def run_mitgcm_zonally_reentrant(mode):
"""Function that shows how to load MITgcm data in a zonally periodic domain"""
data_path = path.join(path.dirname(__file__), "MITgcm_example_data/")
filenames = {
"U": data_path + "mitgcm_UV_surface_zonally_reentrant.nc",
"V": data_path + "mitgcm_UV_surface_zonally_reentrant.nc",
}
variables = {"U": "UVEL", "V": "VVEL"}
dimensions = {
"U": {
"lon": "XG",
"lat": "YG",
"time": "time"
},
"V": {
"lon": "XG",
"lat": "YG",
"time": "time"
},
}
fieldset = FieldSet.from_mitgcm(filenames,
variables,
dimensions,
mesh="flat")
fieldset.add_periodic_halo(zonal=True)
fieldset.add_constant('domain_width', 1000000)
def periodicBC(particle, fieldset, time):
if particle.lon < 0:
particle.lon += fieldset.domain_width
elif particle.lon > fieldset.domain_width:
particle.lon -= fieldset.domain_width
# Release particles 5 cells away from the Eastern boundary
pset = ParticleSet.from_line(
fieldset,
pclass=ptype[mode],
start=(fieldset.U.grid.lon[-5], fieldset.U.grid.lat[5]),
finish=(fieldset.U.grid.lon[-5], fieldset.U.grid.lat[-5]),
size=10,
)
pfile = ParticleFile("MIT_particles_" + str(mode) + ".nc",
pset,
outputdt=delta(days=1))
kernels = AdvectionRK4 + pset.Kernel(periodicBC)
pset.execute(kernels,
runtime=delta(days=5),
dt=delta(minutes=30),
output_file=pfile)
pfile.close()
def run_microbes_eac(outfile, startdate):
fieldset = set_hycom_fieldset(t0=startdate)
fieldset.add_constant('maxage', 90. * 86400)
fieldset.Kh = 100. # diffusion constant
i0 = len(fieldset.U.time)
nperloc = 100
sitelat38 = np.tile([-32.788], [nperloc])
sitelon38 = np.tile([153.785], [nperloc])
sitelat40 = np.tile([-30.621], [nperloc])
sitelon40 = np.tile([153.371], [nperloc])
class MicrobeParticle(JITParticle):
temp = Variable('temp', dtype=np.float32, initial=fieldset.temp)
age = Variable('age', dtype=np.float32, initial=0.)
pset = {}
pfile = {}
pset[40] = ParticleSet(fieldset=fieldset,
pclass=MicrobeParticle,
lon=sitelon40,
lat=sitelat40,
time=fieldset.U.time[-1])
pfile[40] = ParticleFile(outfile + '40', pset[40])
pfile[40].write(pset[40], pset[40][0].time)
kernels = pset[40].Kernel(
AdvectionRK4) + BrownianDiffusion + SampleTemp + Age
for s in range(i0, 90, 1):
if s is i0 + 1:
pset[38] = ParticleSet(fieldset=fieldset,
pclass=MicrobeParticle,
lon=sitelon38,
lat=sitelat38,
time=fieldset.U.time[-1])
pfile[38] = ParticleFile(outfile + '38', pset[38])
pfile[38].write(pset[38], pset[38][0].time)
for p in pset:
pset[p].execute(
kernels,
starttime=pset[p][0].time,
runtime=delta(days=1),
dt=delta(minutes=-5),
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
pfile[p].write(pset[p], pset[p][0].time)
fieldset.advancetime(set_hycom_fieldset(t0=startdate, t=s))
def run_corefootprintparticles(dirwrite,outfile,lonss,lonsz,latss,latsz,dep):
snapshots = snapshot_function(date(2000, 1, 3), date(2005, 12, 29), delta(days=3))
fieldset = set_ofes_fieldset(snapshots)
fieldset.add_periodic_halo(zonal=True)
fieldset.add_constant('dwellingdepth', np.float(dd))
fieldset.add_constant('maxage', 300000.*86400)
fieldset.add_constant('surface', 2.6)
class FixParticle(JITParticle):
temp = Variable('temp', dtype=np.float32, initial=np.nan)
age = Variable('age', dtype=np.float32, initial=0., to_write = False)
salin = Variable('salin', dtype=np.float32, initial=np.nan)
psets = ParticleSet.from_list(fieldset=fieldset, pclass=FixParticle,
lon=lonsz.tolist(), lat=latsz.tolist(),
depth=dep, time = np.datetime64('2005-12-25'))#
pfiles = ParticleFile(dirwrite + 'surface' + outfile, psets, outputdt=delta(days=3))
kernelss = psets.Kernel(SampleSurf) + psets.Kernel(Age)
psets.execute(kernelss, runtime=delta(days=2170), dt=delta(days=-1), output_file=pfiles, recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
def run_nemo_curvilinear(mode, outfile):
