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test_particle_sets.py
484 lines (390 loc) · 21 KB
/
test_particle_sets.py
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from parcels import (FieldSet, Field, ScipyParticle, JITParticle,
Variable, StateCode, OperationCode, CurvilinearZGrid)
from parcels import ParticleSetSOA, ParticleFileSOA, KernelSOA # noqa
from parcels import ParticleSetAOS, ParticleFileAOS, KernelAOS # noqa
import numpy as np
import pytest
pset_modes = ['soa', 'aos']
ptype = {'scipy': ScipyParticle, 'jit': JITParticle}
pset_type = {'soa': {'pset': ParticleSetSOA, 'pfile': ParticleFileSOA, 'kernel': KernelSOA},
'aos': {'pset': ParticleSetAOS, 'pfile': ParticleFileAOS, 'kernel': KernelAOS}}
def fieldset(xdim=40, ydim=100):
U = np.zeros((ydim, xdim), dtype=np.float32)
V = np.zeros((ydim, xdim), dtype=np.float32)
lon = np.linspace(0, 1, xdim, dtype=np.float32)
lat = np.linspace(-60, 60, ydim, dtype=np.float32)
depth = np.zeros(1, dtype=np.float32)
data = {'U': np.array(U, dtype=np.float32), 'V': np.array(V, dtype=np.float32)}
dimensions = {'lat': lat, 'lon': lon, 'depth': depth}
return FieldSet.from_data(data, dimensions)
@pytest.fixture(name="fieldset")
def fieldset_fixture(xdim=40, ydim=100):
return fieldset(xdim=xdim, ydim=ydim)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_create_lon_lat(fieldset, pset_mode, mode, npart=100):
lon = np.linspace(0, 1, npart, dtype=np.float32)
lat = np.linspace(1, 0, npart, dtype=np.float32)
pset = pset_type[pset_mode]['pset'](fieldset, lon=lon, lat=lat, pclass=ptype[mode])
assert np.allclose([p.lon for p in pset], lon, rtol=1e-12)
assert np.allclose([p.lat for p in pset], lat, rtol=1e-12)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
@pytest.mark.parametrize('lonlatdepth_dtype', [np.float64, np.float32])
def test_pset_create_line(fieldset, pset_mode, mode, lonlatdepth_dtype, npart=100):
lon = np.linspace(0, 1, npart, dtype=lonlatdepth_dtype)
lat = np.linspace(1, 0, npart, dtype=lonlatdepth_dtype)
pset = pset_type[pset_mode]['pset'].from_line(fieldset, size=npart, start=(0, 1), finish=(1, 0),
pclass=ptype[mode], lonlatdepth_dtype=lonlatdepth_dtype)
assert np.allclose([p.lon for p in pset], lon, rtol=1e-12)
assert np.allclose([p.lat for p in pset], lat, rtol=1e-12)
assert isinstance(pset[0].lat, lonlatdepth_dtype)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_create_list_with_customvariable(fieldset, pset_mode, mode, npart=100):
lon = np.linspace(0, 1, npart, dtype=np.float32)
lat = np.linspace(1, 0, npart, dtype=np.float32)
class MyParticle(ptype[mode]):
v = Variable('v')
v_vals = np.arange(npart)
pset = pset_type[pset_mode]['pset'].from_list(fieldset, lon=lon, lat=lat, v=v_vals, pclass=MyParticle)
assert np.allclose([p.lon for p in pset], lon, rtol=1e-12)
assert np.allclose([p.lat for p in pset], lat, rtol=1e-12)
assert np.allclose([p.v for p in pset], v_vals, rtol=1e-12)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
@pytest.mark.parametrize('restart', [True, False])
def test_pset_create_fromparticlefile(fieldset, pset_mode, mode, restart, tmpdir):
filename = tmpdir.join("pset_fromparticlefile.zarr")
lon = np.linspace(0, 1, 10, dtype=np.float32)
lat = np.linspace(1, 0, 10, dtype=np.float32)
class TestParticle(ptype[mode]):
p = Variable('p', np.float32, initial=0.33)
p2 = Variable('p2', np.float32, initial=1, to_write=False)
p3 = Variable('p3', np.float32, to_write='once')
pset = pset_type[pset_mode]['pset'](fieldset, lon=lon, lat=lat, depth=[4]*len(lon), pclass=TestParticle, p3=np.arange(len(lon)))
pfile = pset.ParticleFile(filename, outputdt=1)
def Kernel(particle, fieldset, time):
particle.p = 2.
