def setup_model():
print 'initializing the model'
# start with default time,duration...this will be changed when model is run
model = Model(
) #change to use all defaults and set time_step also in Setup_TAP!!
mapfile = os.path.join(setup.MapFileDir, setup.MapFileName)
print 'adding the map: ', mapfile
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
print 'adding a GridCurrentMover:'
c_mover = GridCurrentMover(filename=setup.curr_fn, extrapolate=True)
model.movers += c_mover
print 'adding a WindMover:'
w = Wind(filename=setup.wind_fn)
w_mover = WindMover(w)
# w_mover = GridWindMover(wind_file=setup.w_filelist)
model.movers += w_mover
if setup.diff_coef is not None:
print 'adding a RandomMover:'
random_mover = RandomMover(diffusion_coef=setup.diff_coef) #in cm/s
model.movers += random_mover
return model
def CurrentsAndWinds(timeStep, start_time, duration, weatheringSteps, mapfile, 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:'
print (data_path, map_path, mapfile)
mapfile = get_datafile(os.path.join(data_path, map_path, mapfile))
model.map = MapFromBNA(mapfile, refloat_halflife=reFloatHalfLife)
print 'adding a renderer'
model.outputters += Renderer(mapfile, output_path, size=(800, 600), output_timestep=timedelta(hours=timestep_outputs))
if save_nc:
nc_outputter = NetCDFOutput('currentsAndWinds_example.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=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)
return model
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_simple_run_with_map():
'''
pretty much all this tests is that the model will run
'''
start_time = datetime(2012, 9, 15, 12, 0)
model = Model()
model.map = gnome.map.MapFromBNA(testmap, refloat_halflife=6) # hours
a_mover = SimpleMover(velocity=(1., 2., 0.))
model.movers += a_mover
assert len(model.movers) == 1
spill = point_line_release_spill(num_elements=10,
start_position=(0., 0., 0.),
release_time=start_time)
model.spills += spill
assert len(model.spills) == 1
model.start_time = spill.release.release_time
# test iterator
for step in model:
print 'just ran time step: %s' % step
assert step['step_num'] == model.current_time_step
# reset and run again
model.reset()
# test iterator is repeatable
for step in model:
print 'just ran time step: %s' % step
assert step['step_num'] == model.current_time_step
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 10, 25, 0, 1)
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=6),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'nyharbor.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = point_line_release_spill(num_elements=1000,
start_position=(-74.15, 40.5, 0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
model.movers += constant_wind_mover(4, 270, units='m/s')
print 'adding a current mover:'
# url is broken, fix and include the following section
# url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml')
# # cf = roms_field('nos.tbofs.fields.n000.20160406.t00z_sgrid.nc')
# cf = GridCurrent.from_netCDF(url)
# renderer.add_grid(cf.grid)
# renderer.delay = 25
# u_mover = PyCurrentMover(cf, default_num_method='Euler')
# model.movers += u_mover
#
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2015, 9, 24, 3, 0)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours = 48),
time_step=3600)
mapfile = get_datafile(os.path.join(base_dir, 'Perfland.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=1, raster_size=1024*1024) # 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, image_size=(800, 600),
output_timestep=timedelta(hours=1),
timestamp_attrib={'size': 'medium', 'color':'uncert_LE'})
renderer.set_timestamp_attrib(format='%a %c')
renderer.graticule.set_DMS(True)
# renderer.viewport = ((-124.25, 47.5), (-122.0, 48.70))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = point_line_release_spill(num_elements=5000,
start_position=(0.0,
0.0,
0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
model.movers += constant_wind_mover(13, 270, units='m/s')
print 'adding a current mover:'
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
#
# # uncertain_time_delay in hours
# c_mover = GridCurrentMover(curr_file)
# c_mover.uncertain_cross = 0 # default is .25
#
# model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2015, 9, 24, 3, 0)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours = 48),
time_step=3600)
mapfile = get_datafile(os.path.join(base_dir, 'Perfland.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=1, raster_size=1024*1024) # 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, image_size=(800, 600),
output_timestep=timedelta(hours=1),
timestamp_attrib={'size': 'medium', 'color':'uncert_LE'})
renderer.set_timestamp_attrib(format='%a %c')
renderer.graticule.set_DMS(True)
# renderer.viewport = ((-124.25, 47.5), (-122.0, 48.70))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = point_line_release_spill(num_elements=5000,
start_position=(0.0,
0.0,
0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
model.movers += constant_wind_mover(13, 270, units='m/s')
print 'adding a current mover:'
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
#
# # uncertain_time_delay in hours
# c_mover = GridCurrentMover(curr_file)
# c_mover.uncertain_cross = 0 # default is .25
#
# model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2013, 1, 1, 1) # data starts at 1:00 instead of 0:00
model = Model(start_time=start_time, duration=timedelta(days=1),
time_step=900, uncertain=False)
try:
mapfile = get_datafile(os.path.join(base_dir, './pearl_harbor.bna'))
except HTTPError:
print ('Could not download Pearl Harbor data from server - '
'returning empty model')
return model
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=1) # hours
#
# Add the outputters -- render to images, and save out as netCDF
#
print 'adding renderer and netcdf output'
model.outputters += Renderer(mapfile, images_dir, size=(800, 600))
netcdf_output_file = os.path.join(base_dir, 'pearl_harbor_output.nc')
scripting.remove_netcdf(netcdf_output_file)
model.outputters += NetCDFOutput(netcdf_output_file, which_data='all')
# #
# # Set up the movers:
# #
print 'adding a random mover:'
model.movers += RandomMover(diffusion_coef=10000)
print 'adding a wind mover:'
series = np.zeros((3, ), dtype=datetime_value_2d)
series[0] = (start_time, (4, 180))
series[1] = (start_time + timedelta(hours=12), (2, 270))
series[2] = (start_time + timedelta(hours=24), (4, 180))
w_mover = WindMover(Wind(timeseries=series, units='knots'))
model.movers += w_mover
model.environment += w_mover.wind
print 'adding a current mover:'
# this is CH3D currents
curr_file = os.path.join(base_dir, r"./ch3d2013.nc")
topology_file = os.path.join(base_dir, r"./PearlHarborTop.dat")
model.movers += GridCurrentMover(curr_file, topology_file)
# #
# # Add a spill (sources of elements)
# #
print 'adding spill'
model.spills += point_line_release_spill(num_elements=1000,
start_position=(-157.97064,
21.331524, 0.0),
release_time=start_time)
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2015, 9, 24, 1, 1)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=48),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'columbia_river.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(600, 1200))
renderer.graticule.set_DMS(True)
# renderer.viewport = ((-123.35, 45.6), (-122.68, 46.13))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = point_line_release_spill(num_elements=1000,
start_position=(-122.625, 45.609, 0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
# model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
model.movers += constant_wind_mover(0.5, 0, units='m/s')
print 'adding a current mover:'
curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# uncertain_time_delay in hours
# vec_field = TriVectorField('COOPSu_CREOFS24.nc')
# u_mover = UGridCurrentMover(vec_field)
c_mover = GridCurrentMover(curr_file)
# c_mover.uncertain_cross = 0 # default is .25
# model.movers += u_mover
model.movers += c_mover
model.save
return model
def make_model(images_dir=os.path.join(base_dir, "images")):
print "initializing the model"
# set up the modeling environment
start_time = datetime(2004, 12, 31, 13, 0)
model = Model(start_time=start_time, duration=timedelta(days=3), time_step=30 * 60, uncertain=False)
print "adding the map"
model.map = GnomeMap() # this is a "water world -- no land anywhere"
# renderere is only top-down view on 2d -- but it's something
renderer = Renderer(output_dir=images_dir, size=(1024, 768), output_timestep=timedelta(hours=1))
renderer.viewport = ((-0.15, -0.35), (0.15, 0.35))
print "adding outputters"
model.outputters += renderer
# Also going to write the results out to a netcdf file
netcdf_file = os.path.join(base_dir, "script_plume.nc")
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(
netcdf_file,
which_data="most",
# output most of the data associated with the elements
output_timestep=timedelta(hours=2),
)
print "adding Horizontal and Vertical diffusion"
# Horizontal Diffusion
# model.movers += RandomMover(diffusion_coef=5)
# vertical diffusion (different above and below the mixed layer)
model.movers += RandomVerticalMover(
vertical_diffusion_coef_above_ml=5, vertical_diffusion_coef_below_ml=0.11, mixed_layer_depth=10
)
print "adding Rise Velocity"
# droplets rise as a function of their density and radius
model.movers += RiseVelocityMover()
print "adding a circular current and eastward current"
# This is .3 m/s south
model.movers += PyGridCurrentMover(current=vg, default_num_method="Trapezoid", extrapolate=True)
model.movers += SimpleMover(velocity=(0.0, -0.1, 0.0))
# Now to add in the TAMOC "spill"
print "Adding TAMOC spill"
model.spills += tamoc_spill.TamocSpill(
release_time=start_time,
start_position=(0, 0, 1000),
num_elements=1000,
end_release_time=start_time + timedelta(days=1),
name="TAMOC plume",
TAMOC_interval=None, # how often to re-run TAMOC
)
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2015, 9, 24, 1, 1)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours = 48),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'columbia_river.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(600, 1200))
