def __init__(self,
lon,
lat,
depth,
time=None,
time_origin=None,
mesh='flat'):
super(CurvilinearSGrid, self).__init__(lon, lat, time, time_origin,
mesh)
assert (isinstance(depth, np.ndarray) and len(depth.shape)
in [3, 4]), 'depth is not a 4D numpy array'
self.gtype = GridCode.CurvilinearSGrid
self.depth = depth
self.zdim = self.depth.shape[-3]
self.z4d = len(self.depth.shape) == 4
if self.z4d:
# self.depth.shape[0] is 0 for S grids loaded from netcdf file
assert self.tdim == self.depth.shape[0] or self.depth.shape[
0] == 0, 'depth dimension has the wrong format. It should be [tdim, zdim, ydim, xdim]'
assert self.xdim == self.depth.shape[-1] or self.depth.shape[
-1] == 0, 'depth dimension has the wrong format. It should be [tdim, zdim, ydim, xdim]'
assert self.ydim == self.depth.shape[-2] or self.depth.shape[
-2] == 0, 'depth dimension has the wrong format. It should be [tdim, zdim, ydim, xdim]'
else:
assert self.xdim == self.depth.shape[
-1], 'depth dimension has the wrong format. It should be [zdim, ydim, xdim]'
assert self.ydim == self.depth.shape[
-2], 'depth dimension has the wrong format. It should be [zdim, ydim, xdim]'
if not self.depth.dtype == np.float32:
logger.warning_once("Casting depth data to np.float32")
self.depth = self.depth.astype(np.float32)
def check_fieldsets_in_kernels(self, pyfunc):
"""
function checks the integrity of the fieldset with the kernels.
This function is to be called from the derived class when setting up the 'pyfunc'.
"""
if self.fieldset is not None:
if pyfunc is AdvectionRK4_3D:
warning = False
if isinstance(self._fieldset.W, Field) and self._fieldset.W.creation_log != 'from_nemo' and \
self._fieldset.W._scaling_factor is not None and self._fieldset.W._scaling_factor > 0:
warning = True
if type(self._fieldset.W) in [SummedField, NestedField]:
for f in self._fieldset.W:
if f.creation_log != 'from_nemo' and f._scaling_factor is not None and f._scaling_factor > 0:
warning = True
if warning:
logger.warning_once(
'Note that in AdvectionRK4_3D, vertical velocity is assumed positive towards increasing z.\n'
' If z increases downward and w is positive upward you can re-orient it downwards by setting fieldset.W.set_scaling_factor(-1.)'
)
elif pyfunc is AdvectionAnalytical:
if self._ptype.uses_jit:
raise NotImplementedError(
'Analytical Advection only works in Scipy mode')
if self._fieldset.U.interp_method != 'cgrid_velocity':
raise NotImplementedError(
'Analytical Advection only works with C-grids')
if self._fieldset.U.grid.gtype not in [
GridCode.CurvilinearZGrid, GridCode.RectilinearZGrid
]:
raise NotImplementedError(
'Analytical Advection only works with Z-grids in the vertical'
)
def __init__(self,
lon,
lat,
depth,
time=None,
time_origin=None,
mesh='flat'):
super(RectilinearSGrid, self).__init__(lon, lat, time, time_origin,
mesh)
assert (isinstance(depth, np.ndarray) and len(depth.shape)
in [3, 4]), 'depth is not a 3D or 4D numpy array'
self.gtype = GridCode.RectilinearSGrid
self.depth = depth
self.zdim = self.depth.shape[-3]
self.z4d = len(self.depth.shape) == 4
if self.z4d:
assert self.tdim == self.depth.shape[
0], 'depth dimension has the wrong format. It should be [tdim, zdim, ydim, xdim]'
assert self.xdim == self.depth.shape[
-1], 'depth dimension has the wrong format. It should be [tdim, zdim, ydim, xdim]'
assert self.ydim == self.depth.shape[
-2], 'depth dimension has the wrong format. It should be [tdim, zdim, ydim, xdim]'
else:
assert self.xdim == self.depth.shape[
-1], 'depth dimension has the wrong format. It should be [zdim, ydim, xdim]'
assert self.ydim == self.depth.shape[
-2], 'depth dimension has the wrong format. It should be [zdim, ydim, xdim]'
if not self.depth.dtype == np.float32:
logger.warning_once("Casting depth data to np.float32")
self.depth = self.depth.astype(np.float32)
if self.lat_flipped:
self.depth = np.flip(self.depth, axis=-2)
def advancetime(self, fieldset_new):
"""Replace oldest time on FieldSet with new FieldSet
:param fieldset_new: FieldSet snapshot with which the oldest time has to be replaced"""
logger.warning_once("Fieldset.advancetime() is deprecated.\n \
Parcels deals automatically with loading only 3 time steps simustaneously\
such that the total allocated memory remains limited."
)
advance = 0
for gnew in fieldset_new.gridset.grids:
gnew.advanced = False
for fnew in fieldset_new.get_fields():
if isinstance(fnew, VectorField):
continue
f = getattr(self, fnew.name)
gnew = fnew.grid
if not gnew.advanced:
g = f.grid
advance2 = g.advancetime(gnew)
if advance2 * advance < 0:
raise RuntimeError(
"Some Fields of the Fieldset are advanced forward and other backward"
)
advance = advance2
gnew.advanced = True
f.advancetime(fnew, advance == 1)
def add_periodic_halo(self, zonal, meridional, halosize=5):
"""Add a 'halo' to the Grid, through extending the Grid (and lon/lat)
similarly to the halo created for the Fields
:param zonal: Create a halo in zonal direction (boolean)
:param meridional: Create a halo in meridional direction (boolean)
:param halosize: size of the halo (in grid points). Default is 5 grid points
"""
if zonal:
lonshift = self.lon[:, -1] - 2 * self.lon[:, 0] + self.lon[:, 1]
if not np.allclose(self.lon[:, 1]-self.lon[:, 0], self.lon[:, -1]-self.lon[:, -2]):
logger.warning_once("The zonal halo is located at the east and west of current grid, with a dx = lon[:,1]-lon[:,0] between the last nodes of the original grid and the first ones of the halo. In your grid, lon[:,1]-lon[:,0] != lon[:,-1]-lon[:,-2]. Is the halo computed as you expect?")
self.lon = np.concatenate((self.lon[:, -halosize:] - lonshift[:, np.newaxis],
self.lon, self.lon[:, 0:halosize] + lonshift[:, np.newaxis]),
axis=len(self.lon.shape)-1)
self.lat = np.concatenate((self.lat[:, -halosize:],
self.lat, self.lat[:, 0:halosize]),
axis=len(self.lat.shape)-1)
self.xdim = self.lon.shape[1]
self.ydim = self.lat.shape[0]
self.zonal_periodic = True
self.zonal_halo = halosize
if meridional:
if not np.allclose(self.lat[1, :]-self.lat[0, :], self.lat[-1, :]-self.lat[-2, :]):
logger.warning_once("The meridional halo is located at the north and south of current grid, with a dy = lat[1,:]-lat[0,:] between the last nodes of the original grid and the first ones of the halo. In your grid, lat[1,:]-lat[0,:] != lat[-1,:]-lat[-2,:]. Is the halo computed as you expect?")
