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example_moving_eddies.py
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example_moving_eddies.py
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import gc
import math
from argparse import ArgumentParser
from datetime import timedelta as delta
from os import path
import numpy as np
import pytest
from parcels import AdvectionEE
from parcels import AdvectionRK4
from parcels import AdvectionRK45
from parcels import FieldSet
from parcels import JITParticle
from parcels import ParticleSet
from parcels import ScipyParticle
ptype = {'scipy': ScipyParticle, 'jit': JITParticle}
method = {'RK4': AdvectionRK4, 'EE': AdvectionEE, 'RK45': AdvectionRK45}
def moving_eddies_fieldset(xdim=200, ydim=350, mesh='flat'):
"""Generate a fieldset encapsulating the flow field consisting of two
moving eddies, one moving westward and the other moving northwestward.
:param xdim: Horizontal dimension of the generated fieldset
:param xdim: Vertical dimension of the generated fieldset
:param mesh: String indicating the type of mesh coordinates and
units used during velocity interpolation:
1. spherical: Lat and lon in degree, with a
correction for zonal velocity U near the poles.
2. flat (default): No conversion, lat/lon are assumed to be in m.
Note that this is not a proper geophysical flow. Rather, a Gaussian eddy is moved
artificially with uniform velocities. Velocities are calculated from geostrophy.
"""
# Set Parcels FieldSet variables
time = np.arange(0., 8. * 86400., 86400., dtype=np.float64)
# Coordinates of the test fieldset (on A-grid in m)
if mesh == 'spherical':
lon = np.linspace(0, 4, xdim, dtype=np.float32)
lat = np.linspace(45, 52, ydim, dtype=np.float32)
else:
lon = np.linspace(0, 4.e5, xdim, dtype=np.float32)
lat = np.linspace(0, 7.e5, ydim, dtype=np.float32)
# Grid spacing in m
def cosd(x):
return math.cos(math.radians(float(x)))
dx = (lon[1] - lon[0]) * 1852 * 60 * cosd(lat.mean()) if mesh == 'spherical' else lon[1] - lon[0]
dy = (lat[1] - lat[0]) * 1852 * 60 if mesh == 'spherical' else lat[1] - lat[0]
# Define arrays U (zonal), V (meridional), and P (sea surface height) on A-grid
U = np.zeros((lon.size, lat.size, time.size), dtype=np.float32)
V = np.zeros((lon.size, lat.size, time.size), dtype=np.float32)
P = np.zeros((lon.size, lat.size, time.size), dtype=np.float32)
# Some constants
corio_0 = 1.e-4 # Coriolis parameter
h0 = 1 # Max eddy height
sig = 0.5 # Eddy e-folding decay scale (in degrees)
g = 10 # Gravitational constant
eddyspeed = 0.1 # Translational speed in m/s
dX = eddyspeed * 86400 / dx # Grid cell movement of eddy max each day
dY = eddyspeed * 86400 / dy # Grid cell movement of eddy max each day
[x, y] = np.mgrid[:lon.size, :lat.size]
for t in range(time.size):
hymax_1 = lat.size / 7.
