def test_fieldset_defer_loading_with_diff_time_origin(
tmpdir, fail, filename='test_parcels_defer_loading'):
filepath = tmpdir.join(filename)
data0, dims0 = generate_fieldset(10, 10, 1, 10)
dims0['time'] = np.arange(0, 10, 1) * 3600
fieldset_out = FieldSet.from_data(data0, dims0)
fieldset_out.U.grid.time_origin = TimeConverter(
np.datetime64('2018-04-20'))
fieldset_out.V.grid.time_origin = TimeConverter(
np.datetime64('2018-04-20'))
data1, dims1 = generate_fieldset(10, 10, 1, 10)
if fail:
dims1['time'] = np.arange(0, 10, 1) * 3600
else:
dims1['time'] = np.arange(0, 10, 1) * 1800 + (24 + 25) * 3600
if fail:
Wtime_origin = TimeConverter(np.datetime64('2018-04-22'))
else:
Wtime_origin = TimeConverter(np.datetime64('2018-04-18'))
gridW = RectilinearZGrid(dims1['lon'],
dims1['lat'],
dims1['depth'],
dims1['time'],
time_origin=Wtime_origin)
fieldW = Field('W', np.zeros(data1['U'].shape), grid=gridW)
fieldset_out.add_field(fieldW)
fieldset_out.write(filepath)
fieldset = FieldSet.from_parcels(filepath, extra_fields={'W': 'W'})
assert fieldset.U.creation_log == 'from_parcels'
pset = ParticleSet.from_list(fieldset,
pclass=JITParticle,
lon=[0.5],
lat=[0.5],
depth=[0.5],
time=[datetime.datetime(2018, 4, 20, 1)])
pset.execute(AdvectionRK4_3D, runtime=delta(hours=4), dt=delta(hours=1))
def test_curvilinear_grids(mode):
x = np.linspace(0, 1e3, 7, dtype=np.float32)
y = np.linspace(0, 1e3, 5, dtype=np.float32)
(xx, yy) = np.meshgrid(x, y)
r = np.sqrt(xx * xx + yy * yy)
theta = np.arctan2(yy, xx)
theta = theta + np.pi / 6.
lon = r * np.cos(theta)
lat = r * np.sin(theta)
time = np.array([0, 86400], dtype=np.float64)
grid = CurvilinearZGrid(lon, lat, time=time)
u_data = np.ones((2, y.size, x.size), dtype=np.float32)
v_data = np.zeros((2, y.size, x.size), dtype=np.float32)
u_data[0, :, :] = lon[:, :] + lat[:, :]
u_field = Field('U', u_data, grid=grid, transpose=False)
v_field = Field('V', v_data, grid=grid, transpose=False)
field_set = FieldSet(u_field, v_field)
def sampleSpeed(particle, fieldset, time):
u = fieldset.U[time, particle.depth, particle.lat, particle.lon]
v = fieldset.V[time, particle.depth, particle.lat, particle.lon]
particle.speed = math.sqrt(u * u + v * v)
class MyParticle(ptype[mode]):
speed = Variable('speed', dtype=np.float32, initial=0.)
pset = ParticleSet.from_list(field_set,
MyParticle,
lon=[400, -200],
lat=[600, 600])
pset.execute(pset.Kernel(sampleSpeed), runtime=0, dt=0)
assert (np.allclose(pset[0].speed, 1000))
""" Defining the particle set """
rho_pls = [
30, 30, 30, 30, 30, 840, 840, 840, 840, 840, 920, 920, 920, 920, 920
] # add/remove here if more needed
r_pls = [
1e-3, 1e-4, 1e-5, 1e-6, 1e-7, 1e-3, 1e-4, 1e-5, 1e-6, 1e-7, 1e-3, 1e-4,
1e-5, 1e-6, 1e-7
] # add/remove here if more needed
pset = ParticleSet.from_list(
fieldset=fieldset, # the fields on which the particles are advected
pclass=
plastic_particle, # the type of particles (JITParticle or ScipyParticle)
lon=lon_release, #-160., # a vector of release longitudes
lat=lat_release, #36.,
time=np.datetime64('%s-%s-05' % (yr1, mon)),
depth=z_release,
r_pl=r_pls[0] * np.ones(np.array(lon_release).size),
rho_pl=rho_pls[0] * np.ones(np.array(lon_release).size),
r_tot=r_pls[0] * np.ones(np.array(lon_release).size),
rho_tot=rho_pls[0] * np.ones(np.array(lon_release).size))
for r_pl, rho_pl in zip(r_pls[1:], rho_pls[1:]):
pset.add(
ParticleSet.from_list(
fieldset=fieldset, # the fields on which the particles are advected
pclass=
plastic_particle, # the type of particles (JITParticle or ScipyParticle)
lon=lon_release, #-160., # a vector of release longitudes
lat=lat_release, #36.,
time=np.datetime64('%s-%s-05' % (yr1, mon)),
def test_periodic(mode, time_periodic, dt_sign):
lon = np.array([0, 1], dtype=np.float32)
lat = np.array([0, 1], dtype=np.float32)
depth = np.array([0, 1], dtype=np.float32)
tsize = 24 * 60 + 1
period = 86400
time = np.linspace(0, period, tsize, dtype=np.float64)
def temp_func(time):
return 20 + 2 * np.sin(time * 2 * np.pi / period)
temp_vec = temp_func(time)
U = np.zeros((2, 2, 2, tsize), dtype=np.float32)
V = np.zeros((2, 2, 2, tsize), dtype=np.float32)
V[0, 0, 0, :] = 1e-5
W = np.zeros((2, 2, 2, tsize), dtype=np.float32)
temp = np.zeros((2, 2, 2, tsize), dtype=np.float32)
temp[:, :, :, :] = temp_vec
data = {'U': U, 'V': V, 'W': W, 'temp': temp}
dimensions = {'lon': lon, 'lat': lat, 'depth': depth, 'time': time}
fieldset = FieldSet.from_data(data,
dimensions,
mesh='flat',
time_periodic=time_periodic,
transpose=True,
allow_time_extrapolation=True)
def sampleTemp(particle, fieldset, time):
