def setup_test(self, end_time_delay, num_les, ts=900.):
stime = datetime(2015, 1, 1, 12, 0)
etime = stime + end_time_delay
st_pos = (0, 0, 0)
oil = test_oil
m1 = Model(start_time=stime, time_step=ts)
m1.environment += [constant_wind(0, 0), Water()]
m1.weatherers += Evaporation()
m1.spills += point_line_release_spill(num_les[0],
st_pos,
stime,
end_release_time=etime,
substance=oil,
amount=36000,
units='kg')
m1.outputters += WeatheringOutput()
m2 = Model(start_time=stime, time_step=ts)
m2.environment += [constant_wind(0, 0), Water()]
m2.weatherers += Evaporation()
m2.spills += point_line_release_spill(num_les[1],
st_pos,
stime,
end_release_time=etime,
substance=oil,
amount=36000,
units='kg')
m2.outputters += WeatheringOutput()
return (m1, m2)
def test_weathering_data_attr():
'''
mass_balance is initialized/written if we have weatherers
'''
ts = 900
s1_rel = datetime.now().replace(microsecond=0)
s2_rel = s1_rel + timedelta(seconds=ts)
s = [point_line_release_spill(10, (0, 0, 0), s1_rel),
point_line_release_spill(10, (0, 0, 0), s2_rel)]
model = Model(time_step=ts, start_time=s1_rel)
model.spills += s
model.step()
for sc in model.spills.items():
assert len(sc.mass_balance) == 2
for key in ('beached', 'off_maps'):
assert key in sc.mass_balance
model.environment += [Water(), constant_wind(0., 0)]
model.weatherers += [Evaporation(model.environment[0],
model.environment[1])]
# use different element_type and initializers for both spills
s[0].amount = 10.0
s[0].units = 'kg'
model.rewind()
model.step()
for sc in model.spills.items():
# since no substance is defined, all the LEs are marked as
# nonweathering
assert sc.mass_balance['non_weathering'] == sc['mass'].sum()
assert sc.mass_balance['non_weathering'] == s[0].amount
s[1].amount = 5.0
s[1].units = 'kg'
model.rewind()
exp_rel = 0.0
for ix in range(2):
model.step()
exp_rel += s[ix].amount
for sc in model.spills.items():
assert sc.mass_balance['non_weathering'] == sc['mass'].sum()
assert sc.mass_balance['non_weathering'] == exp_rel
model.rewind()
assert sc.mass_balance == {}
# weathering data is now empty for all steps
del model.weatherers[0]
for ix in xrange(2):
model.step()
for sc in model.spills.items():
assert len(sc.mass_balance) == 2
assert (len(set(sc.mass_balance.keys()) -
{'beached', 'off_maps'}) == 0)
def mk_objs(cls, sample_model_fcn2):
model = sample_model_weathering2(sample_model_fcn2, test_oil, 333.0)
model.set_make_default_refs(True)
model.environment += [waves, wind, water]
model.weatherers += Evaporation(wind=wind, water=water)
model.weatherers += Emulsification(waves=waves)
return (model.spills.items()[0], model)
def test_full_run(sample_model_fcn, oil, temp):
'''
test evaporation outputs for a full run of model.
This contains a mover so at some point several elements end up on_land.
This test also checks the evap_decay_constant for elements that are not
in water is 0 so mass is unchanged.
'''
model = sample_model_weathering(sample_model_fcn, oil, temp, 10)
model.environment += [Water(temp), constant_wind(1., 0)]
model.weatherers += [
Evaporation(model.environment[-2], model.environment[-1])
]
released = 0
init_rho = model.spills[0].substance.density_at_temp(temp)
init_vis = model.spills[0].substance.kvis_at_temp(temp)
for step in model:
for sc in model.spills.items():
assert_helper(sc, sc.num_released - released)
released = sc.num_released
if sc.num_released > 0:
assert np.all(sc['density'] >= init_rho)
assert np.all(sc['viscosity'] >= init_vis)
mask = sc['status_codes'] == oil_status.in_water
assert sc.mass_balance['floating'] == np.sum(sc['mass'][mask])
print("Amount released: {0}".format(
sc.mass_balance['amount_released']))
print "Mass floating: {0}".format(sc.mass_balance['floating'])
print "Mass evap: {0}".format(sc.mass_balance['evaporated'])
print "LEs in water: {0}".format(sum(mask))
print "Mass on land: {0}".format(np.sum(sc['mass'][~mask]))
print "Completed step: {0}\n".format(step['step_num'])
def model(sample_model_fcn, output_filename):
"""
Use fixture model_surface_release_spill and add a few things to it for the
test
"""
model = sample_model_fcn['model']
model.cache_enabled = True
model.spills += \
point_line_release_spill(num_elements=5,
start_position=sample_model_fcn['release_start_pos'],
release_time=model.start_time,
end_release_time=model.start_time + model.duration,
substance=test_oil,
amount=1000,
units='kg')
water = Water()
model.movers += RandomMover(diffusion_coef=100000)
model.movers += constant_wind_mover(1.0, 0.0)
model.weatherers += Evaporation(water=water, wind=model.movers[-1].wind)
model.outputters += NetCDFOutput(output_filename)
model.rewind()
return model
def model(sample_model, output_dir):
model = sample_model_weathering(sample_model, test_oil)
rel_start_pos = sample_model['release_start_pos']
rel_end_pos = sample_model['release_end_pos']
model.cache_enabled = True
model.uncertain = True
water, wind = Water(), constant_wind(1., 0)
model.environment += [water, wind]
model.weatherers += Evaporation(water, wind)
et = floating(substance=model.spills[0].substance.name)
N = 10 # a line of ten points
line_pos = np.zeros((N, 3), dtype=np.float64)
line_pos[:, 0] = np.linspace(rel_start_pos[0], rel_end_pos[0], N)
line_pos[:, 1] = np.linspace(rel_start_pos[1], rel_end_pos[1], N)
# print start_points
model.spills += point_line_release_spill(1,
start_position=rel_start_pos,
release_time=model.start_time,
end_position=rel_end_pos,
element_type=et,
amount=100,
units='tons')
model.outputters += TrajectoryGeoJsonOutput(output_dir=output_dir)
model.rewind()
return model
def test_full_run(sample_model_fcn2, oil, temp, dispersed):
'''
test dispersion 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 += Emulsification(waves)
model.weatherers += NaturalDispersion()
# set make_default_refs to True for objects contained in model after adding
# objects to the model
model.set_make_default_refs(True)
for step in model:
for sc in model.spills.items():
if step['step_num'] > 0:
