sort order for Dissolution weatherer'
wind = constant_wind(15., 0)
waves = Waves(wind, Water())
diss = Dissolution(waves)
assert weatherer_sort(diss) == 8
def test_prepare_for_model_run():
'test sort order for Dissolution weatherer'
et = floating(substance='oil_bahia')
diss = Dissolution(waves)
# we don't want to query the oil database, but get the sample oil
assert et.substance.record.id is None
(sc, _time_step) = weathering_data_arrays(diss.array_types,
water,
element_type=et)[:2]
assert 'partition_coeff' in sc.data_arrays
assert 'dissolution' not in sc.mass_balance
diss.prepare_for_model_run(sc)
assert 'dissolution' in sc.mass_balance
def test_prepare_for_model_run():
'test sort order for Dissolution weatherer'
et = floating(substance='oil_bahia')
diss = Dissolution(waves)
# we don't want to query the oil database, but get the sample oil
assert et.substance.record.id is None
(sc, _time_step) = weathering_data_arrays(diss.array_types,
water,
element_type=et)[:2]
assert 'partition_coeff' in sc.data_arrays
assert 'dissolution' not in sc.mass_balance
diss.prepare_for_model_run(sc)
assert 'dissolution' in sc.mass_balance
def test_init():
'test initialization'
wind = constant_wind(15., 0)
waves = Waves(wind, Water())
diss = Dissolution(waves)
print diss.array_types
assert all([(at in diss.array_types)
for at in ('mass', 'viscosity', 'density')])
def test_dissolution_droplet_size(oil, temp, num_elems, drop_size, on):
'''
Here we are testing that the molar averaged oil/water partition
coefficient (K_ow) is getting calculated with reasonable values
'''
et = floating(substance=oil)
disp = NaturalDispersion(waves, water)
diss = Dissolution(waves)
(sc, time_step) = weathering_data_arrays(diss.array_types,
water,
element_type=et,
num_elements=num_elems)[:2]
print 'num_spills:', len(sc.spills)
print 'spill[0] amount:', sc.spills[0].amount, sc.spills[0].units
model_time = (sc.spills[0]
.release_time + timedelta(seconds=time_step))
print 'model_time = ', model_time
print 'time_step = ', time_step
# we don't want to query the oil database, but get the sample oil
assert sc.spills[0].element_type.substance.record.id is None
disp.on = on
diss.on = on
disp.prepare_for_model_run(sc)
diss.prepare_for_model_run(sc)
disp.initialize_data(sc, sc.num_released)
diss.initialize_data(sc, sc.num_released)
for i in range(3):
disp.prepare_for_model_step(sc, time_step, model_time)
diss.prepare_for_model_step(sc, time_step, model_time)
disp.weather_elements(sc, time_step, model_time)
diss.weather_elements(sc, time_step, model_time)
print 'droplet_avg_size:', sc._data_arrays['droplet_avg_size']
assert np.allclose(sc._data_arrays['droplet_avg_size'], drop_size[i])
def test_full_run_no_evap(sample_model_fcn2, oil, temp, expected_balance):
'''
test dissolution outputs post step for a full run of model. Dump json
for 'weathering_model.json' in dump directory
'''
low_wind = constant_wind(1., 270, 'knots')
low_waves = Waves(low_wind, Water(temp))
model = sample_model_weathering2(sample_model_fcn2, oil, temp)
model.environment += [Water(temp), low_wind, low_waves]
# model.weatherers += Evaporation(Water(temp), low_wind)
model.weatherers += NaturalDispersion(low_waves, Water(temp))
model.weatherers += Dissolution(low_waves, low_wind)
print ('Model start time: {}, Duration: {}, Time step: {}'
.format(model.start_time, model.duration, model.time_step))
for sc in model.spills.items():
print '\nSpill dict keys: ', sc.__dict__.keys()
print '\nSpill data arrays: ', sc._data_arrays
print 'num spills:', len(sc.spills)
print ('spill[0] amount: {} {} ({})'
.format(sc.spills[0].amount, sc.spills[0].units,
sc.spills[0].substance.name)
)
original_amount = sc.spills[0].amount
# set make_default_refs to True for objects contained in model after adding
# objects to the model
model.set_make_default_refs(True)
model.setup_model_run()
dissolved = []
for step_num, step in enumerate(model):
for sc in model.spills.items():
if step['step_num'] > 0:
assert (sc.mass_balance['dissolution'] > 0)
assert (sc.mass_balance['natural_dispersion'] > 0)
assert (sc.mass_balance['sedimentation'] > 0)
dissolved.append(sc.mass_balance['dissolution'])
print ('\n#Step: {}'.format(step_num))
print ("Dissolved: {0}".