if particle.lon == 1.:
particle.delete()
pset.execute(Kernel, runtime=2, dt=1, output_file=pfile)
pfile.close()
pset_new = pset_type[pset_mode]['pset'].from_particlefile(fieldset, pclass=TestParticle, filename=filename,
restart=restart, repeatdt=1)
for var in ['lon', 'lat', 'depth', 'time', 'p', 'p2', 'p3']:
assert np.allclose([getattr(p, var) for p in pset], [getattr(p, var) for p in pset_new])
if restart:
assert np.allclose([p.id for p in pset], [p.id for p in pset_new])
pset_new.execute(Kernel, runtime=2, dt=1)
assert len(pset_new) == 3*len(pset)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy'])
@pytest.mark.parametrize('lonlatdepth_dtype', [np.float64, np.float32])
def test_pset_create_field(fieldset, pset_mode, mode, lonlatdepth_dtype, npart=100):
np.random.seed(123456)
shape = (fieldset.U.lon.size, fieldset.U.lat.size)
K = Field('K', lon=fieldset.U.lon, lat=fieldset.U.lat,
data=np.ones(shape, dtype=np.float32), transpose=True)
pset = pset_type[pset_mode]['pset'].from_field(fieldset, size=npart, pclass=ptype[mode],
start_field=K, lonlatdepth_dtype=lonlatdepth_dtype)
assert (np.array([p.lon for p in pset]) <= K.lon[-1]).all()
assert (np.array([p.lon for p in pset]) >= K.lon[0]).all()
assert (np.array([p.lat for p in pset]) <= K.lat[-1]).all()
assert (np.array([p.lat for p in pset]) >= K.lat[0]).all()
assert isinstance(pset[0].lat, lonlatdepth_dtype)
@pytest.mark.parametrize('pset_mode', pset_modes)
def test_pset_create_field_curvi(pset_mode, npart=100):
np.random.seed(123456)
r_v = np.linspace(.25, 2, 20)
theta_v = np.linspace(0, np.pi/2, 200)
dtheta = theta_v[1]-theta_v[0]
dr = r_v[1]-r_v[0]
(r, theta) = np.meshgrid(r_v, theta_v)
x = -1 + r * np.cos(theta)
y = -1 + r * np.sin(theta)
grid = CurvilinearZGrid(x, y)
u = np.ones(x.shape)
v = np.where(np.logical_and(theta > np.pi/4, theta < np.pi/3), 1, 0)
ufield = Field('U', u, grid=grid)
vfield = Field('V', v, grid=grid)
fieldset = FieldSet(ufield, vfield)
pset = pset_type[pset_mode]['pset'].from_field(fieldset, size=npart, pclass=ptype['scipy'], start_field=fieldset.V)
lons = np.array([p.lon+1 for p in pset])
lats = np.array([p.lat+1 for p in pset])
thetas = np.arctan2(lats, lons)
rs = np.sqrt(lons*lons + lats*lats)
test = np.pi/4-dtheta < thetas
test *= thetas < np.pi/3+dtheta
test *= rs > .25-dr
test *= rs < 2+dr
assert np.all(test)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_create_with_time(fieldset, pset_mode, mode, npart=100):
lon = np.linspace(0, 1, npart)
lat = np.linspace(1, 0, npart)
time = 5.
pset = pset_type[pset_mode]['pset'](fieldset, lon=lon, lat=lat, pclass=ptype[mode], time=time)
assert np.allclose([p.time for p in pset], time, rtol=1e-12)
pset = pset_type[pset_mode]['pset'].from_list(fieldset, lon=lon, lat=lat, pclass=ptype[mode],
time=[time]*npart)
assert np.allclose([p.time for p in pset], time, rtol=1e-12)
pset = pset_type[pset_mode]['pset'].from_line(fieldset, size=npart, start=(0, 1), finish=(1, 0),
pclass=ptype[mode], time=time)
assert np.allclose([p.time for p in pset], time, rtol=1e-12)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_not_multipldt_time(fieldset, pset_mode, mode):
times = [0, 1.1]
pset = pset_type[pset_mode]['pset'](fieldset, lon=[0]*2, lat=[0]*2, pclass=ptype[mode], time=times)
def Addlon(particle, fieldset, time):
particle.lon += particle.dt
pset.execute(Addlon, dt=1, runtime=2)
assert np.allclose([p.lon for p in pset], [2 - t for t in times])
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_repeated_release(fieldset, pset_mode, mode, npart=10):
time = np.arange(0, npart, 1) # release 1 particle every second
pset = pset_type[pset_mode]['pset'](fieldset, lon=np.zeros(npart), lat=np.zeros(npart),
pclass=ptype[mode], time=time)
assert np.allclose([p.time for p in pset], time)
def IncrLon(particle, fieldset, time):
particle.lon += 1.