hxmax_1 = .75 * lon.size - dX * t
hymax_2 = 3. * lat.size / 7. + dY * t
hxmax_2 = .75 * lon.size - dX * t
P[:, :, t] = h0 * np.exp(-(x-hxmax_1)**2/(sig*lon.size/4.)**2-(y-hymax_1)**2/(sig*lat.size/7.)**2)
P[:, :, t] += h0 * np.exp(-(x-hxmax_2)**2/(sig*lon.size/4.)**2-(y-hymax_2)**2/(sig*lat.size/7.)**2)
V[:-1, :, t] = -np.diff(P[:, :, t], axis=0) / dx / corio_0 * g
V[-1, :, t] = V[-2, :, t] # Fill in the last column
U[:, :-1, t] = np.diff(P[:, :, t], axis=1) / dy / corio_0 * g
U[:, -1, t] = U[:, -2, t] # Fill in the last row
data = {'U': U, 'V': V, 'P': P}
dimensions = {'lon': lon, 'lat': lat, 'time': time}
return FieldSet.from_data(data, dimensions, transpose=True, mesh=mesh)
def moving_eddies_example(fieldset, outfile, npart=2, mode='jit', verbose=False,
method=AdvectionRK4):
"""Configuration of a particle set that follows two moving eddies
:arg fieldset: :class FieldSet: that defines the flow field
:arg npart: Number of particles to initialise"""
# Determine particle class according to mode
start = (3.3, 46.) if fieldset.U.grid.mesh == 'spherical' else (3.3e5, 1e5)
finish = (3.3, 47.8) if fieldset.U.grid.mesh == 'spherical' else (3.3e5, 2.8e5)
pset = ParticleSet.from_line(fieldset=fieldset, size=npart, pclass=ptype[mode],
start=start, finish=finish)
if verbose:
print("Initial particle positions:\n%s" % pset)
# Execute for 1 week, with 1 hour timesteps and hourly output
runtime = delta(days=7)
print("MovingEddies: Advecting %d particles for %s" % (npart, str(runtime)))
pset.execute(method, runtime=runtime, dt=delta(hours=1),
output_file=pset.ParticleFile(name=outfile, outputdt=delta(hours=1)),
moviedt=None)
if verbose:
print("Final particle positions:\n%s" % pset)
return pset
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
@pytest.mark.parametrize('mesh', ['flat', 'spherical'])
def test_moving_eddies_fwdbwd(mode, mesh, tmpdir, npart=2):
method = AdvectionRK4
fieldset = moving_eddies_fieldset(mesh=mesh)
# Determine particle class according to mode
lons = [3.3, 3.3] if fieldset.U.grid.mesh == 'spherical' else [3.3e5, 3.3e5]
lats = [46., 47.8] if fieldset.U.grid.mesh == 'spherical' else [1e5, 2.8e5]
pset = ParticleSet(fieldset=fieldset, pclass=ptype[mode], lon=lons, lat=lats)
# Execte for 14 days, with 30sec timesteps and hourly output
runtime = delta(days=1)
dt = delta(minutes=5)
outputdt = delta(hours=1)
print("MovingEddies: Advecting %d particles for %s" % (npart, str(runtime)))
outfile = tmpdir.join("EddyParticlefwd")
pset.execute(method, runtime=runtime, dt=dt,
output_file=pset.ParticleFile(name=outfile, outputdt=outputdt))
print("Now running in backward time mode")
outfile = tmpdir.join("EddyParticlebwd")
pset.execute(method, endtime=0, dt=-dt,
output_file=pset.ParticleFile(name=outfile, outputdt=outputdt))
assert np.allclose([p.lon for p in pset], lons)
assert np.allclose([p.lat for p in pset], lats)
return pset
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
@pytest.mark.parametrize('mesh', ['flat', 'spherical'])
def test_moving_eddies_fieldset(mode, mesh, tmpdir):
fieldset = moving_eddies_fieldset(mesh=mesh)
outfile = tmpdir.join("EddyParticle")
pset = moving_eddies_example(fieldset, outfile, 2, mode=mode)
if mesh == 'flat':
assert (pset[0].lon < 2.2e5 and 1.1e5 < pset[0].lat < 1.2e5)
assert (pset[1].lon < 2.2e5 and 3.7e5 < pset[1].lat < 3.8e5)
else:
assert(pset[0].lon < 2.0 and 46.2 < pset[0].lat < 46.25)
assert(pset[1].lon < 2.0 and 48.8 < pset[1].lat < 48.85)
def fieldsetfile(mesh, tmpdir):
"""Generate fieldset files for moving_eddies test"""
filename = tmpdir.join('moving_eddies')
fieldset = moving_eddies_fieldset(200, 350, mesh=mesh)
fieldset.write(filename)
