def test_nestedfields(mode, k_sample_p):
xdim = 10
ydim = 20
U1 = Field('U1',
0.1 * np.ones((ydim, xdim), dtype=np.float32),
lon=np.linspace(0., 1., xdim, dtype=np.float32),
lat=np.linspace(0., 1., ydim, dtype=np.float32))
V1 = Field('V1',
0.2 * np.ones((ydim, xdim), dtype=np.float32),
lon=np.linspace(0., 1., xdim, dtype=np.float32),
lat=np.linspace(0., 1., ydim, dtype=np.float32))
U2 = Field('U2',
0.3 * np.ones((ydim, xdim), dtype=np.float32),
lon=np.linspace(0., 2., xdim, dtype=np.float32),
lat=np.linspace(0., 2., ydim, dtype=np.float32))
V2 = Field('V2',
0.4 * np.ones((ydim, xdim), dtype=np.float32),
lon=np.linspace(0., 2., xdim, dtype=np.float32),
lat=np.linspace(0., 2., ydim, dtype=np.float32))
U = NestedField('U', [U1, U2])
V = NestedField('V', [V1, V2])
fieldset = FieldSet(U, V)
P1 = Field('P1',
0.1 * np.ones((ydim, xdim), dtype=np.float32),
lon=np.linspace(0., 1., xdim, dtype=np.float32),
lat=np.linspace(0., 1., ydim, dtype=np.float32))
P2 = Field('P2',
0.2 * np.ones((ydim, xdim), dtype=np.float32),
lon=np.linspace(0., 2., xdim, dtype=np.float32),
lat=np.linspace(0., 2., ydim, dtype=np.float32))
P = NestedField('P', [P1, P2])
fieldset.add_field(P)
def Recover(particle, fieldset, time):
particle.lon = -1
particle.lat = -1
particle.p = 999
particle.time = particle.time + particle.dt
pset = ParticleSet(fieldset, pclass=pclass(mode), lon=[0], lat=[.3])
pset.execute(AdvectionRK4 + pset.Kernel(k_sample_p), runtime=1, dt=1)
assert np.isclose(pset.lat[0], .5)
assert np.isclose(pset.p[0], .1)
pset = ParticleSet(fieldset, pclass=pclass(mode), lon=[0], lat=[1.3])
pset.execute(AdvectionRK4 + pset.Kernel(k_sample_p), runtime=1, dt=1)
assert np.isclose(pset.lat[0], 1.7)
assert np.isclose(pset.p[0], .2)
pset = ParticleSet(fieldset, pclass=pclass(mode), lon=[0], lat=[2.3])
pset.execute(AdvectionRK4 + pset.Kernel(k_sample_p),
runtime=1,
dt=1,
recovery={ErrorCode.ErrorOutOfBounds: Recover})
assert np.isclose(pset.lat[0], -1)
assert np.isclose(pset.p[0], 999)
assert np.allclose(fieldset.UV[0][0, 0, 0, 0], [.1, .2])
def set_diffusion_MERCATOR(
fieldset, diffusivity): # create fields needed for the brownian motion
if type(fieldset.U) == Field:
size2D = (fieldset.U.grid.ydim, fieldset.U.grid.xdim)
lat1 = fieldset.U.grid.lat
lon1 = fieldset.U.grid.lon
fieldset.add_field(
Field('Kh_zonal',
data=diffusivity * np.ones(size2D),
lon=lon1,
lat=lat1,
allow_time_extrapolation=True))
fieldset.add_field(
Field('Kh_meridional',
data=diffusivity * np.ones(size2D),
lon=lon1,
lat=lat1,
allow_time_extrapolation=True))
else:
size2D_0083 = (fieldset.U[0].grid.ydim, fieldset.U[0].grid.xdim)
size2D_025 = (fieldset.U[1].grid.ydim, fieldset.U[1].grid.xdim)
Kh_zonal = NestedField('Kh_zonal', [
Field('Kh_zonal',
data=diffusivity * np.ones(size2D_0083),
lat=fieldset.U[0].grid.lat,
lon=fieldset.U[0].grid.lon,
mesh='spherical',
allow_time_extrapolation=True),
Field('Kh_zonal',
data=diffusivity * np.ones(size2D_025),