# print ("Dispersed: {0}".
# format(sc.mass_balance['natural_dispersion']))
# print ("Sedimentation: {0}".
# format(sc.mass_balance['sedimentation']))
# print "Completed step: {0}\n".format(step['step_num'])
assert (sc.mass_balance['natural_dispersion'] > 0)
assert (sc.mass_balance['sedimentation'] > 0)
sc = model.spills.items()[0]
print (sc.mass_balance['natural_dispersion'], dispersed)
assert np.isclose(sc.mass_balance['natural_dispersion'], dispersed,
atol=0.001)
def allWeatherers(timeStep, start_time, duration, weatheringSteps, map, uncertain, data_path, curr_path, wind_path, map_path, reFloatHalfLife, windFile, currFile, tidalFile, num_elements, depths, lat, lon, output_path, wind_scale, save_nc, timestep_outputs, weatherers, td):
print 'initializing the model:'
model = Model(time_step=timeStep, start_time=start_time, duration=duration)
print 'adding the map:'
map_folder = os.path.join(data_path, map_path)
if not(os.path.exists(map_folder)):
print('The map folder is incorrectly set:', map_folder)
mapfile = get_datafile( os.path.join(map_folder,map) )
model.map = MapFromBNA(mapfile, refloat_halflife=reFloatHalfLife)
print 'adding a renderer'
model.outputters += Renderer(mapfile, output_path, size=(800, 600), output_timestep=timedelta(hours=1))
if save_nc:
nc_outputter = NetCDFOutput(netcdf_file, which_data='most', output_timestep=timedelta(hours=1))
model.outputters += nc_outputter
print 'adding a wind mover:'
wind_file = get_datafile(os.path.join(data_path, wind_path, windFile))
wind = GridWindMover(wind_file)
wind.wind_scale = wind_scale
model.movers += wind
print 'adding a current mover: '
curr_file = get_datafile(os.path.join(data_path, curr_path, currFile))
model.movers += GridCurrentMover(curr_file, num_method='RK4')
if td:
random_mover = RandomMover(diffusion_coef=10000)
model.movers += random_mover
print 'adding spill'
model.spills += point_line_release_spill(num_elements=num_elements, start_position=(lon, lat, 0), release_time=start_time, end_release_time=start_time + duration)
print 'adding weatherers'
water = Water(280.92)
wind = constant_wind(20.0, 117, 'knots')
waves = Waves(wind, water)
model.weatherers += Evaporation(water, wind)
model.weatherers += Emulsification(waves)
model.weatherers += NaturalDispersion(waves, water)
return model
def test_setup_model_run(model):
'turn of movers/weatherers and ensure data_arrays change'
model.environment += Water()
model.rewind()
model.step()
exp_keys = {
'windages', 'windage_range', 'mass_components', 'windage_persist'
}
# no exp_keys in model data_arrays
assert not exp_keys.intersection(model.spills.LE_data)
cwm = gnome.movers.constant_wind_mover(1., 0.)
model.weatherers += [HalfLifeWeatherer(), Evaporation()]
model.movers += cwm
model.rewind()
model.step()
assert exp_keys.issubset(model.spills.LE_data)
cwm.on = False
for w in xrange(2):
model.weatherers[w].on = False
model.rewind()
model.step()
assert not exp_keys.intersection(model.spills.LE_data)
def test_load_location_file(self, saveloc_, model):
'''
create a model
load save file from script_boston which contains a spill. Then merge
the created model into the model loaded from save file
'''
m = Model()
m.environment += [Water(), constant_wind(1., 0.)]