format(sc.mass_balance['dissolution']))
print ("Mass: {0}".
format(sc._data_arrays['mass']))
print ("Mass Components: {0}".
format(sc._data_arrays['mass_components']))
print ('Fraction dissolved after full run: {}'
.format(dissolved[-1] / original_amount))
assert dissolved[0] == 0.0
assert np.isclose(dissolved[-1], expected_balance)
def test_serialize_deseriailize():
'test serialize/deserialize for webapi'
wind = constant_wind(15., 0)
water = Water()
waves = Waves(wind, water)
diss = Dissolution(waves)
json_ = diss.serialize()
pp.pprint(json_)
assert json_['waves'] == waves.serialize()
# deserialize and ensure the dict's are correct
d_ = Dissolution.deserialize(json_)
assert d_['waves'] == Waves.deserialize(json_['waves'])
d_['waves'] = waves
diss.update_from_dict(d_)
assert diss.waves is waves
def test_full_run(sample_model_fcn2, oil, temp, expected_balance):
'''
test dissolution outputs post step for a full run of model. Dump json
for 'weathering_model.json' in dump directory
'''
model = sample_model_weathering2(sample_model_fcn2, oil, temp)
model.environment += [Water(temp), wind, waves]
model.weatherers += Evaporation()
model.weatherers += NaturalDispersion()
model.weatherers += Dissolution(waves, wind)
for sc in model.spills.items():
print sc.__dict__.keys()
print sc._data_arrays
print 'num spills:', len(sc.spills)
print 'spill[0] amount:', sc.spills[0].amount
original_amount = sc.spills[0].amount
# we don't want to query the oil database, but get the sample oil
#assert sc.spills[0].substance.record.id is None
# set make_default_refs to True for objects contained in model after adding
# objects to the model
model.set_make_default_refs(True)
model.setup_model_run()
dissolved = []
for step in model:
for sc in model.spills.items():
if step['step_num'] > 0:
assert (sc.mass_balance['dissolution'] > 0)
assert (sc.mass_balance['natural_dispersion'] > 0)
assert (sc.mass_balance['sedimentation'] > 0)
dissolved.append(sc.mass_balance['dissolution'])
# print ("\nDissolved: {0}".
# format(sc.mass_balance['dissolution']))
# print ("Mass: {0}".
# format(sc._data_arrays['mass']))
# print ("Mass Components: {0}".
# format(sc._data_arrays['mass_components']))
print ('Fraction dissolved after full run: {}'
.format(dissolved[-1] / original_amount))
assert dissolved[0] == 0.0
assert np.isclose(dissolved[-1], expected_balance, rtol=1e-4)
def test_sort_order():
'test sort order for Dissolution weatherer'
wind = constant_wind(15., 0)
waves = Waves(wind, Water())
diss = Dissolution(waves, wind)
disp = NaturalDispersion(waves=waves, water=waves.water)
weathering_data = WeatheringData(water=waves.water)
# dissolution is dependent upon droplet distribution generated by
# natural dispersion
assert weatherer_sort(disp) < weatherer_sort(diss)
# dissolution needs to happen before we treat our weathering data
assert weatherer_sort(diss) < weatherer_sort(weathering_data)
def test_full_run_dissolution_not_active(sample_model_fcn):
'no water/wind/waves object and no evaporation'
model = sample_model_weathering(sample_model_fcn, 'oil_4')
model.environment += [Water(288.7), wind, waves]
model.weatherers += Evaporation()
model.weatherers += NaturalDispersion()
model.weatherers += Dissolution(waves=waves, wind=wind, on=False)
model.outputters += WeatheringOutput()
for step in model:
'''
if no weatherers, then no weathering output - need to add on/off
switch to WeatheringOutput
'''
assert 'dissolution' not in step['WeatheringOutput']
assert ('time_stamp' in step['WeatheringOutput'])
print ("Completed step: {0}".format(step['step_num']))
def test_dissolution_not_active(oil, temp, num_elems):
'''
Fuel Oil #6 does not exist...
