Python parcels.Grid類代碼示例

def test_grid_from_nemo(xdim, ydim, tmpdir, filename='test_nemo'):
    """ Simple test for grid initialisation from NEMO file format. """
    filepath = tmpdir.join(filename)
    u, v, lon, lat, depth, time = generate_grid(xdim, ydim)
    grid_out = Grid.from_data(u, lon, lat, v, lon, lat, depth, time)
    grid_out.write(filepath)
    grid = Grid.from_nemo(filepath)
    u_t = np.transpose(u).reshape((lat.size, lon.size))
    v_t = np.transpose(v).reshape((lat.size, lon.size))
    assert len(grid.U.data.shape) == 3  # Will be 4 once we use depth
    assert len(grid.V.data.shape) == 3
    assert np.allclose(grid.U.data[0, :], u_t, rtol=1e-12)
    assert np.allclose(grid.V.data[0, :], v_t, rtol=1e-12)

def test_meridionalflow_sperical(mode, xdim=100, ydim=200):
    """ Create uniform NORTHWARD flow on sperical earth and advect particles

    As flow is so simple, it can be directly compared to analytical solution
    """

    maxvel = 1.
    lon = np.linspace(-180, 180, xdim, dtype=np.float32)
    lat = np.linspace(-90, 90, ydim, dtype=np.float32)
    U = np.zeros([xdim, ydim])
    V = maxvel * np.ones([xdim, ydim])

    grid = Grid.from_data(np.array(U, dtype=np.float32), lon, lat,
                          np.array(V, dtype=np.float32), lon, lat)

    lonstart = [0, 45]
    latstart = [0, 45]
    endtime = delta(hours=24)
    pset = grid.ParticleSet(2, pclass=pclass(mode), lon=lonstart, lat=latstart)
    pset.execute(pset.Kernel(AdvectionRK4), endtime=endtime, dt=delta(hours=1))

    assert(pset[0].lat - (latstart[0] + endtime.total_seconds() * maxvel / 1852 / 60) < 1e-4)
    assert(pset[0].lon - lonstart[0] < 1e-4)
    assert(pset[1].lat - (latstart[1] + endtime.total_seconds() * maxvel / 1852 / 60) < 1e-4)
    assert(pset[1].lon - lonstart[1] < 1e-4)

def radial_rotation_grid(xdim=200, ydim=200):  # Define 2D flat, square grid for testing purposes.

    lon = np.linspace(0, 60, xdim, dtype=np.float32)
    lat = np.linspace(0, 60, ydim, dtype=np.float32)

    x0 = 30.                                   # Define the origin to be the centre of the grid.
    y0 = 30.

    U = np.zeros((xdim, ydim), dtype=np.float32)
    V = np.zeros((xdim, ydim), dtype=np.float32)

    T = delta(days=1)
    omega = 2*np.pi/T.total_seconds()          # Define the rotational period as 1 day.

    for i in range(lon.size):
        for j in range(lat.size):

            r = np.sqrt((lon[i]-x0)**2 + (lat[j]-y0)**2)  # Define radial displacement.
            assert(r >= 0.)
            assert(r <= np.sqrt(x0**2 + y0**2))

            theta = math.atan2((lat[j]-y0), (lon[i]-x0))  # Define the polar angle.
            assert(abs(theta) <= np.pi)

            U[i, j] = r * math.sin(theta) * omega
            V[i, j] = -r * math.cos(theta) * omega

    return Grid.from_data(U, lon, lat, V, lon, lat, mesh='flat')

def test_zonalflow_sperical(mode, k_sample_p, xdim=100, ydim=200):
    """ Create uniform EASTWARD flow on sperical earth and advect particles

    As flow is so simple, it can be directly compared to analytical solution
    Note that in this case the cosine conversion is needed
    """
    maxvel = 1.
    p_fld = 10
    lon = np.linspace(-180, 180, xdim, dtype=np.float32)
    lat = np.linspace(-90, 90, ydim, dtype=np.float32)
    V = np.zeros([xdim, ydim])
    U = maxvel * np.ones([xdim, ydim])
    P = p_fld * np.ones([xdim, ydim])

    grid = Grid.from_data(np.array(U, dtype=np.float32), lon, lat,
                          np.array(V, dtype=np.float32), lon, lat,
                          field_data={'P': np.array(P, dtype=np.float32)})

    lonstart = [0, 45]
    latstart = [0, 45]
    endtime = delta(hours=24)
    pset = grid.ParticleSet(2, pclass=pclass(mode), lon=lonstart, lat=latstart)
    pset.execute(pset.Kernel(AdvectionRK4) + k_sample_p,
                 endtime=endtime, dt=delta(hours=1))

    assert(pset[0].lat - latstart[0] < 1e-4)
    assert(pset[0].lon - (lonstart[0] + endtime.total_seconds() * maxvel / 1852 / 60
                          / cos(latstart[0] * pi / 180)) < 1e-4)
    assert(abs(pset[0].p - p_fld) < 1e-4)
    assert(pset[1].lat - latstart[1] < 1e-4)
    assert(pset[1].lon - (lonstart[1] + endtime.total_seconds() * maxvel / 1852 / 60
                          / cos(latstart[1] * pi / 180)) < 1e-4)
    assert(abs(pset[1].p - p_fld) < 1e-4)

def test_delay_start_example(mode, npart=10, show_movie=False):
    """Example script that shows how to 'delay' the start of particle advection.
    This is useful for example when particles need to be started at different times

