def test_pset_create_fromparticlefile(fieldset, mode, restart, tmpdir):
filename = tmpdir.join("pset_fromparticlefile.nc")
lon = np.linspace(0, 1, 10, dtype=np.float32)
lat = np.linspace(1, 0, 10, dtype=np.float32)
pset = ParticleSet(fieldset, lon=lon, lat=lat, pclass=ptype[mode])
pfile = pset.ParticleFile(filename, outputdt=1)
def DeleteLast(particle, fieldset, time):
if particle.lon == 1.:
particle.delete()
pset.execute(DeleteLast, runtime=2, dt=1, output_file=pfile)
pfile.close()
if restart:
ptype[mode].setLastID(0) # need to reset to zero
pset_new = ParticleSet.from_particlefile(fieldset,
pclass=ptype[mode],
filename=filename,
restart=restart)
for var in ['lon', 'lat', 'depth', 'time']:
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])
def test_globcurrent_pset_fromfile(mode, dt, pid_offset, tmpdir):
filename = tmpdir.join("pset_fromparticlefile.nc")
fieldset = set_globcurrent_fieldset()
ptype[mode].setLastID(pid_offset)
pset = ParticleSet(fieldset, pclass=ptype[mode], lon=25, lat=-35)
pfile = pset.ParticleFile(filename, outputdt=delta(hours=6))
pset.execute(AdvectionRK4, runtime=delta(days=1), dt=dt, output_file=pfile)
pfile.close()
restarttime = np.nanmax if dt > 0 else np.nanmin
pset_new = ParticleSet.from_particlefile(fieldset, pclass=ptype[mode], filename=filename, restarttime=restarttime)
pset.execute(AdvectionRK4, runtime=delta(days=1), dt=dt)
pset_new.execute(AdvectionRK4, runtime=delta(days=1), dt=dt)
for var in ['lon', 'lat', 'depth', 'time', 'id']:
assert np.allclose([getattr(p, var) for p in pset], [getattr(p, var) for p in pset_new])
def test_pset_create_fromparticlefile(fieldset, mode, restart, tmpdir):
filename = tmpdir.join("pset_fromparticlefile.nc")
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 = ParticleSet(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 = ParticleSet.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)
def sequential(start_date,
end_date,
config,
name='',
winds=True,
diffusion=True,
unbeaching=True,
restart_file=""):
# years = config[WorldLitter.years]
years = np.arange(start_date.year, end_date.year + 1)
base_folder = config[GlobalModel.base_folder]
release_loc_folder = config[GlobalModel.loc_folder]
output_file = join(config[GlobalModel.output_folder], name)
unbeach_file = config[GlobalModel.unbeach_file]
lat_files = config[GlobalModel.lat_files]
lon_files = config[GlobalModel.lon_files]
dt = config[GlobalModel.dt]
kh = 1
repeat_release = config[GlobalModel.repeat_release]
run_time = timedelta(seconds=(end_date - start_date).total_seconds())
file_names = read_files(base_folder,
years,
wind=winds,
start_date=start_date,
end_date=end_date)
if len(file_names) == 0:
raise Exception("ERROR: We couldn't read any file!")
print("Reading initial positions.....")
lat0 = functools.reduce(lambda a, b: np.concatenate((a, b), axis=0), [
np.genfromtxt(join(release_loc_folder, x), delimiter='')
for x in lat_files
])
lon0 = functools.reduce(lambda a, b: np.concatenate((a, b), axis=0), [
np.genfromtxt(join(release_loc_folder, x), delimiter='')
for x in lon_files
])
variables = {'U': 'surf_u', 'V': 'surf_v'}
dimensions = {'lat': 'latitude', 'lon': 'longitude', 'time': 'time'}
print("Reading netcdf files.....", flush=True)
# Adding the vector fields it may be currents or currents + winds
main_fieldset = FieldSet.from_netcdf(file_names,
variables,
dimensions,
allow_time_extrapolation=True,
field_chunksize=(2048, 2048))
# ------- Making syntetic diffusion coefficient
U_grid = main_fieldset.U.grid
lat = U_grid.lat
lon = U_grid.lon
# Getting proporcional size by degree
if diffusion:
print("Adding diffusion .....")
add_Kh(main_fieldset, lat, lon, kh)
if unbeaching:
print("Adding unbeaching.....")
add_unbeaching_field(main_fieldset, lat, lon, unbeach_file)
# ------- Adding constants for periodic halo
main_fieldset.add_constant('halo_west', main_fieldset.U.grid.lon[0])
main_fieldset.add_constant('halo_east', main_fieldset.U.grid.lon[-1])
main_fieldset.add_periodic_halo(zonal=True) #create a zonal halo
print("Setting up everything.....")
if unbeaching:
particle_class = LitterParticle
else:
particle_class = JITParticle
if restart_file != '':
print(F"Using restart file {restart_file}")
pset = ParticleSet.from_particlefile(fieldset=main_fieldset,
pclass=particle_class,
filename=restart_file,
repeatdt=repeat_release)
else:
pset = ParticleSet(fieldset=main_fieldset,
pclass=particle_class,
lon=lon0,
lat=lat0,
repeatdt=repeat_release)
out_parc_file = pset.ParticleFile(name=output_file,
outputdt=config[GlobalModel.output_freq])
t = time.time()
print(F"Adding kernels...")
if unbeaching:
kernels = pset.Kernel(AdvectionRK4Beached)
else:
kernels = pset.Kernel(AdvectionRK4)
if unbeaching:
kernels += pset.Kernel(BeachTesting_2D)
kernels += pset.Kernel(UnBeaching)
if diffusion:
kernels += pset.Kernel(BrownianMotion2DUnbeaching)
kernels += pset.Kernel(BeachTesting_2D)
else:
if diffusion:
kernels += pset.Kernel(BrownianMotion2D)
kernels += pset.Kernel(periodicBC)
print(F"Running with {pset.size} number of particles for {run_time}",
flush=True)
pset.execute(kernels,
runtime=run_time,
dt=dt,
output_file=out_parc_file,
recovery={ErrorCode.ErrorOutOfBounds: outOfBounds})
print(F"Done time={time.time()-t}.....")
print(F"Saving output to {output_file}!!!!!")
# domain = {'N': 31, 'S': 16, 'E': -76, 'W': -98}
# pset.show(field=main_fieldset.U, domain=domain) # Draw current particles
out_parc_file.export() # Save trajectories to file
if MPI:
print(
F"----- Waiting for file to be saved proc {MPI.COMM_WORLD.Get_rank()} ... ---------",
flush=True)
MPI.COMM_WORLD.Barrier()
# out_parc_file.close()
# del pset
# del kernels
# del main_fieldset
# # plotTrajectoriesFile(output_file) # Plotting trajectories
# print("Forcing gc.collect")
# gc.collect()
print("Done!!!!!!!!!!!! YEAH BABE!!!!!!!!", flush=True)