latshift = self.lat[-1, :] - 2 * self.lat[0, :] + self.lat[1, :]
self.lat = np.concatenate((self.lat[-halosize:, :] - latshift[np.newaxis, :],
self.lat, self.lat[0:halosize, :] + latshift[np.newaxis, :]),
axis=len(self.lat.shape)-2)
self.lon = np.concatenate((self.lon[-halosize:, :],
self.lon, self.lon[0:halosize, :]),
axis=len(self.lon.shape)-2)
self.xdim = self.lon.shape[1]
self.ydim = self.lat.shape[0]
self.meridional_halo = halosize
def add_periodic_halo(self, zonal, meridional, halosize=5):
"""Add a 'halo' to the Grid, through extending the Grid (and lon/lat)
similarly to the halo created for the Fields
:param zonal: Create a halo in zonal direction (boolean)
:param meridional: Create a halo in meridional direction (boolean)
:param halosize: size of the halo (in grid points). Default is 5 grid points
"""
if zonal:
lonshift = (self.lon[-1] - 2 * self.lon[0] + self.lon[1])
if not np.allclose(self.lon[1]-self.lon[0], self.lon[-1]-self.lon[-2]):
logger.warning_once("The zonal halo is located at the east and west of current grid, with a dx = lon[1]-lon[0] between the last nodes of the original grid and the first ones of the halo. In your grid, lon[1]-lon[0] != lon[-1]-lon[-2]. Is the halo computed as you expect?")
self.lon = np.concatenate((self.lon[-halosize:] - lonshift,
self.lon, self.lon[0:halosize] + lonshift))
self.xdim = self.lon.size
self.zonal_periodic = True
self.zonal_halo = halosize
if meridional:
if not np.allclose(self.lat[1]-self.lat[0], self.lat[-1]-self.lat[-2]):
logger.warning_once("The meridional halo is located at the north and south of current grid, with a dy = lat[1]-lat[0] between the last nodes of the original grid and the first ones of the halo. In your grid, lat[1]-lat[0] != lat[-1]-lat[-2]. Is the halo computed as you expect?")
latshift = (self.lat[-1] - 2 * self.lat[0] + self.lat[1])
self.lat = np.concatenate((self.lat[-halosize:] - latshift,
self.lat, self.lat[0:halosize] + latshift))
self.ydim = self.lat.size
self.meridional_halo = halosize
self.lonlat_minmax = np.array([np.nanmin(self.lon), np.nanmax(self.lon), np.nanmin(self.lat), np.nanmax(self.lat)], dtype=np.float32)
if isinstance(self, RectilinearSGrid):
self.add_Sdepth_periodic_halo(zonal, meridional, halosize)
def execute_python(self, pset, endtime, dt):
"""Performs the core update loop via Python"""
# sign of dt: { [0, 1]: forward simulation; -1: backward simulation }
sign_dt = np.sign(dt)
analytical = False
if 'AdvectionAnalytical' in self._pyfunc.__name__:
analytical = True
if not np.isinf(dt):
logger.warning_once(
'dt is not used in AnalyticalAdvection, so is set to np.inf'
)
dt = np.inf
if self.fieldset is not None:
for f in self.fieldset.get_fields():
if type(f) in [VectorField, NestedField, SummedField]:
continue
f.data = np.array(f.data)
for p in pset:
self.evaluate_particle(p,
endtime,
sign_dt,
dt,
analytical=analytical)
def __init__(self):
ptype = self.getPType()
# Explicit initialisation of all particle variables
for v in ptype.variables:
if isinstance(v.initial, attrgetter):
initial = v.initial(self)
elif isinstance(v.initial, Field):
lon = self.getInitialValue(ptype, name='lon')
lat = self.getInitialValue(ptype, name='lat')
depth = self.getInitialValue(ptype, name='depth')
time = self.getInitialValue(ptype, name='time')
if time is None:
raise RuntimeError(
'Cannot initialise a Variable with a Field if no time provided. '
'Add a "time=" to ParticleSet construction')
v.initial.fieldset.computeTimeChunk(time, 0)
initial = v.initial[time, depth, lat, lon]
logger.warning_once(
"Particle initialisation from field can be very slow as it is computed in scipy mode."
)
else:
initial = v.initial
# Enforce type of initial value
if v.dtype != c_void_p:
setattr(self, v.name, v.dtype(initial))
# Placeholder for explicit error handling
self.exception = None
def to_dict(self, pfile, time, deleted_only=False):
"""Convert all Particle data from one time step to a python dictionary.
:param pfile: ParticleFile object requesting the conversion
:param time: Time at which to write ParticleSet
:param deleted_only: Flag to write only the deleted Particles
returns two dictionaries: one for all variables to be written each outputdt,
and one for all variables to be written once
"""
data_dict = {}
data_dict_once = {}
time = time.total_seconds() if isinstance(time, delta) else time
pd = self.particle_data
if pfile.lasttime_written != time and \
(pfile.write_ondelete is False or deleted_only is not False):
if pd['id'].size == 0:
logger.warning(
"ParticleSet is empty on writing as array at time %g" %
time)
else:
if deleted_only is not False:
to_write = deleted_only
else:
to_write = _to_write_particles(pd, time)
if np.any(to_write) > 0:
for var in pfile.var_names:
data_dict[var] = pd[var][to_write]
pfile.maxid_written = np.maximum(pfile.maxid_written,
np.max(data_dict['id']))
pset_errs = (to_write & (pd['state'] != OperationCode.Delete)
& np.less(1e-3,
np.abs(time - pd['time']),
where=np.isfinite(pd['time'])))
if np.count_nonzero(pset_errs) > 0:
logger.warning_once(
'time argument in pfile.write() is {}, but particles have time {}'
.format(time, pd['time'][pset_errs]))
if time not in pfile.time_written:
pfile.time_written.append(time)
if len(pfile.var_names_once) > 0:
first_write = (_to_write_particles(pd, time) & np.isin(
pd['id'], pfile.written_once, invert=True))
if np.any(first_write):
data_dict_once['id'] = np.array(
pd['id'][first_write]).astype(dtype=np.int64)
for var in pfile.var_names_once:
data_dict_once[var] = pd[var][first_write]
pfile.written_once.extend(pd['id'][first_write])
if deleted_only is False:
pfile.lasttime_written = time
return data_dict, data_dict_once
def __enter__(self):
"""
This function enters the physical file (equivalent to a 'with open(...)' statement) and returns a file object.
In Dask, with dynamic loading, this is the point where we have access to the header-information of the file.
Hence, this function initializes the dynamic loading by parsing the chunksize-argument and maps the requested
chunksizes onto the variables found in the file. For auto-chunking, educated guesses are made (e.g. with the
dask configuration file in the background) to determine the ideal chunk sizes. This is also the point
where - due to the chunking, the file is 'locked', meaning that it cannot be simultaneously accessed by
another process. This is significant in a cluster setup.
"""
if self.chunksize not in [False, None, 'auto'] and type(
self.chunksize) is not dict:
raise AttributeError(
"'chunksize' is of wrong type. Parameter is expected to be a dict per data dimension, or be False, None or 'auto'."
)
if isinstance(self.chunksize, list):
self.chunksize = tuple(self.chunksize)
init_chunk_dict = None
if self.chunksize not in [False, None]:
init_chunk_dict = self._get_initial_chunk_dictionary()
try:
# Unfortunately we need to do if-else here, cause the lock-parameter is either False or a Lock-object
# (which we would rather want to have being auto-managed).
# If 'lock' is not specified, the Lock-object is auto-created and managed by xarray internally.
if self.lock_file:
self.dataset = xr.open_dataset(str(self.filename),
decode_cf=True,
engine=self.netcdf_engine,
chunks=init_chunk_dict)
else:
self.dataset = xr.open_dataset(str(self.filename),
decode_cf=True,
engine=self.netcdf_engine,
chunks=init_chunk_dict,
lock=False)
self.dataset['decoded'] = True
except:
logger.warning_once(
"File %s could not be decoded properly by xarray (version %s).\n It will be opened with no decoding. Filling values might be wrongly parsed."