"""Function that shows how to read in curvilinear grids, in this case from NEMO"""
data_path = path.join(path.dirname(__file__), 'NemoCurvilinear_data/')
filenames = {'U': {'lon': data_path + 'mesh_mask.nc4',
'lat': data_path + 'mesh_mask.nc4',
'data': data_path + 'U_purely_zonal-ORCA025_grid_U.nc4'},
'V': {'lon': data_path + 'mesh_mask.nc4',
'lat': data_path + 'mesh_mask.nc4',
'data': data_path + 'V_purely_zonal-ORCA025_grid_V.nc4'}}
variables = {'U': 'U', 'V': 'V'}
dimensions = {'lon': 'glamf', 'lat': 'gphif'}
field_set = FieldSet.from_nemo(filenames, variables, dimensions)
# Now run particles as normal
npart = 20
lonp = 30 * np.ones(npart)
latp = [i for i in np.linspace(-70, 88, npart)]
def periodicBC(particle, fieldSet, time):
if particle.lon > 180:
particle.lon -= 360
pset = ParticleSet.from_list(field_set, ptype[mode], lon=lonp, lat=latp)
pfile = ParticleFile(outfile, pset, outputdt=delta(days=1))
kernels = pset.Kernel(AdvectionRK4) + periodicBC
pset.execute(kernels, runtime=delta(days=1)*160, dt=delta(hours=6),
output_file=pfile)
assert np.allclose([pset[i].lat - latp[i] for i in range(len(pset))], 0, atol=2e-2)
def compute_OFAM_particle_advection(field_set, mode, lonp, latp):
def DeleteParticle(particle, fieldset, time):
particle.delete()
def RenewParticle(particle, fieldset, time):
# particle.lon = random.random() * 360.0
particle.lon = -20.0 - 5.0 + random.random() * 2.0 * 5.0
particle.lat = -75.0 + random.random() * 2.0 * 75.0
particle.state = ErrorCode.Evaluate
def periodicBC(particle, fieldSet, time):
dlon = 360.0
dlat = 75.0 + 75.0
if particle.lon > 360.0:
particle.lon -= dlon
if particle.lon < 0.0:
particle.lon += dlon
if particle.lat > 75.0:
particle.lat -= dlat
if particle.lat < -75.0:
particle.lat += dlat
pset = ParticleSet.from_list(field_set, ptype[mode], lon=lonp, lat=latp)
pfile = ParticleFile("OFAM_particles_chunk", pset, outputdt=delta(days=7))
kernels = pset.Kernel(periodicBC) + pset.Kernel(AdvectionRK4_3D)
pset.execute(kernels,
runtime=delta(days=60),
dt=delta(hours=12),
output_file=pfile,
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
return pset
def run_corefootprintparticles(outfile):
snapshots = range(3165, 3288)
fieldset = set_ofes_fieldset(snapshots)
fieldset.add_constant('dwellingdepth', 50.)
fieldset.add_constant('sinkspeed', 200. / 86400)
fieldset.add_constant('maxage', 30. * 86400)
corelon = [17.30]
corelat = [-34.70]
coredepth = [2440]
class ForamParticle(JITParticle):
temp = Variable('temp', dtype=np.float32, initial=fieldset.temp)
age = Variable('age', dtype=np.float32, initial=0.)
pset = ParticleSet(
fieldset=fieldset,
pclass=ForamParticle,
lon=corelon,
lat=corelat,
depth=coredepth,
time=fieldset.U.grid.time[-1],
repeatdt=delta(days=3)
) # the new argument 'repeatdt' means no need to call pset.add() anymore in for-loop
pfile = ParticleFile(outfile, pset, outputdt=delta(
days=1)) # `interval` argument has changed to `outputdt`
kernels = pset.Kernel(AdvectionRK4_3D) + Sink + SampleTemp + Age
pset.execute(kernels,
dt=delta(minutes=-5),
output_file=pfile,
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
def run_corefootprintparticles(dirwrite,outfile,lonss,lonsz,latss,latsz,dep,time):
snapshots = snapshot_function(date(2000, 1, 3), date(2005, 12, 29), delta(days=3))
fieldset = set_ofes_fieldset(snapshots)
fieldset.add_periodic_halo(zonal=True)
fieldset.B.allow_time_extrapolation = True
fieldset.add_constant('dwellingdepth', np.float(dd))
#constants needed for the sinking. Linear increase between 100m and 2000m from 6m/day to 45m/day
fieldset.add_constant('sp_depth1', np.float(increasedepth))
fieldset.add_constant('sp_depth2', np.float(spconstantdepth))
fieldset.add_constant('sinkspeed', sp/86400.)
fieldset.add_constant('sinkspeed2', spd/86400.)