'''
diss = Dissolution(waves)
et = floating(substance=oil)
(sc, time_step) = weathering_data_arrays(diss.array_types, water,
element_type=et)[:2]
sc.amount = 10000
model_time = (sc.spills[0].get('release_time') +
timedelta(seconds=time_step))
diss.prepare_for_model_run(sc)
new_model_time = (sc.spills[0].get('release_time') +
timedelta(seconds=3600))
diss.active_start = new_model_time
diss.prepare_for_model_step(sc, time_step, model_time)
diss.weather_elements(sc, time_step, model_time)
assert np.all(sc.mass_balance['dissolution'] == 0)
def test__deserialize():
'test serialize/deserialize for webapi'
wind = constant_wind(15., 0)
water = Water()
waves = Waves(wind, water)
diss = Dissolution(waves, wind)
json_ = diss.serialize()
pp.pprint(json_)
assert json_['waves'] == waves.serialize()
# deserialize and ensure the dict's are correct
d_ = Dissolution.deserialize(json_)
assert d_['waves'] == Waves.deserialize(json_['waves'])
d_['waves'] = waves
diss.update_from_dict(d_)
assert diss.waves is waves
def test_dissolution_mass_balance(oil, temp, num_elems, expected_mb, on):
'''
Fuel Oil #6 does not exist...
'''
et = floating(substance=oil)
diss = Dissolution(waves)
(sc, time_step) = weathering_data_arrays(diss.array_types,
water,
element_type=et,
num_elements=num_elems)[:2]
print 'num spills:', len(sc.spills)
print 'spill[0] amount:', sc.spills[0].amount
model_time = (sc.spills[0].get('release_time') +
timedelta(seconds=time_step))
diss.on = on
diss.prepare_for_model_run(sc)
diss.initialize_data(sc, sc.num_released)
diss.prepare_for_model_step(sc, time_step, model_time)
diss.weather_elements(sc, time_step, model_time)
if on:
assert np.isclose(sc.mass_balance['dissolution'], expected_mb)
else:
assert 'dissolution' not in sc.mass_balance
def test_dissolution_droplet_size(oil, temp, num_elems, drop_size, on):
'''
Here we are testing that the molar averaged oil/water partition
coefficient (K_ow) is getting calculated with reasonable values
'''
disp = NaturalDispersion(waves, water)
diss = Dissolution(waves, wind)
(sc, time_step) = weathering_data_arrays(diss.array_types,
water,
num_elements=num_elems)[:2]
print 'num_spills:', len(sc.spills)
print 'spill[0] amount:', sc.spills[0].amount, sc.spills[0].units
model_time = (sc.spills[0]
.release_time + timedelta(seconds=time_step))
print 'model_time = ', model_time
print 'time_step = ', time_step
# we don't want to query the oil database, but get the sample oil
#assert sc.spills[0].substance.record.id is None
disp.on = on
diss.on = on
disp.prepare_for_model_run(sc)
diss.prepare_for_model_run(sc)
disp.initialize_data(sc, sc.num_released)
diss.initialize_data(sc, sc.num_released)
for i in range(3):
disp.prepare_for_model_step(sc, time_step, model_time)
diss.prepare_for_model_step(sc, time_step, model_time)
disp.weather_elements(sc, time_step, model_time)
diss.weather_elements(sc, time_step, model_time)
print 'droplet_avg_size:', sc._data_arrays['droplet_avg_size']
assert np.allclose(sc._data_arrays['droplet_avg_size'], drop_size[i])
def test_dissolution_k_ow(oil, temp, num_elems, k_ow, on):
'''
Here we are testing that the molar averaged oil/water partition
coefficient (K_ow) is getting calculated with reasonable values
Note: for now droplets are calculated in natural dispersion so
natural dispersion is required for the dissolution algorithm
'''
diss = Dissolution(waves, wind)
disp = NaturalDispersion(waves, water)
(sc, time_step) = weathering_data_arrays(diss.array_types,
water,
substance=oil,
num_elements=num_elems)[:2]
print 'num spills:', len(sc.spills)
print 'spill[0] amount:', sc.spills[0].amount
# we don't want to query the oil database, but get the sample oil
#assert sc.spills[0].substance.record.id is None
model_time = (sc.spills[0].release_time +
timedelta(seconds=time_step))
disp.on = on
diss.on = on
disp.prepare_for_model_run(sc)
diss.prepare_for_model_run(sc)
disp.initialize_data(sc, sc.num_released)
diss.initialize_data(sc, sc.num_released)
disp.prepare_for_model_step(sc, time_step, model_time)
diss.prepare_for_model_step(sc, time_step, model_time)
disp.weather_elements(sc, time_step, model_time)
diss.weather_elements(sc, time_step, model_time)
assert all(np.isclose(sc._data_arrays['partition_coeff'], k_ow))
def test_dissolution_k_ow(oil, temp, num_elems, k_ow, on):
'''
Here we are testing that the molar averaged oil/water partition
coefficient (K_ow) is getting calculated with reasonable values
'''
et = floating(substance=oil)
diss = Dissolution(waves)
(sc, time_step) = weathering_data_arrays(diss.array_types,
water,
element_type=et,
num_elements=num_elems)[:2]
print 'num spills:', len(sc.spills)
print 'spill[0] amount:', sc.spills[0].amount
# we don't want to query the oil database, but get the sample oil
assert sc.spills[0].element_type.substance.record.id is None
model_time = (sc.spills[0].release_time + timedelta(seconds=time_step))
diss.on = on
diss.prepare_for_model_run(sc)
diss.initialize_data(sc, sc.num_released)
diss.prepare_for_model_step(sc, time_step, model_time)
diss.weather_elements(sc, time_step, model_time)
assert all(np.isclose(sc._data_arrays['partition_coeff'], k_ow))
def test_dissolution_mass_balance(oil, temp, wind_speed,
num_elems, expected_mb, on):
'''
Test a single dissolution step.