pset.execute(IncrLon, dt=1., runtime=npart)
assert np.allclose([p.lon for p in pset], np.arange(npart, 0, -1))
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_dt0(fieldset, pset_mode, mode, npart=10):
pset = pset_type[pset_mode]['pset'](fieldset, lon=np.zeros(npart), lat=np.zeros(npart),
pclass=ptype[mode])
def IncrLon(particle, fieldset, time):
particle.lon += 1
pset.execute(IncrLon, dt=0., runtime=npart)
assert np.allclose([p.lon for p in pset], 1.)
assert np.allclose([p.time for p in pset], 0.)
@pytest.mark.parametrize('pset_mode', pset_modes)
def test_pset_repeatdt_check_dt(pset_mode, fieldset):
pset = pset_type[pset_mode]['pset'](fieldset, lon=[0], lat=[0], pclass=ScipyParticle, repeatdt=5)
def IncrLon(particle, fieldset, time):
particle.lon = 1.
pset.execute(IncrLon, dt=2, runtime=21)
assert np.allclose([p.lon for p in pset], 1) # if p.dt is nan, it won't be executed so p.lon will be 0
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_repeatdt_custominit(fieldset, pset_mode, mode):
class MyParticle(ptype[mode]):
sample_var = Variable('sample_var')
pset = pset_type[pset_mode]['pset'](fieldset, lon=0, lat=0, pclass=MyParticle, repeatdt=1, sample_var=5)
def DoNothing(particle, fieldset, time):
return StateCode.Success
pset.execute(DoNothing, dt=1, runtime=21)
assert np.allclose([p.sample_var for p in pset], 5.)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_stop_simulation(fieldset, pset_mode, mode):
pset = pset_type[pset_mode]['pset'](fieldset, lon=0, lat=0, pclass=ptype[mode])
def Delete(particle, fieldset, time):
if time == 4:
return OperationCode.StopExecution
pset.execute(Delete, dt=1, runtime=21)
assert pset[0].time == 4
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_access(fieldset, pset_mode, mode, npart=100):
lon = np.linspace(0, 1, npart, dtype=np.float32)
lat = np.linspace(1, 0, npart, dtype=np.float32)
pset = pset_type[pset_mode]['pset'](fieldset, lon=lon, lat=lat, pclass=ptype[mode])
assert pset.size == 100
assert np.allclose([pset[i].lon for i in range(pset.size)], lon, rtol=1e-12)
assert np.allclose([pset[i].lat for i in range(pset.size)], lat, rtol=1e-12)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_custom_ptype(fieldset, pset_mode, mode, npart=100):
class TestParticle(ptype[mode]):
p = Variable('p', np.float32, initial=0.33)
n = Variable('n', np.int32, initial=2)
pset = pset_type[pset_mode]['pset'](fieldset, pclass=TestParticle,
lon=np.linspace(0, 1, npart),
lat=np.linspace(1, 0, npart))
assert pset.size == npart
assert np.allclose([p.p - 0.33 for p in pset], np.zeros(npart), atol=1e-5)
assert np.allclose([p.n - 2 for p in pset], np.zeros(npart), rtol=1e-12)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_add_explicit(fieldset, pset_mode, mode, npart=100):
lon = np.linspace(0, 1, npart)
lat = np.linspace(1, 0, npart)
pset = pset_type[pset_mode]['pset'](fieldset, lon=[], lat=[], pclass=ptype[mode], lonlatdepth_dtype=np.float64)
for i in range(npart):
particle = pset_type[pset_mode]['pset'](pclass=ptype[mode], lon=lon[i], lat=lat[i],
fieldset=fieldset, lonlatdepth_dtype=np.float64)
pset.add(particle)
assert pset.size == npart
assert np.allclose([p.lon for p in pset], lon, rtol=1e-12)
assert np.allclose([p.lat for p in pset], lat, rtol=1e-12)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_add_shorthand(fieldset, pset_mode, mode, npart=100):
lon = np.linspace(0, 1, npart, dtype=np.float32)