m.weatherers += Evaporation(m.environment[0], m.environment[-1])
m.spills += point_line_release_spill(10, (0, 0, 0),
datetime(2014, 1, 1, 12, 0))
# create save model
sample_save_file = os.path.join(saveloc_, 'SampleSaveModel.zip')
model.save(saveloc_, name='SampleSaveModel.zip')
if os.path.exists(sample_save_file):
model = load(sample_save_file)
model.merge(m)
for oc in m._oc_list:
for item in getattr(m, oc):
model_oc = getattr(model, oc)
assert item is model_oc[item.id]
for spill in m.spills:
assert spill is model.spills[spill.id]
# merge the other way and ensure model != m
m.merge(model)
assert model != m
def test_serialize_deseriailize():
'test serialize/deserialize for webapi'
e = Evaporation()
wind = constant_wind(1., 0)
water = Water()
json_ = e.serialize()
json_['wind'] = wind.serialize()
json_['water'] = water.serialize()
# deserialize and ensure the dict's are correct
d_ = Evaporation.deserialize(json_)
assert d_['wind'] == Wind.deserialize(json_['wind'])
assert d_['water'] == Water.deserialize(json_['water'])
d_['wind'] = wind
d_['water'] = water
e.update_from_dict(d_)
assert e.wind is wind
assert e.water is water
def test_evaporation_no_wind():
evap = Evaporation(Water(), wind=constant_wind(0., 0))
(sc, time_step) = weathering_data_arrays(evap.array_types, evap.water)[:2]
model_time = (sc.spills[0].release_time + timedelta(seconds=time_step))
evap.prepare_for_model_run(sc)
evap.prepare_for_model_step(sc, time_step, model_time)
evap.weather_elements(sc, time_step, model_time)
for spill in sc.spills:
mask = sc.get_spill_mask(spill)
assert np.all(sc['evap_decay_constant'][mask, :] < 0.0)
def test_contains_object(sample_model_fcn):
'''
Test that we can find all contained object types with a model.
'''
model = sample_model_weathering(sample_model_fcn, test_oil)
gnome_map = model.map = gnome.map.GnomeMap() # make it all water
rel_time = model.spills[0].get('release_time')
model.start_time = rel_time - timedelta(hours=1)
model.duration = timedelta(days=1)
water, wind = Water(), constant_wind(1., 0)
model.environment += [water, wind]
et = floating(substance=model.spills[0].get('substance').name)
sp = point_line_release_spill(500, (0, 0, 0),
rel_time + timedelta(hours=1),
element_type=et,
amount=100,
units='tons')
rel = sp.release
initializers = et.initializers
model.spills += sp
movers = [m for m in model.movers]
evaporation = Evaporation()
skim_start = sp.get('release_time') + timedelta(hours=1)
skimmer = Skimmer(.5 * sp.amount,
units=sp.units,
efficiency=0.3,
active_start=skim_start,
active_stop=skim_start + timedelta(hours=1))
burn = burn_obj(sp)
disp_start = skim_start + timedelta(hours=1)
dispersion = ChemicalDispersion(0.1,
active_start=disp_start,
active_stop=disp_start +
timedelta(hours=1))
model.weatherers += [evaporation, dispersion, burn, skimmer]
renderer = Renderer(images_dir='junk', size=(400, 300))
model.outputters += renderer
for o in (gnome_map, sp, rel, et, water, wind, evaporation, dispersion,
burn, skimmer, renderer):
assert model.contains_object(o.id)
for o in initializers:
assert model.contains_object(o.id)
for o in movers:
assert model.contains_object(o.id)
def model(sample_model):
model = sample_model['model']
model.make_default_refs = True
rel_start_pos = sample_model['release_start_pos']
rel_end_pos = sample_model['release_end_pos']
model.cache_enabled = True
model.uncertain = False
model.environment += Water(311.15)
print 'adding a Weatherer'
model.environment += constant_wind(1.0, 0.0)
N = 10 # a line of ten points
line_pos = np.zeros((N, 3), dtype=np.float64)
line_pos[:, 0] = np.linspace(rel_start_pos[0], rel_end_pos[0], N)
line_pos[:, 1] = np.linspace(rel_start_pos[1], rel_end_pos[1], N)
# print start_points
model.duration = timedelta(hours=6)
end_time = model.start_time + timedelta(hours=1)
spill = point_line_release_spill(1000,
start_position=rel_start_pos,
release_time=model.start_time,
end_release_time=end_time,
end_position=rel_end_pos,
substance=test_oil,
amount=1000,
units='kg')
model.spills += spill
# figure out mid-run save for weathering_data attribute, then add this in
rel_time = model.spills[0].get('release_time')
skim_start = rel_time + timedelta(hours=1)
amount = model.spills[0].amount
units = model.spills[0].units
skimmer = Skimmer(.3 * amount,
units=units,
efficiency=0.3,
active_start=skim_start,
active_stop=skim_start + timedelta(hours=1))