% (self.filename, xr.__version__))
if self.lock_file:
self.dataset = xr.open_dataset(str(self.filename),
decode_cf=False,
engine=self.netcdf_engine,
chunks=init_chunk_dict)
else:
self.dataset = xr.open_dataset(str(self.filename),
decode_cf=False,
engine=self.netcdf_engine,
chunks=init_chunk_dict,
lock=False)
self.dataset['decoded'] = False
for inds in self.indices.values():
if type(inds) not in [list, range]:
raise RuntimeError(
'Indices for field subsetting need to be a list')
return self
def toDictionary(self, pfile, time, deleted_only=False):
"""
Convert all Particle data from one time step to a python dictionary.
:param pfile: ParticleFile object requesting the conversion
:param time: Time at which to write ParticleSet
:param deleted_only: Flag to write only the deleted Particles
returns two dictionaries: one for all variables to be written each outputdt,
and one for all variables to be written once
This function depends on the specific collection in question and thus needs to be specified in specific
derivative classes.
"""
data_dict = {}
data_dict_once = {}
time = time.total_seconds() if isinstance(time, delta) else time
indices_to_write = []
if pfile.lasttime_written != time and \
(pfile.write_ondelete is False or deleted_only is not False):
if self._data['id'].size == 0:
logger.warning("ParticleSet is empty on writing as array at time %g" % time)
else:
if deleted_only is not False:
if type(deleted_only) not in [list, np.ndarray] and deleted_only in [True, 1]:
indices_to_write = np.where(np.isin(self._data['state'],
[OperationCode.Delete]))[0]
elif type(deleted_only) in [list, np.ndarray]:
indices_to_write = deleted_only
else:
indices_to_write = _to_write_particles(self._data, time)
if np.any(indices_to_write) > 0:
for var in pfile.var_names:
data_dict[var] = self._data[var][indices_to_write]
pfile.maxid_written = np.maximum(pfile.maxid_written, np.max(data_dict['id']))
pset_errs = ((self._data['state'][indices_to_write] != OperationCode.Delete) & np.greater(np.abs(time - self._data['time'][indices_to_write]), 1e-3, where=np.isfinite(self._data['time'][indices_to_write])))
if np.count_nonzero(pset_errs) > 0:
logger.warning_once('time argument in pfile.write() is {}, but particles have time {}'.format(time, self._data['time'][pset_errs]))
# ==== this function should probably move back somewhere into the particle-file instead of the to_dict ==== #
if time not in pfile.time_written:
pfile.time_written.append(time)
if len(pfile.var_names_once) > 0:
first_write = (_to_write_particles(self._data, time) & _is_particle_started_yet(self._data, time) & np.isin(self._data['id'], pfile.written_once, invert=True))
if np.any(first_write):
data_dict_once['id'] = np.array(self._data['id'][first_write]).astype(dtype=np.int64)
for var in pfile.var_names_once:
data_dict_once[var] = self._data[var][first_write]
pfile.written_once.extend(np.array(self._data['id'][first_write]).astype(dtype=np.int64).tolist())
if deleted_only is False:
pfile.lasttime_written = time
return data_dict, data_dict_once
def write(self, pset, time, sync=True, deleted_only=False):
"""Write :class:`parcels.particleset.ParticleSet` data to file
:param pset: ParticleSet object to write
:param time: Time at which to write ParticleSet
:param sync: Optional argument whether to write data to disk immediately. Default is True
"""
if self.dataset is None:
self.open_dataset()
if isinstance(time, delta):
time = time.total_seconds()
if self.lasttime_written != time and \
(self.write_ondelete is False or deleted_only is True):
if pset.size > 0:
first_write = [
p for p in pset if (p.fileid < 0 or len(self.idx) == 0)
and _is_particle_started_yet(p, time)
] # len(self.idx)==0 in case pset is written to new ParticleFile
for p in first_write:
p.fileid = self.lasttraj # particle id in current file
self.lasttraj += 1
self.idx = np.append(self.idx, np.zeros(len(first_write)))
for p in pset:
if _is_particle_started_yet(p, time):
i = p.fileid
self.id[i, self.idx[i]] = p.id
self.time[i, self.idx[i]] = p.time
self.lat[i, self.idx[i]] = p.lat
self.lon[i, self.idx[i]] = p.lon
self.z[i, self.idx[i]] = p.depth
for var in self.user_vars:
getattr(self, var)[i,
self.idx[i]] = getattr(p, var)
if p.state != ErrorCode.Delete and not np.allclose(
p.time, time):
logger.warning_once(
'time argument in pfile.write() is %g, but a particle has time %g.'
% (time, p.time))
for p in first_write:
for var in self.user_vars_once:
getattr(self, var)[p.fileid] = getattr(p, var)
else:
logger.warning(
"ParticleSet is empty on writing as array at time %g" %
time)
if not deleted_only:
self.idx += 1
self.lasttime_written = time
if sync:
self.sync()
def cleanup_unload_lib(lib):
# Clean-up the in-memory dynamic linked libraries.
# This is not really necessary, as these programs are not that large, but with the new random
# naming scheme which is required on Windows OS'es to deal with updates to a Parcels' kernel.
if lib is not None:
try:
_ctypes.FreeLibrary(lib._handle) if platform == 'win32' else _ctypes.dlclose(lib._handle)
except:
logger.warning_once("compiled library already freed.")
def add_grid(self, field):
grid = field.grid
existing_grid = False
for g in self.grids:
if field.field_chunksize != grid.master_chunksize:
logger.warning_once(
"Field chunksize and Grid master chunksize are not equal - erroneous behaviour expected."
)
break
if g == grid:
existing_grid = True
break
sameGrid = True
sameDims = True
if grid.time_origin != g.time_origin:
sameDims = False
continue
for attr in ['lon', 'lat', 'depth', 'time']:
gattr = getattr(g, attr)
gridattr = getattr(grid, attr)
if gattr.shape != gridattr.shape or not np.allclose(
gattr, gridattr):
sameGrid = False
sameDims = False
break
if not sameDims:
continue
sameGrid &= (grid.master_chunksize == g.master_chunksize) or (
grid.master_chunksize in [False, None]
and g.master_chunksize in [False, None])
if not sameGrid and sameDims and grid.master_chunksize is not None:
res = False
if (isinstance(grid.master_chunksize, tuple) and isinstance(g.master_chunksize, tuple)) or \
(isinstance(grid.master_chunksize, dict) and isinstance(g.master_chunksize, dict)):
res |= functools.reduce(
lambda i, j: i and j,
map(lambda m, k: m == k, grid.master_chunksize,
g.master_chunksize), True)
if res:
sameGrid = True
logger.warning_once(
"Trying to initialize a shared grid with different chunking sizes - action prohibited. Replacing requested field_chunksize with grid's master chunksize."
)
else:
raise ValueError(
"Conflict between grids of the same gridset: major grid chunksize and requested sibling-grid chunksize as well as their chunk-dimension names are not equal - Please apply the same chunksize to all fields in a shared grid!"
)
break
if sameGrid:
existing_grid = True
field.grid = g
break
if not existing_grid:
self.grids.append(grid)
field.igrid = self.grids.index(field.grid)
def convert_pset_to_dict(self, pset, time, deleted_only=False):
"""Convert all Particle data from one time step to a python dictionary.