lat = np.linspace(1, 0, npart, dtype=np.float32)
pset = pset_type[pset_mode]['pset'](fieldset, lon=[], lat=[], pclass=ptype[mode])
for i in range(npart):
pset += pset_type[pset_mode]['pset'](pclass=ptype[mode], lon=lon[i], lat=lat[i], fieldset=fieldset)
assert pset.size == npart
assert np.allclose([p.lon for p in pset], lon, rtol=1e-12)
assert np.allclose([p.lat for p in pset], lat, rtol=1e-12)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_add_execute(fieldset, pset_mode, mode, npart=10):
def AddLat(particle, fieldset, time):
particle.lat += 0.1
pset = pset_type[pset_mode]['pset'](fieldset, lon=[], lat=[], pclass=ptype[mode])
for i in range(npart):
pset += pset_type[pset_mode]['pset'](pclass=ptype[mode], lon=0.1, lat=0.1, fieldset=fieldset)
for _ in range(3):
pset.execute(pset.Kernel(AddLat), runtime=1., dt=1.0)
assert np.allclose(np.array([p.lat for p in pset]), 0.4, rtol=1e-12)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_merge_inplace(fieldset, pset_mode, mode, npart=100):
pset1 = pset_type[pset_mode]['pset'](fieldset, pclass=ptype[mode],
lon=np.linspace(0, 1, npart),
lat=np.linspace(1, 0, npart))
pset2 = pset_type[pset_mode]['pset'](fieldset, pclass=ptype[mode],
lon=np.linspace(0, 1, npart),
lat=np.linspace(0, 1, npart))
assert pset1.size == npart
assert pset2.size == npart
pset1.add(pset2)
assert pset1.size == 2*npart
@pytest.mark.xfail(reason="ParticleSet duplication has not been implemented yet")
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_merge_duplicate(fieldset, pset_mode, mode, npart=100):
pset1 = pset_type[pset_mode]['pset'](fieldset, pclass=ptype[mode],
lon=np.linspace(0, 1, npart),
lat=np.linspace(1, 0, npart))
pset2 = pset_type[pset_mode]['pset'](fieldset, pclass=ptype[mode],
lon=np.linspace(0, 1, npart),
lat=np.linspace(0, 1, npart))
pset3 = pset1 + pset2
assert pset1.size == npart
assert pset2.size == npart
assert pset3.size == 2*npart
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_remove_index(fieldset, pset_mode, mode, npart=100):
lon = np.linspace(0, 1, npart)
lat = np.linspace(1, 0, npart)
pset = pset_type[pset_mode]['pset'](fieldset, lon=lon, lat=lat, pclass=ptype[mode], lonlatdepth_dtype=np.float64)
for ilon, ilat in zip(lon[::-1], lat[::-1]):
assert pset[-1].lon == ilon
assert pset[-1].lat == ilat
pset.remove_indices(-1)
assert pset.size == 0
@pytest.mark.xfail(reason="Particle removal has not been implemented yet")
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_remove_particle(fieldset, pset_mode, mode, npart=100):
lon = np.linspace(0, 1, npart)
lat = np.linspace(1, 0, npart)
pset = pset_type[pset_mode]['pset'](fieldset, lon=lon, lat=lat, pclass=ptype[mode])
for ilon, ilat in zip(lon[::-1], lat[::-1]):
assert pset.lon[-1] == ilon
assert pset.lat[-1] == ilat
pset.remove_indices(pset[-1])
assert pset.size == 0
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_remove_kernel(fieldset, pset_mode, mode, npart=100):
def DeleteKernel(particle, fieldset, time):
if particle.lon >= .4:
particle.delete()
pset = pset_type[pset_mode]['pset'](fieldset, pclass=ptype[mode],
lon=np.linspace(0, 1, npart),
lat=np.linspace(1, 0, npart))
pset.execute(pset.Kernel(DeleteKernel), endtime=1., dt=1.0)
assert pset.size == 40
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_multi_execute(fieldset, pset_mode, mode, npart=10, n=5):
def AddLat(particle, fieldset, time):