lat=fieldset.U[1].grid.lat,
lon=fieldset.U[1].grid.lon,
mesh='spherical',
allow_time_extrapolation=True)
])
Kh_meridional = NestedField('Kh_meridional', [
Field('Kh_meridional',
data=diffusivity * np.ones(size2D_0083),
lat=fieldset.U[0].grid.lat,
lon=fieldset.U[0].grid.lon,
mesh='spherical',
allow_time_extrapolation=True),
Field('Kh_meridional',
data=diffusivity * np.ones(size2D_025),
lat=fieldset.U[1].grid.lat,
lon=fieldset.U[1].grid.lon,
mesh='spherical',
allow_time_extrapolation=True)
])
fieldset.add_field(Kh_zonal)
fieldset.add_field(Kh_meridional)
return fieldset
def set_cmems(fieldset):
data_dir = '/projects/0/topios/hydrodynamic_data/CMEMS/NORTHWESTSHELF_REANALYSIS_PHYS_004_009/MetO-NWS-REAN-PHYS-daily-CUR/'
fnames = []
years = range(2000, 2005)
for y in years:
basepath = data_dir + str(
y) + '/*/' + 'metoffice_foam1_amm7_NWS_RFVL_dm*.nc'
fnames += sorted(glob(str(basepath)))
dimensionsU = {'lon': 'lon', 'lat': 'lat', 'time': 'time'}
dimensionsV = {'lon': 'lon', 'lat': 'lat', 'time': 'time'}
indices = {
'lon': range(1, 296),
'lat': range(1, 374)
} # cmems puts nan values at its borders
Ucmems = Field.from_netcdf(fnames, ('Ucmems', 'vozocrtx'),
dimensionsU,
fieldtype='U',
indices=indices,
allow_time_extrapolation=False)
Vcmems = Field.from_netcdf(fnames, ('Vcmems', 'vomecrty'),
dimensionsV,
fieldtype='V',
indices=indices,
allow_time_extrapolation=False,
grid=Ucmems.grid,
dataFiles=Ucmems.dataFiles)
fieldset.add_field(Ucmems)
fieldset.add_field(Vcmems)
fieldset.Ucmems.vmax = 5
fieldset.Vcmems.vmax = 5
fieldset.Unemo = fieldset.U
fieldset.Unemo.name = 'Unemo'
fieldset.Vnemo = fieldset.V
fieldset.Vnemo.name = 'Vnemo'
U = NestedField('U', [fieldset.Ucmems, fieldset.Unemo])
V = NestedField('V', [fieldset.Vcmems, fieldset.Vnemo])
fieldset.U = U
fieldset.V = V
fieldset.cmems = True
def set_unbeaching(fieldset):
files = '/home/philippe/data/ORCA%s-N06_unbeaching_vel.nc' % fieldset.nemo_res
filenames = files
variables = {'Unemo_unbeach': 'unBeachU', 'Vnemo_unbeach': 'unBeachV'}
dimensions = {'lon': 'glamf', 'lat': 'gphif'}
fieldsetUnBeach = FieldSet.from_nemo(filenames,
variables,
dimensions,
tracer_interp_method='cgrid_velocity')
fieldset.add_field(fieldsetUnBeach.Unemo_unbeach)
fieldset.add_field(fieldsetUnBeach.Vnemo_unbeach)
if fieldset.cmems:
fname = '/home/philippe/data/cmems_NWS_rean_004_009_unbeaching_vel.nc'
dimensionsU = {'lon': 'lon', 'lat': 'lat'}
Ucmems_unbeach = Field.from_netcdf(fname,
('Ucmems_unbeach', 'unBeachU'),
dimensionsU,
fieldtype='U')
dimensionsV = {'lon': 'lon', 'lat': 'lat'}
Vcmems_unbeach = Field.from_netcdf(fname,
('Vcmems_unbeach', 'unBeachV'),
dimensionsV,
fieldtype='V')
fieldset.add_field(Ucmems_unbeach)
fieldset.add_field(Vcmems_unbeach)
UVnemo_unbeach = VectorField('UVnemo_unbeach', fieldset.Unemo_unbeach,
fieldset.Vnemo_unbeach)
UVcmems_unbeach = VectorField('UVcmems_unbeach',
fieldset.Ucmems_unbeach,
fieldset.Vcmems_unbeach)
UVunbeach = NestedField('UVunbeach', [UVcmems_unbeach, UVnemo_unbeach])