:param pset: ParticleSet object to write
:param time: Time at which to write ParticleSet
:param deleted_only: Flag to write only the deleted Particles
returns two dictionaries: one for all variables to be written each outputdt,
and one for all variables to be written once
"""
data_dict = {}
data_dict_once = {}
time = time.total_seconds() if isinstance(time, delta) else time
if self.lasttime_written != time and \
(self.write_ondelete is False or deleted_only is True):
if pset.size == 0:
logger.warning("ParticleSet is empty on writing as array at time %g" % time)
else:
for var in self.var_names:
data_dict[var] = np.nan * np.zeros(len(pset))
i = 0
for p in pset:
if p.dt*p.time <= p.dt*time:
for var in self.var_names:
data_dict[var][i] = getattr(p, var)
if p.state != ErrorCode.Delete and not np.allclose(p.time, time):
logger.warning_once('time argument in pfile.write() is %g, but a particle has time %g.' % (time, p.time))
self.maxid_written = np.max([self.maxid_written, p.id])
i += 1
save_ind = np.isfinite(data_dict["id"])
for key in self.var_names:
data_dict[key] = data_dict[key][save_ind]
if time not in self.time_written:
self.time_written.append(time)
if len(self.var_names_once) > 0:
first_write = [p for p in pset if (p.id not in self.written_once) and _is_particle_started_yet(p, time)]
data_dict_once['id'] = np.nan * np.zeros(len(first_write))
for var in self.var_names_once:
data_dict_once[var] = np.nan * np.zeros(len(first_write))
i = 0
for p in first_write:
self.written_once.append(p.id)
data_dict_once['id'][i] = p.id
for var in self.var_names_once:
data_dict_once[var][i] = getattr(p, var)
i += 1
if not deleted_only:
self.lasttime_written = time
return data_dict, data_dict_once
def execute_python(self, pset, endtime, dt):
"""Performs the core update loop via Python
InteractionKernels do not implement ways to catch or recover from
errors caused during execution of the kernel function(s).
It is strongly recommended not to sample from fields inside an
InteractionKernel.
"""
if self.fieldset is not None:
for f in self.fieldset.get_fields():
if type(f) in [VectorField, NestedField, SummedField]:
continue
f.data = np.array(f.data)
reset_particle_idx = []
for pyfunc in self._pyfunc:
pset.compute_neighbor_tree(endtime, dt)
active_idx = pset._active_particle_idx
mutator = defaultdict(lambda: [])
# Loop only over particles that are in a positive state and have started.
for particle_idx in active_idx:
p = pset[particle_idx]
# Don't use particles that are not started.
if (endtime - p.time) / dt <= -1e-7:
continue
elif (endtime - p.time) / dt < 1:
p.dt = endtime - p.time
reset_particle_idx.append(particle_idx)
neighbors = pset.neighbors_by_index(particle_idx)
try:
res = pyfunc(p, pset.fieldset, p.time, neighbors, mutator)
except Exception as e:
res = ErrorCode.Error
p.exception = e
# InteractionKernels do not implement a way to recover
# from errors.
if res != StateCode.Success:
logger.warning_once(
"Some InteractionKernel was not completed succesfully, likely because a Particle threw an error that was not captured."
)
for particle_idx in active_idx:
p = pset[particle_idx]
try:
for mutator_func, args in mutator[p.id]:
mutator_func(p, *args)
except KeyError:
pass
for particle_idx in reset_particle_idx:
pset[particle_idx].dt = dt
def __init__(self, lon, lat, depth=None, time=None, time_origin=None, mesh='flat'):
super(CurvilinearZGrid, self).__init__(lon, lat, time, time_origin, mesh)
if isinstance(depth, np.ndarray):
assert(len(depth.shape) == 1), 'depth is not a vector'
self.gtype = GridCode.CurvilinearZGrid
self.depth = np.zeros(1, dtype=np.float32) if depth is None else depth
self.zdim = self.depth.size
self.z4d = -1 # only for SGrid
if not self.depth.dtype == np.float32:
logger.warning_once("Casting depth data to np.float32")
self.depth = self.depth.astype(np.float32)
def __init__(self, lon, lat, time, time_origin, mesh):
assert(isinstance(lon, np.ndarray) and len(lon.shape) == 1), 'lon is not a numpy vector'
assert(isinstance(lat, np.ndarray) and len(lat.shape) == 1), 'lat is not a numpy vector'
assert (isinstance(time, np.ndarray) or not time), 'time is not a numpy array'
if isinstance(time, np.ndarray):
assert(len(time.shape) == 1), 'time is not a vector'
super(RectilinearGrid, self).__init__(lon, lat, time, time_origin, mesh)
self.xdim = self.lon.size
self.ydim = self.lat.size
self.tdim = self.time.size
if self.lat[-1] < self.lat[0]:
self.lat = np.flip(self.lat, axis=0)
self.lat_flipped = True
logger.warning_once("Flipping lat data from North-South to South-North")
def __enter__(self):
try:
# Unfortunately we need to do if-else here, cause the lock-parameter is either False or a Lock-object
# (which we would rather want to have being auto-managed).
# If 'lock' is not specified, the Lock-object is auto-created and managed by xarray internally.
self.dataset = xr.open_dataset(str(self.filename), decode_cf=True, engine=self.netcdf_engine)
self.dataset['decoded'] = True
except:
logger.warning_once("File %s could not be decoded properly by xarray (version %s).\n "
"It will be opened with no decoding. Filling values might be wrongly parsed."
% (self.filename, xr.__version__))
self.dataset = xr.open_dataset(str(self.filename), decode_cf=False, engine=self.netcdf_engine)
self.dataset['decoded'] = False
for inds in self.indices.values():
if type(inds) not in [list, range]:
raise RuntimeError('Indices for field subsetting need to be a list')
return self
def __init__(self, lon, lat, time, time_origin, mesh):
self.lon = lon
self.lat = lat
self.time = np.zeros(1, dtype=np.float64) if time is None else time
if not self.lon.dtype == np.float32:
logger.warning_once("Casting lon data to np.float32")
self.lon = self.lon.astype(np.float32)
if not self.lat.dtype == np.float32:
logger.warning_once("Casting lat data to np.float32")
self.lat = self.lat.astype(np.float32)
if not self.time.dtype == np.float64:
assert isinstance(self.time[0], (np.integer, np.floating, float, int)), 'Time vector must be an array of int or floats'
logger.warning_once("Casting time data to np.float64")
self.time = self.time.astype(np.float64)
self.time_full = self.time # needed for deferred_loaded Fields
self.time_origin = TimeConverter() if time_origin is None else time_origin
assert isinstance(self.time_origin, TimeConverter), 'time_origin needs to be a TimeConverter object'
self.mesh = mesh
self.cstruct = None
self.cell_edge_sizes = {}
self.zonal_periodic = False
self.zonal_halo = 0
self.meridional_halo = 0
self.lat_flipped = False
self.defer_load = False
self.lonlat_minmax = np.array([np.nanmin(lon), np.nanmax(lon), np.nanmin(lat), np.nanmax(lat)], dtype=np.float32)
self.periods = 0
def __init__(self, lon, lat, time, time_origin, mesh):
assert (isinstance(lon, np.ndarray)
and len(lon.shape) <= 1), 'lon is not a numpy vector'
assert (isinstance(lat, np.ndarray)
and len(lat.shape) <= 1), 'lat is not a numpy vector'
assert (isinstance(time, np.ndarray)
or not time), 'time is not a numpy array'
if isinstance(time, np.ndarray):
assert (len(time.shape) == 1), 'time is not a vector'
super(RectilinearGrid, self).__init__(lon, lat, time, time_origin,
mesh)
self.xdim = self.lon.size
self.ydim = self.lat.size
self.tdim = self.time.size
if self.ydim > 1 and self.lat[-1] < self.lat[0]:
self.lat = np.flip(self.lat, axis=0)
self.lat_flipped = True
logger.warning_once(
"Flipping lat data from North-South to South-North. "
"Note that this may lead to wrong sign for meridional velocity, so tread very carefully"
)
def execute_python(self, pset, endtime, dt):
"""Performs the core update loop via Python"""
sign_dt = np.sign(dt)
if 'AdvectionAnalytical' in self.pyfunc.__name__:
analytical = True
if not np.isinf(dt):
logger.warning_once('dt is not used in AnalyticalAdvection, so is set to np.inf')
dt = np.inf
else:
analytical = False
particles = pset.data_accessor()
# back up variables in case of OperationCode.Repeat
p_var_back = {}
if self.fieldset is not None:
for f in self.fieldset.get_fields():
if type(f) in [VectorField, NestedField, SummedField]:
continue
f.data = np.array(f.data)
for p in range(pset.size):
particles.set_index(p)
# Don't execute particles that aren't started yet
sign_end_part = np.sign(endtime - particles.time)
# Compute min/max dt for first timestep
dt_pos = min(abs(particles.dt), abs(endtime - particles.time))
# ==== numerically stable; also making sure that continuously-recovered particles do end successfully,
# as they fulfil the condition here on entering at the final calculation here. ==== #
if ((sign_end_part != sign_dt) or np.isclose(dt_pos, 0)) and not np.isclose(dt, 0):
if abs(particles.time) >= abs(endtime):
particles.set_state(StateCode.Success)
continue
while particles.state in [StateCode.Evaluate, OperationCode.Repeat] or np.isclose(dt, 0):
for var in pset.ptype.variables:
p_var_back[var.name] = getattr(particles, var.name)
try:
pdt_prekernels = sign_dt * dt_pos
particles.dt = pdt_prekernels
state_prev = particles.state
res = self.pyfunc(particles, pset.fieldset, particles.time)
if res is None:
res = StateCode.Success
if res is StateCode.Success and particles.state != state_prev:
res = particles.state
if not analytical and res == StateCode.Success and not np.isclose(particles.dt, pdt_prekernels):
res = OperationCode.Repeat
except FieldOutOfBoundError as fse_xy:
res = ErrorCode.ErrorOutOfBounds
particles.exception = fse_xy
except FieldOutOfBoundSurfaceError as fse_z:
res = ErrorCode.ErrorThroughSurface
particles.exception = fse_z
except TimeExtrapolationError as fse_t:
res = ErrorCode.ErrorTimeExtrapolation
particles.exception = fse_t
except Exception as e:
res = ErrorCode.Error
particles.exception = e
# Handle particle time and time loop
if res in [StateCode.Success, OperationCode.Delete]:
# Update time and repeat
particles.time += particles.dt
particles.update_next_dt()
if analytical:
particles.dt = np.inf
dt_pos = min(abs(particles.dt), abs(endtime - particles.time))
sign_end_part = np.sign(endtime - particles.time)
if res != OperationCode.Delete and not np.isclose(dt_pos, 0) and (sign_end_part == sign_dt):
res = StateCode.Evaluate
if sign_end_part != sign_dt:
dt_pos = 0
particles.set_state(res)
if np.isclose(dt, 0):
break
else:
particles.set_state(res)
# Try again without time update
for var in pset.ptype.variables:
if var.name not in ['dt', 'state']:
setattr(particles, var.name, p_var_back[var.name])
dt_pos = min(abs(particles.dt), abs(endtime - particles.time))
sign_end_part = np.sign(endtime - particles.time)
if sign_end_part != sign_dt:
dt_pos = 0
break
def execute(self,
pyfunc=AdvectionRK4,
endtime=None,
runtime=None,
dt=1.,
moviedt=None,
recovery=None,
output_file=None,
movie_background_field=None,
verbose_progress=None):
"""Execute a given kernel function over the particle set for
multiple timesteps. Optionally also provide sub-timestepping
for particle output.
:param pyfunc: Kernel function to execute. This can be the name of a
defined Python function or a :class:`parcels.kernel.Kernel` object.
Kernels can be concatenated using the + operator
:param endtime: End time for the timestepping loop.
It is either a datetime object or a positive double.
:param runtime: Length of the timestepping loop. Use instead of endtime.
It is either a timedelta object or a positive double.
:param dt: Timestep interval to be passed to the kernel.
It is either a timedelta object or a double.
Use a negative value for a backward-in-time simulation.
:param moviedt: Interval for inner sub-timestepping (leap), which dictates
the update frequency of animation.
It is either a timedelta object or a positive double.
None value means no animation.
:param output_file: :mod:`parcels.particlefile.ParticleFile` object for particle output
:param recovery: Dictionary with additional `:mod:parcels.tools.error`
recovery kernels to allow custom recovery behaviour in case of
kernel errors.
:param movie_background_field: field plotted as background in the movie if moviedt is set.
'vector' shows the velocity as a vector field.
:param verbose_progress: Boolean for providing a progress bar for the kernel execution loop.
"""
# check if pyfunc has changed since last compile. If so, recompile
if self.kernel is None or (self.kernel.pyfunc is not pyfunc
and self.kernel is not pyfunc):
# Generate and store Kernel
if isinstance(pyfunc, Kernel):
self.kernel = pyfunc
else:
self.kernel = self.Kernel(pyfunc)
# Prepare JIT kernel execution
if self.ptype.uses_jit:
self.kernel.remove_lib()
self.kernel.compile(compiler=GNUCompiler())
self.kernel.load_lib()
# Convert all time variables to seconds
if isinstance(endtime, delta):
raise RuntimeError('endtime must be either a datetime or a double')
if isinstance(endtime, datetime):
endtime = np.datetime64(endtime)
if isinstance(endtime, np.datetime64):
if self.time_origin.calender is None:
raise NotImplementedError(
'If fieldset.time_origin is not a date, execution endtime must be a double'
)
endtime = self.time_origin.reltime(endtime)
if isinstance(runtime, delta):
runtime = runtime.total_seconds()
if isinstance(dt, delta):
dt = dt.total_seconds()
outputdt = output_file.outputdt if output_file else np.infty
if isinstance(outputdt, delta):
outputdt = outputdt.total_seconds()
if isinstance(moviedt, delta):
moviedt = moviedt.total_seconds()
assert runtime is None or runtime >= 0, 'runtime must be positive'
assert outputdt is None or outputdt >= 0, 'outputdt must be positive'
assert moviedt is None or moviedt >= 0, 'moviedt must be positive'
# Set particle.time defaults based on sign of dt, if not set at ParticleSet construction
for p in self:
if np.isnan(p.time):
mintime, maxtime = self.fieldset.gridset.dimrange('time_full')
p.time = mintime if dt >= 0 else maxtime
# Derive _starttime and endtime from arguments or fieldset defaults
if runtime is not None and endtime is not None:
raise RuntimeError(
'Only one of (endtime, runtime) can be specified')
_starttime = min([p.time for p in self]) if dt >= 0 else max(
[p.time for p in self])
if self.repeatdt is not None and self.repeat_starttime is None:
self.repeat_starttime = _starttime
if runtime is not None:
endtime = _starttime + runtime * np.sign(dt)
elif endtime is None:
mintime, maxtime = self.fieldset.gridset.dimrange('time_full')
endtime = maxtime if dt >= 0 else mintime
if abs(endtime - _starttime) < 1e-5 or dt == 0 or runtime == 0:
dt = 0
runtime = 0
endtime = _starttime
logger.warning_once(
"dt or runtime are zero, or endtime is equal to Particle.time. "
"The kernels will be executed once, without incrementing time")