renderer.graticule.set_DMS(True)
# renderer.viewport = ((-123.35, 45.6), (-122.68, 46.13))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = point_line_release_spill(num_elements=5000,
start_position=(-122.625,
45.609,
0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=5000)
print 'adding a wind mover:'
# model.movers += constant_wind_mover(8, 90, units='m/s')
print 'adding a current mover:'
curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# uncertain_time_delay in hours
c_mover = GridCurrentMover(curr_file)
c_mover.uncertain_cross = 0 # default is .25
model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2006, 3, 31, 20, 0)
model = Model(start_time=start_time,
duration=timedelta(days=3),
time_step=30 * 60,
uncertain=True)
print 'adding the map'
mapfile = get_datafile(os.path.join(base_dir, 'coastSF.bna'))
model.map = MapFromBNA(mapfile, refloat_halflife=1) # seconds
renderer = Renderer(mapfile,
images_dir,
image_size=(800, 600),
draw_ontop='forecast')
renderer.viewport = ((-124.5, 37.), (-120.5, 39))
print 'adding outputters'
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_sf_bay.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding a spill'
spill = point_line_release_spill(
num_elements=1000,
start_position=(-123.57152, 37.369436, 0.0),
release_time=start_time,
substance=NonWeatheringSubstance(windage_range=(0.01, .04))
#element_type=floating(windage_range=(0.01,
# 0.04)
# )
)
model.spills += spill
# print 'adding a RandomMover:'
# r_mover = gnome.movers.RandomMover(diffusion_coef=50000)
# model.movers += r_mover
print 'adding a grid wind mover:'
wind_file = get_datafile(os.path.join(base_dir, 'WindSpeedDirSubset.nc'))
topology_file = get_datafile(
os.path.join(base_dir, 'WindSpeedDirSubsetTop.dat'))
w_mover = GridWindMover(wind_file, topology_file)
# w_mover.uncertain_time_delay = 6
# w_mover.uncertain_duration = 6
w_mover.uncertain_speed_scale = 1
w_mover.uncertain_angle_scale = 0.2 # default is .4
w_mover.wind_scale = 2
model.movers += w_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2006, 3, 31, 20, 0)
model = Model(start_time=start_time,
duration=timedelta(days=3), time_step=30 * 60,
uncertain=True)
print 'adding the map'
mapfile = get_datafile(os.path.join(base_dir, './coastSF.bna'))
model.map = MapFromBNA(mapfile, refloat_halflife=1) # seconds
renderer = Renderer(mapfile, images_dir, size=(800, 600),
draw_ontop='forecast')
renderer.viewport = ((-124.5, 37.), (-120.5, 39))
print 'adding outputters'
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_sf_bay.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding a spill'
spill = point_line_release_spill(num_elements=1000,
start_position=(-123.57152, 37.369436,
0.0),
release_time=start_time,
element_type=floating(windage_range=(0.01,
0.04)
)
)
model.spills += spill
# print 'adding a RandomMover:'
# r_mover = gnome.movers.RandomMover(diffusion_coef=50000)
# model.movers += r_mover
print 'adding a grid wind mover:'
wind_file = get_datafile(os.path.join(base_dir, r"./WindSpeedDirSubset.nc")
)
topology_file = get_datafile(os.path.join(base_dir,
r"./WindSpeedDirSubsetTop.dat"))
w_mover = GridWindMover(wind_file, topology_file)
#w_mover.uncertain_time_delay = 6
#w_mover.uncertain_duration = 6
w_mover.uncertain_speed_scale = 1
w_mover.uncertain_angle_scale = 0.2 # default is .4
w_mover.wind_scale = 2
model.movers += w_mover
return model
def make_models():
print 'initializing the model'
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
models = []
start_time = datetime(2012, 10, 27, 0, 30)
duration_hrs=23
time_step=450
num_steps = duration_hrs * 3600 / time_step
names = [
'Euler',
'Trapezoid',
'RK4',
]
mapfile = get_datafile(os.path.join(base_dir, 'long_beach.bna'))
print 'gen map'
map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
fn = ('00_dir_roms_display.ncml.nc4')
curr = GridCurrent.from_netCDF(filename=fn)
models = []
for method in names:
mod = Model(start_time=start_time,
duration=timedelta(hours=duration_hrs),
time_step=time_step)
mod.map = map
spill = point_line_release_spill(num_elements=1000,
start_position=(-74.1,
39.7525,
0.0),
release_time=start_time)
mod.spills += spill
mod.movers += RandomMover(diffusion_coef=100)
mod.movers += PyGridCurrentMover(current=curr, default_num_method=method)
images_dir = method + '-' + str(time_step / 60) + 'min-' + str(num_steps) + 'steps'
renderer = Renderer(mapfile, images_dir, image_size=(1024, 768))
renderer.delay = 25
# renderer.add_grid(curr.grid)
mod.outputters += renderer
netCDF_fn = os.path.join(base_dir, images_dir + '.nc')
mod.outputters += NetCDFOutput(netCDF_fn, which_data='all')
models.append(mod)
print 'returning models'
return models
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 make_model(base_dir='.'):
#,images_dir=os.path.join(base_dir, 'images',gdat_dir='/data/dylan/ArcticTAP/data_gnome/ROMS_h2ouv/')):
print 'initializing the model'
print base_dir
start_time = datetime(1985, 1, 1, 13, 31)
# start with generic times...this will be changed when model is run
model = Model(start_time=start_time, time_step=setup.time_step)
mapfile = get_datafile(os.path.join(base_dir, setup.MapFileName))
print mapfile
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
return model
def make_model(base_dir='.'):
#,images_dir=os.path.join(base_dir, 'images',gdat_dir='/data/dylan/ArcticTAP/data_gnome/ROMS_h2ouv/')):
print 'initializing the model'
print base_dir
start_time = datetime(1985, 1, 1, 13, 31)
# start with generic times...this will be changed when model is run
model = Model(start_time=start_time,
duration=timedelta(hours=96),
time_step=120*60)
mapfile = get_datafile(os.path.join(base_dir, 'arctic_coast3.bna'))
print mapfile
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
return model
def test_simple_run_rewind():
'''
Pretty much all this tests is that the model will run
and the seed is set during first run, then set correctly
after it is rewound and run again
'''
start_time = datetime(2012, 9, 15, 12, 0)
model = Model()
model.map = gnome.map.GnomeMap()
a_mover = SimpleMover(velocity=(1., 2., 0.))
model.movers += a_mover
assert len(model.movers) == 1
spill = point_line_release_spill(num_elements=10,
start_position=(0., 0., 0.),
release_time=start_time)
model.spills += spill
assert len(model.spills) == 1
# model.add_spill(spill)
model.start_time = spill.release.release_time
# test iterator
for step in model:
print 'just ran time step: %s' % model.current_time_step
assert step['step_num'] == model.current_time_step
pos = np.copy(model.spills.LE('positions'))
# rewind and run again:
print 'rewinding'
model.rewind()
# test iterator is repeatable
for step in model:
print 'just ran time step: %s' % model.current_time_step
assert step['step_num'] == model.current_time_step
assert np.all(model.spills.LE('positions') == pos)
def test_simple_run_rewind():
'''
Pretty much all this tests is that the model will run
and the seed is set during first run, then set correctly
after it is rewound and run again
'''
start_time = datetime(2012, 9, 15, 12, 0)
model = Model()
model.map = gnome.map.GnomeMap()
a_mover = SimpleMover(velocity=(1., 2., 0.))
model.movers += a_mover
assert len(model.movers) == 1
spill = point_line_release_spill(num_elements=10,
start_position=(0., 0., 0.),
release_time=start_time)
model.spills += spill
assert len(model.spills) == 1
# model.add_spill(spill)
model.start_time = spill.release.release_time
# test iterator
for step in model:
print 'just ran time step: %s' % model.current_time_step
assert step['step_num'] == model.current_time_step
pos = np.copy(model.spills.LE('positions'))
# rewind and run again:
print 'rewinding'
model.rewind()
# test iterator is repeatable
for step in model:
print 'just ran time step: %s' % model.current_time_step
assert step['step_num'] == model.current_time_step
assert np.all(model.spills.LE('positions') == pos)
def only_Winds(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:'
mapfile = get_datafile(os.path.join(data_path, map_path, 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=timestep_outputs))
if save_nc:
nc_outputter = NetCDFOutput(netcdf_file, which_data='most', 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 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)
return model
def test_simple_run_with_map():
"""
pretty much all this tests is that the model will run
"""
start_time = datetime(2012, 9, 15, 12, 0)
model = Model()
model.map = gnome.map.MapFromBNA(testmap, refloat_halflife=6) # hours
a_mover = SimpleMover(velocity=(1., 2., 0.))
model.movers += a_mover
assert len(model.movers) == 1
spill = PointLineSource(num_elements=10,
start_position=(0., 0., 0.), release_time=start_time)
model.spills += spill
# model.add_spill(spill)
assert len(model.spills) == 1
model.start_time = spill.release_time
# test iterator:
for step in model:
print 'just ran time step: %s' % step
# reset and run again:
model.reset()
# test iterator:
for step in model:
print 'just ran time step: %s' % step
assert True
def setup_model():
print 'initializing the model'
# start with default time,duration...this will be changed when model is run
model = Model() #change to use all defaults and set time_step also in Setup_TAP!!
mapfile = os.path.join(setup.MapFileDir, setup.MapFileName)
print 'adding the map: ', mapfile
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
print 'adding a GridCurrentMover:'
c_mover = GridCurrentMover(filename=setup.curr_fn,topology_file=setup.curr_topo)
model.movers += c_mover
# print 'adding a GridWindMover:'
# w_mover = GridWindMover(wind_file=setup.w_filelist,topology_file=setup.w_Topology)
# w_mover = GridWindMover(wind_file=setup.w_filelist)
# model.movers += w_mover
if setup.diff_coef is not None:
print 'adding a RandomMover:'
random_mover = RandomMover(diffusion_coef=setup.diff_coef) #in cm/s
model.movers += random_mover
return model
def test_simple_run_with_map():
'''
pretty much all this tests is that the model will run
'''
start_time = datetime(2012, 9, 15, 12, 0)
model = Model()
model.map = gnome.map.MapFromBNA(testdata['MapFromBNA']['testmap'],
refloat_halflife=6) # hours
a_mover = SimpleMover(velocity=(1., 2., 0.))