# thickness = 1m so area is just 20% of volume
volume = spill.get_mass() / spill.get('substance').get_density()
burn = Burn(0.2 * volume, 1.0, active_start=skim_start, efficiency=0.9)
c_disp = ChemicalDispersion(.1,
efficiency=0.5,
active_start=skim_start,
active_stop=skim_start + timedelta(hours=1))
model.weatherers += [Evaporation(), c_disp, burn, skimmer]
model.outputters += WeatheringOutput()
model.rewind()
return model
def make_model(timeStep,start_time, duration, weatheringSteps, map, uncertain, data_path, reFloatHalfLife, windFile, currFile, tidalFile,
num_elements, depths, lat, lon, output_path, evaporation):
#initalizing the model
print 'initializing the model:'
# model = Model(time_step = timeStep, start_time= start_time, duration=duration, uncertain = uncertain)
model = Model(time_step = timeStep, start_time= start_time, duration=duration)
#adding the map
print 'adding the map:'
print 'pinche path', data_path
mapfile = get_datafile(os.path.join(data_path, map))
model.map = MapFromBNA(mapfile, refloat_halflife = reFloatHalfLife)
#model.map = GnomeMap()
print 'adding a renderer'
# renderer is a class that writes map images for GNOME results
model.outputters += Renderer(mapfile, output_path, size=(800, 600), output_timestep=timedelta(hours=1))
##scripting.remove_netcdf(netcdf_file)
#nc_outputter = NetCDFOutput(netcdf_file, which_data='most', output_timestep=timedelta(hours=1))
#model.outputters += nc_outputter
#adding the movers
print 'adding a wind mover:'
wind_file = get_datafile(os.path.join(data_path, windFile))
wind = GridWindMover(wind_file)
wind.wind_scale = 2
model.movers += wind
print 'adding a current mover: '
curr_file = get_datafile(os.path.join(data_path,currFile))
model.movers+= GridCurrentMover(curr_file, num_method='RK4')
#random_mover = RandomMover(diffusion_coef=10000) #in cm/sdfd
#model.movers += random_mover
if evaporation:
#wind for evaporation
print'adding evaporation'
wind = constant_wind(1, 0, 'knots')
water = Water(temperature=300.0, salinity=35.0)
model.weatherers += Evaporation(wind=wind, water=water)
#
print 'adding a spill'
# for i in depths:
# model.spills+= point_line_release_spill(num_elements=num_elements, start_position=(lon,lat,i), release_time=start_time)
model.spills+= point_line_release_spill(num_elements=num_elements, start_position=(lon,lat,0), release_time=start_time,
end_release_time=start_time+timedelta(days=93))
return model
def test_weatherer_sort():
'''
Sample model with weatherers - only tests sorting of weathereres. The
Model will likely not run
'''
model = Model()
skimmer = Skimmer(100, 'kg', efficiency=0.3,
active_start=datetime(2014, 1, 1, 0, 0),
active_stop=datetime(2014, 1, 1, 0, 3))
burn = Burn(100, 1, active_start=datetime(2014, 1, 1, 0, 0))
c_disp = ChemicalDispersion(.3,
active_start=datetime(2014, 1, 1, 0, 0),
active_stop=datetime(2014, 1, 1, 0, 3),
efficiency=0.2)
weatherers = [Emulsification(),
Evaporation(Water(),
constant_wind(1, 0)),
burn,
c_disp,
skimmer]
exp_order = [weatherers[ix] for ix in (3, 4, 2, 1, 0)]
model.environment += [Water(), constant_wind(5, 0), Waves()]
model.weatherers += weatherers
# WeatheringData and FayGravityViscous automatically get added to
# weatherers. Only do assertion on weatherers contained in list above
assert model.weatherers.values()[:len(exp_order)] != exp_order
model.setup_model_run()
assert model.weatherers.values()[:len(exp_order)] == exp_order
# check second time around order is kept
model.rewind()
assert model.weatherers.values()[:len(exp_order)] == exp_order
# Burn, ChemicalDispersion are at same sorting level so appending
# another Burn to the end of the list will sort it to be just after
# ChemicalDispersion so index 2
burn = Burn(50, 1, active_start=datetime(2014, 1, 1, 0, 0))
exp_order.insert(3, burn)
model.weatherers += exp_order[3] # add this and check sorting still works
assert model.weatherers.values()[:len(exp_order)] != exp_order
model.setup_model_run()
assert model.weatherers.values()[:len(exp_order)] == exp_order
def test_full_run_evap_not_active(sample_model_fcn):
'no water/wind object'
model = sample_model_weathering(sample_model_fcn, 'oil_6')
model.weatherers += Evaporation(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 'evaporated' not in step['WeatheringOutput']
assert ('time_stamp' in step['WeatheringOutput'])
print("Completed step: {0}".format(step['step_num']))
def test_evaporation(oil, temp, num_elems, on):
'''
still working on tests ..