fieldset.add_constant('maxage', 300000.*86400)
fieldset.add_constant('surface', 2.6)
class DinoOfesParticle(JITParticle):
temp = Variable('temp', dtype=np.float32, initial=np.nan)
age = Variable('age', dtype=np.float32, initial=0.)
salin = Variable('salin', dtype=np.float32, initial=np.nan)
lon0 = Variable('lon0', dtype=np.float32, initial=0.)
lat0 = Variable('lat0', dtype=np.float32, initial=0.)
depth0 = Variable('depth0',dtype=np.float32, initial=0., to_write=False)
time0 = Variable('time0',dtype=np.float32, initial=0., to_write=False)
pset = ParticleSet.from_list(fieldset=fieldset, pclass=DinoOfesParticle, lon=lonss.tolist(), lat=latss.tolist(), time = time) #depth=depths,
pfile = ParticleFile(dirwrite + outfile, pset, write_ondelete=True)
kernels = pset.Kernel(initials) + Sink + pset.Kernel(AdvectionRK4_3D) + Age + periodicBC
pset.execute(kernels, runtime=delta(days=2170), dt=delta(minutes=-60), output_file=pfile, recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
def convert_npydir_to_netcdf(tempwritedir):
"""Convert npy files in tempwritedir to a NetCDF file
:param tempwritedir: directory where the temporary npy files are stored (can be obtained from ParticleFile.tempwritedir attribute)
"""
pyset_file = path.join(tempwritedir, 'pset_info.npy')
if not path.isdir(tempwritedir):
raise ValueError('Output directory "%s" does not exist' % tempwritedir)
if not path.isfile(pyset_file):
raise ValueError(
'Output directory "%s" does not contain a pset_info.npy file' %
tempwritedir)
pset_info = np.load(pyset_file, allow_pickle=True).item()
pfile = ParticleFile(None, None, pset_info=pset_info)
pfile.export()
pfile.dataset.close()
def convert_npydir_to_netcdf(tempwritedir_base, delete_tempfiles=False):
"""Convert npy files in tempwritedir to a NetCDF file
:param tempwritedir_base: directory where the directories for temporary npy files
are stored (can be obtained from ParticleFile.tempwritedir_base attribute)
"""
tempwritedir = sorted(glob(path.join("%s" % tempwritedir_base, "*")),
key=lambda x: int(path.basename(x)))[0]
pyset_file = path.join(tempwritedir, 'pset_info.npy')
if not path.isdir(tempwritedir):
raise ValueError('Output directory "%s" does not exist' % tempwritedir)
if not path.isfile(pyset_file):
raise ValueError('Output directory "%s" does not contain a pset_info.npy file' % tempwritedir)
pset_info = np.load(pyset_file, allow_pickle=True).item()
pfile = ParticleFile(None, None, pset_info=pset_info, tempwritedir=tempwritedir_base, convert_at_end=False)
pfile.close(delete_tempfiles)
def compute_globcurrent_particle_advection(field_set, mode, lonp, latp):
pset = ParticleSet(field_set, pclass=ptype[mode], lon=lonp, lat=latp)
pfile = ParticleFile("globcurrent_particles_chunk",
pset,
outputdt=delta(hours=2))
pset.execute(AdvectionRK4,
runtime=delta(days=1),
dt=delta(minutes=5),
output_file=pfile)
return pset
def compute_pop_particle_advection(field_set, mode, lonp, latp):
pset = ParticleSet.from_list(field_set, ptype[mode], lon=lonp, lat=latp)
pfile = ParticleFile("globcurrent_particles_chunk",
pset,
outputdt=delta(days=15))
pset.execute(AdvectionRK4,
runtime=delta(days=90),
dt=delta(days=2),
output_file=pfile)
return pset
def compute_ofam_particle_advection(field_set, mode, lonp, latp, depthp):
pset = ParticleSet(field_set,
pclass=ptype[mode],
lon=lonp,
lat=latp,
depth=depthp)
pfile = ParticleFile("ofam_particles_chunk", pset, outputdt=delta(days=1))
pset.execute(AdvectionRK4,
runtime=delta(days=10),
dt=delta(minutes=5),
output_file=pfile)
return pset
def compute_swash_particle_advection(field_set, mode, lonp, latp, depthp):
pset = ParticleSet.from_list(field_set,
ptype[mode],
lon=lonp,
lat=latp,
depth=depthp)
pfile = ParticleFile("swash_particles_chunk",
pset,
outputdt=delta(seconds=0.05))
pset.execute(AdvectionRK4,
runtime=delta(seconds=0.2),
dt=delta(seconds=0.005),
output_file=pfile)
return pset
def run_corefootprintparticles(dirwrite,outfile,lonss,latss,dep):
files = sorted(glob(dirread_pop+'control_PD_1egree_extra_BOLUS/tavg/t.*'))
dfile = [dirread_pop+'control_PD_1egree/t.x1_SAMOC_flux.160001.interp.nc']
bfile = [dirread_pop+'bathymetry_POP_lowres_320t384.nc']
dimfile = [dirread_pop+'coordinates_curvilinear_pop_grid_320x384.nc']
afile = [dirread_pop+'spinup_B_2000_cam5_f09_g16.pop.h.1000-01.nc']
if(gmbol):
fieldset = setf.set_pop_fieldset_bolus(files, dimfile, dfile, bfile,afile, indices = ind)
else:
fieldset = setf.set_pop_fieldset(files, dimfile, dfile, bfile, afile, indices = ind)
fieldset.add_periodic_halo(zonal=True, halosize=20)
fieldset.add_constant('dwellingdepth', np.float(dd))
fieldset.add_constant('sinkspeed', sp/86400.)