particle.lat += 0.1
pset = pset_type[pset_mode]['pset'](fieldset, pclass=ptype[mode],
lon=np.linspace(0, 1, npart),
lat=np.zeros(npart))
k_add = pset.Kernel(AddLat)
for _ in range(n):
pset.execute(k_add, runtime=1., dt=1.0)
assert np.allclose([p.lat - n*0.1 for p in pset], np.zeros(npart), rtol=1e-12)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
def test_pset_multi_execute_delete(fieldset, pset_mode, mode, npart=10, n=5):
def AddLat(particle, fieldset, time):
particle.lat += 0.1
pset = pset_type[pset_mode]['pset'](fieldset, pclass=ptype[mode],
lon=np.linspace(0, 1, npart),
lat=np.zeros(npart))
k_add = pset.Kernel(AddLat)
for _ in range(n):
pset.execute(k_add, runtime=1., dt=1.0)
pset.remove_indices(-1)
assert np.allclose([p.lat - n*0.1 for p in pset], np.zeros(npart - n), rtol=1e-12)
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('mode', ['scipy', 'jit'])
@pytest.mark.parametrize('area_scale', [True, False])
def test_density(fieldset, pset_mode, mode, area_scale):
lons, lats = np.meshgrid(np.linspace(0.05, 0.95, 10), np.linspace(-30, 30, 20))
pset = pset_type[pset_mode]['pset'](fieldset, pclass=ptype[mode], lon=lons, lat=lats)
arr = pset.density(area_scale=area_scale)
if area_scale:
assert np.allclose(arr, 1 / fieldset.U.cell_areas(), rtol=1e-3) # check that density equals 1/area
else:
assert np.sum(arr) == lons.size # check conservation of particles
inds = np.where(arr)
for i in range(len(inds[0])): # check locations (low atol because of coarse grid)
assert np.allclose(fieldset.U.lon[inds[1][i]], pset[i].lon, atol=fieldset.U.lon[1]-fieldset.U.lon[0])
assert np.allclose(fieldset.U.lat[inds[0][i]], pset[i].lat, atol=fieldset.U.lat[1]-fieldset.U.lat[0])
@pytest.mark.parametrize('pset_mode', pset_modes)
@pytest.mark.parametrize('staggered_grid', ['Agrid', 'Cgrid'])
def test_from_field_exact_val(pset_mode, staggered_grid):
xdim = 4
ydim = 3
lon = np.linspace(-1, 2, xdim, dtype=np.float32)
lat = np.linspace(50, 52, ydim, dtype=np.float32)
dimensions = {'lat': lat, 'lon': lon}
if staggered_grid == 'Agrid':
U = np.zeros((ydim, xdim), dtype=np.float32)
V = np.zeros((ydim, xdim), dtype=np.float32)
data = {'U': np.array(U, dtype=np.float32), 'V': np.array(V, dtype=np.float32)}
mask = np.array([[1, 1, 0, 0],
[1, 1, 1, 0],
[1, 1, 1, 1]])
fieldset = FieldSet.from_data(data, dimensions, mesh='flat')
FMask = Field('mask', mask, lon, lat)
fieldset.add_field(FMask)
elif staggered_grid == 'Cgrid':
U = np.array([[0, 0, 0, 0],
[1, 0, 0, 0],
[1, 1, 0, 0]])
V = np.array([[0, 1, 0, 0],
[0, 1, 0, 0],
[0, 1, 1, 0]])
data = {'U': np.array(U, dtype=np.float32), 'V': np.array(V, dtype=np.float32)}
mask = np.array([[-1, -1, -1, -1],
[-1, 1, 0, 0],
[-1, 1, 1, 0]])
fieldset = FieldSet.from_data(data, dimensions, mesh='flat')
fieldset.U.interp_method = 'cgrid_velocity'
fieldset.V.interp_method = 'cgrid_velocity'
FMask = Field('mask', mask, lon, lat, interp_method='cgrid_tracer')
fieldset.add_field(FMask)
class SampleParticle(ptype['scipy']):
mask = Variable('mask', initial=fieldset.mask)
pset = pset_type[pset_mode]['pset'].from_field(fieldset, size=400, pclass=SampleParticle, start_field=FMask, time=0)
# pset.show(field=FMask)
assert np.allclose([p.mask for p in pset], 1)
assert (np.array([p.lon for p in pset]) <= 1).all()
test = np.logical_or(np.array([p.lon for p in pset]) <= 0, np.array([p.lat for p in pset]) >= 51)
assert test.all()