def test_fieldKh_SpatiallyVaryingBrownianMotion(mesh,
mode,
xdim=200,
ydim=100):
"""Test SpatiallyVaryingDiffusion on a non-uniform diffusivity field
with a linear gradient in one direction"""
mesh_conversion = 1 / 1852. / 60 if mesh is 'spherical' else 1
fieldset = zeros_fieldset(mesh=mesh,
xdim=xdim,
ydim=ydim,
mesh_conversion=mesh_conversion)
Kh = np.zeros((ydim, xdim), dtype=np.float32)
for x in range(xdim):
Kh[:, x] = np.tanh(fieldset.U.lon[x] / fieldset.U.lon[-1] *
10.) * xdim / 2. + xdim / 2. + 100.
grid = RectilinearZGrid(lon=fieldset.U.lon, lat=fieldset.U.lat, mesh=mesh)
fieldset.add_field(Field('Kh_zonal', Kh, grid=grid))
fieldset.add_field(Field('Kh_meridional', Kh, grid=grid))
dKh_zonal_dx, _ = fieldset.Kh_zonal.gradient()
_, dKh_meridional_dy = fieldset.Kh_meridional.gradient()
fieldset.add_field(Field('dKh_zonal_dx', dKh_zonal_dx, grid=grid))
fieldset.add_field(Field('dKh_meridional_dy', dKh_meridional_dy,
grid=grid))
if mesh is 'spherical':
fieldset.dKh_zonal_dx.units = GeographicPolar()
fieldset.dKh_meridional_dy.units = Geographic()
npart = 100
runtime = delta(days=1)
random.seed(1234)
pset = ParticleSet(fieldset=fieldset,
pclass=ptype[mode],
lon=np.zeros(npart),
lat=np.zeros(npart))
pset.execute(pset.Kernel(SpatiallyVaryingBrownianMotion2D),
runtime=runtime,
dt=delta(hours=1))
lats = np.array([p.lat for p in pset])
lons = np.array([p.lon for p in pset])
tol = 2000 * mesh_conversion # effectively 2000 m errors (because of low numbers of particles)
assert np.allclose(np.mean(lons), 0, atol=tol)
assert np.allclose(np.mean(lats), 0, atol=tol)
assert (stats.skew(lons) > stats.skew(lats))
},
'borV': {
'time': 'time',
'lat': 'lat',
'lon': 'lon'
},
}
#%%
#Create the fieldset with the periodic halo and time extrapolation for the EKE
print 'Creating the fieldset'
fieldset = FieldSet.from_netcdf(filenames,
variables,
dimensions,
allow_time_extrapolation=True)
fieldset.add_periodic_halo(zonal=True)
fieldset.uuss.units = GeographicPolar()
fieldset.vuss.units = Geographic()
#The starting coordinates of the Particles, for the North Pacific. They are generated
#by the code NAgrid.py, graciously send to me by David.
lons = np.load(
'/home/students/4056094/Desktop/Thesis/ParcelsOutput/North Atlantic/InputDistribution/LonsTestgrid0_5.npy'
)
lats = np.load(
'/home/students/4056094/Desktop/Thesis/ParcelsOutput/North Atlantic/InputDistribution/LatsTestgrid0_5.npy'
)
#lons, lats = np.meshgrid(lon,lat)
lons[lons < 0] += 360
#And now we define what sort of particles we are actually dealing with
class SampleParticle(JITParticle):
dimensions={
'lon': 'lon_rho',
'lat': 'lat_rho'
},
interp_method='linear',
mesh='spherical',
allow_time_extrapolation=True)
fieldset.add_field(iso_psi_all)
fieldset.add_field(source_id_psi)
fieldset.add_field(sink_id_psi)
fieldset.add_field(cdist)
fieldset.add_field(cnormx)
fieldset.add_field(cnormy)
fieldset.cnormx_rho.units = GeographicPolar()
fieldset.cnormy_rho.units = Geographic()
# ADD THE PERIODIC BOUNDARY
fieldset.add_constant('halo_west', -180.)
fieldset.add_constant('halo_east', 180.)
fieldset.add_periodic_halo(zonal=True)
# ADD DIFFUSION
if param['Kh']:
fieldset.add_constant_field('Kh_zonal', param['Kh'], mesh='spherical')
fieldset.add_constant_field('Kh_meridional', param['Kh'], mesh='spherical')
# ADD MAXIMUM PARTICLE AGE (IF LIMITED AGE)
fieldset.add_constant('max_age', param['max_age'])
'lat': 'latitude',
'lon': 'longitude',
'time': 'time'
},
}
fieldset = FieldSet.from_netcdf(filenames,
variables,
dimensions,
allow_time_extrapolation=True)
###############################################################################
# Adding the Stokes drift to the HYCOM currents #
###############################################################################
if stokes == 0:
fieldset.Ust.units = GeographicPolar()
fieldset.Vst.units = Geographic()
fieldset = FieldSet(
U=fieldset.U + fieldset.Ust,
V=fieldset.V + fieldset.Vst,
)
###############################################################################
# Adding the border current, which applies for all scenarios except for 0 #
###############################################################################
datasetBor = Dataset(dataInputdirec + 'boundary_velocities_HYCOM.nc')
borU = datasetBor.variables['MaskUvel'][:]
borU[borU != 0] = borU[borU != 0] / abs(borU[borU != 0])
borV = datasetBor.variables['MaskVvel'][:]
borV[borV != 0] = borV[borV != 0] / abs(borV[borV != 0])
borMag = np.sqrt(np.square(borU) + np.square(borV))
'vwnd':'vwnd',
'borU':'MaskUvel',
'borV':'MaskVvel'}
dimensions = {'U':{'time':'time','lat':'lat','lon':'lon'},
'V':{'time':'time','lat':'lat','lon':'lon'},
'uwnd':{'time':'time','lat':'latitude','lon':'longitude'},
'vwnd':{'time':'time','lat':'latitude','lon':'longitude'},
'borU':{'time':'time','lat':'lat','lon':'lon'},
'borV': {'time':'time','lat':'lat','lon':'lon'},
}
#%%
#Create the fieldset with the periodic halo and time extrapolation for the EKE
print 'Creating the fieldset'
fieldset = FieldSet.from_netcdf(filenames, variables, dimensions,allow_time_extrapolation=True)
fieldset.add_periodic_halo(zonal=True)
fieldset.uwnd.units=GeographicPolar()
fieldset.vwnd.units=Geographic()
#The starting coordinates of the Particles, for the North Pacific. They are generated
#by the code NAgrid.py, graciously send to me by David.
lons=np.load('/home/students/4056094/Desktop/Thesis/ParcelsOutput/North Atlantic/InputDistribution/LonsTestgrid0_5.npy')
lats=np.load('/home/students/4056094/Desktop/Thesis/ParcelsOutput/North Atlantic/InputDistribution/LatsTestgrid0_5.npy')
#lons, lats = np.meshgrid(lon,lat)
lons[lons<0]+=360
#And now we define what sort of particles we are actually dealing with
class SampleParticle(JITParticle):
# #Now the part to determine the age of the particle
Age=Variable('Age',initial=0.,dtype=np.float32)#agr is gonna be in seconds
prev_time=Variable('prev_time',initial=attrgetter('time'),to_write=False)