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_Water_init():
w = Water()
assert w.temperature == 300.0
assert w.salinity == 35.0
w = Water(temperature=273, salinity=0)
assert w.temperature == 273.0
assert w.salinity == 0.0
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_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_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_validate_model_env_obj(self, obj_make_default_refs):
'''
test that Model is invalid if make_default_refs is True and referenced
objects are not in model's environment collection
'''
# object is complete but model must contain
(model, waves) = self.make_model_incomplete_waves()
waves.water = Water()
waves.wind = constant_wind(5, 0)
assert len(model.environment) == 1
waves.make_default_refs = obj_make_default_refs
(msgs, isvalid) = model.validate()
print msgs
if obj_make_default_refs:
assert not isvalid
assert len(msgs) > 0
assert ('warning: Model: water not found in environment collection'
in msgs)
assert ('warning: Model: wind not found in environment collection'
in msgs)
else:
assert isvalid
assert len(msgs) == 0
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_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 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 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 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 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 weathering_data_arrays(n_arrays,
water=None,
time_step=15.*60,
element_type=None,
langmuir=False):
'''
function to initialize data_arrays set by WeatheringData. Weatherer tests
can use this function to release elements and initialize data without
defining a model
'''
if water is None:
water = Water()
rqd_weatherers = [WeatheringData(water), FayGravityViscous(water)]
arrays = set()
arrays.update(n_arrays)
for wd in rqd_weatherers:
arrays.update(wd.array_types)
if element_type is None:
element_type = floating(substance=test_oil)
sc = sample_sc_release(num_elements=2,
element_type=element_type,
arr_types=arrays,
time_step=time_step)
for wd in rqd_weatherers:
wd.prepare_for_model_run(sc)
wd.initialize_data(sc, sc.num_released)
return (sc, time_step, rqd_weatherers)
def test_get_emulsification_wind():
wind = constant_wind(3., 0)
water = Water()
w = Waves(wind, water)
print w.get_emulsification_wind(start_time)
assert w.get_emulsification_wind(start_time) == 3.0
def test_sort_order():
'test sort order for Biodegradation weatherer'
wind = constant_wind(15., 0)
waves = Waves(wind, Water())
bio_deg = Biodegradation(waves)
assert weatherer_sort(bio_deg) == 11
def test_Water_get(attr, unit, val, si_val):
w = Water()
setattr(w, attr, val)
w.units[attr] = unit
assert w.get(attr) == si_val
assert w.get(attr, unit) == val
def build_waves_obj(wind_speed, wind_units, direction_deg, temperature):
# also test with lower wind no dispersion
wind = constant_wind(wind_speed, direction_deg, wind_units)
water = Water(temperature=temperature)
waves = Waves(wind, water)
return waves
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 mk_test_objs(cls, water=None):
'''
create SpillContainer and test WeatheringData object test objects so
we can run Skimmer, Burn like a model without using a full on Model
NOTE: Use this function to define class level objects. Other methods
in this class expect sc, and weatherers to be class level objects
'''
# spreading does not need to be initialized correctly for these tests,
# but since we are mocking the model, let's do it correctly
if water is None:
water = Water()
# keep this order
weatherers = [WeatheringData(water), FayGravityViscous(water)]
weatherers.sort(key=weatherer_sort)
sc = SpillContainer()
print "******************"
print "Adding a spill to spill container"
sc.spills += point_line_release_spill(10, (0, 0, 0),
rel_time,
substance=test_oil,
amount=amount,
units='kg',
water=water)
return (sc, weatherers)
def sample_model_weathering(sample_model_fcn,
oil,
temp=311.16,
num_les=10):
model = sample_model_fcn['model']
rel_pos = sample_model_fcn['release_start_pos']
# update model the same way for multiple tests
model.uncertain = False # fixme: with uncertainty, copying spill fails!
model.duration = timedelta(hours=4)
et = gnome.spill.elements.floating(substance=oil)
start_time = model.start_time + timedelta(hours=1)
end_time = start_time + timedelta(seconds=model.time_step*3)
spill = gnome.spill.point_line_release_spill(num_les,
rel_pos,
start_time,
end_release_time=end_time,
element_type=et,
amount=100,
units='kg')
model.spills += spill
# define environment objects that weatherers require
model.environment += [constant_wind(1, 0), Water(), Waves()]
return model
def sample_sc_intrinsic(self, num_elements, rel_time, add_at=None):
'''
initialize Sample SC and WeatheringData object
objects are constructed and prepare_for_model_run() is invoked on all
'''
wd = WeatheringData(Water())
end_time = rel_time + timedelta(hours=1)
spills = [
point_line_release_spill(num_elements, (0, 0, 0),
rel_time,
end_release_time=end_time,
amount=100,
units='kg',
substance=test_oil)
]
sc = SpillContainer()
sc.spills += spills
at = wd.array_types
if add_at is not None:
at.update(add_at)
sc.prepare_for_model_run(at)
# test initialization as well
wd.prepare_for_model_run(sc)
for val in sc.mass_balance.values():
assert val == 0.0
# test initialization as well
return (sc, wd)
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_one_weather(self):
'''
calls one weathering step and checks that we decayed at the expected
rate. Needs more tests with varying half_lives
'''
time_step = 15. * 60
hl = tuple([time_step] * subs.num_components)
weatherer = HalfLifeWeatherer(half_lives=hl)
sc = weathering_data_arrays(weatherer.array_types, Water(),
time_step)[0]
print '\nsc["mass"]:\n', sc['mass']
orig_mc = np.copy(sc['mass_components'])
model_time = rel_time
weatherer.prepare_for_model_run(sc)
weatherer.prepare_for_model_step(sc, time_step, model_time)
weatherer.weather_elements(sc, time_step, model_time)
weatherer.model_step_is_done()
print '\nsc["mass"]:\n', sc['mass']
assert np.allclose(0.5 * orig_mc.sum(1), sc['mass'])
assert np.allclose(0.5 * orig_mc, sc['mass_components'])
def test_exceptions(attr, unit):
w = Water()
with pytest.raises(InvalidUnitError):
w.get(attr, unit)
with pytest.raises(InvalidUnitError):
w.set(attr, 5, unit)
def test_init():
wind = constant_wind(15., 0)
waves = Waves(wind, Water())
bio_deg = Biodegradation(waves)
print(bio_deg.array_types)
assert all([(at in bio_deg.array_types)
for at in ('mass', 'droplet_avg_size')])
def test_not_implemented_in_water():
sample_time = 60 * 60 * 24 * 365 * 30 # seconds
w = Water()
with raises(AttributeError):
w.data_start = sample_time
with raises(AttributeError):
w.data_stop = sample_time
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_properties_in_si(attr, unit, val, exp_si):
'''
set properties in non SI units and check default get() returns it in SI
'''
kw = {attr: val, 'units': {attr: unit}}
w = Water(**kw)
assert getattr(w, attr) == val
assert w.units[attr] == unit
assert w.get(attr) == exp_si
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 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)