# Note that fieldset.temp is interpolated at time=time+dt.
# Indeed, sampleTemp is called at time=time, but the result is written
# at time=time+dt, after the Kernel update
particle.temp = fieldset.temp[time + particle.dt, particle.depth,
particle.lat, particle.lon]
# test if we can interpolate UV and UVW together
(particle.u1, particle.v1) = fieldset.UV[time + particle.dt,
particle.depth, particle.lat,
particle.lon]
(particle.u2, particle.v2,
w_) = fieldset.UVW[time + particle.dt, particle.depth, particle.lat,
particle.lon]
class MyParticle(ptype[mode]):
temp = Variable('temp', dtype=np.float32, initial=20.)
u1 = Variable('u1', dtype=np.float32, initial=0.)
u2 = Variable('u2', dtype=np.float32, initial=0.)
v1 = Variable('v1', dtype=np.float32, initial=0.)
v2 = Variable('v2', dtype=np.float32, initial=0.)
pset = ParticleSet.from_list(fieldset,
pclass=MyParticle,
lon=[0.5],
lat=[0.5],
depth=[0.5])
pset.execute(AdvectionRK4_3D + pset.Kernel(sampleTemp),
runtime=delta(hours=51),
dt=delta(hours=dt_sign * 1))
if time_periodic is not False:
t = pset.time[0]
temp_theo = temp_func(t)
elif dt_sign == 1:
temp_theo = temp_vec[-1]
elif dt_sign == -1:
temp_theo = temp_vec[0]
assert np.allclose(temp_theo, pset.temp[0], atol=1e-5)
assert np.allclose(pset.u1[0], pset.u2[0])
assert np.allclose(pset.v1[0], pset.v2[0])
def test_multi_structured_grids(mode):
def temp_func(lon, lat):
return 20 + lat / 1000. + 2 * np.sin(lon * 2 * np.pi / 5000.)
a = 10000
b = 10000
# Grid 0
xdim_g0 = 201
ydim_g0 = 201
# Coordinates of the test fieldset (on A-grid in deg)
lon_g0 = np.linspace(0, a, xdim_g0, dtype=np.float32)
lat_g0 = np.linspace(0, b, ydim_g0, dtype=np.float32)
time_g0 = np.linspace(0., 1000., 2, dtype=np.float64)
grid_0 = RectilinearZGrid(lon_g0, lat_g0, time=time_g0)
# Grid 1
xdim_g1 = 51
ydim_g1 = 51
# Coordinates of the test fieldset (on A-grid in deg)
lon_g1 = np.linspace(0, a, xdim_g1, dtype=np.float32)
lat_g1 = np.linspace(0, b, ydim_g1, dtype=np.float32)
time_g1 = np.linspace(0., 1000., 2, dtype=np.float64)
grid_1 = RectilinearZGrid(lon_g1, lat_g1, time=time_g1)
u_data = np.ones((lon_g0.size, lat_g0.size, time_g0.size),
dtype=np.float32)
u_data = 2 * u_data
u_field = Field('U', u_data, grid=grid_0, transpose=True)
temp0_data = np.empty((lon_g0.size, lat_g0.size, time_g0.size),
dtype=np.float32)
for i in range(lon_g0.size):
for j in range(lat_g0.size):
temp0_data[i, j, :] = temp_func(lon_g0[i], lat_g0[j])
temp0_field = Field('temp0', temp0_data, grid=grid_0, transpose=True)
v_data = np.zeros((lon_g1.size, lat_g1.size, time_g1.size),
dtype=np.float32)
v_field = Field('V', v_data, grid=grid_1, transpose=True)
temp1_data = np.empty((lon_g1.size, lat_g1.size, time_g1.size),
dtype=np.float32)
for i in range(lon_g1.size):
for j in range(lat_g1.size):
temp1_data[i, j, :] = temp_func(lon_g1[i], lat_g1[j])
temp1_field = Field('temp1', temp1_data, grid=grid_1, transpose=True)
other_fields = {}
other_fields['temp0'] = temp0_field
other_fields['temp1'] = temp1_field
field_set = FieldSet(u_field, v_field, fields=other_fields)
def sampleTemp(particle, fieldset, time, dt):
# Note that fieldset.temp is interpolated at time=time+dt.
# Indeed, sampleTemp is called at time=time, but the result is written
# at time=time+dt, after the Kernel update
particle.temp0 = fieldset.temp0[time + dt, particle.lon, particle.lat,
particle.depth]
particle.temp1 = fieldset.temp1[time + dt, particle.lon, particle.lat,
particle.depth]
class MyParticle(ptype[mode]):
temp0 = Variable('temp0', dtype=np.float32, initial=20.)
temp1 = Variable('temp1', dtype=np.float32, initial=20.)