    In this example, we use pset.add statements to add one particle every hour
    in the peninsula grid. Note that the title in the movie may not show correct time"""

    grid = Grid.from_nemo('examples/Peninsula_data/peninsula', extra_vars={'P': 'P'})

    # Initialise particles as in the Peninsula example
    x = 3. * (1. / 1.852 / 60)  # 3 km offset from boundary
    y = (grid.U.lat[0] + x, grid.U.lat[-1] - x)  # latitude range, including offsets

    lat = np.linspace(y[0], y[1], npart, dtype=np.float32)
    pset = grid.ParticleSet(0, lon=[], lat=[], pclass=ptype[mode])

    delaytime = delta(hours=1)  # delay time between particle releases
    for t in range(npart):
        pset.add(ptype[mode](lon=x, lat=lat[t], grid=grid))
        pset.execute(AdvectionRK4, runtime=delaytime, dt=delta(minutes=5),
                     interval=delta(hours=1), show_movie=show_movie)

    # Note that time on the movie is not parsed correctly
    pset.execute(AdvectionRK4, runtime=delta(hours=24)-npart*delaytime,
                 dt=delta(minutes=5), interval=delta(hours=1), show_movie=show_movie)

    londist = np.array([(p.lon - x) for p in pset])
    assert(londist > 0.1).all()

def set_ofam_grid():
    filenames = {'U': "examples/OFAM_example_data/OFAM_simple_U.nc",
                 'V': "examples/OFAM_example_data/OFAM_simple_V.nc"}
    variables = {'U': 'u', 'V': 'v'}
    dimensions = {'lat': 'yu_ocean', 'lon': 'xu_ocean', 'depth': 'st_ocean',
                  'time': 'Time'}
    return Grid.from_netcdf(filenames, variables, dimensions)

def set_globcurrent_grid():
    filenames = {'U': "examples/GlobCurrent_example_data/20*-GLOBCURRENT-L4-CUReul_hs-ALT_SUM-v02.0-fv01.0.nc",
                 'V': "examples/GlobCurrent_example_data/20*-GLOBCURRENT-L4-CUReul_hs-ALT_SUM-v02.0-fv01.0.nc"}
    variables = {'U': 'eastward_eulerian_current_velocity', 'V': 'northward_eulerian_current_velocity'}
    dimensions = {'lat': 'lat', 'lon': 'lon',
                  'time': 'time'}
    return Grid.from_netcdf(filenames, variables, dimensions)

def moving_eddies_grid(xdim=200, ydim=350):
    """Generate a grid encapsulating the flow field consisting of two
    moving eddies, one moving westward and the other moving northwestward.

    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 NEMO grid variables
    depth = np.zeros(1, dtype=np.float32)
    time = np.arange(0.0, 25.0 * 86400.0, 86400.0, dtype=np.float64)

    # Coordinates of the test grid (on A-grid in deg)
    lon = np.linspace(0, 4, xdim, dtype=np.float32)
    lat = np.linspace(45, 52, 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())
    dy = (lat[1] - lat[0]) * 1852 * 60

    # Define arrays U (zonal), V (meridional), W (vertical) and P (sea
    # surface height) all 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 = 1.0e-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 / 7.0
        hxmax_1 = 0.75 * lon.size - dX * t
        hymax_2 = 3.0 * lat.size / 7.0 + dY * t
        hxmax_2 = 0.75 * lon.size - dX * t

        P[:, :, t] = h0 * np.exp(
            -(x - hxmax_1) ** 2 / (sig * lon.size / 4.0) ** 2 - (y - hymax_1) ** 2 / (sig * lat.size / 7.0) ** 2
        )
        P[:, :, t] += h0 * np.exp(
            -(x - hxmax_2) ** 2 / (sig * lon.size / 4.0) ** 2 - (y - hymax_2) ** 2 / (sig * lat.size / 7.0) ** 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

    return Grid.from_data(U, lon, lat, V, lon, lat, depth, time, field_data={"P": P})

def grid(xdim=20, ydim=20):
    """ Standard unit mesh grid """
    lon = np.linspace(0., 1., xdim, dtype=np.float32)
    lat = np.linspace(0., 1., ydim, dtype=np.float32)
    U, V = np.meshgrid(lat, lon)
    return Grid.from_data(np.array(U, dtype=np.float32), lon, lat,
                          np.array(V, dtype=np.float32), lon, lat,
                          mesh='flat')