- for this, we need a dispersion weatherer to give us a droplet size
distribution.
Fuel Oil #6 does not exist...
'''
et = floating(substance=oil)
waves = build_waves_obj(wind_speed, 'knots', 270, temp)
water = waves.water
disp = NaturalDispersion(waves, water)
diss = Dissolution(waves)
all_array_types = diss.array_types.union(disp.array_types)
(sc, time_step) = weathering_data_arrays(all_array_types,
water,
element_type=et,
num_elements=num_elems,
units='kg',
amount_per_element=1.0
)[:2]
print 'time_step: {}'.format(time_step)
print 'num spills:', len(sc.spills)
print 'spill[0] amount: {} {}'.format(sc.spills[0].amount,
sc.spills[0].units)
print 'temperature = ', temp
print 'wind = ',
print '\n'.join(['\t{} {}'.format(ts[1][0], waves.wind.units)
for ts in waves.wind.timeseries])
print
# we don't want to query the oil database, but get the sample oil
assert sc.spills[0].element_type.substance.record.id is None
initial_amount = sc.spills[0].amount
model_time = (sc.spills[0].release_time +
timedelta(seconds=time_step))
disp.on = on
disp.prepare_for_model_run(sc)
disp.initialize_data(sc, sc.num_released)
diss.on = on
diss.prepare_for_model_run(sc)
diss.initialize_data(sc, sc.num_released)
disp.prepare_for_model_step(sc, time_step, model_time)
diss.prepare_for_model_step(sc, time_step, model_time)
disp.weather_elements(sc, time_step, model_time)
diss.weather_elements(sc, time_step, model_time)
if on:
print ('fraction dissolved: {}'
.format(sc.mass_balance['dissolution'] / initial_amount)
)
print ('fraction dissolved: {:.2%}'
.format(sc.mass_balance['dissolution'] / initial_amount)
)
print sc.mass_balance['dissolution'], expected_mb
assert np.isclose(sc.mass_balance['dissolution'], expected_mb)
else:
assert 'dissolution' not in sc.mass_balance
def make_model():
"""
Set up a GNOME simulation that uses TAMOC
Set up a spill scenario in GNOME that uses TAMOC to simulate a subsurface
blowout and then pass the TAMOC solution to GNOME for the far-field
particle tracking
"""
# Set up the directory structure for the model
base_dir, images_dir, outfiles_dir = set_directory_structure()
# Set up the modeling environment
print '\n-- Initializing the Model --'
start_time = "2019-06-01T12:00"
model = gs.Model(start_time=start_time,
duration=gs.days(3),
time_step=gs.minutes(30),
uncertain=False)
# Add a map
print '\n-- Adding a Map --'
model.map = gs.GnomeMap()
# Add image output
print '\n-- Adding Image Outputters --'
renderer = gs.Renderer(output_dir=images_dir,
image_size=(1024, 768),
output_timestep=gs.hours(1),
viewport=((-0.15, -0.35), (0.15, 0.35)))
model.outputters += renderer
# Add NetCDF output
print '\n-- Adding NetCDF Outputter --'
if not os.path.exists(outfiles_dir):
os.mkdir(outfiles_dir)
netcdf_file = os.path.join(outfiles_dir, 'script_tamoc.nc')
gs.remove_netcdf(netcdf_file)
file_writer = gs.NetCDFOutput(netcdf_file,
which_data='all',
output_timestep=gs.hours(2))
model.outputters += file_writer
# Add a spill object
print '\n-- Adding a Point Spill --'
end_release_time = model.start_time + gs.hours(12)
point_source = ts.TamocSpill(num_elements=100,
start_position=(0.0, 0.0, 1000.),
release_duration=gs.hours(24),
release_time=start_time,
substance='AD01554',
release_rate=20000.,
units='bbl/day',
gor=500.,
d0=0.5,
phi_0=-np.pi / 2.,
theta_0=0.,
windage_range=(0.01, 0.04),
windage_persist=900,
name='Oil Well Blowout')
model.spills += point_source
# Create an ocean environment
water, wind, waves = base_environment(water_temp=273.15 + 21.,
wind_speed=5.,
wind_dir=225.)