fieldset.add_constant('maxage', 300000.*86400)
fieldset.add_constant('surface', 5.00622)
fieldset.add_constant('gmbol', gmbol)
fieldset.add_constant('Cs', Cs)
class DinoParticle(JITParticle):
temp = Variable('temp', dtype=np.float32, initial=np.nan)
age = Variable('age', dtype=np.float32, initial=0.)
salin = Variable('salin', dtype=np.float32, initial=np.nan)
lon0 = Variable('lon0', dtype=np.float32, initial=0.)
lat0 = Variable('lat0', dtype=np.float32, initial=0.)
depth0 = Variable('depth0',dtype=np.float32, initial=0.)
beached = Variable('beached',dtype=np.float32, initial=0.)
pset = ParticleSet.from_list(fieldset=fieldset, pclass=DinoParticle, lon=lonss.tolist(), lat=latss.tolist(),
time = time)
pfile = ParticleFile(dirwrite + outfile, pset, write_ondelete=True)
if(gmbol):
advectionkernel = pset.Kernel(popk.AdvectionRK4_3D_addbolus)
if(Cs>0):
advectionkernel += popk.smagorinsky_bolus
else:
advectionkernel = pset.Kernel(AdvectionRK4_3D)
if(Cs>0):
advectionkernel += popk.smagorinsky
kernels = pset.Kernel(popk.initials) + popk.Sink + advectionkernel + popk.Age + popk.periodicBC
pset.execute(kernels, runtime=delta(days=5*365), dt=delta(minutes=-15), output_file=pfile, verbose_progress=False, recovery={ErrorCode.ErrorOutOfBounds: popk.DeleteParticle})
print('Execution finished')
def run_nemo_curvilinear(mode, outfile, advtype='RK4'):
"""Function that shows how to read in curvilinear grids, in this case from NEMO"""
data_path = path.join(path.dirname(__file__), 'NemoCurvilinear_data/')
filenames = {
'U': {
'lon': data_path + 'mesh_mask.nc4',
'lat': data_path + 'mesh_mask.nc4',
'data': data_path + 'U_purely_zonal-ORCA025_grid_U.nc4'
},
'V': {
'lon': data_path + 'mesh_mask.nc4',
'lat': data_path + 'mesh_mask.nc4',
'data': data_path + 'V_purely_zonal-ORCA025_grid_V.nc4'
}
}
variables = {'U': 'U', 'V': 'V'}
dimensions = {'lon': 'glamf', 'lat': 'gphif'}
field_chunksize = {'y': 2, 'x': 2}
field_set = FieldSet.from_nemo(filenames,
variables,
dimensions,
field_chunksize=field_chunksize)
assert field_set.U.field_chunksize == field_chunksize
# Now run particles as normal
npart = 20
lonp = 30 * np.ones(npart)
if advtype == 'RK4':
latp = np.linspace(-70, 88, npart)
runtime = delta(days=160)
else:
latp = np.linspace(-70, 70, npart)
runtime = delta(days=15)
def periodicBC(particle, fieldSet, time):
if particle.lon > 180:
particle.lon -= 360
pset = ParticleSet.from_list(field_set, ptype[mode], lon=lonp, lat=latp)
pfile = ParticleFile(outfile, pset, outputdt=delta(days=1))
kernels = pset.Kernel(advection[advtype]) + periodicBC
pset.execute(kernels,
runtime=runtime,
dt=delta(hours=6),
output_file=pfile)
assert np.allclose(pset.lat - latp, 0, atol=2e-2)
def compute_nemo_particle_advection(field_set, mode, lonp, latp):
def periodicBC(particle, fieldSet, time):
if particle.lon > 15.0:
particle.lon -= 15.0
if particle.lon < 0:
particle.lon += 15.0
if particle.lat > 60.0:
particle.lat -= 11.0
if particle.lat < 49.0:
particle.lat += 11.0
pset = ParticleSet.from_list(field_set, ptype[mode], lon=lonp, lat=latp)
pfile = ParticleFile("nemo_particles_chunk", pset, outputdt=delta(days=1))
kernels = pset.Kernel(AdvectionRK4) + periodicBC
pset.execute(kernels, runtime=delta(days=4), dt=delta(hours=6), output_file=pfile)
return pset
def run_corefootprintparticles(dirwrite, outfile, lonss, latss, dep):
ufiles = sorted(glob(dirread_top + 'means/ORCA0083-N06_200?????d05U.nc'))
vfiles = sorted(glob(dirread_top + 'means/ORCA0083-N06_200?????d05V.nc'))
wfiles = sorted(glob(dirread_top + 'means/ORCA0083-N06_200?????d05W.nc'))
tfiles = sorted(glob(dirread_top + 'means/ORCA0083-N06_200?????d05T.nc'))
bfile = dirread_top + 'domain/bathymetry_ORCA12_V3.3.nc'
fieldset = set_nemo_fieldset(ufiles, vfiles, wfiles, tfiles, bfile,
dirread_pal + 'domain/coordinates.nc')
fieldset.B.allow_time_extrapolation = True
fieldset.add_constant('dwellingdepth', np.float(dd))
fieldset.add_constant('sinkspeed', sp / 86400.)