'''
et = floating(substance=oil)
time_step = 15. * 60
evap = Evaporation(Water(), wind=constant_wind(1., 0))
evap.on = on
sc = weathering_data_arrays(evap.array_types, evap.water, time_step, et)[0]
model_time = (sc.spills[0].release_time +
timedelta(seconds=time_step))
evap.prepare_for_model_run(sc)
evap.prepare_for_model_step(sc, time_step, model_time)
init_mass = sc['mass_components'].copy()
evap.weather_elements(sc, time_step, model_time)
if on:
assert np.all(sc['frac_lost'] > 0) and np.all(sc['frac_lost'] < 1.0)
# all elements experience the same evaporation
assert np.all(sc['frac_lost'][0] == sc['frac_lost'])
for spill in sc.spills:
mask = sc.get_spill_mask(spill)
if on:
assert np.all(sc['evap_decay_constant'][mask, :] < 0.0)
else:
assert np.all(sc['evap_decay_constant'][mask, :] == 0.0)
print '\nevap_decay_const', sc['evap_decay_constant']
print 'frac_lost', sc['frac_lost']
if on:
assert sc.mass_balance['evaporated'] > 0.0
print 'total evaporated', sc.mass_balance['evaporated']
else:
assert 'evaporated' not in sc.mass_balance
assert np.all(sc['mass_components'] == init_mass)
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_evaporation_no_wind():
evap = Evaporation(Water(), wind=constant_wind(0., 0))
(sc, time_step) = weathering_data_arrays(evap.array_types, evap.water)[:2]
model_time = (sc.spills[0].get('release_time') +
timedelta(seconds=time_step))
evap.prepare_for_model_run(sc)
evap.prepare_for_model_step(sc, time_step, model_time)
evap.weather_elements(sc, time_step, model_time)
for spill in sc.spills:
mask = sc.get_spill_mask(spill)
assert np.all(sc['evap_decay_constant'][mask, :] < 0.0)
def test_callback_add_weather():
'''
Test callback when weatherer is added
'''
model = Model()
water = Water()
wind = constant_wind(1, 30)
assert len(model.environment) == 0
model.weatherers += Evaporation(water, wind)
# wind and water added to environment collection
assert len(model.environment) == 2
assert wind in model.environment
assert water in model.environment
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_evaporation(oil, temp, num_elems, on):
'''
still working on tests ..
'''
et = floating(substance=oil)
time_step = 15. * 60
evap = Evaporation(Water(), wind=constant_wind(1., 0))
evap.on = on
sc = weathering_data_arrays(evap.array_types, evap.water, time_step, et)[0]
model_time = (sc.spills[0].get('release_time') +
timedelta(seconds=time_step))
evap.prepare_for_model_run(sc)
evap.prepare_for_model_step(sc, time_step, model_time)
init_mass = sc['mass_components'].copy()
evap.weather_elements(sc, time_step, model_time)
if on:
assert np.all(sc['frac_lost'] > 0) and np.all(sc['frac_lost'] < 1.0)
# all elements experience the same evaporation
assert np.all(sc['frac_lost'][0] == sc['frac_lost'])
for spill in sc.spills:
mask = sc.get_spill_mask(spill)
if on:
assert np.all(sc['evap_decay_constant'][mask, :] < 0.0)
else:
assert np.all(sc['evap_decay_constant'][mask, :] == 0.0)
print '\nevap_decay_const', sc['evap_decay_constant']
print 'frac_lost', sc['frac_lost']
if on:
assert sc.mass_balance['evaporated'] > 0.0
print 'total evaporated', sc.mass_balance['evaporated']
else:
assert 'evaporated' not in sc.mass_balance
assert np.all(sc['mass_components'] == init_mass)
def test_full_run(sample_model_fcn, oil, temp):
'''
test emulsification outputs post step for a full run of model. Dump json
for 'weathering_model.json' in dump directory
'''
model = sample_model_weathering2(sample_model_fcn, oil, temp)
model.environment += [Waves(), wind, Water(temp)]
model.weatherers += Evaporation()
model.weatherers += Emulsification()
model.set_make_default_refs(True)
for step in model:
for sc in model.spills.items():
# need or condition to account for water_content = 0.9000000000012
# or just a little bit over 0.9
assert (sc.mass_balance['water_content'] <= .9
or np.isclose(sc.mass_balance['water_content'], 0.9))
print("Water fraction: {0}".format(
sc.mass_balance['water_content']))
print "Completed step: {0}\n".format(step['step_num'])
def test_bio_degradation_full_run(sample_model_fcn2, oil, temp,
expected_balance):
'''
test bio degradation 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.duration = timedelta(days=5)
model.environment += [Water(temp), wind, waves]
model.weatherers += Evaporation()
model.weatherers += NaturalDispersion()
# model.weatherers += Dissolution(waves)
model.weatherers += Biodegradation()
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
# 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()
bio_degradated = []
for step in model:
for sc in model.spills.items():
if step['step_num'] > 0:
assert (sc.mass_balance['bio_degradation'] > 0)
if 'bio_degradation' in sc.mass_balance:
bio_degradated.append(sc.mass_balance['bio_degradation'])