model.movers += a_mover
assert len(model.movers) == 1
spill = point_line_release_spill(num_elements=10,
start_position=(0., 0., 0.),
release_time=start_time)
model.spills += spill
assert len(model.spills) == 1
model.start_time = spill.release.release_time
# test iterator
for step in model:
print 'just ran time step: %s' % step
assert step['step_num'] == model.current_time_step
# reset and run again
model.reset()
# test iterator is repeatable
for step in model:
print 'just ran time step: %s' % step
assert step['step_num'] == model.current_time_step
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(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2016, 4, 5, 18, 0)
model = Model(start_time=start_time,
duration=timedelta(hours=12),
time_step=.25 * 3600)
mapfile = (os.path.join(base_dir, 'coast.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = point_line_release_spill(num_elements=500,
start_position=(-82.73888, 27.5475, 0.0),
release_time=start_time,
end_release_time=start_time +
timedelta(hours=24))
spill2 = point_line_release_spill(num_elements=500,
start_position=(-82.73888, 27.545, 0.0),
release_time=start_time,
end_release_time=start_time +
timedelta(hours=24))
spill3 = point_line_release_spill(num_elements=500,
start_position=(-82.73888, 27.5425, 0.0),
release_time=start_time,
end_release_time=start_time +
timedelta(hours=24))
spill4 = point_line_release_spill(num_elements=500,
start_position=(-82.73988, 27.5475, 0.0),
release_time=start_time,
end_release_time=start_time +
timedelta(hours=24))
spill5 = point_line_release_spill(num_elements=500,
start_position=(-82.73988, 27.5450, 0.0),
release_time=start_time,
end_release_time=start_time +
timedelta(hours=24))
spill6 = point_line_release_spill(num_elements=500,
start_position=(-82.73988, 27.5425, 0.0),
release_time=start_time,
end_release_time=start_time +
timedelta(hours=24))
model.spills += spill1
model.spills += spill2
model.spills += spill3
model.spills += spill4
model.spills += spill5
model.spills += spill6
model.spills._spill_container.spills.remove(0)
print 'adding a current mover:'
fn = 'nos.tbofs.fields.n000.20160406.t00z_sgrid.nc'
#fn = 'dbofs_newFormat.nc'
cf = GridCurrent.from_netCDF(filename=fn)
u_mover = PyGridCurrentMover(cf, extrapolate=True)
#u_mover = GridCurrentMover(fn)
renderer.add_grid(cf.grid)
# renderer.add_vec_prop(cf)
model.movers += u_mover
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 10, 25, 0, 1)
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=6),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'nyharbor.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = point_line_release_spill(num_elements=1000,
start_position=(-74.15,
40.5,
0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
model.movers += constant_wind_mover(4, 270, units='m/s')
print 'adding a current mover:'
url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml')
# cf = roms_field('nos.tbofs.fields.n000.20160406.t00z_sgrid.nc')
cf = GridCurrent.from_netCDF(url)
renderer.add_grid(cf.grid)
renderer.delay = 25
u_mover = PyGridCurrentMover(cf, default_num_method='Euler')
model.movers += u_mover
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(1985, 1, 1, 13, 31)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=4),
time_step=7200)
# mapfile = get_datafile(os.path.join(base_dir, 'ak_arctic.bna'))
mapfile = get_datafile('arctic_coast3.bna')
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
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),
# spill1 = point_line_release_spill(num_elements=10000,
# start_position=(-163.75,
# 69.75,
# 0.0),
# release_time=start_time)
#
spill1 = point_line_release_spill(num_elements=50000,
start_position=(196.25,
69.75,
0.0),
release_time=start_time)
model.spills += spill1
# model.spills += spill2
print 'adding a wind mover:'
# model.movers += constant_wind_mover(0.5, 0, units='m/s')
print 'adding a current mover:'
fn = ['arctic_avg2_0001_gnome.nc',
'arctic_avg2_0002_gnome.nc']
# fn = ['C:\\Users\\jay.hennen\\Documents\\Code\\pygnome\\py_gnome\\scripts\\script_TAP\\arctic_avg2_0001_gnome.nc',
# 'C:\\Users\\jay.hennen\\Documents\\Code\\pygnome\\py_gnome\\scripts\\script_TAP\\arctic_avg2_0002_gnome.nc']
gt = {'node_lon': 'lon',
'node_lat': 'lat'}
# fn='arctic_avg2_0001_gnome.nc'
wind_method = 'Euler'
method = 'RK2'
print 'adding outputters'
# 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, image_size=(1024, 768))
model.outputters += renderer
netcdf_file = os.path.join(base_dir, str(model.time_step / 60) + method + '.nc')
scripting.remove_netcdf(netcdf_file)
print 'adding movers'
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'loading entire current data'
ice_aware_curr = IceAwareCurrent.from_netCDF(filename=fn,
grid_topology=gt)
# env1 = get_env_from_netCDF(filename)
# mov = PyCurrentMover.from_netCDF(filename)
ice_aware_curr.ice_velocity.variables[0].dimension_ordering = ['time', 'x', 'y']
ice_aware_wind = IceAwareWind.from_netCDF(filename=fn,
ice_velocity=ice_aware_curr.ice_velocity,
ice_concentration=ice_aware_curr.ice_concentration,
grid=ice_aware_curr.grid)
curr = GridCurrent.from_netCDF(filename=fn)
# GridCurrent.is_gridded()
# import pprint as pp
# from gnome.utilities.orderedcollection import OrderedCollection
# model.environment = OrderedCollection(dtype=Environment)
# model.environment.add(ice_aware_curr)
# from gnome.environment import WindTS
print 'loading entire wind data'
# i_c_mover = PyCurrentMover(current=ice_aware_curr)
# i_c_mover = PyCurrentMover(current=ice_aware_curr, default_num_method='Euler')
i_c_mover = PyCurrentMover(current=ice_aware_curr, default_num_method=method, extrapolate=True)
i_w_mover = PyWindMover(wind=ice_aware_wind, default_num_method=wind_method)
# ice_aware_curr.grid.node_lon = ice_aware_curr.grid.node_lon[:]-360
# ice_aware_curr.grid.build_celltree()
model.movers += i_c_mover
model.movers += i_w_mover
print 'adding an IceAwareRandomMover:'
model.movers += IceAwareRandomMover(ice_concentration=ice_aware_curr.ice_concentration,
diffusion_coef=1000)
# renderer.add_grid(ice_aware_curr.grid)
# renderer.add_vec_prop(ice_aware_curr)
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
# model.environment.add(WindTS.constant(10, 300))
# print('Saving')
# model.environment[0].ice_velocity.variables[0].serialize()
# IceVelocity.deserialize(model.environment[0].ice_velocity.serialize())
# model.save('.')
# from gnome.persist.save_load import load
# print('Loading')
# model2 = load('./Model.zip')
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
# set up the modeling environment
start_time = datetime(2016, 9, 18, 1, 0)
model = Model(start_time=start_time,
duration=timedelta(days=3),
time_step=30 * 60,
uncertain=False)
print 'adding the map'
model.map = GnomeMap() # this is a "water world -- no land anywhere"
# renderere is only top-down view on 2d -- but it's something
renderer = Renderer(output_dir=images_dir,
size=(1024, 768),
output_timestep=timedelta(hours=1),
)
renderer.viewport = ((-87.095, 27.595), (-87.905, 28.405))
print 'adding outputters'
model.outputters += renderer
# Also going to write the results out to a netcdf file
netcdf_file = os.path.join(base_dir, 'gulf_tamoc.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file,
which_data='most',
# output most of the data associated with the elements
output_timestep=timedelta(hours=2))
print "adding Horizontal and Vertical diffusion"
# Horizontal Diffusion
model.movers += RandomMover(diffusion_coef=100000)
# vertical diffusion (different above and below the mixed layer)
model.movers += RandomVerticalMover(vertical_diffusion_coef_above_ml=50,
vertical_diffusion_coef_below_ml=10,
horizontal_diffusion_coef_above_ml=100000,
horizontal_diffusion_coef_below_ml=100,
mixed_layer_depth=10)
print 'adding Rise Velocity'
# droplets rise as a function of their density and radius
model.movers += TamocRiseVelocityMover()
print 'adding the 3D current mover'
gc = GridCurrent.from_netCDF('HYCOM_3d.nc')
model.movers += GridCurrentMover('HYCOM_3d.nc')
# model.movers += SimpleMover(velocity=(0., 0, 0.))
# model.movers += constant_wind_mover(5, 315, units='knots')
# Wind from a buoy
w = Wind(filename='KIKT.osm')
model.movers += WindMover(w)
# Now to add in the TAMOC "spill"
print "Adding TAMOC spill"
model.spills += tamoc_spill.TamocSpill(release_time=start_time,
start_position=(-87.5, 28.0, 2000),
num_elements=30000,
end_release_time=start_time + timedelta(days=2),
name='TAMOC plume',
TAMOC_interval=None, # how often to re-run TAMOC
)
model.spills[0].data_sources['currents'] = gc
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
# set up the modeling environment
start_time = datetime(2016, 9, 23, 0, 0)
model = Model(start_time=start_time,
duration=timedelta(days=2),
time_step=30 * 60,
uncertain=False)
print 'adding the map'
model.map = GnomeMap() # this is a "water world -- no land anywhere"
# renderere is only top-down view on 2d -- but it's something
renderer = Renderer(output_dir=images_dir,
image_size=(1024, 768),
output_timestep=timedelta(hours=1),
)
renderer.viewport = ((196.14, 71.89), (196.18, 71.93))
print 'adding outputters'
model.outputters += renderer
# Also going to write the results out to a netcdf file
netcdf_file = os.path.join(base_dir, 'script_arctic_plume.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file,
which_data='most',
# output most of the data associated with the elements
output_timestep=timedelta(hours=2))
print "adding Horizontal and Vertical diffusion"
# Horizontal Diffusion
model.movers += RandomMover(diffusion_coef=500)
# vertical diffusion (different above and below the mixed layer)
model.movers += RandomMover3D(vertical_diffusion_coef_above_ml=5,
vertical_diffusion_coef_below_ml=.11,
mixed_layer_depth=10)
print 'adding Rise Velocity'
# droplets rise as a function of their density and radius
model.movers += TamocRiseVelocityMover()
print 'adding a circular current and eastward current'
fn = 'hycom_glb_regp17_2016092300_subset.nc'
fn_ice = 'hycom-cice_ARCu0.08_046_2016092300_subset.nc'
iconc = IceConcentration.from_netCDF(filename=fn_ice)
ivel = IceVelocity.from_netCDF(filename=fn_ice, grid = iconc.grid)
ic = IceAwareCurrent.from_netCDF(ice_concentration = iconc, ice_velocity= ivel, filename=fn)
model.movers += PyCurrentMover(current = ic)
model.movers += SimpleMover(velocity=(0., 0., 0.))
model.movers += constant_wind_mover(20, 315, units='knots')
# Now to add in the TAMOC "spill"
print "Adding TAMOC spill"
model.spills += tamoc_spill.TamocSpill(release_time=start_time,
start_position=(196.16, 71.91, 40.0),
num_elements=1000,
end_release_time=start_time + timedelta(days=1),
name='TAMOC plume',
TAMOC_interval=None, # how often to re-run TAMOC
)
model.spills[0].data_sources['currents'] = ic
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 10, 25, 0, 1)
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=24),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'nyharbor.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = point_line_release_spill(num_elements=1000,
start_position=(-74.15,
40.5,
0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
# model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
series = []
for i in [(1, (5, 90)), (7, (5, 180)), (13, (5, 270)), (19, (5, 0)), (25, (5, 90))]:
series.append((start_time + timedelta(hours=i[0]), i[1]))
wind1 = WindTS.constant_wind('wind1', 5, 270, 'knots')
wind2 = WindTS(timeseries = series, units='knots', extrapolate=True)
wind = Wind(timeseries=series, units='knots')
model.movers += PyWindMover(wind=wind2)
# model.movers += WindMover(wind)
# print 'adding a current mover:'
#
# url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml')
# # cf = roms_field('nos.tbofs.fields.n000.20160406.t00z_sgrid.nc')
# cf = roms_field(url)
# cf.set_appearance(on=True)
# renderer.grids += [cf]
# renderer.delay = 25
# u_mover = UGridCurrentMover(cf)
# model.movers += u_mover
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 10, 25, 0, 1)
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=2),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'nyharbor.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_ny_plume.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding two spills'