pset = ParticleSet.from_list(field_set, MyParticle, lon=[3001], lat=[5001])
pset.execute(AdvectionRK4 + pset.Kernel(sampleTemp), runtime=1, dt=1)
assert np.allclose(pset.particles[0].temp0,
pset.particles[0].temp1,
atol=1e-3)
def SampleTemp(particle, fieldset, time):
particle.temp = fieldset.temp[time, particle.depth, particle.lat,
particle.lon]
def SampleBathy(particle, fieldset, time):
particle.bathy = fieldset.bathy[0, 0, particle.lat, particle.lon]
time0 = fieldset.U.grid.time[0]
time = [time0] * len(lon)
pset = ParticleSet.from_list(fieldset,
pclass=SampleParticle,
lon=lon,
lat=lat,
time=time,
repeatdt=repeatdt)
pfile = pset.ParticleFile(out_file, outputdt=delta(days=1))
kernels = pset.Kernel(
AdvectionRK4
) + SampleAge + SampleTemp + SampleBathy + SampleDistance + BrownianMotion2D
pset.execute(kernels,
dt=delta(minutes=5),
output_file=pfile,
verbose_progress=True,
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle},
endtime=end_time)
def test_nemo_grid(mode):
data_path = path.join(path.dirname(__file__), 'test_data/')
mesh_filename = data_path + 'mask_nemo_cross_180lon.nc'
rotation_angles_filename = data_path + 'rotation_angles_nemo_cross_180lon.nc'
compute_curvilinearGrid_rotationAngles(mesh_filename,
rotation_angles_filename)
filenames = {
'U': data_path + 'Uu_eastward_nemo_cross_180lon.nc',
'V': data_path + 'Vv_eastward_nemo_cross_180lon.nc',
'cosU': rotation_angles_filename,
'sinU': rotation_angles_filename,
'cosV': rotation_angles_filename,
'sinV': rotation_angles_filename
}
variables = {
'U': 'U',
'V': 'V',
'cosU': 'cosU',
'sinU': 'sinU',
'cosV': 'cosV',
'sinV': 'sinV'
}
dimensions = {
'U': {
'lon': 'nav_lon_u',
'lat': 'nav_lat_u'
},
'V': {
'lon': 'nav_lon_v',
'lat': 'nav_lat_v'
},
'cosU': {
'lon': 'glamu',
'lat': 'gphiu'
},
'sinU': {
'lon': 'glamu',
'lat': 'gphiu'
},
'cosV': {
'lon': 'glamv',
'lat': 'gphiv'
},
'sinV': {
'lon': 'glamv',
'lat': 'gphiv'
}
}
field_set = FieldSet.from_netcdf(filenames,
variables,
dimensions,
mesh='spherical')
def sampleVel(particle, fieldset, time, dt):
(particle.zonal, particle.meridional) = fieldset.UV[time, particle.lon,
particle.lat,
particle.depth]
class MyParticle(ptype[mode]):
zonal = Variable('zonal', dtype=np.float32, initial=0.)
meridional = Variable('meridional', dtype=np.float32, initial=0.)
lonp = 175.5
latp = 81.5
pset = ParticleSet.from_list(field_set, MyParticle, lon=[lonp], lat=[latp])
pset.execute(pset.Kernel(sampleVel), runtime=0, dt=0)
u = field_set.U.units.to_source(pset[0].zonal, lonp, latp, 0)
v = field_set.V.units.to_source(pset[0].meridional, lonp, latp, 0)
assert abs(u - 1) < 1e-4
assert abs(v) < 1e-4
def test_cgrid_uniform_3dvel_spherical(mode, vert_mode, time):
data_path = path.join(path.dirname(__file__), 'test_data/')
dim_file = xr.open_dataset(data_path + 'mask_nemo_cross_180lon.nc')
u_file = xr.open_dataset(data_path + 'Uu_eastward_nemo_cross_180lon.nc')
v_file = xr.open_dataset(data_path + 'Vv_eastward_nemo_cross_180lon.nc')
j = 4
i = 11
lon = np.array(dim_file.glamf[0, j:j + 2, i:i + 2])
lat = np.array(dim_file.gphif[0, j:j + 2, i:i + 2])
U = np.array(u_file.U[0, j:j + 2, i:i + 2])
V = np.array(v_file.V[0, j:j + 2, i:i + 2])
trash = np.zeros((2, 2))
U = np.stack((U, trash))
V = np.stack((V, trash))
w0 = 1
w1 = 1
W = np.array([[[-99, -99], [-99, w0]], [[-99, -99], [-99, w1]]])
if vert_mode == 'zlev':
depth = np.array([0, 1])
elif vert_mode == 'slev1':
depth = np.array([[[0, 0], [0, 0]], [[1, 1], [1, 1]]])
if time:
U = np.stack((U, U))
V = np.stack((V, V))
W = np.stack((W, W))
dimensions = {
'lat': lat,
'lon': lon,
'depth': depth,
'time': np.array([0, 10])
}
else:
dimensions = {'lat': lat, 'lon': lon, 'depth': depth}
data = {
'U': np.array(U, dtype=np.float32),
'V': np.array(V, dtype=np.float32),
'W': np.array(W, dtype=np.float32)
}
fieldset = FieldSet.from_data(data, dimensions, mesh='spherical')
fieldset.U.interp_method = 'cgrid_velocity'
fieldset.V.interp_method = 'cgrid_velocity'
fieldset.W.interp_method = 'cgrid_velocity'
def sampleVel(particle, fieldset, time):
(particle.zonal, particle.meridional,
particle.vertical) = fieldset.UVW[time, particle.depth, particle.lat,
particle.lon]
class MyParticle(ptype[mode]):
zonal = Variable('zonal', dtype=np.float32, initial=0.)
meridional = Variable('meridional', dtype=np.float32, initial=0.)
vertical = Variable('vertical', dtype=np.float32, initial=0.)