print('Bio degradated amount: {}'.format(bio_degradated[-1]))
print('Fraction bio degradated after full run: {}'.format(
bio_degradated[-1] / original_amount))
assert bio_degradated[0] == 0.0
def test_serialize_deseriailize():
'test serialize/deserialize for webapi'
e = Evaporation()
wind = constant_wind(1., 0)
water = Water()
json_ = e.serialize()
json_['wind'] = wind.serialize()
json_['water'] = water.serialize()
# deserialize and ensure the dict's are correct
d_ = Evaporation.deserialize(json_)
assert d_['wind'] == Wind.deserialize(json_['wind'])
assert d_['water'] == Water.deserialize(json_['water'])
d_['wind'] = wind
d_['water'] = water
e.update_from_dict(d_)
assert e.wind is wind
assert e.water is water
def make_modelF(timeStep, start_time, duration, weatheringSteps, map, uncertain, data_path, curr_path, wind_path, map_path, reFloatHalfLife, windFile, currFile, num_elements, depths, lat, lon, output_path, wind_scale, save_nc, timestep_outputs, weatherers, td, dif_coef,temp_water):
print 'initializing the model:'
model = Model(time_step=timeStep, start_time=start_time, duration=duration, uncertain=uncertain)
print 'adding the map:'
mapfile = get_datafile(os.path.join(data_path, map_path, map))
model.map = MapFromBNA(mapfile, refloat_halflife=reFloatHalfLife)
print 'adding a renderer'
if save_nc:
scripting.remove_netcdf(output_path+'/'+'output.nc')
nc_outputter = NetCDFOutput(output_path+'/'+'output.nc', which_data='standard', output_timestep=timedelta(hours=timestep_outputs))
model.outputters += nc_outputter
print 'adding a wind mover:'
wind_file = get_datafile(os.path.join(data_path, wind_path, windFile))
wind = GridWindMover(wind_file)
# wind.wind_scale = wind_scale
model.movers += wind
print 'adding a current mover:'
curr_file = get_datafile(os.path.join(data_path, curr_path, currFile))
model.movers += GridCurrentMover(curr_file, num_method='RK4')
if td:
random_mover = RandomMover(diffusion_coef=dif_coef)
model.movers += random_mover
print 'adding spill'
model.spills += point_line_release_spill(num_elements=num_elements, start_position=(lon, lat, 0), release_time=start_time, end_release_time=start_time + duration)#, substance='AD04001', amount=9600000, units='kg')
if weatherers:
print 'adding weatherers'
water = Water(temp_water)
wind = constant_wind(0.0001, 0, 'knots')
waves = Waves(wind, water)
model.weatherers += Evaporation(water, wind)
# model.weatherers += Emulsification(waves)
model.weatherers += NaturalDispersion(waves, water)
return model
def make_model(uncertain=False, mode='gnome'):
'''
Create a model from the data in sample_data/boston_data
It contains:
- the GeoProjection
- wind mover
- random mover
- cats shio mover
- cats ossm mover
- plain cats mover
'''
start_time = datetime(2013, 2, 13, 9, 0)
model = Model(start_time=start_time,
duration=timedelta(days=2),
time_step=timedelta(minutes=30).total_seconds(),
uncertain=uncertain,
map=MapFromBNA(testdata['boston_data']['map'],
refloat_halflife=1),
mode=mode)
print 'adding a spill'
start_position = (144.664166, 13.441944, 0.0)
end_release_time = start_time + timedelta(hours=6)
spill_amount = 1000.0
spill_units = 'kg'
model.spills += point_line_release_spill(num_elements=1000,
start_position=start_position,
release_time=start_time,
end_release_time=end_release_time,
amount=spill_amount,
units=spill_units,
substance=test_oil)
spill = model.spills[-1]
spill_volume = spill.get_mass() / spill.substance.density_at_temp()
# need a scenario for SimpleMover
# model.movers += SimpleMover(velocity=(1.0, -1.0, 0.0))
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=100000)
print 'adding a wind mover:'
series = np.zeros((2, ), dtype=datetime_value_2d)
series[0] = (start_time, (5, 180))
series[1] = (start_time + timedelta(hours=18), (5, 180))
w_mover = WindMover(Wind(timeseries=series, units='m/s'))
model.movers += w_mover
model.environment += w_mover.wind
print 'adding a cats shio mover:'
c_mover = CatsMover(testdata['boston_data']['cats_curr2'],
tide=Tide(testdata['boston_data']['cats_shio']))
# c_mover.scale_refpoint should automatically get set from tide object
c_mover.scale = True # default value
c_mover.scale_value = -1
# tide object automatically gets added by model
model.movers += c_mover
print 'adding a cats ossm mover:'
c_mover = CatsMover(testdata['boston_data']['cats_curr2'],
tide=Tide(testdata['boston_data']['cats_ossm']))
c_mover.scale = True # but do need to scale (based on river stage)
c_mover.scale_refpoint = (-70.65, 42.58333, 0.0)
c_mover.scale_value = 1.
print 'adding a cats mover:'
c_mover = CatsMover(testdata['boston_data']['cats_curr3'])
c_mover.scale = True # but do need to scale (based on river stage)
c_mover.scale_refpoint = (-70.78333, 42.39333, 0.0)