# Break the spill into two spills, first with the larger droplets
# and second with the smaller droplets.
# Split the total spill volume (100 m^3) to have most
# in the larger droplet spill.
# Smaller droplets start at a lower depth than larger
end_time = start_time + model.duration
# wd = WeibullDistribution(alpha=1.8,
# lambda_=.00456,
# min_=.0002) # 200 micron min
#
# spill = subsurface_plume_spill(num_elements=10,
# start_position=(-74.15,
# 40.5,
# 7.2),
# release_time=start_time,
# distribution=wd,
# amount=90, # default volume_units=m^3
# units='m^3',
# end_release_time=end_time,
# density=600)
#
# model.spills += spill
# wd = WeibullDistribution(alpha=1.8,
# lambda_=.00456,
# max_=.0002) # 200 micron max
wd = UniformDistribution(low=.0002,
high=.0002)
spill = point_line_release_spill(num_elements=10, amount=90,
units='m^3',
start_position=(-74.15,
40.5,
7.2),
release_time=start_time,
element_type=plume(distribution=wd,
substance_name='ALASKA NORTH SLOPE (MIDDLE PIPELINE)')
)
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a RiseVelocityMover:'
model.movers += RiseVelocityMover()
print 'adding a RandomVerticalMover:'
# model.movers += RandomVerticalMover(vertical_diffusion_coef_above_ml=5,
# vertical_diffusion_coef_below_ml=.11,
# mixed_layer_depth=10)
url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml')
gc = GridCurrent.from_netCDF(url)
u_mover = PyGridCurrentMover(gc, default_num_method='Trapezoid')
model.movers += u_mover
# print 'adding a wind mover:'
# series = np.zeros((2, ), dtype=gnome.basic_types.datetime_value_2d)
# series[0] = (start_time, (30, 90))
# series[1] = (start_time + timedelta(hours=23), (30, 90))
# wind = Wind(timeseries=series, units='knot')
#
# default is .4 radians
# w_mover = gnome.movers.WindMover(wind, uncertain_angle_scale=0)
#
# model.movers += w_mover
print 'adding a simple mover:'
# s_mover = SimpleMover(velocity=(0.0, -.3, 0.0))
# model.movers += s_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
# set up the modeling environment
start_time = datetime(2016, 9, 23, 0, 0)
model = Model(start_time=start_time,
duration=timedelta(days=2),
time_step=30 * 60,
uncertain=False)
print 'adding the map'
model.map = GnomeMap() # this is a "water world -- no land anywhere"
# renderere is only top-down view on 2d -- but it's something
renderer = Renderer(output_dir=images_dir,
image_size=(1024, 768),
output_timestep=timedelta(hours=1),
)
renderer.viewport = ((196.14, 71.89), (196.18, 71.93))
print 'adding outputters'
model.outputters += renderer
# Also going to write the results out to a netcdf file
netcdf_file = os.path.join(base_dir, 'script_arctic_plume.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file,
which_data='most',
# output most of the data associated with the elements
output_timestep=timedelta(hours=2))
print "adding Horizontal and Vertical diffusion"
# Horizontal Diffusion
model.movers += RandomMover(diffusion_coef=500)
# vertical diffusion (different above and below the mixed layer)
model.movers += RandomVerticalMover(vertical_diffusion_coef_above_ml=5,
vertical_diffusion_coef_below_ml=.11,
mixed_layer_depth=10)
print 'adding Rise Velocity'
# droplets rise as a function of their density and radius
model.movers += TamocRiseVelocityMover()
print 'adding a circular current and eastward current'
fn = 'hycom_glb_regp17_2016092300_subset.nc'
fn_ice = 'hycom-cice_ARCu0.08_046_2016092300_subset.nc'
iconc = IceConcentration.from_netCDF(filename=fn_ice)
ivel = IceVelocity.from_netCDF(filename=fn_ice, grid = iconc.grid)
ic = IceAwareCurrent.from_netCDF(ice_concentration = iconc, ice_velocity= ivel, filename=fn)
model.movers += PyCurrentMover(current = ic)
model.movers += SimpleMover(velocity=(0., 0., 0.))
model.movers += constant_wind_mover(20, 315, units='knots')
# Now to add in the TAMOC "spill"
print "Adding TAMOC spill"
model.spills += tamoc_spill.TamocSpill(release_time=start_time,
start_position=(196.16, 71.91, 40.0),
num_elements=1000,
end_release_time=start_time + timedelta(days=1),
name='TAMOC plume',
TAMOC_interval=None, # how often to re-run TAMOC
)
model.spills[0].data_sources['currents'] = ic
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2015, 9, 24, 1, 1)
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=47),
time_step=300)
mapfile = get_datafile(os.path.join(base_dir, 'columbia_river.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(600, 1200))
renderer.delay=15
# renderer.viewport = ((-123.35, 45.6), (-122.68, 46.13))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = continuous_release_spill(initial_elements=10000,
num_elements=400,
start_position=(-122.625,
45.609,
0.0),
release_time=start_time,
end_position=(-122.6, 45.605, 0.0),
end_release_time=start_time + timedelta(seconds=36000))
model.spills += spill1
print 'adding a RandomMover:'
# model.movers += RandomMover(diffusion_coef=10000)
print 'adding a wind mover:'
series = []
for i in [(1, (5, 90)), (7, (5, 180)), (13, (5, 270)), (19, (5, 0)), (25, (5, 90))]:
series.append((start_time + timedelta(hours=i[0]), i[1]))
wind1 = WindTS.constant_wind('wind1', 0.5, 0, 'm/s')
wind2 = WindTS(timeseries = series, units='knots', extrapolate=True)
# wind = Wind(timeseries=series, units='knots')
model.movers += PyWindMover(wind=wind1)
print 'adding a current mover:'
# url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml')
# test = GridCurrent.from_netCDF(name='gc1', filename=url)
curr_file = get_datafile('COOPSu_CREOFS24.nc')
curr = GridCurrent.from_netCDF(name='gc2', filename=curr_file,)
c_mover = PyGridCurrentMover(curr, extrapolate = True, default_num_method='Trapezoid')
# renderer.add_grid(curr.grid)
# renderer.add_vec_prop(curr)
model.movers += c_mover
print 'adding a random mover'
model.movers += RandomMover(diffusion_coef=1000)
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
def main(RootDir, Data_Dir, StartSite, RunSite, NumStarts, RunStarts,
ReleaseLength, TrajectoryRunLength, StartTimeFiles, TrajectoriesPath,
NumLEs, MapFileName, refloat, current_files, wind_files,
diffusion_coef, model_timestep, windage_range, windage_persist,
OutputTimestep):
timingRecord = open(os.path.join(RootDir, "timing.txt"), "w")
count = len(StartTimeFiles) * len(RunStarts)
timingRecord.write("This file tracks the time to process " + str(count) +
" gnome runs")
# model timing
release_duration = timedelta(hours=ReleaseLength)
run_time = timedelta(hours=TrajectoryRunLength)
# initiate model
model = Model(duration=run_time, time_step=model_timestep, uncertain=False)
# determine boundary for model
print "Adding the map:", MapFileName
mapfile = get_datafile(os.path.join(Data_Dir, MapFileName))
# model.map = MapFromBNA(mapfile, refloat_halflife=refloat) no, model map needs to inclde mudflats. later
# loop through seasons
for Season in StartTimeFiles:
timer1 = datetime.now()
SeasonName = Season[1]
start_times = open(Season[0], 'r').readlines()[:NumStarts]
SeasonTrajDir = os.path.join(RootDir, TrajectoriesPath, SeasonName)
if not os.path.isdir(SeasonTrajDir):
print "Creating directory: ", SeasonTrajDir
make_dir(SeasonTrajDir)
print " Season:", SeasonName
# get and parse start times in this season
start_dt = []
for start_time in start_times:
start_time = [int(i) for i in start_time.split(',')]
start_time = datetime(start_time[0], start_time[1], start_time[2],
start_time[3], start_time[4])
start_dt.append(start_time)
## loop through start times
for time_idx in RunStarts:
timer2 = datetime.now()
gc.collect()
model.movers.clear()
## set the start location
start_time = start_dt[time_idx]
end_time = start_time + run_time
model.start_time = start_time
print " ", start_time, "to", end_time
## get a list of the only data files needed for the start time (less data used)
## note: requires data files in year increments
#Todo: needs fixing before real run
years = range(start_time.year, end_time.year + 1)
years = [str(i) for i in years]
wind = [s for s in wind_files if any(xs in s for xs in years)]
current = [
s for s in current_files if any(xs in s for xs in years)
]
#Todo: add mudflats. Does it work like this?
topology = {'node_lon': 'x', 'node_lat': 'y'}
## add wind movers
w_mover = PyWindMover(filename=wind)
model.movers += w_mover
## add current movers
current_mover = gs.GridCurrent.from_netCDF(current,
grid_topology=topology)
c_mover = PyCurrentMover(current=current_mover)
model.movers += c_mover
tideflat = Matroos_Mudflats(current, grid_topology=topology)
land_map = gs.MapFromBNA(mapfile)
model.map = TideflatMap(land_map, tideflat)
## add diffusion
model.movers += RandomMover(diffusion_coef=diffusion_coef)
## loop through start locations
timer3 = datetime.now()
#Todo: can it deal with the test.location.txt file??
start_position = [float(i) for i in StartSite.split(',')]
OutDir = os.path.join(RootDir, TrajectoriesPath, SeasonName,
'pos_%03i' % (RunSite + 1))
make_dir(OutDir)
print " ", RunSite, time_idx
print " Running: start time:", start_time,
print "at start location:", start_position
## set the spill to the location
spill = surface_point_line_spill(
num_elements=NumLEs,
start_position=(start_position[0], start_position[1], 0.0),
release_time=start_time,
end_release_time=start_time + release_duration,
windage_range=windage_range,
windage_persist=windage_persist)
# print "adding netcdf output"
netcdf_output_file = os.path.join(
OutDir,
'pos_%03i-t%03i_%08i.nc' %
(RunSite + 1, time_idx, int(start_time.strftime('%y%m%d%H'))),
)
model.outputters.clear()
model.outputters += NetCDFOutput(
netcdf_output_file,
output_timestep=timedelta(hours=OutputTimestep))
model.spills.clear()
model.spills += spill
model.full_run(rewind=True)
timer4 = datetime.now()
diff = round((timer4 - timer3).total_seconds() / 60, 2)
timingRecord.write("\t\t" + str(RunSite) + " took " + str(diff) +
" minutes to complete")
diff = round((timer4 - timer1).total_seconds() / 3600, 2)
count = len(RunStarts)
timingRecord.write("\t" + str(SeasonName) + " took " + str(diff) +
" hours to finish " + str(count) + " Gnome runs")
#OutDir.close
timingRecord.close
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 10, 25, 0, 1)
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=24),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'nyharbor.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = point_line_release_spill(num_elements=1000,
start_position=(-74.15, 40.5, 0.0),
release_time=start_time)
model.spills += spill1
print 'adding a RandomMover:'
# model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
series = []
for i in [(1, (5, 90)), (7, (5, 180)), (13, (5, 270)), (19, (5, 0)),
(25, (5, 90))]:
series.append((start_time + timedelta(hours=i[0]), i[1]))
wind1 = WindTS.constant_wind('wind1', 5, 270, 'knots')
wind2 = WindTS(timeseries=series, units='knots', extrapolate=True)
wind = Wind(timeseries=series, units='knots')
model.movers += PyWindMover(wind=wind2)
# model.movers += WindMover(wind)
# print 'adding a current mover:'
#
# url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml')
# # cf = roms_field('nos.tbofs.fields.n000.20160406.t00z_sgrid.nc')
# cf = roms_field(url)
# cf.set_appearance(on=True)
# renderer.grids += [cf]
# renderer.delay = 25
# u_mover = UGridCurrentMover(cf)
# model.movers += u_mover
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2012, 10, 25, 0, 1)
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=2),
time_step=900)
mapfile = get_datafile(os.path.join(base_dir, 'nyharbor.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_ny_plume.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding two spills'