# Initialise particle timestepping
for p in self:
p.dt = dt
# First write output_file, because particles could have been added
if output_file:
output_file.write(self, _starttime)
if moviedt:
self.show(field=movie_background_field,
show_time=_starttime,
animation=True)
if moviedt is None:
moviedt = np.infty
time = _starttime
if self.repeatdt:
next_prelease = self.repeat_starttime + (
abs(time - self.repeat_starttime) // self.repeatdt +
1) * self.repeatdt * np.sign(dt)
else:
next_prelease = np.infty if dt > 0 else -np.infty
next_output = time + outputdt if dt > 0 else time - outputdt
next_movie = time + moviedt if dt > 0 else time - moviedt
next_input = self.fieldset.computeTimeChunk(time, np.sign(dt))
tol = 1e-12
if verbose_progress is None:
walltime_start = time_module.time()
if verbose_progress:
try:
pbar = progressbar.ProgressBar(
max_value=abs(endtime - _starttime)).start()
except: # for old versions of progressbar
pbar = progressbar.ProgressBar(
maxvalue=abs(endtime - _starttime)).start()
while (time < endtime and dt > 0) or (time > endtime
and dt < 0) or dt == 0:
if verbose_progress is None and time_module.time(
) - walltime_start > 10:
# Showing progressbar if runtime > 10 seconds
pbar = progressbar.ProgressBar(
max_value=abs(endtime - _starttime)).start()
verbose_progress = True
if dt > 0:
time = min(next_prelease, next_input, next_output, next_movie,
endtime)
else:
time = max(next_prelease, next_input, next_output, next_movie,
endtime)
self.kernel.execute(self,
endtime=time,
dt=dt,
recovery=recovery,
output_file=output_file)
if abs(time - next_prelease) < tol:
pset_new = ParticleSet(fieldset=self.fieldset,
time=time,
lon=self.repeatlon,
lat=self.repeatlat,
depth=self.repeatdepth,
pclass=self.repeatpclass)
for p in pset_new:
p.dt = dt
self.add(pset_new)
next_prelease += self.repeatdt * np.sign(dt)
if abs(time - next_output) < tol:
if output_file:
output_file.write(self, time)
next_output += outputdt * np.sign(dt)
if abs(time - next_movie) < tol:
self.show(field=movie_background_field,
show_time=time,
animation=True)
next_movie += moviedt * np.sign(dt)
next_input = self.fieldset.computeTimeChunk(time, dt)
if dt == 0:
break
if verbose_progress:
pbar.update(abs(time - _starttime))
if output_file:
output_file.write(self, time)
if verbose_progress:
pbar.finish()
def __init__(self,
fieldset=None,
pclass=JITParticle,
lon=None,
lat=None,
depth=None,
time=None,
repeatdt=None,
lonlatdepth_dtype=None,
pid_orig=None,
**kwargs):
self.fieldset = fieldset
if self.fieldset is None:
logger.warning_once(
"No FieldSet provided in ParticleSet generation. "
"This breaks most Parcels functionality")
else:
self.fieldset.check_complete()
partitions = kwargs.pop('partitions', None)
def convert_to_array(var):
# Convert lists and single integers/floats to one-dimensional numpy arrays
if isinstance(var, np.ndarray):
return var.flatten()
elif isinstance(var, (int, float, np.float32, np.int32)):
return np.array([var])
else:
return np.array(var)
lon = np.empty(shape=0) if lon is None else convert_to_array(lon)
lat = np.empty(shape=0) if lat is None else convert_to_array(lat)
if isinstance(pid_orig, (type(None), type(False))):
pid_orig = np.arange(lon.size)
pid = pid_orig + pclass.lastID
if depth is None:
mindepth = self.fieldset.gridset.dimrange(
'depth')[0] if self.fieldset is not None else 0
depth = np.ones(lon.size) * mindepth
else:
depth = convert_to_array(depth)
assert lon.size == lat.size and lon.size == depth.size, (
'lon, lat, depth don'
't all have the same lenghts')
time = convert_to_array(time)
time = np.repeat(time, lon.size) if time.size == 1 else time
def _convert_to_reltime(time):
if isinstance(time, np.datetime64) or (hasattr(time, 'calendar')
and time.calendar
in _get_cftime_calendars()):
return True
return False
if time.size > 0 and type(time[0]) in [datetime, date]:
time = np.array([np.datetime64(t) for t in time])
self.time_origin = fieldset.time_origin if self.fieldset is not None else 0
if time.size > 0 and isinstance(
time[0], np.timedelta64) and not self.time_origin:
raise NotImplementedError(
'If fieldset.time_origin is not a date, time of a particle must be a double'
)
time = np.array([
self.time_origin.reltime(t) if _convert_to_reltime(t) else t
for t in time
])
assert lon.size == time.size, (
'time and positions (lon, lat, depth) don'
't have the same lengths.')
if partitions is not None and partitions is not False:
partitions = convert_to_array(partitions)
for kwvar in kwargs:
kwargs[kwvar] = convert_to_array(kwargs[kwvar])
assert lon.size == kwargs[kwvar].size, (
'%s and positions (lon, lat, depth) don'
't have the same lengths.' % kwvar)
offset = np.max(pid) if len(pid) > 0 else -1
if MPI:
mpi_comm = MPI.COMM_WORLD
mpi_rank = mpi_comm.Get_rank()
mpi_size = mpi_comm.Get_size()
if lon.size < mpi_size and mpi_size > 1:
raise RuntimeError(
'Cannot initialise with fewer particles than MPI processors'
)
if mpi_size > 1:
if partitions is not False:
if partitions is None:
if mpi_rank == 0:
coords = np.vstack((lon, lat)).transpose()
kmeans = KMeans(n_clusters=mpi_size,
random_state=0).fit(coords)
partitions = kmeans.labels_
else:
partitions = None
partitions = mpi_comm.bcast(partitions, root=0)
elif np.max(partitions) >= mpi_size:
raise RuntimeError(
'Particle partitions must vary between 0 and the number of mpi procs'
)
lon = lon[partitions == mpi_rank]
lat = lat[partitions == mpi_rank]
time = time[partitions == mpi_rank]
depth = depth[partitions == mpi_rank]
pid = pid[partitions == mpi_rank]
for kwvar in kwargs:
kwargs[kwvar] = kwargs[kwvar][partitions == mpi_rank]
offset = MPI.COMM_WORLD.allreduce(offset, op=MPI.MAX)
self.repeatdt = repeatdt.total_seconds() if isinstance(
repeatdt, delta) else repeatdt
if self.repeatdt:
if self.repeatdt <= 0:
raise ('Repeatdt should be > 0')
if time[0] and not np.allclose(time, time[0]):
raise (
'All Particle.time should be the same when repeatdt is not None'
)
self.repeat_starttime = time[0]
self.repeatlon = lon
self.repeatlat = lat
self.repeatpid = pid - pclass.lastID
self.repeatdepth = depth
self.repeatpclass = pclass
self.partitions = partitions
self.repeatkwargs = kwargs
pclass.setLastID(offset + 1)
if lonlatdepth_dtype is None:
if fieldset is not None:
self.lonlatdepth_dtype = self.lonlatdepth_dtype_from_field_interp_method(
fieldset.U)
else:
self.lonlatdepth_dtype = np.float32
else:
self.lonlatdepth_dtype = lonlatdepth_dtype
assert self.lonlatdepth_dtype in [np.float32, np.float64], \
'lon lat depth precision should be set to either np.float32 or np.float64'
pclass.set_lonlatdepth_dtype(self.lonlatdepth_dtype)
self.ptype = pclass.getPType()
self.kernel = None
# store particle data as an array per variable (structure of arrays approach)
self.particle_data = {}
initialised = set()
for v in self.ptype.variables:
if v.name in ['xi', 'yi', 'zi', 'ti']:
ngrid = fieldset.gridset.size if fieldset is not None else 1
self.particle_data[v.name] = np.empty((len(lon), ngrid),
dtype=v.dtype)
else:
self.particle_data[v.name] = np.empty(len(lon), dtype=v.dtype)
if lon is not None and lat is not None:
# Initialise from lists of lon/lat coordinates
assert self.size == len(lon) and self.size == len(lat), (
'Size of ParticleSet does not match length of lon and lat.')