lonp = 179.8
latp = 81.35
pset = ParticleSet.from_list(fieldset,
MyParticle,
lon=lonp,
lat=latp,
depth=.2)
pset.execute(pset.Kernel(sampleVel), runtime=0, dt=0)
pset[0].zonal = fieldset.U.units.to_source(pset[0].zonal, lonp, latp, 0)
pset[0].meridional = fieldset.V.units.to_source(pset[0].meridional, lonp,
latp, 0)
assert abs(pset[0].zonal - 1) < 1e-3
assert abs(pset[0].meridional) < 1e-3
assert abs(pset[0].vertical - 1) < 1e-3
def test_popgrid(mode, vert_discretisation, deferred_load):
mesh = path.join(path.join(path.dirname(__file__), 'test_data'),
'POPtestdata_time.nc')
if vert_discretisation == 'zlevel':
w_dep = 'w_dep'
elif vert_discretisation == 'slevel':
w_dep = 'w_deps' # same as zlevel, but defined as slevel
elif vert_discretisation == 'slevel2':
w_dep = 'w_deps2' # contains shaved cells
filenames = mesh
variables = {'U': 'U', 'V': 'V', 'W': 'W', 'T': 'T'}
dimensions = {'lon': 'lon', 'lat': 'lat', 'depth': w_dep, 'time': 'time'}
field_set = FieldSet.from_pop(filenames,
variables,
dimensions,
mesh='flat',
deferred_load=deferred_load)
def sampleVel(particle, fieldset, time):
(particle.zonal, particle.meridional,
particle.vert) = fieldset.UVW[time, particle.depth, particle.lat,
particle.lon]
particle.tracer = fieldset.T[time, particle.depth, particle.lat,
particle.lon]
def OutBoundsError(particle, fieldset, time):
particle.out_of_bounds = 1
particle.depth -= 3
class MyParticle(ptype[mode]):
zonal = Variable('zonal', dtype=np.float32, initial=0.)
meridional = Variable('meridional', dtype=np.float32, initial=0.)
vert = Variable('vert', dtype=np.float32, initial=0.)
tracer = Variable('tracer', dtype=np.float32, initial=0.)
out_of_bounds = Variable('out_of_bounds', dtype=np.float32, initial=0.)
pset = ParticleSet.from_list(field_set,
MyParticle,
lon=[3, 5, 1],
lat=[3, 5, 1],
depth=[3, 7, 11])
pset.execute(pset.Kernel(sampleVel),
runtime=1,
dt=1,
recovery={ErrorCode.ErrorOutOfBounds: OutBoundsError})
if vert_discretisation == 'slevel2':
assert np.isclose(pset.vert[0], 0.)
assert np.isclose(pset.zonal[0], 0.)
assert np.isclose(pset.tracer[0], 99.)
assert np.isclose(pset.vert[1], -0.0066666666)
assert np.isclose(pset.zonal[1], .015)
assert np.isclose(pset.tracer[1], 1.)
assert pset.out_of_bounds[0] == 0
assert pset.out_of_bounds[1] == 0
assert pset.out_of_bounds[2] == 1
else:
assert np.allclose(pset.zonal, 0.015)
assert np.allclose(pset.meridional, 0.01)
assert np.allclose(pset.vert, -0.01)
assert np.allclose(pset.tracer, 1)
def compute_swash_particle_advection(field_set, mode, lonp, latp, depthp):
pset = ParticleSet.from_list(field_set, ptype[mode], lon=lonp, lat=latp, depth=depthp)
pfile = ParticleFile("swash_particles_chunk", pset, outputdt=delta(seconds=0.05))
pset.execute(AdvectionRK4, runtime=delta(seconds=0.2), dt=delta(seconds=0.005), output_file=pfile)
return pset
def compute_pop_particle_advection(field_set, mode, lonp, latp):
pset = ParticleSet.from_list(field_set, ptype[mode], lon=lonp, lat=latp)
pfile = ParticleFile("globcurrent_particles_chunk", pset, outputdt=delta(days=15))
pset.execute(AdvectionRK4, runtime=delta(days=90), dt=delta(days=2), output_file=pfile)
return pset
def get_traj_with_parcels(date, runtime, delta_time, particle_grid_step,
stream_data_fname):
"""Compute trajectories of particles in the sea using parcels library.
Compute trajectories of particles in the sea at a given date, in a static 2D
field of stream. Trajectories are saved in a .nc file.
Args:
date (int) : Day in number of days relatively to the data time origin at
which the stream data should be taken.
runtime (int) : Total duration in hours of the field integration.
Trajectories length increases with the runtime.
delta_time (int) : Time step in hours of the integration.
particle_grid_step (int) : Grid step size for the initial positions of
the particles. The unit is the data index step, ie data dx and dy.
stream_data_fname (str) : Complete name of the stream data file.
Returns:
stream_line_list (list of classes.StreamLine) : The list of trajectories
Notes:
The input file is expected to contain the daily mean fields of east- and
northward ocean current velocity (uo,vo) in a format as described here:
http://marine.copernicus.eu/documents/PUM/CMEMS-GLO-PUM-001-024.pdf.