# Break the spill into two spills, first with the larger droplets
# and second with the smaller droplets.
# Split the total spill volume (100 m^3) to have most
# in the larger droplet spill.
# Smaller droplets start at a lower depth than larger
end_time = start_time + model.duration
# wd = WeibullDistribution(alpha=1.8,
# lambda_=.00456,
# min_=.0002) # 200 micron min
#
# spill = subsurface_plume_spill(num_elements=10,
# start_position=(-74.15,
# 40.5,
# 7.2),
# release_time=start_time,
# distribution=wd,
# amount=90, # default volume_units=m^3
# units='m^3',
# end_release_time=end_time,
# density=600)
#
# model.spills += spill
# wd = WeibullDistribution(alpha=1.8,
# lambda_=.00456,
# max_=.0002) # 200 micron max
oil_name = 'ALASKA NORTH SLOPE (MIDDLE PIPELINE, 1997)'
wd = UniformDistribution(low=.0002,
high=.0002)
spill = point_line_release_spill(num_elements=10, amount=90,
units='m^3',
start_position=(-74.15,
40.5,
7.2),
release_time=start_time,
substance = GnomeOil(oil_name,initializers=plume_initializers(distribution=wd))
#element_type=plume(distribution=wd,
#substance_name='ALASKA NORTH SLOPE (MIDDLE PIPELINE, 1997)')
)
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a RiseVelocityMover:'
model.movers += RiseVelocityMover()
print 'adding a RandomMover3D:'
# model.movers += RandomMover3D(vertical_diffusion_coef_above_ml=5,
# vertical_diffusion_coef_below_ml=.11,
# mixed_layer_depth=10)
# the url is broken, update and include the following four lines
# url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml')
# gc = GridCurrent.from_netCDF(url)
# u_mover = PyCurrentMover(gc, default_num_method='RK2')
# model.movers += u_mover
# print 'adding a wind mover:'
# series = np.zeros((2, ), dtype=gnome.basic_types.datetime_value_2d)
# series[0] = (start_time, (30, 90))
# series[1] = (start_time + timedelta(hours=23), (30, 90))
# wind = Wind(timeseries=series, units='knot')
#
# default is .4 radians
# w_mover = gnome.movers.WindMover(wind, uncertain_angle_scale=0)
#
# model.movers += w_mover
print 'adding a simple mover:'
# s_mover = SimpleMover(velocity=(0.0, -.3, 0.0))
# model.movers += s_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2013, 2, 13, 9, 0)
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=2),
time_step=30 * 60,
uncertain=False)
print 'adding the map'
mapfile = get_datafile(os.path.join(base_dir, 'GuamMap.bna'))
model.map = MapFromBNA(mapfile, refloat_halflife=6) # hours
print 'adding outputters'
renderer = Renderer(mapfile, images_dir, image_size=(800, 600))
renderer.viewport = ((144.6, 13.4), (144.7, 13.5))
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_guam.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding a spill'
end_time = start_time + timedelta(hours=6)
spill = point_line_release_spill(num_elements=10,
start_position=(144.664166, 13.441944,
0.0),
release_time=start_time,
end_release_time=end_time)
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
series = np.zeros((4, ), dtype=datetime_value_2d)
series[0] = (start_time, (5, 135))
series[1] = (start_time + timedelta(hours=23), (5, 135))
series[2] = (start_time + timedelta(hours=25), (5, 0))
series[3] = (start_time + timedelta(hours=48), (5, 0))
wind = Wind(timeseries=series, units='knot')
w_mover = WindMover(wind)
model.movers += w_mover
model.environment += w_mover.wind
print 'adding a cats mover:'
curr_file = get_datafile(os.path.join(base_dir, 'OutsideWAC.cur'))
c_mover = CatsMover(curr_file)
c_mover.scale = True
c_mover.scale_refpoint = (144.601, 13.42)
c_mover.scale_value = .15
model.movers += c_mover
print 'adding a cats shio mover:'
curr_file = get_datafile(os.path.join(base_dir, 'WACFloodTide.cur'))
tide_file = get_datafile(os.path.join(base_dir, 'WACFTideShioHts.txt'))
c_mover = CatsMover(curr_file, tide=Tide(tide_file))
# this is different from the value in the file!
c_mover.scale_refpoint = (144.621667, 13.45)
c_mover.scale = True
c_mover.scale_value = 1
# will need the fScaleFactor for heights files
# c_mover.time_dep.scale_factor = 1.1864
c_mover.tide.scale_factor = 1.1864
model.movers += c_mover
model.environment += c_mover.tide
return model
def test_all_movers(start_time, release_delay, duration):
'''
Tests that all the movers at least can be run
Add new ones as they come along!
'''
model = Model()
model.time_step = timedelta(hours=1)
model.duration = timedelta(seconds=model.time_step * duration)
model.start_time = start_time
start_loc = (1., 2., 0.) # random non-zero starting points
# a spill - release after 5 timesteps
release_time = (start_time +
timedelta(seconds=model.time_step * release_delay))
model.spills += point_line_release_spill(num_elements=10,
start_position=start_loc,
release_time=release_time)
# the land-water map
model.map = gnome.map.GnomeMap() # the simplest of maps
# simple mover
model.movers += SimpleMover(velocity=(1., -1., 0.))
assert len(model.movers) == 1
# random mover
model.movers += RandomMover(diffusion_coef=100000)
assert len(model.movers) == 2
# wind mover
series = np.array((start_time, (10, 45)), dtype=datetime_value_2d).reshape(
(1, ))
model.movers += WindMover(Wind(timeseries=series,
units='meter per second'))
assert len(model.movers) == 3
# CATS mover
model.movers += CatsMover(testdata['CatsMover']['curr'])
assert len(model.movers) == 4
# run the model all the way...
num_steps_output = 0
for step in model:
num_steps_output += 1
print 'running step:', step
# test release happens correctly for all cases
if release_delay < duration:
# at least one get_move has been called after release
assert np.all(model.spills.LE('positions')[:, :2] != start_loc[:2])
elif release_delay == duration:
# particles are released after last step so no motion,
# only initial _state
assert np.all(model.spills.LE('positions') == start_loc)
else:
# release_delay > duration so nothing released though model ran
assert len(model.spills.LE('positions')) == 0
# there is the zeroth step, too.
calculated_steps = (model.duration.total_seconds() / model.time_step) + 1
assert num_steps_output == calculated_steps
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2013, 5, 18, 0)
model = Model(start_time=start_time, duration=timedelta(days=8),
time_step=1 * 3600, uncertain=False)
mapfile = get_datafile(os.path.join(base_dir, './mariana_island.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=6) # hours
#
# Add the outputters -- render to images, and save out as netCDF
#
print 'adding renderer'
model.outputters += Renderer(mapfile, images_dir, size=(800, 600))
# print "adding netcdf output"
# netcdf_output_file = os.path.join(base_dir,'mariana_output.nc')
# scripting.remove_netcdf(netcdf_output_file)
# model.outputters += gnome.netcdf_outputter.NetCDFOutput(netcdf_output_file,
# which_data='all')
# #
# # Set up the movers:
# #
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=10000)
print 'adding a simple wind mover:'
model.movers += constant_wind_mover(5, 315, units='m/s')
print 'adding a current mover:'
# # this is HYCOM currents
curr_file = get_datafile(os.path.join(base_dir, r"./HYCOM.nc"))
model.movers += GridCurrentMover(curr_file)
# #
# # Add some spills (sources of elements)
# #
print 'adding four spill'
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(145.25, 15.0,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(146.25, 15.0,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(145.75, 15.25,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(145.75, 14.75,
0.0),
release_time=start_time)
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(1985, 1, 1, 13, 31)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=4),
time_step=7200)
# mapfile = get_datafile(os.path.join(base_dir, 'ak_arctic.bna'))
mapfile = get_datafile('arctic_coast3.bna')
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
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),
# spill1 = point_line_release_spill(num_elements=10000,
# start_position=(-163.75,
# 69.75,
# 0.0),
# release_time=start_time)
#
spill1 = point_line_release_spill(num_elements=50000,
start_position=(196.25, 69.75, 0.0),
release_time=start_time)
model.spills += spill1
# model.spills += spill2
print 'adding a wind mover:'
# model.movers += constant_wind_mover(0.5, 0, units='m/s')
print 'adding a current mover:'
fn = ['arctic_avg2_0001_gnome.nc', 'arctic_avg2_0002_gnome.nc']
# fn = ['C:\\Users\\jay.hennen\\Documents\\Code\\pygnome\\py_gnome\\scripts\\script_TAP\\arctic_avg2_0001_gnome.nc',
# 'C:\\Users\\jay.hennen\\Documents\\Code\\pygnome\\py_gnome\\scripts\\script_TAP\\arctic_avg2_0002_gnome.nc']
gt = {'node_lon': 'lon', 'node_lat': 'lat'}
# fn='arctic_avg2_0001_gnome.nc'
wind_method = 'Euler'
method = 'RK2'
print 'adding outputters'
# 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, image_size=(1024, 768))
model.outputters += renderer
netcdf_file = os.path.join(base_dir,
str(model.time_step / 60) + method + '.nc')
scripting.remove_netcdf(netcdf_file)
print 'adding movers'
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'loading entire current data'
ice_aware_curr = IceAwareCurrent.from_netCDF(filename=fn, grid_topology=gt)
# env1 = get_env_from_netCDF(filename)
# mov = PyCurrentMover.from_netCDF(filename)
ice_aware_curr.ice_velocity.variables[0].dimension_ordering = [
'time', 'x', 'y'
]
ice_aware_wind = IceAwareWind.from_netCDF(
filename=fn,
ice_velocity=ice_aware_curr.ice_velocity,
ice_concentration=ice_aware_curr.ice_concentration,
grid=ice_aware_curr.grid)
curr = GridCurrent.from_netCDF(filename=fn)
# GridCurrent.is_gridded()
# import pprint as pp
# from gnome.utilities.orderedcollection import OrderedCollection
# model.environment = OrderedCollection(dtype=Environment)
# model.environment.add(ice_aware_curr)
# from gnome.environment import WindTS
print 'loading entire wind data'
# i_c_mover = PyCurrentMover(current=ice_aware_curr)
# i_c_mover = PyCurrentMover(current=ice_aware_curr, default_num_method='Euler')
i_c_mover = PyCurrentMover(current=ice_aware_curr,
default_num_method=method,
extrapolate=True)
i_w_mover = PyWindMover(wind=ice_aware_wind,
default_num_method=wind_method)
# ice_aware_curr.grid.node_lon = ice_aware_curr.grid.node_lon[:]-360
# ice_aware_curr.grid.build_celltree()
model.movers += i_c_mover
model.movers += i_w_mover
print 'adding an IceAwareRandomMover:'
model.movers += IceAwareRandomMover(
ice_concentration=ice_aware_curr.ice_concentration,
diffusion_coef=1000)