# mimic the variables that get initialised in the constructor
self.particle_data['lat'][:] = lat
self.particle_data['lon'][:] = lon
self.particle_data['depth'][:] = depth
self.particle_data['time'][:] = time
self.particle_data['id'][:] = pid
self.particle_data['fileid'][:] = -1
# special case for exceptions which can only be handled from scipy
self.particle_data['exception'] = np.empty(self.size, dtype=object)
initialised |= {'lat', 'lon', 'depth', 'time', 'id'}
# any fields that were provided on the command line
for kwvar, kwval in kwargs.items():
if not hasattr(pclass, kwvar):
raise RuntimeError(
'Particle class does not have Variable %s' % kwvar)
self.particle_data[kwvar][:] = kwval
initialised.add(kwvar)
# initialise the rest to their default values
for v in self.ptype.variables:
if v.name in initialised:
continue
if isinstance(v.initial, Field):
for i in range(self.size):
if (time[i] is None) or (np.isnan(time[i])):
raise RuntimeError(
'Cannot initialise a Variable with a Field if no time provided. '
'Add a "time=" to ParticleSet construction')
v.initial.fieldset.computeTimeChunk(time[i], 0)
self.particle_data[v.name][i] = v.initial[time[i],
depth[i],
lat[i],
lon[i]]
logger.warning_once(
"Particle initialisation from field can be very slow as it is computed in scipy mode."
)
elif isinstance(v.initial, attrgetter):
self.particle_data[v.name][:] = v.initial(self)
else:
self.particle_data[v.name][:] = v.initial
initialised.add(v.name)
else:
raise ValueError(
"Latitude and longitude required for generating ParticleSet")
def from_netcdf(cls,
filenames,
variables,
dimensions,
indices=None,
mesh='spherical',
timestamps=None,
allow_time_extrapolation=None,
time_periodic=False,
deferred_load=True,
**kwargs):
"""Initialises FieldSet object from NetCDF files
:param filenames: Dictionary mapping variables to file(s). The
filepath may contain wildcards to indicate multiple files
or be a list of file.
filenames can be a list [files], a dictionary {var:[files]},
a dictionary {dim:[files]} (if lon, lat, depth and/or data not stored in same files as data),
or a dictionary of dictionaries {var:{dim:[files]}}.
time values are in filenames[data]
:param variables: Dictionary mapping variables to variable names in the netCDF file(s).
Note that the built-in Advection kernels assume that U and V are in m/s
:param dimensions: Dictionary mapping data dimensions (lon,
lat, depth, time, data) to dimensions in the netCF file(s).
Note that dimensions can also be a dictionary of dictionaries if
dimension names are different for each variable
(e.g. dimensions['U'], dimensions['V'], etc).
:param indices: Optional dictionary of indices for each dimension
to read from file(s), to allow for reading of subset of data.
Default is to read the full extent of each dimension.
Note that negative indices are not allowed.
:param mesh: String indicating the type of mesh coordinates and
units used during velocity interpolation, see also https://nbviewer.jupyter.org/github/OceanParcels/parcels/blob/master/parcels/examples/tutorial_unitconverters.ipynb:
1. spherical (default): Lat and lon in degree, with a
correction for zonal velocity U near the poles.
2. flat: No conversion, lat/lon are assumed to be in m.
:param timestamps: A numpy array containing the timestamps for each of the files in filenames.
Default is None if dimensions includes time.
:param allow_time_extrapolation: boolean whether to allow for extrapolation
(i.e. beyond the last available time snapshot)
Default is False if dimensions includes time, else True
:param time_periodic: boolean whether to loop periodically over the time component of the FieldSet
This flag overrides the allow_time_interpolation and sets it to False
:param deferred_load: boolean whether to only pre-load data (in deferred mode) or
fully load them (default: True). It is advised to deferred load the data, since in
that case Parcels deals with a better memory management during particle set execution.
deferred_load=False is however sometimes necessary for plotting the fields.
:param netcdf_engine: engine to use for netcdf reading in xarray. Default is 'netcdf',
but in cases where this doesn't work, setting netcdf_engine='scipy' could help
"""
# Ensure that times are not provided both in netcdf file and in 'timestamps'.
if timestamps is not None and 'time' in dimensions:
logger.warning_once(
"Time already provided, defaulting to dimensions['time'] over timestamps."
)
timestamps = None
# Typecast timestamps to numpy array & correct shape.
if timestamps is not None:
if isinstance(timestamps, list):
timestamps = np.array(timestamps)
timestamps = np.reshape(timestamps, [timestamps.size, 1])
fields = {}
if 'creation_log' not in kwargs.keys():
kwargs['creation_log'] = 'from_netcdf'
for var, name in variables.items():
# Resolve all matching paths for the current variable
paths = filenames[var] if type(
filenames) is dict and var in filenames else filenames
if type(paths) is not dict:
paths = cls.parse_wildcards(paths, filenames, var)
else:
for dim, p in paths.items():
paths[dim] = cls.parse_wildcards(p, filenames, var)
# Use dimensions[var] and indices[var] if either of them is a dict of dicts
dims = dimensions[var] if var in dimensions else dimensions
cls.checkvaliddimensionsdict(dims)
inds = indices[var] if (indices and var in indices) else indices
grid = None
# check if grid has already been processed (i.e. if other fields have same filenames, dimensions and indices)
for procvar, _ in fields.items():
procdims = dimensions[
procvar] if procvar in dimensions else dimensions
procinds = indices[procvar] if (
indices and procvar in indices) else indices
procpaths = filenames[procvar] if isinstance(
filenames, dict) and procvar in filenames else filenames
nowpaths = filenames[var] if isinstance(
filenames, dict) and var in filenames else filenames
if procdims == dims and procinds == inds and procpaths == nowpaths:
sameGrid = False
if ((not isinstance(filenames, dict))
or filenames[procvar] == filenames[var]):
sameGrid = True
elif isinstance(filenames[procvar], dict):
sameGrid = True
for dim in ['lon', 'lat', 'depth']:
if dim in dimensions:
sameGrid *= filenames[procvar][
dim] == filenames[var][dim]
if sameGrid:
grid = fields[procvar].grid
kwargs['dataFiles'] = fields[procvar].dataFiles
break
fields[var] = Field.from_netcdf(
paths, (var, name),
dims,
inds,
grid=grid,
mesh=mesh,
timestamps=timestamps,
allow_time_extrapolation=allow_time_extrapolation,
time_periodic=time_periodic,
deferred_load=deferred_load,
**kwargs)
u = fields.pop('U', None)
v = fields.pop('V', None)
return cls(u, v, fields=fields)
def convert_pset_to_dict(self, pset, time, deleted_only=False):
"""Convert all Particle data from one time step to a python dictionary.
:param pset: ParticleSet object to write
:param time: Time at which to write ParticleSet
:param deleted_only: Flag to write only the deleted Particles
returns two dictionaries: one for all variables to be written each outputdt,
and one for all variables to be written once
"""
data_dict = {}
data_dict_once = {}
time = time.total_seconds() if isinstance(time, delta) else time
if self.lasttime_written != time and \
(self.write_ondelete is False or deleted_only is True):
if pset.size == 0:
logger.warning(
"ParticleSet is empty on writing as array at time %g" %
time)
else:
if deleted_only:
pset_towrite = pset
elif pset[0].dt > 0:
pset_towrite = [
p for p in pset
if time <= p.time < time + p.dt and np.isfinite(p.id)
]
else:
pset_towrite = [
p for p in pset
if time + p.dt < p.time <= time and np.isfinite(p.id)
]
if len(pset_towrite) > 0:
for var in self.var_names:
data_dict[var] = np.array(
[getattr(p, var) for p in pset_towrite])
self.maxid_written = np.max(
[self.maxid_written,
np.max(data_dict['id'])])
pset_errs = [
p for p in pset_towrite
if p.state != ErrorCode.Delete and abs(time -
p.time) > 1e-3
]
for p in pset_errs:
logger.warning_once(
'time argument in pfile.write() is %g, but a particle has time % g.'