fieldset.add_constant('maxage', 300000. * 86400)
fieldset.add_constant('surface', 2.5)
class DinoParticle(JITParticle):
temp = Variable('temp', dtype=np.float32, initial=np.nan)
age = Variable('age', dtype=np.float32, initial=0.)
salin = Variable('salin', dtype=np.float32, initial=np.nan)
lon0 = Variable('lon0', dtype=np.float32, initial=0.)
lat0 = Variable('lat0', dtype=np.float32, initial=0.)
depth0 = Variable('depth0', dtype=np.float32, initial=0.)
pset = ParticleSet.from_list(fieldset=fieldset,
pclass=DinoParticle,
lon=lonss.tolist(),
lat=latss.tolist(),
time=time)
pfile = ParticleFile(dirwrite + outfile, pset, write_ondelete=True)
kernels = pset.Kernel(initials) + Sink + pset.Kernel(
AdvectionRK4_3D) + Age + periodicBC
pset.execute(kernels,
runtime=delta(days=2170),
dt=delta(minutes=-60),
output_file=pfile,
verbose_progress=False,
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
print 'Execution finished'
def run_corefootprintparticles(dirwrite, outfile, lonss, lonsz, latss, latsz,
startdep, time):
snapshots = snapshot_function(date(2000, 1, 9), date(2010, 6, 15),
delta(days=3))
fieldset = set_ofes_fieldset(snapshots)
fieldset.add_periodic_halo(zonal=True)
fieldset.B.allow_time_extrapolation = True
fieldset.add_constant('dwellingdepth', np.float(dd))
fieldset.add_constant('sinkspeed', sp / 86400.)
fieldset.add_constant('maxage', 30. * 86400)
class ForamParticle(JITParticle):
temp = Variable('temp', dtype=np.float32, initial=np.nan)
age = Variable('age', dtype=np.float32, initial=0.)
salin = Variable('salin', dtype=np.float32, initial=np.nan)
lon0 = Variable('lon0', dtype=np.float32, initial=0.)
lat0 = Variable('lat0', dtype=np.float32, initial=0.)
depth0 = Variable('depth0',
dtype=np.float32,
initial=0.,
to_write=False)
time0 = Variable('time0', dtype=np.float32, initial=0., to_write=False)
shellage = Variable('shellage', dtype=np.float32, initial=0.)
loctemp = Variable('loctemp', dtype=np.float32, initial=np.nan)
pset = ParticleSet.from_list(fieldset=fieldset,
pclass=ForamParticle,
lon=lonss.tolist(),
lat=latss.tolist(),
time=time)
pfile = ParticleFile(dirwrite + outfile, pset, outputdt=delta(days=1))
kernels = pset.Kernel(
initials
) + ShellAge + Age + Sink + AdvectionRK4_3D + SampleTemp + LocalConditions
pset.execute(kernels,
runtime=delta(days=3650),
dt=delta(minutes=-5),
output_file=pfile,
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
def run_corefootprintparticles(dirwrite, outfile, lonss, latss, dep):
snapshots = snapshotfunction(range(0, 365 * 5 + 8,
tempres)) #max is 365*5+7
hormesh = mesh + 'grid_coordinates_pop_tx0.1.nc'
Sdepth = mesh + 'bottom_cell.nc'
fieldset = set_fieldset(snapshots, hormesh, Sdepth)
fieldset.B.allow_time_extrapolation = True
fieldset.add_periodic_halo(zonal=True)
fieldset.add_constant('dwellingdepth', np.float(dd))
fieldset.add_constant('sinkspeed', sp / 86400.)