"""
# Loading data
data_set = nc.Dataset(stream_data_fname)
u_1day = data_set['uo'][date, 0, :]
v_1day = data_set['vo'][date, 0, :]
# Data sizes
data_time_size, data_depth_size, data_lat_size, data_lon_size = np.shape(
data_set['uo'])
longitudes = np.array(data_set['longitude'])
latitudes = np.array(data_set['latitude'])
# Replace the mask (ie the ground areas) with a null vector field.
U = np.array(u_1day)
U[U == -32767] = 0
V = np.array(v_1day)
V[V == -32767] = 0
# Initialize a field set using the data set.
data = {'U': U, 'V': V}
dimensions = {'lon': longitudes, 'lat': latitudes}
fieldset = FieldSet.from_data(data, dimensions, mesh='spherical')
fieldset.U.interp_method = 'cgrid_velocity'
fieldset.V.interp_method = 'cgrid_velocity'
# List of initial positions of the particles. Particles on the ground are
# removed.
init_pos = []
for lon in range(0, data_lon_size, particle_grid_step):
for lat in range(0, data_lat_size, particle_grid_step):
if not u_1day[lat, lon] is np.ma.masked:
init_pos.append([longitudes[lon], latitudes[lat]])
init_pos = np.array(init_pos)
init_longitudes = init_pos[:, 0]
init_latitudes = init_pos[:, 1]
# Initialize particle set
pSet = ParticleSet.from_list(fieldset,
ScipyParticle,
init_longitudes,
init_latitudes,
depth=None,
time=None)
# Initialize output file and run simulation
def DeleteParticle(particle, fieldset, time):
particle.delete()
output = pSet.ParticleFile(name="trajectories_temp.nc",
outputdt=delta(hours=delta_time))
pSet.execute(AdvectionRK4,
runtime=delta(hours=runtime),
dt=np.inf,
output_file=output,
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
output.close()
# Load simulation results and create the stream line list
nc_traj = nc.Dataset("trajectories_temp.nc")
trajectories = np.zeros(
(nc_traj.dimensions['traj'].size, nc_traj.dimensions['obs'].size, 2))
trajectories[:, :, 0] = np.array(nc_traj['lon'])
trajectories[:, :, 1] = np.array(nc_traj['lat'])
stream_line_list = []
for trajectory in trajectories:
stream_line_list.append(
StreamLine(trajectory[np.isfinite(trajectory[:, 0])],
delta_time * 3600))
# Clean working dir
os.system("rm -r trajectories_temp*")
return stream_line_list
prevlon = Variable('prevlon', dtype=np.float64, initial=0., to_write=False)
prevlat = Variable('prevlat', dtype=np.float64, initial=0., to_write=False)
prevdep = Variable('prevdep', dtype=np.float64, initial=0., to_write=False)
if options['hdiffusion']==False and options['vdiffusion']==False:
npart=1
lon0=np.zeros(npart*len(options['x0']));lat0=np.zeros(npart*len(options['x0']));depth0=np.zeros(npart*len(options['x0']));
for i in range(0,len(options['x0'])):
lon0[i*npart:(i+1)*npart] = options['x0'][i]
lat0[i*npart:(i+1)*npart] = options['y0'][i]
depth0[i*npart:(i+1)*npart] = options['z0'][i]
repeatdt=delta(minutes=options['repeatdt']) # release particles every...
pset = ParticleSet.from_list(fieldset=fieldset, pclass=ForCoastParticle,
lon=lon0, lat=lat0, depth=depth0,
time=np.datetime64(options['sdate']),
repeatdt=repeatdt,
lonlatdepth_dtype=np.float64 )
# CHOOSE KERNELS
if options['stokes']:
kernels = pset.Kernel(Dbl_AdvectionRK4_3D_clumsy) if options['run3D'] else pset.Kernel(Dbl_AdvectionRK4)
else:
kernels = pset.Kernel(AdvectionRK4_3D) if options['run3D'] else pset.Kernel(AdvectionRK4, delete_cfiles=False)
if options['hdiffusion']:
print('Using horizontal diffusion')
kernels += DiffusionUniformKh
if options['run3D'] and options['vdiffusion']:
print('Using vertical diffusion')
def parcels_particle_run(k, v):
L.info(f'Received Input: {v}')
L.info("Loading vectors from model...")
datapath = Path(__file__).parent.parent / 'data'
with xr.open_mfdataset(str(datapath / 'ncom_socal' /
'socal_2017-01-0[1-9].nc'),
decode_cf=False) as undecoded:
time_units = undecoded.time.units
time_calendar = undecoded.time.calendar
with xr.open_mfdataset(
str(datapath / 'ncom_socal' / 'socal_2017-01-0[1-9].nc')) as ds:
uv = ds[['water_u', 'water_v']]
uv = uv.isel(depth=0)
variables = {'U': 'water_u', 'V': 'water_v'}
dimensions = {'lat': 'lat', 'lon': 'lon', 'time': 'time'}
xr_fieldset = FieldSet.from_xarray_dataset(
uv, variables, dimensions, allow_time_extrapolation=True)
L.info("Created Fieldset")
expanded_rows = []
df = pd.DataFrame.from_records(v['records'])
for ix, row in df.iterrows():
expanded_rows.append(
pd.concat([row] * int(row.nparticles), ignore_index=True,
axis=1).T)
expanded_df = pd.concat(expanded_rows, axis=0).reset_index()
expanded_df = expanded_df.drop(columns=['index', 'nparticles'])
L.info(f"Expanded and Loaded {len(expanded_df)} Particles!")