# renderer.add_grid(ice_aware_curr.grid)
# renderer.add_vec_prop(ice_aware_curr)
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
# model.environment.add(WindTS.constant(10, 300))
# print('Saving')
# model.environment[0].ice_velocity.variables[0].serialize()
# IceVelocity.deserialize(model.environment[0].ice_velocity.serialize())
# model.save('.')
# from gnome.persist.save_load import load
# print('Loading')
# model2 = load('./Model.zip')
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(1985, 1, 1, 13, 31)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=4),
time_step=3600*2)
mapfile = get_datafile(os.path.join(base_dir, 'arctic_coast3.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
# model.map = GnomeMap()
print 'adding outputters'
# 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, image_size=(1024, 768))
# model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_old_TAPa.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
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),
spill1 = point_line_release_spill(num_elements=10000,
start_position=(196.25,
69.75,
0.0),
release_time=start_time)
#
# spill2 = point_line_release_spill(num_elements=5000,
# start_position=(-163.75,
# 69.5,
# 0.0),
# release_time=start_time)
model.spills += spill1
# model.spills += spill2
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=1000)
print 'adding a wind mover:'
# winds from the ROMS Arctic run, provided by Walter Johnson
wind_file = os.path.join(base_dir, 'arctic_filelist.txt')
print wind_file
topology_file = os.path.join(base_dir, 'arctic_subset_newtopo2.DAT')
model.movers += IceWindMover(wind_file, topology_file)
# model.movers += GridWindMover(wind_file, topology_file)
# model.movers += GridWindMover(wind_file, topology_file)
print 'adding an ice mover:'
# ice from the ROMS Arctic run, provided by Walter Johnson
ice_file = os.path.join(base_dir, 'arctic_filelist.txt')
topology_file = os.path.join(base_dir, 'arctic_subset_newtopo2.DAT')
model.movers += IceMover(ice_file, topology_file)
# model.movers += IceMover(ice_file)
print ice_file
print 'adding a current mover:'
#
# fn = ['N:\\Users\\Dylan.Righi\\OutBox\\ArcticROMS\\arctic_avg2_0001_gnome.nc',
# 'N:\\Users\\Dylan.Righi\\OutBox\\ArcticROMS\\arctic_avg2_0002_gnome.nc']
#
# gt = {'node_lon':'lon',
# 'node_lat':'lat'}
# # fn='arctic_avg2_0001_gnome.nc'
#
# ice_aware_curr = IceAwareCurrent.from_netCDF(filename=fn,
# grid_topology=gt)
# ice_aware_wind = IceAwareWind.from_netCDF(filename=fn,
# grid = ice_aware_curr.grid,)
# method = 'Trapezoid'
#
# # i_c_mover = PyGridCurrentMover(current=ice_aware_curr)
# # i_c_mover = PyGridCurrentMover(current=ice_aware_curr, default_num_method='Euler')
# i_c_mover = PyGridCurrentMover(current=ice_aware_curr, default_num_method=method)
# i_w_mover = PyWindMover(wind = ice_aware_wind, default_num_method=method)
#
# ice_aware_curr.grid.node_lon = ice_aware_curr.grid.node_lon[:]-360
# # ice_aware_curr.grid.build_celltree()
# model.movers += i_c_mover
# model.movers += i_w_mover
# renderer.add_grid(ice_aware_curr.grid)
# renderer.add_vec_prop(ice_aware_curr)
# renderer.set_viewport(((-190.9, 60), (-72, 89)))
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
model.save('.')
return model
def make_model():
print ('initializing the model')
#print (start_date)
start_time = startday
model = Model(start_time=start_time, duration=timedelta(days=30),
#weathering_substeps = 6,
time_step=24 * 3600,
uncertain=False)
mapfile = get_datafile(os.path.join(base_dir,'gulf.bna'))
#mapfile='gulf.bna'
print ('adding the map')
model.map = MapFromBNA(mapfile, refloat_halflife=6) # hours
#
# Add the outputters -- render to images, and save out as netCDF
#
print ("adding shapefile output")
# with open("Result {}".format(spill_num), "w") as fp:
# fp.write("text")
dir_name = os.path.join (base_dir, season, str(position), "Spillnum {}".format(spill_num))
if not os.path.exists(dir_name):
os.makedirs(dir_name)
#os.makedirs(dir_name, exist_ok =True)
for i in range(1, 31, 1):
model.outputters += ShapeOutput(os.path.join(dir_name, 'gnome_result {id}'.format(id=i)),
zip_output=False,
output_timestep=timedelta(days=i))
images_dir = os.path.join(dir_name, 'image')
# print 'adding renderer'
# model.outputters += Renderer(mapfile,
# images_dir,
# image_size=(800, 600))
# print ('adding renderer')
# dir_image = os.path.join(dir_name)
# model.outputters += Renderer(mapfile,
# dir_image,
# size=(800, 600))
#
# Set up the movers:
#
print ('adding a RandomMover:')
model.movers += RandomMover(diffusion_coef=10000)
print ('adding a simple wind mover:')
wind_file = get_datafile(os.path.join(base_dir, 'ECMWF.nc'))
model.movers += GridWindMover(wind_file)
print ('adding a current mover:')
# # this is NEMO currents
curr_file = get_datafile(os.path.join(base_dir, Currents))
model.movers += GridCurrentMover(curr_file,
num_method='Euler');
# # Add some spills (sources of elements)
print ('adding one spill')
spill = point_line_release_spill(num_elements=1000,
amount= 3200000000 * spilldur , units='grams',
start_position = position,
release_time = start_time,
substance = (sub))
model.spills += spill
####### open excel file
print ('adding Excel file')
workbook = xlsxwriter.Workbook(os.path.join(dir_name, 'Result {}_{}.xlsx'.format(spill_num, position)))
worksheet = workbook.add_worksheet ()
a = ((spilldur*3200)**(-0.3))*0.000069
worksheet.write ('A1', a)
workbook.close()
print ('adding weatherers and cleanup options:')
model.environment += [water,wind,waves]
model.weatherers += Evaporation()
model.weatherers += Emulsification()
model.weatherers += NaturalDispersion()
print ('model full run:')
model.full_run()
return model
def make_model(images_dir=os.path.join(base_dir, "images")):
print "initializing the model"
start_time = datetime(1985, 1, 1, 13, 31)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time, duration=timedelta(days=4), time_step=3600)
mapfile = get_datafile(os.path.join(base_dir, "ak_arctic.bna"))
print "adding the map"
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
print "adding outputters"
# 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, image_size=(1024, 768))
# model.outputters += renderer
netcdf_file = os.path.join(base_dir, "script_ice.nc")
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data="all")
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),
spill1 = point_line_release_spill(num_elements=10000, start_position=(-163.75, 69.75, 0.0), release_time=start_time)
#
# spill2 = point_line_release_spill(num_elements=5000,
# start_position=(-163.75,
# 69.5,
# 0.0),
# release_time=start_time)
model.spills += spill1
# model.spills += spill2
print "adding a RandomMover:"
model.movers += RandomMover(diffusion_coef=1000)
print "adding a wind mover:"
# model.movers += constant_wind_mover(0.5, 0, units='m/s')
print "adding a current mover:"
fn = [get_datafile("arctic_avg2_0001_gnome.nc"), get_datafile("arctic_avg2_0002_gnome.nc")]
gt = {"node_lon": "lon", "node_lat": "lat"}
ice_aware_curr = IceAwareCurrent.from_netCDF(filename=fn, grid_topology=gt)
ice_aware_wind = IceAwareWind.from_netCDF(filename=fn, grid=ice_aware_curr.grid)
method = "Trapezoid"
# i_c_mover = PyGridCurrentMover(current=ice_aware_curr)
# i_c_mover = PyGridCurrentMover(current=ice_aware_curr, default_num_method='Euler')
i_c_mover = PyGridCurrentMover(current=ice_aware_curr, default_num_method=method)
i_w_mover = PyWindMover(wind=ice_aware_wind, default_num_method=method)
ice_aware_curr.grid.node_lon = ice_aware_curr.grid.node_lon[:] - 360
# ice_aware_curr.grid.build_celltree()
model.movers += i_c_mover
model.movers += i_w_mover
# renderer.add_grid(ice_aware_curr.grid)
# renderer.add_vec_prop(ice_aware_curr)
# renderer.set_viewport(((-190.9, 60), (-72, 89)))
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2013, 2, 13, 9, 0)
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=2),
time_step=30 * 60,
uncertain=False)
print 'adding the map'
mapfile = get_datafile(os.path.join(base_dir, 'GuamMap.bna'))
model.map = MapFromBNA(mapfile, refloat_halflife=6) # hours
print 'adding outputters'
renderer = Renderer(mapfile, images_dir, image_size=(800, 600))
renderer.viewport = ((144.6, 13.4), (144.7, 13.5))
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_guam.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
print 'adding a spill'
end_time = start_time + timedelta(hours=6)
spill = point_line_release_spill(num_elements=10,
start_position=(144.664166,
13.441944, 0.0),
release_time=start_time,
end_release_time=end_time)
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a wind mover:'
series = np.zeros((4, ), dtype=datetime_value_2d)
series[0] = (start_time, (5, 135))
series[1] = (start_time + timedelta(hours=23), (5, 135))
series[2] = (start_time + timedelta(hours=25), (5, 0))
series[3] = (start_time + timedelta(hours=48), (5, 0))
wind = Wind(timeseries=series, units='knot')
w_mover = WindMover(wind)
model.movers += w_mover
model.environment += w_mover.wind
print 'adding a cats mover:'
curr_file = get_datafile(os.path.join(base_dir, 'OutsideWAC.cur'))
c_mover = CatsMover(curr_file)
c_mover.scale = True
c_mover.scale_refpoint = (144.601, 13.42)
c_mover.scale_value = .15
model.movers += c_mover
print 'adding a cats shio mover:'
curr_file = get_datafile(os.path.join(base_dir, 'WACFloodTide.cur'))
tide_file = get_datafile(os.path.join(base_dir, 'WACFTideShioHts.txt'))
c_mover = CatsMover(curr_file, tide=Tide(tide_file))
# this is different from the value in the file!
c_mover.scale_refpoint = (144.621667, 13.45)
c_mover.scale = True
c_mover.scale_value = 1
# will need the fScaleFactor for heights files
# c_mover.time_dep.scale_factor = 1.1864
c_mover.tide.scale_factor = 1.1864
model.movers += c_mover
model.environment += c_mover.tide
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(1985, 1, 1, 13, 31)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=4),
time_step=3600)
# mapfile = get_datafile(os.path.join(base_dir, 'ak_arctic.bna'))
mapfile = get_datafile('arctic_coast3.bna')
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
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),
# spill1 = point_line_release_spill(num_elements=10000,
# start_position=(-163.75,
# 69.75,
# 0.0),
# release_time=start_time)
#
spill1 = point_line_release_spill(num_elements=50000,
start_position=(196.25,
69.75,
0.0),
release_time=start_time)
model.spills += spill1
# model.spills += spill2
print 'adding a wind mover:'
# model.movers += constant_wind_mover(0.5, 0, units='m/s')
print 'adding a current mover:'
fn = ['arctic_avg2_0001_gnome.nc',
'arctic_avg2_0002_gnome.nc']
gt = {'node_lon': 'lon',
'node_lat': 'lat'}
# fn='arctic_avg2_0001_gnome.nc'
wind_method = 'Euler'
method = 'Trapezoid'
print 'adding outputters'
# 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, image_size=(1024, 768))
# model.outputters += renderer
netcdf_file = os.path.join(base_dir, str(model.time_step / 60) + method + '.nc')
scripting.remove_netcdf(netcdf_file)
print 'adding movers'
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
load = False
print 'loading entire current data'
ice_aware_curr = IceAwareCurrent.from_netCDF(filename=fn,
grid_topology=gt,
load_all=load)
print 'loading entire wind data'
ice_aware_wind = IceAwareWind.from_netCDF(filename=fn,
ice_var=ice_aware_curr.ice_var,
ice_conc_var=ice_aware_curr.ice_conc_var,
grid=ice_aware_curr.grid,
load_all=load)
# i_c_mover = PyGridCurrentMover(current=ice_aware_curr)
# i_c_mover = PyGridCurrentMover(current=ice_aware_curr, default_num_method='Euler')
i_c_mover = PyGridCurrentMover(current=ice_aware_curr, default_num_method=method, extrapolate=True)
i_w_mover = PyWindMover(wind=ice_aware_wind, default_num_method=wind_method)
# ice_aware_curr.grid.node_lon = ice_aware_curr.grid.node_lon[:]-360
# ice_aware_curr.grid.build_celltree()
model.movers += i_c_mover
model.movers += i_w_mover
print 'adding an IceAwareRandomMover:'
model.movers += IceAwareRandomMover(ice_conc_var=ice_aware_curr.ice_conc_var,
diffusion_coef=1000)
# renderer.add_grid(ice_aware_curr.grid)
# renderer.add_vec_prop(ice_aware_curr)
# renderer.set_viewport(((-190.9, 60), (-72, 89)))
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2004, 12, 31, 13, 0)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=1),
time_step=30 * 60,
uncertain=True)
mapfile = get_datafile(os.path.join(base_dir, 'ChesapeakeBay.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,
image_size=(800, 600),
output_timestep=timedelta(hours=2),
draw_ontop='forecast')
# set the viewport to zoom in on the map:
renderer.viewport = ((-76.5, 37.), (-75.8, 38.))