def grid(xdim=100, ydim=100):
    U = np.zeros((xdim, ydim), dtype=np.float32)
    V = np.zeros((xdim, ydim), dtype=np.float32)
    lon = np.linspace(0, 1, xdim, dtype=np.float32)
    lat = np.linspace(0, 1, ydim, dtype=np.float32)
    depth = np.zeros(1, dtype=np.float32)
    time = np.zeros(1, dtype=np.float64)
    return Grid.from_data(U, lon, lat, V, lon, lat, depth, time)

def test_add_field(xdim, ydim, tmpdir, filename="test_add"):
    filepath = tmpdir.join(filename)
    u, v, lon, lat, depth, time = generate_grid(xdim, ydim)
    grid = Grid.from_data(u, lon, lat, v, lon, lat, depth, time)
    field = Field("newfld", grid.U.data, grid.U.lon, grid.U.lat)
    grid.add_field(field)
    assert grid.newfld.data.shape == grid.U.data.shape
    grid.write(filepath)

def peninsula_grid(xdim, ydim):
    """Construct a grid encapsulating the flow field around an
    idealised peninsula.

    :param xdim: Horizontal dimension of the generated grid
    :param xdim: Vertical dimension of the generated grid

    The original test description can be found in Fig. 2.2.3 in:
    North, E. W., Gallego, A., Petitgas, P. (Eds). 2009. Manual of
    recommended practices for modelling physical - biological
    interactions during fish early life.
    ICES Cooperative Research Report No. 295. 111 pp.
    http://archimer.ifremer.fr/doc/00157/26792/24888.pdf

    Note that the problem is defined on an A-grid while NEMO
    normally returns C-grids. However, to avoid accuracy
    problems with interpolation from A-grid to C-grid, we
    return NetCDF files that are on an A-grid.
    """
    # Set NEMO grid variables
    depth = np.zeros(1, dtype=np.float32)
    time = np.zeros(1, dtype=np.float64)

    # Generate the original test setup on A-grid in km
    dx = 100. / xdim / 2.
    dy = 50. / ydim / 2.
    La = np.linspace(dx, 100.-dx, xdim, dtype=np.float32)
    Wa = np.linspace(dy, 50.-dy, ydim, dtype=np.float32)

    # Define arrays U (zonal), V (meridional), W (vertical) and P (sea
    # surface height) all on A-grid
    U = np.zeros((xdim, ydim), dtype=np.float32)
    V = np.zeros((xdim, ydim), dtype=np.float32)
    W = np.zeros((xdim, ydim), dtype=np.float32)
    P = np.zeros((xdim, ydim), dtype=np.float32)

    u0 = 1
    x0 = 50.
    R = 0.32 * 50.

    # Create the fields
    x, y = np.meshgrid(La, Wa, sparse=True, indexing='ij')
    P = u0*R**2*y/((x-x0)**2+y**2)-u0*y
    U = u0-u0*R**2*((x-x0)**2-y**2)/(((x-x0)**2+y**2)**2)
    V = -2*u0*R**2*((x-x0)*y)/(((x-x0)**2+y**2)**2)

    # Set land points to NaN
    I = P >= 0.
    U[I] = np.nan
    V[I] = np.nan
    W[I] = np.nan

    # Convert from km to lat/lon
    lon = La / 1.852 / 60.
    lat = Wa / 1.852 / 60.

    return Grid.from_data(U, lon, lat, V, lon, lat, depth, time, field_data={'P': P})

def test_peninsula_file(gridfile, mode):
    """Open grid files and execute"""
    grid = Grid.from_nemo(gridfile, extra_vars={'P': 'P'})
    pset = pensinsula_example(grid, 100, mode=mode, degree=1)
    # Test advection accuracy by comparing streamline values
    err_adv = np.array([abs(p.p_start - p.p) for p in pset])
    assert(err_adv <= 1.e-3).all()
    # Test grid sampling accuracy by comparing kernel against grid sampling
    err_smpl = np.array([abs(p.p - pset.grid.P[0., p.lon, p.lat]) for p in pset])
    assert(err_smpl <= 1.e-3).all()

def test_grid_from_data(xdim, ydim):
    """ Simple test for grid initialisation from data. """
    u, v, lon, lat, depth, time = generate_grid(xdim, ydim)
    grid = Grid.from_data(u, lon, lat, v, lon, lat, depth, time)
    u_t = np.transpose(u).reshape((lat.size, lon.size))
    v_t = np.transpose(v).reshape((lat.size, lon.size))
    assert len(grid.U.data.shape) == 3  # Will be 4 once we use depth
    assert len(grid.V.data.shape) == 3
    assert np.allclose(grid.U.data[0, :], u_t, rtol=1e-12)
    assert np.allclose(grid.V.data[0, :], v_t, rtol=1e-12)

def grid(xdim=200, ydim=100):
    """ Standard grid spanning the earth's coordinates with U and V
        equivalent to longitude and latitude in deg.
    """
    lon = np.linspace(-180, 180, xdim, dtype=np.float32)
    lat = np.linspace(-90, 90, ydim, dtype=np.float32)
    U, V = np.meshgrid(lat, lon)
    return Grid.from_data(np.array(U, dtype=np.float32), lon, lat,
                          np.array(V, dtype=np.float32), lon, lat,
                          mesh='flat')