# Add a uniform current in the easterly direction
print '\n-- Adding Currents --'
uniform_current = gs.SimpleMover(velocity=(0.1, 0.0, 0.))
model.movers += uniform_current
# Add a wind mover
wind_mover = gs.WindMover(wind)
model.movers += wind_mover
# Add particle diffusion...note, units are in cm^2/s
print '\n-- Adding Particle Diffusion --'
particle_diffusion = gs.RandomMover3D(
horizontal_diffusion_coef_above_ml=100000.,
horizontal_diffusion_coef_below_ml=10000.,
vertical_diffusion_coef_above_ml=100.,
vertical_diffusion_coef_below_ml=10.,
mixed_layer_depth=15.)
model.movers += particle_diffusion
# Add rise velocity for droplets
print '\n-- Adding Particle Rise Velocity --'
# fixme: we do have code for rise velocity:
# gnome.movers.RiseVelocityMover
# let's test that later
slip_velocity = gs.SimpleMover(velocity=(0.0, 0.0, -0.1))
model.movers += slip_velocity
# Add dissolution
print '\n-- Adding Weathering --'
evaporation = Evaporation(water=water, wind=wind)
model.weatherers += evaporation
dissolution = Dissolution(waves=waves, wind=wind)
model.weatherers += dissolution
return model
def test_sort_order():
assert weatherer_sort(Dissolution()) > weatherer_sort(NaturalDispersion())
def test_dissolution_mass_balance(oil, temp, wind_speed,
num_elems, expected_mb, on):
'''
Test a single dissolution step.
- for this, we need a dispersion weatherer to give us a droplet size
distribution.
Fuel Oil #6 does not exist...
'''
waves = build_waves_obj(wind_speed, 'knots', 270, temp)
wind = waves.wind
water = waves.water
disp = NaturalDispersion(waves, water)
diss = Dissolution(waves, wind)
all_array_types = diss.array_types.union(disp.array_types)
(sc, time_step) = weathering_data_arrays(all_array_types,
water,
num_elements=num_elems,
units='kg',
amount_per_element=1.0
)[:2]
print 'time_step: {}'.format(time_step)
print 'num spills:', len(sc.spills)
print 'spill[0] amount: {} {}'.format(sc.spills[0].amount,
sc.spills[0].units)
print 'temperature = ', temp
print 'wind = ',
print '\n'.join(['\t{} {}'.format(ts[1][0], waves.wind.units)
for ts in waves.wind.timeseries])
print
# we don't want to query the oil database, but get the sample oil
#assert sc.spills[0].substance.record.id is None
initial_amount = sc.spills[0].amount
model_time = (sc.spills[0].release_time +
timedelta(seconds=time_step))
disp.on = on
disp.prepare_for_model_run(sc)
disp.initialize_data(sc, sc.num_released)
diss.on = on
diss.prepare_for_model_run(sc)
diss.initialize_data(sc, sc.num_released)
disp.prepare_for_model_step(sc, time_step, model_time)
diss.prepare_for_model_step(sc, time_step, model_time)
disp.weather_elements(sc, time_step, model_time)
diss.weather_elements(sc, time_step, model_time)
if on:
print ('fraction dissolved: {}'
.format(sc.mass_balance['dissolution'] / initial_amount)
)
print ('fraction dissolved: {:.2%}'
.format(sc.mass_balance['dissolution'] / initial_amount)
)
print sc.mass_balance['dissolution'], expected_mb
assert np.isclose(sc.mass_balance['dissolution'], expected_mb,
rtol=1e-4)
else:
assert 'dissolution' not in sc.mass_balance