fieldset.add_vector_field(UVunbeach)
else:
UVunbeach = VectorField('UVunbeach', fieldset.Unemo_unbeach,
fieldset.Vnemo_unbeach)
fieldset.add_vector_field(UVunbeach)
def get_MERCATOR(path,
start_date=0,
finish_date=-1,
chunksize=False,
fieldset=None):
fdir = sorted(glob(path + '*.nc'))
len_path = len(path)
if type(start_date) == datetime:
start_date_str = start_date.strftime("%Y%m%d")
finish_date_str = finish_date.strftime("%Y%m%d")
for i, e in enumerate(fdir):
if e.find(str(start_date_str), len_path) > 0:
start_index = i
elif e.find(str(finish_date_str), len_path) > 0:
finish_index = i
if start_date > finish_date:
filenames = {
'U': fdir[finish_index:start_index + 1],
'V': fdir[finish_index:start_index + 1]
}
else:
filenames = {
'U': fdir[start_index:finish_index + 1],
'V': fdir[start_index:finish_index + 1]
}
if path.find('0083') > 0:
variables = {'U': 'uo', 'V': 'vo'}
else:
variables = {'U': 'u', 'V': 'v'}
dimensions = {
'U': {
'time': 'time',
'depth': 'depth',
'lon': 'longitude',
'lat': 'latitude'
},
'V': {
'time': 'time',
'depth': 'depth',
'lon': 'longitude',
'lat': 'latitude'
}
}
if fieldset:
fieldset.Unemo_old = fieldset.U
fieldset.Unemo_old.name = 'Unemo_old'
fieldset.Vnemo_old = fieldset.V
fieldset.Vnemo_old.name = 'Vnemo_old'
fieldset_new = FieldSet.from_nemo(filenames,
variables,
dimensions,
vmax=5,
vmin=-5,
field_chunksize=chunksize)
fieldset_new.U.name = 'Unemo_new'
fieldset_new.V.name = 'Vnemo_new'
fieldset.add_field(fieldset_new.U)
fieldset.add_field(fieldset_new.V)
fieldset.U = NestedField('U', [fieldset.Unemo_old, fieldset.Unemo_new])
fieldset.V = NestedField('V', [fieldset.Vnemo_old, fieldset.Vnemo_new])
else:
fieldset = FieldSet.from_nemo(filenames,
variables,
dimensions,
vmax=5,
vmin=-5,
field_chunksize=chunksize)
return fieldset
myfieldset.append(get_nemo_fields(ufiles,vfiles,wfiles,mesh_mask,run3D=options['run3D'],chunksize=False,vdiffusion=options['vdiffusion'],beaching=options['beaching']))
if options['nesting']==True:
print('using ',nbgrids,' nested grids')
# NestedFields
ufields=[];vfields=[];wfields=[];Kzfields=[];KzEVDfields=[];tmaskfields=[];
for g in range(nbgrids):
ufields.append(myfieldset[g].U); vfields.append(myfieldset[g].V)
if options['run3D']:
wfields.append(myfieldset[g].W)
if options['vdiffusion']:
Kzfields.append(myfieldset[g].Kz) ; KzEVDfields.append(myfieldset[g].Kz_EVD);
if options['beaching']>0:
tmaskfields.append(myfieldset[g].tmask)
U=NestedField('U', ufields)
V=NestedField('V', vfields)
if options['run3D']:
W=NestedField('W', wfields)
if options['vdiffusion']:
Kz=NestedField('Kz', Kzfields)
Kz_EVD=NestedField('Kz_EVD', KzEVDfields)
if options['beaching']>0:
tmask=NestedField('tmask', tmaskfields)
if options['run3D']:
if options['vdiffusion']:
if options['beaching']>0:
fieldset = FieldSet(U, V, {'W':W, 'Kz':Kz, 'Kz_EVD':Kz_EVD, 'tmask':tmask})
else:
fieldset = FieldSet(U, V, {'W':W, 'Kz':Kz, 'Kz_EVD':Kz_EVD})