L.info("Converting particle release time to the model base unit...")
expanded_df.time = cftime.date2num(pd.DatetimeIndex(
expanded_df.time).to_pydatetime(),
units=time_units,
calendar=time_calendar)
csv_pset = ParticleSet.from_list(fieldset=xr_fieldset,
pclass=JITParticle,
lon=expanded_df.lon,
lat=expanded_df.lat,
time=expanded_df.time.values)
L.info("Created ParticleSet")
runlength = timedelta(days=6)
timestep = timedelta(minutes=5)
rigthnow = datetime.utcnow()
output_file = datapath / 'particle_runs' / f'{v["id"]}_{rigthnow:%Y%m%dT%H%M%S.%f}.nc'
output_file.parent.mkdir(exist_ok=True, parents=True)
output = csv_pset.ParticleFile(name=str(output_file),
outputdt=timedelta(hours=3))
L.info("Running...")
csv_pset.execute(AdvectionRK4,
runtime=runlength,
dt=timestep,
output_file=output)
L.info(f'Complete! Saved output: {output_file}')
kafka_base = 'kafka-int'
p = EasyAvroProducer(schema_registry_url=f'http://{kafka_base}:7002',
kafka_brokers=[f'{kafka_base}:7001'],
kafka_topic='mil-darpa-oot-particle-completed',
key_schema='nokey')
to_send = [(None, {'id': v['id'], 'filepath': str(output_file)})]
p.produce(to_send)
L.info("Sent simulation completed message")
def deleteParticle(particle, fieldset, time):
# Recovery kernel to delete a particle if an error occurs
particle.delete()
##############################################################################
# INITIALISE SIMULATION AND RUN #
##############################################################################
pset = ParticleSet.from_list(fieldset=fieldset,
pclass=debris,
lonlatdepth_dtype=np.float64,
lon=particles['pos']['lon'],
lat=particles['pos']['lat'],
time=particles['pos']['time'],
rp0=particles['pos']['rp0'],
cp0=particles['pos']['cp0'],
source_id=particles['pos']['iso'],
source_cell=particles['pos']['id'])
print(str(len(particles['pos']['time'])) + ' particles released!')
if param['test']:
traj = pset.ParticleFile(name=fh['traj'], outputdt=param['dt_out'])
else:
traj = pset.ParticleFile(name=fh['traj'], write_ondelete=True)
kernels = (pset.Kernel(AdvectionRK4) + pset.Kernel(periodicBC) +
pset.Kernel(antibeach) + pset.Kernel(event))
def test_cgrid_uniform_3dvel(mode, vert_mode, time):
lon = np.array([[0, 2], [.4, 1.5]])
lat = np.array([[0, -.5], [.8, .5]])
u0 = 4.4721359549995793e-01
u1 = 1.3416407864998738e+00
v0 = 1.2126781251816650e+00
v1 = 1.2278812270298409e+00
w0 = 1
w1 = 1
if vert_mode == 'zlev':
depth = np.array([0, 1])
elif vert_mode == 'slev1':
depth = np.array([[[0, 0], [0, 0]], [[1, 1], [1, 1]]])
elif vert_mode == 'slev2':
depth = np.array([[[-1, -.6], [-1.1257142857142859, -.9]],
[[1, 1.5], [0.50857142857142845, .8]]])
w0 = 1.0483007922296661e+00
w1 = 1.3098951476312375e+00
U = np.array([[[-99, -99], [u0, u1]], [[-99, -99], [-99, -99]]])
V = np.array([[[-99, v0], [-99, v1]], [[-99, -99], [-99, -99]]])
W = np.array([[[-99, -99], [-99, w0]], [[-99, -99], [-99, w1]]])
if time:
U = np.stack((U, U))
V = np.stack((V, V))
W = np.stack((W, W))
dimensions = {
'lat': lat,
'lon': lon,
'depth': depth,
'time': np.array([0, 10])
}
else:
dimensions = {'lat': lat, 'lon': lon, 'depth': depth}
data = {
'U': np.array(U, dtype=np.float32),
'V': np.array(V, dtype=np.float32),
'W': np.array(W, dtype=np.float32)
}
fieldset = FieldSet.from_data(data, dimensions, mesh='flat')
fieldset.U.interp_method = 'cgrid_velocity'
fieldset.V.interp_method = 'cgrid_velocity'
fieldset.W.interp_method = 'cgrid_velocity'
def sampleVel(particle, fieldset, time):
(particle.zonal, particle.meridional,
particle.vertical) = fieldset.UVW[time, particle.depth, particle.lat,
particle.lon]
class MyParticle(ptype[mode]):
zonal = Variable('zonal', dtype=np.float32, initial=0.)
meridional = Variable('meridional', dtype=np.float32, initial=0.)
vertical = Variable('vertical', dtype=np.float32, initial=0.)
pset = ParticleSet.from_list(fieldset,
MyParticle,
lon=.7,
lat=.3,
depth=.2)
pset.execute(pset.Kernel(sampleVel), runtime=0, dt=0)
assert abs(pset[0].zonal - 1) < 1e-6
assert abs(pset[0].meridional - 1) < 1e-6
assert abs(pset[0].vertical - 1) < 1e-6
#field_set.U.show()
# Make particles initial position list
nc_fid = Dataset(grid_file, 'r') #open grid file nc to read
#lats = nc_fid.variables['nav_lat'][:] # extract/copy the data
#lons = nc_fid.variables['nav_lon'][:]
#lonE=lons[:,169-3]
#latE=lats[:,169-3]
npart = 30
lonp = [i for i in np.linspace(-88.18, -88.20, npart)]
latp = [i for i in np.linspace(17.52, 17.53, npart)] #this makes a list!