fieldset.add_constant('maxage', 300000. * 86400)
fieldset.add_constant('surface', 5.00622)
class DinoParticle(JITParticle):
temp = Variable('temp', dtype=np.float32, initial=np.nan)
age = Variable('age', dtype=np.float32, initial=0.)
salin = Variable('salin', dtype=np.float32, initial=np.nan)
lon0 = Variable('lon0', dtype=np.float32, initial=0.)
lat0 = Variable('lat0', dtype=np.float32, initial=0.)
depth0 = Variable('depth0', dtype=np.float32, initial=0.)
pset = ParticleSet.from_list(fieldset=fieldset,
pclass=DinoParticle,
lon=lonss.tolist(),
lat=latss.tolist(),
time=time)
pfile = ParticleFile(dirwrite + outfile, pset, write_ondelete=True)
kernels = pset.Kernel(initials) + Sink + pset.Kernel(
AdvectionRK4_3D) + Age + periodicBC
pset.execute(kernels,
runtime=delta(days=365 * 5),
dt=delta(minutes=-5),
output_file=pfile,
verbose_progress=False,
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
print('Execution finished')
def run_corefootprintparticles(dirwrite, outfile):
snapshots = snapshot_function(date(2000, 1, 9), date(2010, 6, 15),
delta(days=3))
# one needs to uses the precise dates of the snapshots in the ofes-data
fieldset = set_ofes_fieldset(snapshots)
fieldset.add_periodic_halo(zonal=True)
fieldset.add_constant('dwellingdepth', np.float(dd))
fieldset.add_constant('sinkspeed', sp / 86400)
fieldset.add_constant('maxage', ls * 86400)
fieldset.add_constant('bottomlon', bottomlon)
fieldset.add_constant('bottomlat', bottomlat)
class ForamParticle(JITParticle):
temp = Variable('temp', dtype=np.float32, initial=fieldset.temp)
age = Variable('age', dtype=np.float32, initial=0.)
salin = Variable('salin', dtype=np.float32, initial=np.nan)
d18ow = Variable('d18ow', dtype=np.float32, initial=0.)
d18oc = Variable('d18oc', dtype=np.float32, initial=0.)
loctemp = Variable('loctemp', dtype=np.float32, initial=0)
d18owL = Variable('d18owL', dtype=np.float32, initial=0.)
d18ocL = Variable('d18ocL', dtype=np.float32, initial=0.)
pset = ParticleSet(fieldset=fieldset,
pclass=ForamParticle,
lon=corelon,
lat=corelat,
depth=coredepth,
time=fieldset.U.grid.time[-1],
repeatdt=delta(days=3))
pfile = ParticleFile(dirwrite + outfile, pset, outputdt=delta(days=1))
kernels = pset.Kernel(
AdvectionRK4_3D
) + Sink + SampleTemp + Age + Sampled18OLoc + LocalConditions
pset.execute(kernels,
dt=delta(minutes=-5),
output_file=pfile,
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
def compute_MITgcm_particle_advection(field_set, mode, lonp, latp):
def periodicBC(particle, fieldSet, time):
dlon = -89.0 + 91.8
dlat = 0.7 + 1.4
if particle.lon > -89.0:
particle.lon -= dlon
if particle.lon < -91.8:
particle.lon += dlon
if particle.lat > 0.7:
particle.lat -= dlat
if particle.lat < -1.4:
particle.lat += dlat
pset = ParticleSet.from_list(field_set, ptype[mode], lon=lonp, lat=latp)
pfile = ParticleFile("MITgcm_particles_chunk",
pset,
outputdt=delta(days=1))
kernels = pset.Kernel(periodicBC) + pset.Kernel(AdvectionRK4)
pset.execute(kernels,
runtime=delta(days=30),
dt=delta(hours=12),
output_file=pfile)
return pset
def run_corefootprintparticles(dirwrite, outfile, lonss, latss, dep):
ufiles = sorted(glob(dirread_top + 'means/ORCA0083-N06_200?????d05U.nc'))
vfiles = sorted(glob(dirread_top + 'means/ORCA0083-N06_200?????d05V.nc'))
wfiles = sorted(glob(dirread_top + 'means/ORCA0083-N06_200?????d05W.nc'))
tfiles = sorted(glob(dirread_top + 'means/ORCA0083-N06_200?????d05T.nc'))
fieldset = set_nemo_fieldset(
ufiles, vfiles, wfiles, tfiles, dirread_pal +
'domain/coordinates.nc') # coordinates.nc is the mesh mask here
fieldset.add_constant('dwellingdepth', np.float(dd))
fieldset.add_constant('maxage', 300000. * 86400)
fieldset.add_constant('surface', 2.5)
class FixParticle(JITParticle):
temp = Variable('temp', dtype=np.float32, initial=np.nan)
age = Variable('age', dtype=np.float32, initial=0.)