# the scale factor is 0 if user inputs no sewage outfall effects
c_mover.scale_value = .04
model.movers += c_mover
# TODO: seg faulting for component mover - comment test for now
# print "adding a component mover:"
# comp_mover = ComponentMover(testdata['boston_data']['component_curr1'],
# testdata['boston_data']['component_curr2'],
# w_mover.wind)
# TODO: callback did not work correctly below - fix!
# comp_mover = ComponentMover(component_file1,
# component_file2,
# Wind(timeseries=series, units='m/s'))
# comp_mover.ref_point = (-70.855, 42.275)
# comp_mover.pat1_angle = 315
# comp_mover.pat1_speed = 19.44
# comp_mover.pat1_speed_units = 1
# comp_mover.pat1ScaleToValue = .138855
# comp_mover.pat2_angle = 225
# comp_mover.pat2_speed = 19.44
# comp_mover.pat2_speed_units = 1
# comp_mover.pat2ScaleToValue = .05121
# model.movers += comp_mover
print 'adding a Weatherer'
model.environment += Water(311.15)
skim_start = start_time + timedelta(hours=3)
model.weatherers += [
Evaporation(),
Skimmer(spill_amount * .5,
spill_units,
efficiency=.3,
active_range=(skim_start, skim_start + timedelta(hours=2))),
Burn(0.2 * spill_volume,
1.0, (skim_start, InfDateTime('inf')),
efficiency=0.9)
]
model.outputters += \
CurrentJsonOutput(model.find_by_attr('_ref_as', 'current_movers',
model.movers, allitems=True))
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2015, 5, 14, 0, 0)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=1.75),
time_step=60 * 60,
uncertain=True)
# mapfile = get_datafile(os.path.join(base_dir, './ak_arctic.bna'))
#
# print 'adding the map'
# model.map = MapFromBNA(mapfile, refloat_halflife=1) # seconds
#
# # draw_ontop can be 'uncertain' or 'forecast'
# # 'forecast' LEs are in black, and 'uncertain' are in red
# # default is 'forecast' LEs draw on top
# renderer = Renderer(mapfile, images_dir, size=(800, 600),
# output_timestep=timedelta(hours=2),
# draw_ontop='forecast')
#
# print 'adding outputters'
# model.outputters += renderer
model.outputters += WeatheringOutput()
netcdf_file = os.path.join(base_dir, 'script_weatherers.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file,
which_data='all',
output_timestep=timedelta(hours=1))
print 'adding a spill'
# for now subsurface spill stays on initial layer
# - will need diffusion and rise velocity
# - wind doesn't act
# - start_position = (-76.126872, 37.680952, 5.0),
end_time = start_time + timedelta(hours=24)
spill = point_line_release_spill(
num_elements=100,
start_position=(-164.791878561, 69.6252597267, 0.0),
release_time=start_time,
end_release_time=end_time,
amount=1000,
substance='ALASKA NORTH SLOPE (MIDDLE PIPELINE)',
units='bbl')
# set bullwinkle to .303 to cause mass goes to zero bug at 24 hours (when continuous release ends)
spill.element_type._substance._bullwinkle = .303
model.spills += spill
print 'adding a RandomMover:'
#model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
series = np.zeros((2, ), dtype=datetime_value_2d)
series[0] = (start_time, (20, 0))
series[1] = (start_time + timedelta(hours=23), (20, 0))
wind2 = Wind(timeseries=series, units='knot')
w_mover = WindMover(wind)
model.movers += w_mover
print 'adding weatherers and cleanup options:'
# define skimmer/burn cleanup options
skim1_start = start_time + timedelta(hours=15.58333)
skim2_start = start_time + timedelta(hours=16)
units = spill.units
skimmer1 = Skimmer(80,
units=units,
efficiency=0.36,
active_start=skim1_start,
active_stop=skim1_start + timedelta(hours=8))
skimmer2 = Skimmer(120,
units=units,
efficiency=0.2,
active_start=skim2_start,
active_stop=skim2_start + timedelta(hours=12))
burn_start = start_time + timedelta(hours=36)
burn = Burn(1000., .1, active_start=burn_start, efficiency=.2)
chem_start = start_time + timedelta(hours=24)
c_disp = ChemicalDispersion(0.5,
efficiency=0.4,
active_start=chem_start,
active_stop=chem_start + timedelta(hours=8))
model.environment += [Water(280.928), wind, waves]
model.weatherers += Evaporation(water, wind)
model.weatherers += Emulsification(waves)
model.weatherers += NaturalDispersion(waves, water)
model.weatherers += skimmer1
model.weatherers += skimmer2
model.weatherers += burn
model.weatherers += c_disp
return model
def make_model(uncertain=False, geojson_output=False):
print 'initializing the model'
start_time = datetime(2012, 9, 15, 12, 0)
mapfile = testdata["lis"]["map"]
gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours
# # the image output renderer
# global renderer
# one hour timestep
model = Model(start_time=start_time,
duration=timedelta(hours=48),
time_step=3600,
map=gnome_map,
uncertain=uncertain,
cache_enabled=False)
print 'adding a spill'
spill = point_line_release_spill(num_elements=1000,
start_position=(-72.419992, 41.202120,
0.0),
release_time=start_time,
amount=1000,
substance=test_oil,
units='kg')
spill.amount_uncertainty_scale = 1.0
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=500000, uncertain_factor=2)
print 'adding a wind mover:'
series = np.zeros((5, ), dtype=datetime_value_2d)
series[0] = (start_time, (20, 45))
series[1] = (start_time + timedelta(hours=18), (20, 90))
series[2] = (start_time + timedelta(hours=30), (20, 135))
series[3] = (start_time + timedelta(hours=42), (20, 180))
series[4] = (start_time + timedelta(hours=54), (20, 225))
wind = Wind(timeseries=series, units='m/s', speed_uncertainty_scale=0.05)
model.movers += WindMover(wind)
print 'adding a cats mover:'
c_mover = CatsMover(testdata["lis"]["cats_curr"],
tide=Tide(testdata["lis"]["cats_tide"]))
model.movers += c_mover
model.environment += c_mover.tide
print 'adding Weatherers'
rel_time = model.spills[0].get('release_time')
skim_start = rel_time + timedelta(hours=4)
amount = spill.amount
units = spill.units
# define skimmer/burn cleanup options
skimmer = Skimmer(0.3 * amount,
units=units,
efficiency=0.3,
active_start=skim_start,
active_stop=skim_start + timedelta(hours=4))
# thickness = 1m so area is just 20% of volume
volume = spill.get_mass() / spill.get('substance').get_density()
burn = Burn(0.2 * volume, 1.0, active_start=skim_start, efficiency=.9)
c_disp = ChemicalDispersion(0.1,
efficiency=0.5,
active_start=skim_start,
active_stop=skim_start + timedelta(hours=1))
water_env = Water(311.15)
model.environment += water_env
model.weatherers += [Evaporation(water_env, wind), c_disp, burn, skimmer]
print 'adding outputters'
model.outputters += WeatheringOutput()
if geojson_output:
model.outputters += TrajectoryGeoJsonOutput()
return model
'test save/load functionality'
_json_, zipfile_, _refs = obj.save(saveloc_)
obj2 = obj.__class__.load(zipfile_)