pset = ParticleSet.from_list(field_set, JITParticle, lon=lonp, lat=latp)
pfile = ParticleFile("tBelize_nemo_particles_30halfD", pset, outputdt=delta(hours=0.5))
kernels = pset.Kernel(AdvectionRK4)
#Plot initial positions
#pset.show()
pset.execute(kernels, runtime=delta(days=0.5), dt=delta(hours=0.1), output_file=pfile)
#plotTrajectoriesFile("Belize_nemo_particles_t2.nc");
#pset.show(domain={'N':-31, 'S':-35, 'E':33, 'W':26})
#pset.show(field=field_set.U)
#pset.show(field=fieldset.U, show_time=datetime(2002, 1, 10, 2))
#pset.show(field=fieldset.U, show_time=datetime(2002, 1, 10, 2), with_particles=False)
end = time.time()
pospartic[0, 0] = -13.072
for i in range(1, numpart):
if numpart == 1:
break
pospartic[i, 0] = pospartic[0, 0] - i * 0.02
pospartic[:, 1] = -38.45
return pospartic
pospartic = criaPosPartic()
#definindo partículas#
pset = ParticleSet.from_list(fieldset=fset,
pclass=JITParticle,
lat=pospartic[:, 0],
lon=pospartic[:, 1],
repeatdt=timedelta(hours=12))
#############################################################################
############################## Criando Output ###############################
#############################################################################
#criando o que fazer em condição de recovery#
def OutOfBounds(particle, fieldset, time):
particle.delete()
output_file = pset.ParticleFile(name=outname, outputdt=timedelta(seconds=3600))
fieldset = FieldSet(U=fieldset_ocean.U + fieldset_wave.U,
V=fieldset_ocean.V + fieldset_wave.V)
def deleteParticle(particle, fieldset, time):
# Recovery kernel to delete a particle if it leaves the domain
# (possible in certain configurations)
particle.delete()
##############################################################################
# INITIALISE SIMULATION AND RUN #
##############################################################################
pset = ParticleSet.from_list(fieldset=fieldset,
pclass=JITParticle,
lon=lon0,
lat=lat0,
time=t0)
traj = pset.ParticleFile(name=fh['traj'], outputdt=param['dt_out'])
kernels = (pset.Kernel(AdvectionRK4))
pset.execute(kernels,
endtime=param['endtime'],
dt=param['dt_RK4'],
recovery={ErrorCode.ErrorOutOfBounds: deleteParticle},
output_file=traj)
traj.export()
def test_advect_nemo(mode):
data_path = path.join(path.dirname(__file__), 'test_data/')
mesh_filename = data_path + 'mask_nemo_cross_180lon.nc'
rotation_angles_filename = data_path + 'rotation_angles_nemo_cross_180lon.nc'
variables = {
'cosU': 'cosU',
'sinU': 'sinU',
'cosV': 'cosV',
'sinV': 'sinV'
}
dimensions = {
'U': {
'lon': 'glamu',
'lat': 'gphiu'
},
'V': {
'lon': 'glamv',
'lat': 'gphiv'
},
'F': {
'lon': 'glamf',
'lat': 'gphif'
}
}
compute_curvilinearGrid_rotationAngles(mesh_filename,
rotation_angles_filename, variables,
dimensions)
filenames = {
'U': data_path + 'Uu_eastward_nemo_cross_180lon.nc',
'V': data_path + 'Vv_eastward_nemo_cross_180lon.nc',
'cosU': rotation_angles_filename,
'sinU': rotation_angles_filename,
'cosV': rotation_angles_filename,
'sinV': rotation_angles_filename
}
variables = {
'U': 'U',
'V': 'V',
'cosU': 'cosU',
'sinU': 'sinU',
'cosV': 'cosV',
'sinV': 'sinV'
}
dimensions = {
'U': {
'lon': 'nav_lon_u',
'lat': 'nav_lat_u'
},
'V': {
'lon': 'nav_lon_v',
'lat': 'nav_lat_v'
},
'cosU': {
'lon': 'glamu',
'lat': 'gphiu'
},
'sinU': {
'lon': 'glamu',
'lat': 'gphiu'
},
'cosV': {
'lon': 'glamv',
'lat': 'gphiv'
},
'sinV': {
'lon': 'glamv',
'lat': 'gphiv'
}
}
field_set = FieldSet.from_netcdf(filenames,
variables,
dimensions,
mesh='spherical',
allow_time_extrapolation=True)
lonp = 175.5
latp = 81.5
pset = ParticleSet.from_list(field_set,
ptype[mode],
lon=[lonp],
lat=[latp])
pset.execute(AdvectionRK4, runtime=delta(days=2), dt=delta(hours=6))
assert abs(pset[0].lat - latp) < 1e-3
particle.delete()
recovery = {
ErrorCode.ErrorOutOfBounds: DeleteParticle,
ErrorCode.ErrorThroughSurface: DeleteParticle
}
#cover domain in particles
lon = np.linspace(ds.lon_rho.min(), ds.lon_rho.max(), num=2**6)
lat = np.linspace(ds.lat_rho.min(), ds.lat_rho.max(), num=2**6)
lons, lats = np.meshgrid(lon, lat)
pset = ParticleSet.from_list(fieldset=fieldset,
pclass=JITParticle,
time=ds.ocean_time.values[0],
lon=lons,
lat=lats,
depth=depth)
kernels = AdvectionRK4
output_file = pset.ParticleFile(name="/work/wtorres/temp/reefParticles",
outputdt=delta(seconds=60))
pset.execute(kernels,
runtime=delta(hours=12.0),
dt=delta(seconds=60),
output_file=output_file,
recovery=recovery)
output_file.export()
output_file.close()
def deleteParticle(particle, fieldset, time):
# Recovery kernel to delete a particle if an error occurs
particle.delete()
##############################################################################
# INITIALISE SIMULATION AND RUN #
##############################################################################
pset = ParticleSet.from_list(fieldset=fieldset,
pclass=debris,
lonlatdepth_dtype=np.float64,
lon=particles['pos']['lon'],
lat=particles['pos']['lat'],
time=particles['pos']['time'],
gfw_num=particles['pos']['gfw'],
lon0=particles['pos']['lon'],
lat0=particles['pos']['lat'])
print(str(len(particles['pos']['time'])) + ' particles released!')