salin = Variable('salin', dtype=np.float32, initial=np.nan)
pset = ParticleSet.from_list(fieldset=fieldset,
pclass=FixParticle,
lon=lonss.tolist(),
lat=latss.tolist(),
time=time)
pfile = ParticleFile(dirwrite + outfile, pset, outputdt=delta(days=6))
kernels = pset.Kernel(SampleSurf) + Age
pset.execute(kernels,
runtime=delta(days=2170),
dt=delta(days=-3),
output_file=pfile,
verbose_progress=False,
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
print 'Execution finished'
def run_corefootprintparticles(dirwrite, outfile, lonss, latss, time):
snapshots = snapshot_function(date(1980, 1, 3), date(2005, 12, 29),
delta(days=3))
fieldset = set_ofes_fieldset(snapshots)
fieldset.add_periodic_halo(zonal=True)
fieldset.B.allow_time_extrapolation = True
fieldset.add_constant('maxage', 300000. * 86400)
fieldset.add_constant('surface', 2.6)
class DinoOfesParticle(JITParticle):
temp = Variable('temp', dtype=np.float32, initial=np.nan)
age = Variable('age', dtype=np.float32, initial=0.)
salin = Variable('salin', dtype=np.float32, initial=np.nan)
lon0 = Variable('lon0', dtype=np.float32, initial=0., to_write=False)
lat0 = Variable('lat0', dtype=np.float32, initial=0., to_write=False)
depth0 = Variable('depth0',
dtype=np.float32,
initial=0.,
to_write=False)
time0 = Variable('time0', dtype=np.float32, initial=0., to_write=False)
pset = ParticleSet.from_list(fieldset=fieldset,
pclass=DinoOfesParticle,
lon=lonss.tolist(),
lat=latss.tolist(),
time=time) #depth=depths,
pfile = ParticleFile(dirwrite + outfile, pset, outputdt=delta(days=6))
kernels = pset.Kernel(initials) + Sink + Age + periodicBC
pset.execute(kernels,
runtime=delta(days=7300),
dt=delta(days=-3),
output_file=pfile,
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
def run_northsea_mp(outfile,
nemo_res='0083',
cmems=False,
stokes=False,
diffusion=0,
run3D=False):
fieldset = get_nemo_fieldset(nemo_res, run3D)
if cmems:
set_cmems(fieldset)
if stokes:
set_stokes(fieldset)
if diffusion > 0:
set_diffusion(fieldset, diffusion)
set_unbeaching(fieldset)
pset = get_particle_set(fieldset, run3D)
kernel = pset.Kernel(AdvectionRK4_3D) if run3D else pset.Kernel(
AdvectionRK4)
BeachTesting = BeachTesting_3D if run3D else BeachTesting_2D
kernel += pset.Kernel(BeachTesting) + pset.Kernel(UnBeaching)
if stokes:
kernel += pset.Kernel(StokesDrag) + pset.Kernel(BeachTesting)
if diffusion > 0:
kernel += pset.Kernel(BrownianMotion2D) + pset.Kernel(BeachTesting)
kernel += pset.Kernel(Ageing)
pfile = ParticleFile(outfile, pset)
pfile.write(pset, pset[0].time)
tic = timelib.time()
ndays = 365 * 4 + 100
for d in range(ndays / 2):
day = 2 * d
print('running %d / %d [time %g s]: %d particles ' %
(day, ndays, timelib.time() - tic, len(pset)))
pset.execute(kernel,
runtime=delta(days=2),
dt=900,
verbose_progress=False,
recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
pfile.write(pset, pset[0].time)
lats = np.concatenate((lat_r.flatten(), lat_t.flatten()))
times = np.arange(np.datetime64('2000-01-05'), np.datetime64('2001-01-05'))
pset = ParticleSet.from_list(fieldset,
PlasticParticle,
lon=np.tile(lons, [len(times)]),
lat=np.tile(lats, [len(times)]),
time=np.repeat(times, len(lons)))
kernel = AdvectionRK4 #+ pset.Kernel(Ageing)
new_write = True
timer.particlefile = timer.Timer('ParticleFile', parent=timer.root)
outfile = './' + __file__[:-3]
pfile = ParticleFile(outfile, pset)
if new_write:
pfile.write_pickle_per_tstep(pset, pset[0].time)
else:
pfile.write(pset, pset[0].time)
timer.particlefile.stop()
tic = timelib.time()
ndays = 100
timer.run = timer.Timer('Execution', parent=timer.root, start=False)
for d in range(ndays / 2):
day = 2 * d
print('running %d / %d [time %g s]: %d particles ' %
time0 = field_set.U.grid.time[0]