assert obj == obj2
# Wind objects need more work - the data is being written out to file in
# 'r-theta' format accurate to 2 decimal places and in knots.
# All the conversions mean the allclose() check on timeseries fails - xfail
# for now. When loading for a file it works fine, no decimal places stored
# in file for magnitude
@pytest.mark.parametrize("obj", (
Wind(timeseries=(sec_to_date(24 * 3600), (1, 30)),
units='meters per second'),
Evaporation(wind=constant_wind(1., 30.), water=Water(333.0)),
))
def test_serialize_deserialize_wind_objs(saveloc_, obj):
'test serialize/deserialize functionality'
json_ = obj.serialize()
obj2 = obj.__class__.deserialize(json_)
assert obj == obj2
@pytest.mark.parametrize("obj", (
Wind(timeseries=(sec_to_date(24 * 3600), (1, 30)),
units='meters per second'),
Evaporation(wind=constant_wind(1., 30.), water=Water(333.0)),
))
def test_save_load_wind_objs(saveloc_, obj):
inputs = b_class[1]
obj = class_(*inputs, name=name)
assert obj.name == name
obj.name = obj.__class__.__name__
assert obj.name == obj.__class__.__name__
t = datetime(2015, 1, 1, 12, 0)
@pytest.mark.parametrize(
("obj", "make_default_refs", "objvalid"),
[(Wind(timeseries=[(t, (0, 1)), (t + timedelta(10),
(0, 2))], units='m/s'), False, True),
(Evaporation(), False, False), (NaturalDispersion(), False, False),
(Evaporation(), True, True)])
def test_base_validate(obj, make_default_refs, objvalid):
'''
base validate checks wind/water/waves objects are not None. Check these
primarily for weatherers.
'''
obj.make_default_refs = make_default_refs
(out, isvalid) = obj.validate()
print out
print isvalid
assert isvalid is objvalid
assert len(out) > 0
def test_make_default_refs():
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 9, 15, 12, 0)
mapfile = get_datafile(os.path.join(base_dir, './LongIslandSoundMap.BNA'))
gnome_map = MapFromBNA(mapfile, refloat_halflife=6) # hours
# # the image output renderer
# global renderer
# one hour timestep
model = Model(start_time=start_time,
duration=timedelta(hours=48), time_step=3600,
map=gnome_map, uncertain=False, cache_enabled=False)
print 'adding a spill'
et = floating_weathering(substance='FUEL OIL NO.6')
spill = point_line_release_spill(num_elements=1000,
start_position=(-72.419992,
41.202120, 0.0),
release_time=start_time,
amount=1000,
units='kg',
element_type=et)
spill.amount_uncertainty_scale = 1.0
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=500000, uncertain_factor=2)
print 'adding a wind mover:'
series = np.zeros((5, ), dtype=datetime_value_2d)
series[0] = (start_time, (10, 45))
series[1] = (start_time + timedelta(hours=18), (10, 90))
series[2] = (start_time + timedelta(hours=30), (10, 135))
series[3] = (start_time + timedelta(hours=42), (10, 180))
series[4] = (start_time + timedelta(hours=54), (10, 225))
wind = Wind(timeseries=series, units='m/s',
speed_uncertainty_scale=0.5)
model.movers += WindMover(wind)
print 'adding a cats mover:'
curr_file = get_datafile(os.path.join(base_dir, r"./LI_tidesWAC.CUR"))
tide_file = get_datafile(os.path.join(base_dir, r"./CLISShio.txt"))
c_mover = CatsMover(curr_file, tide=Tide(tide_file))
model.movers += c_mover
model.environment += c_mover.tide
print 'adding Weatherers'
water_env = Water(311.15)
model.environment += water_env
model.weatherers += [Evaporation(water_env, wind),
Dispersion(),
Burn(),
Skimmer()]
print 'adding outputters'
model.outputters += WeatheringOutput()
return model