# add the raster map, so we can see it...
# note: this is really slow, so only use for diagnostics
# renderer.raster_map = model.map
print 'adding outputters'
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_chesapeake_bay.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file,
which_data='all',
output_timestep=timedelta(hours=2))
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),
spill = point_line_release_spill(num_elements=1000,
start_position=(-76.126872, 37.680952,
0.0),
release_time=start_time)
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, (30, 0))
series[1] = (start_time + timedelta(hours=23), (30, 0))
wind = Wind(timeseries=series, units='knot')
# default is .4 radians
w_mover = WindMover(wind, uncertain_angle_scale=0)
wind.extrapolation_is_allowed = True
model.movers += w_mover
print 'adding a current mover:'
curr_file = get_datafile(os.path.join(base_dir, 'ChesapeakeBay.nc'))
topology_file = get_datafile(os.path.join(base_dir, 'ChesapeakeBay.dat'))
# uncertain_time_delay in hours
c_mover = GridCurrentMover(curr_file,
topology_file,
uncertain_time_delay=3)
c_mover.uncertain_along = 0 # default is .5
# c_mover.uncertain_cross = 0 # default is .25
model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2015, 9, 24, 1, 1)
# start_time = datetime(2015, 12, 18, 06, 01)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(hours=47),
time_step=300)
mapfile = get_datafile(os.path.join(base_dir, 'columbia_river.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(600, 1200))
renderer.delay = 15
# renderer.viewport = ((-123.35, 45.6), (-122.68, 46.13))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = continuous_release_spill(initial_elements=10000,
num_elements=400,
start_position=(-122.625, 45.609, 0.0),
release_time=start_time,
end_position=(-122.6, 45.605, 0.0),
end_release_time=start_time +
timedelta(seconds=36000))
model.spills += spill1
print 'adding a RandomMover:'
# model.movers += RandomMover(diffusion_coef=10000)
print 'adding a wind mover:'
series = []
for i in [(1, (5, 90)), (7, (5, 180)), (13, (5, 270)), (19, (5, 0)),
(25, (5, 90))]:
series.append((start_time + timedelta(hours=i[0]), i[1]))
wind1 = WindTS.constant_wind('wind1', 0.5, 0, 'm/s')
wind2 = WindTS(timeseries=series, units='knots', extrapolate=True)
# wind = Wind(timeseries=series, units='knots')
model.movers += PyWindMover(wind=wind1)
print 'adding a current mover:'
# url = ('http://geoport.whoi.edu/thredds/dodsC/clay/usgs/users/jcwarner/Projects/Sandy/triple_nest/00_dir_NYB05.ncml')
# test = GridCurrent.from_netCDF(name='gc1', filename=url)
curr_file = get_datafile('COOPSu_CREOFS24.nc')
curr = GridCurrent.from_netCDF(
name='gc2',
filename=curr_file,
)
c_mover = PyGridCurrentMover(curr,
extrapolate=True,
default_num_method='Trapezoid')
# renderer.add_grid(curr.grid)
# renderer.add_vec_prop(curr)
model.movers += c_mover
print 'adding a random mover'
model.movers += RandomMover(diffusion_coef=1000)
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(1985, 1, 1, 13, 31)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=4),
time_step=3600 * 2)
# mapfile = get_datafile(os.path.join(base_dir, 'ak_arctic.bna'))
mapfile = get_datafile('arctic_coast3.bna')
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # seconds
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),
# spill1 = point_line_release_spill(num_elements=10000,
# start_position=(-163.75,
# 69.75,
# 0.0),
# release_time=start_time)
#
spill1 = point_line_release_spill(num_elements=100,
start_position=(196.25, 69.75, 0.0),
release_time=start_time)
model.spills += spill1
# model.spills += spill2
print 'adding a wind mover:'
# model.movers += constant_wind_mover(0.5, 0, units='m/s')
print 'adding a current mover:'
fn = ['arctic_avg2_0001_gnome.nc', 'arctic_avg2_0002_gnome.nc']
gt = {'node_lon': 'lon', 'node_lat': 'lat'}
# fn='arctic_avg2_0001_gnome.nc'
wind_method = 'Euler'
method = 'Trapezoid'
print 'adding outputters'
# 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, image_size=(1024, 768))
# model.outputters += renderer
netcdf_file = os.path.join(base_dir,
str(model.time_step / 60) + method + '.nc')
scripting.remove_netcdf(netcdf_file)
print 'adding movers'
model.outputters += NetCDFOutput(netcdf_file, which_data='all')
ice_aware_curr = IceAwareCurrent.from_netCDF(filename=fn, grid_topology=gt)
ice_aware_wind = IceAwareWind.from_netCDF(
filename=fn,
ice_var=ice_aware_curr.ice_var,
ice_conc_var=ice_aware_curr.ice_conc_var,
grid=ice_aware_curr.grid,
)
# i_c_mover = PyGridCurrentMover(current=ice_aware_curr)
# i_c_mover = PyGridCurrentMover(current=ice_aware_curr, default_num_method='Euler')
i_c_mover = PyGridCurrentMover(current=ice_aware_curr,
default_num_method=method)
i_w_mover = PyWindMover(wind=ice_aware_wind,
default_num_method=wind_method)
# ice_aware_curr.grid.node_lon = ice_aware_curr.grid.node_lon[:]-360
# ice_aware_curr.grid.build_celltree()
model.movers += i_c_mover
model.movers += i_w_mover
print 'adding an IceAwareRandomMover:'
model.movers += IceAwareRandomMover(
ice_conc_var=ice_aware_curr.ice_conc_var, diffusion_coef=1000)
# renderer.add_grid(ice_aware_curr.grid)
# renderer.add_vec_prop(ice_aware_curr)
# renderer.set_viewport(((-190.9, 60), (-72, 89)))
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
def test_all_movers(start_time, release_delay, duration):
'''
Tests that all the movers at least can be run
Add new ones as they come along!
'''
model = Model()
model.time_step = timedelta(hours=1)
model.duration = timedelta(seconds=model.time_step * duration)
model.start_time = start_time
start_loc = (1., 2., 0.) # random non-zero starting points
# a spill - release after 5 timesteps
release_time = (start_time +
timedelta(seconds=model.time_step * release_delay))
model.spills += point_line_release_spill(num_elements=10,
start_position=start_loc,
release_time=release_time)
# the land-water map
model.map = gnome.map.GnomeMap() # the simplest of maps
# simple mover
model.movers += SimpleMover(velocity=(1., -1., 0.))
assert len(model.movers) == 1
# random mover
model.movers += RandomMover(diffusion_coef=100000)
assert len(model.movers) == 2
# wind mover
series = np.array((start_time, (10, 45)),
dtype=datetime_value_2d).reshape((1, ))
model.movers += WindMover(Wind(timeseries=series,
units='meter per second'))
assert len(model.movers) == 3
# CATS mover
model.movers += CatsMover(testdata['CatsMover']['curr'])
assert len(model.movers) == 4
# run the model all the way...
num_steps_output = 0
for step in model:
num_steps_output += 1
print 'running step:', step
# test release happens correctly for all cases
if release_delay < duration:
# at least one get_move has been called after release
assert np.all(model.spills.LE('positions')[:, :2] != start_loc[:2])
elif release_delay == duration:
# particles are released after last step so no motion,
# only initial _state
assert np.all(model.spills.LE('positions') == start_loc)
else:
# release_delay > duration so nothing released though model ran
assert len(model.spills.LE('positions')) == 0
# there is the zeroth step, too.
calculated_steps = (model.duration.total_seconds() / model.time_step) + 1
assert num_steps_output == calculated_steps
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
# set up the modeling environment
start_time = datetime(2004, 12, 31, 13, 0)
model = Model(start_time=start_time,
duration=timedelta(days=3),
time_step=30 * 60,
uncertain=False)
print 'adding the map'
model.map = GnomeMap() # this is a "water world -- no land anywhere"
# renderere is only top-down view on 2d -- but it's something
renderer = Renderer(
output_dir=images_dir,
size=(1024, 768),
output_timestep=timedelta(hours=1),
)
renderer.viewport = ((-.15, -.35), (.15, .35))
print 'adding outputters'
model.outputters += renderer
# Also going to write the results out to a netcdf file
netcdf_file = os.path.join(base_dir, 'script_plume.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(
netcdf_file,
which_data='most',
# output most of the data associated with the elements
output_timestep=timedelta(hours=2))
print "adding Horizontal and Vertical diffusion"
# Horizontal Diffusion
# model.movers += RandomMover(diffusion_coef=5)
# vertical diffusion (different above and below the mixed layer)
model.movers += RandomVerticalMover(vertical_diffusion_coef_above_ml=5,
vertical_diffusion_coef_below_ml=.11,
mixed_layer_depth=10)
print 'adding Rise Velocity'
# droplets rise as a function of their density and radius
model.movers += RiseVelocityMover()
print 'adding a circular current and eastward current'
# This is .3 m/s south
model.movers += PyCurrentMover(current=vg,
default_num_method='Trapezoid',
extrapolate=True)
model.movers += SimpleMover(velocity=(0., -0.1, 0.))