lonv = np.arange(-6, 10.1, .2)
latv = np.arange(50, 63, .2)
lon, lat = np.meshgrid(lonv, latv)
lon = lon.flatten()
lat = lat.flatten()
time = time0 * np.ones(lon.shape)
pset = ParticleSet.from_list(field_set,
JITParticle,
lon=lon,
lat=lat,
time=time)
kernel = AdvectionRK4
timer.particlefile = timer.Timer('ParticleFile', parent=timer.root)
outfile = __file__[:-3]
pfile = ParticleFile(outfile, pset)
pfile.write(pset, pset[0].time)
timer.particlefile.stop()
tic = timelib.time()
ndays = 60
timer.run = timer.Timer('Execution', parent=timer.root, start=False)
for d in range(ndays):
print('running %d / %d: time %g' % (d + 1, ndays, timelib.time() - tic))
timer.run.start()
pset.execute(
kernel, runtime=86400,
dt=900) #, recovery={ErrorCode.ErrorOutOfBounds: DeleteParticle})
timer.run.stop()
timer.particlefile.start()
pfile.write(pset, pset[0].time)
timer.particlefile.stop()
-18.78, -18.69, -18.56, -18.46, -18.41, -18.43, -18.42, -18.53, -18.75,
-18.55, -18.6, -18.61, -18.54, -18.46, -18.32, -18.21, -18.13, -18.17
]
N = 100
def SampleWind(particle, fieldset, time):
particle.uwind = fieldset.uwind[time, particle.depth, particle.lat,
particle.lon]
particle.vwind = fieldset.vwind[time, particle.depth, particle.lat,
particle.lon]
class PumiceParticle(JITParticle):
uwind = Variable('uwind', initial=fieldset.uwind)
vwind = Variable('vwind', initial=fieldset.vwind)
pset = ParticleSet(fieldset=fieldset,
pclass=PumiceParticle,
lon=np.tile(obslon[0], N),
lat=np.tile(obslat[0], N),
time=np.tile(datetime(2019, 8, 7), N))
pfile = ParticleFile(fname, pset, outputdt=delta(days=1))
pset.execute(AdvectionRK4 + pset.Kernel(BrownianMotion2D) + SampleWind,
dt=delta(hours=1),
output_file=pfile)
pfile.close()
depth=z_release,
r_pl=r_pl * np.ones(np.array(lon_release).size),
rho_pl=rho_pl * np.ones(np.array(lon_release).size),
r_tot=r_pl * np.ones(np.array(lon_release).size),
rho_tot=rho_pl * np.ones(np.array(lon_release).size)))
""" Kernal + Execution"""
kernels = pset.Kernel(AdvectionRK4) + pset.Kernel(
PolyTEOS10_bsq) + pset.Kernel(Profiles) + pset.Kernel(
Kooi) #pset.Kernel(AdvectionRK4_3D_vert) pset.Kernel(periodicBC) +
outfile = '/home/dlobelle/Kooi_data/data_output/allrho/res_' + res + '/allr/3yr_uvAdvOnly_NPac_3D_grid' + res + '_allrho_allr_' + str(
round(simdays, 2)) + 'days_' + str(secsdt) + 'dtsecs_' + str(
round(hrsoutdt, 2)) + 'hrsoutdt'
pfile = ParticleFile(outfile, pset, outputdt=delta(hours=hrsoutdt))
pset.execute(kernels,
runtime=delta(days=simdays),
dt=delta(seconds=secsdt),
output_file=pfile,
verbose_progress=True,
recovery={
ErrorCode.ErrorOutOfBounds: DeleteParticle,
ErrorCode.ErrorInterpolation: DeleteParticle
})
pfile.close()
print('Execution finished')
# Make particles initial position list
nc_fid = Dataset(grid_file, 'r') #open grid file nc to read
#lats = nc_fid.variables['nav_lat'][:] # extract/copy the data
#lons = nc_fid.variables['nav_lon'][:]
#lonE=lons[:,169-3]
#latE=lats[:,169-3]
npart = 30
lonp = [i for i in np.linspace(-88.18, -88.20, npart)]
latp = [i for i in np.linspace(17.52, 17.53, npart)] #this makes a list!
pset = ParticleSet.from_list(field_set, JITParticle, lon=lonp, lat=latp)
pfile = ParticleFile("tBelize_nemo_particles_30halfD", pset, outputdt=delta(hours=0.5))
kernels = pset.Kernel(AdvectionRK4)
#Plot initial positions
#pset.show()
pset.execute(kernels, runtime=delta(days=0.5), dt=delta(hours=0.1), output_file=pfile)
#plotTrajectoriesFile("Belize_nemo_particles_t2.nc");
#pset.show(domain={'N':-31, 'S':-35, 'E':33, 'W':26})
#pset.show(field=field_set.U)
#pset.show(field=fieldset.U, show_time=datetime(2002, 1, 10, 2))
#pset.show(field=fieldset.U, show_time=datetime(2002, 1, 10, 2), with_particles=False)
end = time.time()
print(end-start)