return filename
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
@pytest.mark.parametrize('mesh', ['flat', 'spherical'])
def test_moving_eddies_file(mode, mesh, tmpdir):
gc.collect()
fieldset = FieldSet.from_parcels(fieldsetfile(mesh, tmpdir), extra_fields={'P': 'P'})
outfile = tmpdir.join("EddyParticle")
pset = moving_eddies_example(fieldset, outfile, 2, mode=mode)
if mesh == 'flat':
assert (pset[0].lon < 2.2e5 and 1.1e5 < pset[0].lat < 1.2e5)
assert (pset[1].lon < 2.2e5 and 3.7e5 < pset[1].lat < 3.8e5)
else:
assert(pset[0].lon < 2.0 and 46.2 < pset[0].lat < 46.25)
assert(pset[1].lon < 2.0 and 48.8 < pset[1].lat < 48.85)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_periodic_and_computeTimeChunk_eddies(mode):
filename = path.join(path.dirname(__file__), 'MovingEddies_data', 'moving_eddies')
fieldset = FieldSet.from_parcels(filename)
fieldset.add_constant('halo_west', fieldset.U.grid.lon[0])
fieldset.add_constant('halo_east', fieldset.U.grid.lon[-1])
fieldset.add_constant('halo_south', fieldset.U.grid.lat[0])
fieldset.add_constant('halo_north', fieldset.U.grid.lat[-1])
fieldset.add_periodic_halo(zonal=True, meridional=True)
pset = ParticleSet.from_list(fieldset=fieldset,
pclass=ptype[mode],
lon=[3.3, 3.3],
lat=[46.0, 47.8])
def periodicBC(particle, fieldset, time):
if particle.lon < fieldset.halo_west:
particle.lon += fieldset.halo_east - fieldset.halo_west
elif particle.lon > fieldset.halo_east:
particle.lon -= fieldset.halo_east - fieldset.halo_west
if particle.lat < fieldset.halo_south:
particle.lat += fieldset.halo_north - fieldset.halo_south
elif particle.lat > fieldset.halo_north:
particle.lat -= fieldset.halo_north - fieldset.halo_south
def slowlySouthWestward(particle, fieldset, time):
particle.lon = particle.lon - 5 * particle.dt / 1e5
particle.lat -= 3 * particle.dt / 1e5
kernels = pset.Kernel(AdvectionRK4)+slowlySouthWestward+periodicBC
pset.execute(kernels, runtime=delta(days=6), dt=delta(hours=1))
if __name__ == "__main__":
p = ArgumentParser(description="""
Example of particle advection around an idealised peninsula""")
p.add_argument('mode', choices=('scipy', 'jit'), nargs='?', default='jit',
help='Execution mode for performing RK4 computation')
p.add_argument('-p', '--particles', type=int, default=2,
help='Number of particles to advect')
p.add_argument('-v', '--verbose', action='store_true', default=False,
help='Print particle information before and after execution')
p.add_argument('--profiling', action='store_true', default=False,
help='Print profiling information after run')
p.add_argument('-f', '--fieldset', type=int, nargs=2, default=None,
help='Generate fieldset file with given dimensions')
p.add_argument('-m', '--method', choices=('RK4', 'EE', 'RK45'), default='RK4',
help='Numerical method used for advection')
args = p.parse_args()
filename = path.join(path.dirname(__file__), 'MovingEddies_data', 'moving_eddies')
# Generate fieldset files according to given dimensions
if args.fieldset is not None:
fieldset = moving_eddies_fieldset(args.fieldset[0], args.fieldset[1], mesh='flat')
fieldset.write(filename)
# Open fieldset files
fieldset = FieldSet.from_parcels(filename, extra_fields={'P': 'P'})
outfile = "EddyParticle"
if args.profiling:
from cProfile import runctx
from pstats import Stats
runctx("moving_eddies_example(fieldset, outfile, args.particles, mode=args.mode, \
verbose=args.verbose, method=method[args.method])",
globals(), locals(), "Profile.prof")
Stats("Profile.prof").strip_dirs().sort_stats("time").print_stats(10)
else:
moving_eddies_example(fieldset, outfile, args.particles, mode=args.mode,
verbose=args.verbose, method=method[args.method])