# Now to add in the TAMOC "spill"
print "Adding TAMOC spill"
model.spills += tamoc_spill.TamocSpill(
release_time=start_time,
start_position=(0, 0, 1000),
num_elements=1000,
end_release_time=start_time + timedelta(days=1),
name='TAMOC plume',
TAMOC_interval=None, # how often to re-run TAMOC
)
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2013, 5, 18, 0)
model = Model(start_time=start_time, duration=timedelta(days=8),
time_step=4 * 3600, uncertain=False)
mapfile = get_datafile(os.path.join(base_dir, 'mariana_island.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=6) # hours
#
# Add the outputters -- render to images, and save out as netCDF
#
print 'adding renderer'
rend = Renderer(mapfile,
images_dir,
size=(800, 600),
draw_map_bounds=True
)
rend.draw_raster_map()
model.outputters += rend
# draw_back_to_fore=True)
# print "adding netcdf output"
# netcdf_output_file = os.path.join(base_dir,'mariana_output.nc')
# scripting.remove_netcdf(netcdf_output_file)
# model.outputters += NetCDFOutput(netcdf_output_file, which_data='all')
#
# Set up the movers:
#
rend.zoom(0.5)
rend.zoom(2)
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=10000)
print 'adding a simple wind mover:'
model.movers += constant_wind_mover(7, 90, units='m/s')
print 'adding a current mover:'
# # # this is HYCOM currents
# curr_file = get_datafile(os.path.join(base_dir, 'HYCOM.nc'))
# model.movers += GridCurrentMover(curr_file,
# num_method=numerical_methods.euler);
# #
# # Add some spills (sources of elements)
# #
print 'adding four spill'
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(146, 15.25,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(146, 15.125,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(146, 15.0,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(146, 14.875,
0.0),
release_time=start_time)
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2004, 12, 31, 13, 0)
# 1 day of data in file
# 1/2 hr in seconds
model = Model(start_time=start_time,
duration=timedelta(days=1),
time_step=30 * 60,
uncertain=True)
mapfile = get_datafile(os.path.join(base_dir, 'ChesapeakeBay.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='uncertain')
renderer.viewport = ((-76.5, 37.), (-75.8, 38.))
print 'adding outputters'
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_chesapeake_bay.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='all',
output_timestep=timedelta(hours=2))
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),
spill = point_line_release_spill(num_elements=1000,
start_position=(-76.126872,
37.680952,
0.0),
release_time=start_time)
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, (30, 0))
series[1] = (start_time + timedelta(hours=23), (30, 0))
wind = Wind(timeseries=series, units='knot')
# default is .4 radians
w_mover = WindMover(wind, uncertain_angle_scale=0)
model.movers += w_mover
print 'adding a current mover:'
curr_file = get_datafile(os.path.join(base_dir, 'ChesapeakeBay.nc'))
topology_file = get_datafile(os.path.join(base_dir, 'ChesapeakeBay.dat'))
# uncertain_time_delay in hours
c_mover = GridCurrentMover(curr_file, topology_file,
uncertain_time_delay=3)
c_mover.uncertain_along = 0 # default is .5
# c_mover.uncertain_cross = 0 # default is .25
model.movers += c_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2004, 12, 31, 13, 0)
model = Model(start_time=start_time, duration=timedelta(days=3),
time_step=30 * 60, uncertain=False)
print 'adding the map'
model.map = GnomeMap()
# 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(images_dir=images_dir,
#size=(800, 600),
output_timestep=timedelta(hours=1),
draw_ontop='uncertain')
renderer.viewport = ((-76.5, 37.), (-75.8, 38.))
print 'adding outputters'
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_plume.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file, which_data='most',
output_timestep=timedelta(hours=2))
print 'adding two spills'
# Break the spill into two spills, first with the larger droplets
# and second with the smaller droplets.
# Split the total spill volume (100 m^3) to have most
# in the larger droplet spill.
# Smaller droplets start at a lower depth than larger
wd = WeibullDistribution(alpha=1.8, lambda_=.00456,
min_=.0002) # 200 micron min
end_time = start_time + timedelta(hours=24)
spill = point_line_release_spill(num_elements=1000,
volume=90, # default volume_units=m^3
start_position=(-76.126872, 37.680952,
1700),
release_time=start_time,
end_release_time=end_time,
element_type=plume(distribution=wd))
model.spills += spill
wd = WeibullDistribution(alpha=1.8, lambda_=.00456,
max_=.0002) # 200 micron max
spill = point_line_release_spill(num_elements=1000, volume=10,
start_position=(-76.126872, 37.680952,
1800),
release_time=start_time,
element_type=plume(distribution=wd))
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a RiseVelocityMover:'
model.movers += RiseVelocityMover()
print 'adding a RandomVerticalMover:'
model.movers += RandomVerticalMover(vertical_diffusion_coef_above_ml=5,
vertical_diffusion_coef_below_ml=.11,
mixed_layer_depth=10)
# print 'adding a wind mover:'
# series = np.zeros((2, ), dtype=gnome.basic_types.datetime_value_2d)
# series[0] = (start_time, (30, 90))
# series[1] = (start_time + timedelta(hours=23), (30, 90))
# wind = Wind(timeseries=series, units='knot')
#
# default is .4 radians
# w_mover = gnome.movers.WindMover(wind, uncertain_angle_scale=0)
#
# model.movers += w_mover
print 'adding a simple mover:'
s_mover = SimpleMover(velocity=(0.0, -.1, 0.0))
model.movers += s_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2004, 12, 31, 13, 0)
model = Model(start_time=start_time,
duration=timedelta(days=3),
time_step=30 * 60,
uncertain=False)
print 'adding the map'
model.map = GnomeMap()
# 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(
output_dir=images_dir,
# size=(800, 600),
output_timestep=timedelta(hours=1),
draw_ontop='uncertain')
renderer.viewport = ((-76.5, 37.), (-75.8, 38.))
print 'adding outputters'
model.outputters += renderer
netcdf_file = os.path.join(base_dir, 'script_plume.nc')
scripting.remove_netcdf(netcdf_file)
model.outputters += NetCDFOutput(netcdf_file,
which_data='most',
output_timestep=timedelta(hours=2))
print 'adding two spills'
# Break the spill into two spills, first with the larger droplets
# and second with the smaller droplets.
# Split the total spill volume (100 m^3) to have most
# in the larger droplet spill.
# Smaller droplets start at a lower depth than larger
wd = WeibullDistribution(alpha=1.8, lambda_=.00456,
min_=.0002) # 200 micron min
end_time = start_time + timedelta(hours=24)
# spill = point_line_release_spill(num_elements=10,
# amount=90, # default volume_units=m^3
# units='m^3',
# start_position=(-76.126872, 37.680952,
# 1700),
# release_time=start_time,
# end_release_time=end_time,
# element_type=plume(distribution=wd,
# density=600)
# )
spill = subsurface_plume_spill(
num_elements=10,
start_position=(-76.126872, 37.680952, 1700),
release_time=start_time,
distribution=wd,
amount=90, # default volume_units=m^3
units='m^3',
end_release_time=end_time,
density=600)
model.spills += spill
wd = WeibullDistribution(alpha=1.8, lambda_=.00456,
max_=.0002) # 200 micron max
spill = point_line_release_spill(
num_elements=10,
amount=90,
units='m^3',
start_position=(-76.126872, 37.680952, 1800),
release_time=start_time,
element_type=plume(distribution=wd, substance_name='oil_crude'))
model.spills += spill
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=50000)
print 'adding a RiseVelocityMover:'
model.movers += RiseVelocityMover()
print 'adding a RandomVerticalMover:'
model.movers += RandomVerticalMover(vertical_diffusion_coef_above_ml=5,
vertical_diffusion_coef_below_ml=.11,
mixed_layer_depth=10)
# print 'adding a wind mover:'
# series = np.zeros((2, ), dtype=gnome.basic_types.datetime_value_2d)
# series[0] = (start_time, (30, 90))
# series[1] = (start_time + timedelta(hours=23), (30, 90))
# wind = Wind(timeseries=series, units='knot')
#
# default is .4 radians
# w_mover = gnome.movers.WindMover(wind, uncertain_angle_scale=0)
#
# model.movers += w_mover
print 'adding a simple mover:'
s_mover = SimpleMover(velocity=(0.0, -.3, 0.0))
model.movers += s_mover
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2013, 5, 18, 0)
model = Model(start_time=start_time,
duration=timedelta(days=8),
time_step=4 * 3600,
uncertain=False)
mapfile = get_datafile(os.path.join(base_dir, 'mariana_island.bna'))
print 'adding the map'
model.map = MapFromBNA(mapfile, refloat_halflife=6) # hours
#
# Add the outputters -- render to images, and save out as netCDF
#
print 'adding renderer'
model.outputters += Renderer(
mapfile,
images_dir,
size=(800, 600),
)
# draw_back_to_fore=True)
# print "adding netcdf output"
# netcdf_output_file = os.path.join(base_dir,'mariana_output.nc')
# scripting.remove_netcdf(netcdf_output_file)
# model.outputters += NetCDFOutput(netcdf_output_file, which_data='all')
#
# Set up the movers:
#
print 'adding a RandomMover:'
model.movers += RandomMover(diffusion_coef=10000)
print 'adding a simple wind mover:'
model.movers += constant_wind_mover(5, 315, units='m/s')
print 'adding a current mover:'
# # this is HYCOM currents
curr_file = get_datafile(os.path.join(base_dir, 'HYCOM.nc'))
model.movers += GridCurrentMover(curr_file,
num_method=numerical_methods.euler)
# #
# # Add some spills (sources of elements)
# #
print 'adding four spill'
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(145.25, 15.0,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(146.25, 15.0,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(145.75, 15.25,
0.0),
release_time=start_time)
model.spills += point_line_release_spill(num_elements=NUM_ELEMENTS // 4,
start_position=(145.75, 14.75,
0.0),
release_time=start_time)
return model
def make_model(images_dir=os.path.join(base_dir, 'images')):
print 'initializing the model'
start_time = datetime(2016, 4, 5, 18, 0)
model = Model(start_time=start_time,
duration=timedelta(hours=12),
time_step=.25*3600)
mapfile = (os.path.join(base_dir, 'coast.bna'))
print 'adding the map'
'''TODO: sort out MapFromBna's map_bounds parameter...
it does nothing right now, and the spill is out of bounds'''
model.map = MapFromBNA(mapfile, refloat_halflife=0.0) # 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, image_size=(1024, 768))
# renderer.viewport = ((-73.5, 40.5), (-73.1, 40.75))
# renderer.viewport = ((-122.9, 45.6), (-122.6, 46.0))
print 'adding outputters'
model.outputters += renderer
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),
spill1 = point_line_release_spill(num_elements=500,
start_position=(-82.73888,
27.5475,
0.0),
release_time=start_time,
end_release_time=start_time+timedelta(hours=24))
spill2 = point_line_release_spill(num_elements=500,
start_position=(-82.73888,
27.545,
0.0),
release_time=start_time,
end_release_time=start_time+timedelta(hours=24))
spill3 = point_line_release_spill(num_elements=500,
start_position=(-82.73888,
27.5425,
0.0),
release_time=start_time,
end_release_time=start_time+timedelta(hours=24))
spill4 = point_line_release_spill(num_elements=500,
start_position=(-82.73988,
27.5475,
0.0),
release_time=start_time,
end_release_time=start_time+timedelta(hours=24))
spill5 = point_line_release_spill(num_elements=500,
start_position=(-82.73988,
27.5450,
0.0),
release_time=start_time,
end_release_time=start_time+timedelta(hours=24))
spill6 = point_line_release_spill(num_elements=500,
start_position=(-82.73988,
27.5425,
0.0),
release_time=start_time,
end_release_time=start_time+timedelta(hours=24))
model.spills += spill1
model.spills += spill2
model.spills += spill3
model.spills += spill4
model.spills += spill5
model.spills += spill6
model.spills._spill_container.spills.remove(0)
print 'adding a current mover:'
fn = 'nos.tbofs.fields.n000.20160406.t00z_sgrid.nc'
#fn = 'dbofs_newFormat.nc'
cf = GridCurrent.from_netCDF(filename=fn)
u_mover = PyGridCurrentMover(cf, extrapolate=True)
#u_mover = GridCurrentMover(fn)
renderer.add_grid(cf.grid)
# renderer.add_vec_prop(cf)
model.movers += u_mover
# curr_file = get_datafile(os.path.join(base_dir, 'COOPSu_CREOFS24.nc'))
# c_mover = GridCurrentMover(curr_file)
# model.movers += c_mover
return model