if param['test']:
traj = pset.ParticleFile(name=fh['traj'], outputdt=param['dt_out'])
else:
traj = pset.ParticleFile(name=fh['traj'], write_ondelete=True)
kernels = (pset.Kernel(AdvectionRK4) + pset.Kernel(periodicBC) +
pset.Kernel(antibeach) + pset.Kernel(event))
xsi*eta * latCorners[2] + (1-xsi)*eta * latCorners[3]
lonCorners = [1.37941658, 1.63887346, 1.67183721, 1.41217935]
latCorners = [51.58309555, 51.56196213, 51.71636581, 51.73773575]
lon_t = (1-xsi)*(1-eta) * lonCorners[0] + xsi*(1-eta) * lonCorners[1] + \
xsi*eta * lonCorners[2] + (1-xsi)*eta * lonCorners[3]
lat_t = (1-xsi)*(1-eta) * latCorners[0] + xsi*(1-eta) * latCorners[1] + \
xsi*eta * latCorners[2] + (1-xsi)*eta * latCorners[3]
lons = np.concatenate((lon_r.flatten(), lon_t.flatten()))
lats = np.concatenate((lat_r.flatten(), lat_t.flatten()))
times = np.arange(np.datetime64('2000-01-05'), np.datetime64('2001-01-05'))
pset = ParticleSet.from_list(fieldset,
PlasticParticle,
lon=np.tile(lons, [len(times)]),
lat=np.tile(lats, [len(times)]),
time=np.repeat(times, len(lons)))
kernel = AdvectionRK4 #+ pset.Kernel(Ageing)
new_write = True
timer.particlefile = timer.Timer('ParticleFile', parent=timer.root)
outfile = './' + __file__[:-3]
pfile = ParticleFile(outfile, pset)
if new_write:
pfile.write_pickle_per_tstep(pset, pset[0].time)
else:
pfile.write(pset, pset[0].time)
def test_rectilinear_s_grid_sampling(mode, z4d):
lon_g0 = np.linspace(-3e4, 3e4, 61, dtype=np.float32)
lat_g0 = np.linspace(0, 1000, 2, dtype=np.float32)
time_g0 = np.linspace(0, 1000, 2, dtype=np.float64)
if z4d:
depth_g0 = np.zeros((time_g0.size, 5, lat_g0.size, lon_g0.size),
dtype=np.float32)
else:
depth_g0 = np.zeros((5, lat_g0.size, lon_g0.size), dtype=np.float32)
def bath_func(lon):
bath = (lon <= -2e4) * 20.
bath += (lon > -2e4) * (lon < 2e4) * (
110. + 90 * np.sin(lon / 2e4 * np.pi / 2.))
bath += (lon >= 2e4) * 200.
return bath
bath = bath_func(lon_g0)
zdim = depth_g0.shape[-3]
for i in range(depth_g0.shape[-1]):
for k in range(zdim):
if z4d:
depth_g0[:, k, :, i] = bath[i] * k / (zdim - 1)
else:
depth_g0[k, :, i] = bath[i] * k / (zdim - 1)
grid = RectilinearSGrid(lon_g0, lat_g0, depth=depth_g0, time=time_g0)
u_data = np.zeros((grid.tdim, grid.zdim, grid.ydim, grid.xdim),
dtype=np.float32)
v_data = np.zeros((grid.tdim, grid.zdim, grid.ydim, grid.xdim),
dtype=np.float32)
temp_data = np.zeros((grid.tdim, grid.zdim, grid.ydim, grid.xdim),
dtype=np.float32)
for k in range(1, zdim):
temp_data[:, k, :, :] = k / (zdim - 1.)
u_field = Field('U', u_data, grid=grid)
v_field = Field('V', v_data, grid=grid)
temp_field = Field('temp', temp_data, grid=grid)
other_fields = {}
other_fields['temp'] = temp_field
field_set = FieldSet(u_field, v_field, fields=other_fields)
def sampleTemp(particle, fieldset, time, dt):
particle.temp = fieldset.temp[time, particle.lon, particle.lat,
particle.depth]
class MyParticle(ptype[mode]):
temp = Variable('temp', dtype=np.float32, initial=20.)
lon = 400
lat = 0
ratio = .3
pset = ParticleSet.from_list(field_set,
MyParticle,
lon=[lon],
lat=[lat],
depth=[bath_func(lon) * ratio])
pset.execute(pset.Kernel(sampleTemp), runtime=0, dt=0)
assert np.allclose(pset.particles[0].temp, ratio, atol=1e-4)
timer.fieldset = timer.Timer('FieldSet', parent=timer.root)
field_set = get_cmems_fieldset(2013)
timer.fieldset.stop()
kernel = AdvectionRK4
time0 = field_set.U.grid.time[0]
lonv = np.arange(-6, 10.1, .2)
latv = np.arange(50, 63, .2)
lon, lat = np.meshgrid(lonv, latv)
lon = lon.flatten()
lat = lat.flatten()
time = time0 * np.ones(lon.shape)
pset = ParticleSet.from_list(field_set,
JITParticle,
lon=lon,
lat=lat,
time=time)
kernel = AdvectionRK4
timer.particlefile = timer.Timer('ParticleFile', parent=timer.root)
outfile = __file__[:-3]
pfile = ParticleFile(outfile, pset)
pfile.write(pset, pset[0].time)
timer.particlefile.stop()
tic = timelib.time()
ndays = 60
timer.run = timer.Timer('Execution', parent=timer.root, start=False)
for d in range(ndays):
print('running %d / %d: time %g' % (d + 1, ndays, timelib.time() - tic))
timer.run.start()
pset.execute(