% (time, p.time))
if time not in self.time_written:
self.time_written.append(time)
if len(self.var_names_once) > 0:
first_write = [
p for p in pset if (p.id not in self.written_once)
and _is_particle_started_yet(p, time)
]
data_dict_once['id'] = np.array(
[p.id for p in first_write])
for var in self.var_names_once:
data_dict_once[var] = np.array(
[getattr(p, var) for p in first_write])
self.written_once += [p.id for p in first_write]
if not deleted_only:
self.lasttime_written = time
return data_dict, data_dict_once
def plotfield(field,
show_time=None,
domain=None,
depth_level=0,
projection=None,
land=True,
vmin=None,
vmax=None,
savefile=None,
**kwargs):
"""Function to plot a Parcels Field
:param show_time: Time at which to show the Field
:param domain: dictionary (with keys 'N', 'S', 'E', 'W') defining domain to show
:param depth_level: depth level to be plotted (default 0)
:param projection: type of cartopy projection to use (default PlateCarree)
:param land: Boolean whether to show land. This is ignored for flat meshes
:param vmin: minimum colour scale (only in single-plot mode)
:param vmax: maximum colour scale (only in single-plot mode)
:param savefile: Name of a file to save the plot to
:param animation: Boolean whether result is a single plot, or an animation
"""
if type(field) is VectorField:
spherical = True if field.U.grid.mesh == 'spherical' else False
field = [field.U, field.V]
plottype = 'vector'
elif type(field) is Field:
spherical = True if field.grid.mesh == 'spherical' else False
field = [field]
plottype = 'scalar'
else:
raise RuntimeError('field needs to be a Field or VectorField object')
if field[0].grid.gtype in [
GridCode.CurvilinearZGrid, GridCode.CurvilinearSGrid
]:
logger.warning(
'Field.show() does not always correctly determine the domain for curvilinear grids. '
'Use plotting with caution and perhaps use domain argument as in the NEMO 3D tutorial'
)
plt, fig, ax, cartopy = create_parcelsfig_axis(spherical,
land,
projection=projection)
if plt is None:
return None, None, None, None # creating axes was not possible
data = {}
plotlon = {}
plotlat = {}
for i, fld in enumerate(field):
show_time = fld.grid.time[0] if show_time is None else show_time
if fld.grid.defer_load:
fld.fieldset.computeTimeChunk(show_time, 1)
(idx, periods) = fld.time_index(show_time)
show_time -= periods * (fld.grid.time_full[-1] - fld.grid.time_full[0])
if show_time > fld.grid.time[-1] or show_time < fld.grid.time[0]:
raise TimeExtrapolationError(show_time, field=fld, msg='show_time')
latN, latS, lonE, lonW = parsedomain(domain, fld)
if isinstance(fld.grid, CurvilinearGrid):
plotlon[i] = fld.grid.lon[latS:latN, lonW:lonE]
plotlat[i] = fld.grid.lat[latS:latN, lonW:lonE]
else:
plotlon[i] = fld.grid.lon[lonW:lonE]
plotlat[i] = fld.grid.lat[latS:latN]
if i > 0 and not np.allclose(plotlon[i], plotlon[0]):
raise RuntimeError(
'VectorField needs to be on an A-grid for plotting')
if fld.grid.time.size > 1:
if fld.grid.zdim > 1:
data[i] = np.squeeze(
fld.temporal_interpolate_fullfield(idx,
show_time))[depth_level,
latS:latN,
lonW:lonE]
else:
data[i] = np.squeeze(
fld.temporal_interpolate_fullfield(idx,
show_time))[latS:latN,
lonW:lonE]
else:
if fld.grid.zdim > 1:
data[i] = np.squeeze(fld.data)[depth_level, latS:latN,
lonW:lonE]
else:
data[i] = np.squeeze(fld.data)[latS:latN, lonW:lonE]
if plottype == 'vector':
if field[0].interp_method == 'cgrid_velocity':
logger.warning_once(
'Plotting a C-grid velocity field is achieved via an A-grid projection, reducing the plot accuracy'
)
d = np.empty_like(data[0])
d[:-1, :] = (data[0][:-1, :] + data[0][1:, :]) / 2.
d[-1, :] = data[0][-1, :]
data[0] = d
d = np.empty_like(data[0])
d[:, :-1] = (data[0][:, :-1] + data[0][:, 1:]) / 2.
d[:, -1] = data[0][:, -1]
data[1] = d
spd = data[0]**2 + data[1]**2
speed = np.where(spd > 0, np.sqrt(spd), 0)
vmin = speed.min() if vmin is None else vmin
vmax = speed.max() if vmax is None else vmax
if isinstance(field[0].grid, CurvilinearGrid):
x, y = plotlon[0], plotlat[0]
else:
x, y = np.meshgrid(plotlon[0], plotlat[0])
u = np.where(speed > 0., data[0] / speed, 0)
v = np.where(speed > 0., data[1] / speed, 0)
if cartopy:
cs = ax.quiver(np.asarray(x),
np.asarray(y),
np.asarray(u),
np.asarray(v),
speed,
cmap=plt.cm.gist_ncar,
clim=[vmin, vmax],
scale=50,
transform=cartopy.crs.PlateCarree())
else:
cs = ax.quiver(x,
y,
u,
v,
speed,
cmap=plt.cm.gist_ncar,
clim=[vmin, vmax],
scale=50)
else:
vmin = data[0].min() if vmin is None else vmin
vmax = data[0].max() if vmax is None else vmax
assert len(data[0].shape) == 2
if field[0].interp_method == 'cgrid_tracer':
d = data[0][1:, 1:]
elif field[0].interp_method == 'cgrid_velocity':
if field[0].fieldtype == 'U':
d = np.empty_like(data[0])
d[:-1, :-1] = (data[0][1:, :-1] + data[0][1:, 1:]) / 2.
elif field[0].fieldtype == 'V':
d = np.empty_like(data[0])
d[:-1, :-1] = (data[0][:-1, 1:] + data[0][1:, 1:]) / 2.
else: # W
d = data[0][1:, 1:]
else: # if A-grid
d = (data[0][:-1, :-1] + data[0][1:, :-1] + data[0][:-1, 1:] +
data[0][1:, 1:]) / 4.
d = np.where(data[0][:-1, :-1] == 0, 0, d)
d = np.where(data[0][1:, :-1] == 0, 0, d)
d = np.where(data[0][1:, 1:] == 0, 0, d)
d = np.where(data[0][:-1, 1:] == 0, 0, d)
if cartopy:
cs = ax.pcolormesh(plotlon[0],
plotlat[0],
d,
transform=cartopy.crs.PlateCarree())
else:
cs = ax.pcolormesh(plotlon[0], plotlat[0], d)
if cartopy is None:
ax.set_xlim(np.nanmin(plotlon[0]), np.nanmax(plotlon[0]))
ax.set_ylim(np.nanmin(plotlat[0]), np.nanmax(plotlat[0]))
elif domain is not None:
ax.set_extent([
np.nanmin(plotlon[0]),
np.nanmax(plotlon[0]),
np.nanmin(plotlat[0]),
np.nanmax(plotlat[0])
],
crs=cartopy.crs.PlateCarree())
cs.cmap.set_over('k')
cs.cmap.set_under('w')
cs.set_clim(vmin, vmax)
cartopy_colorbar(cs, plt, fig, ax)
timestr = parsetimestr(field[0].grid.time_origin, show_time)
titlestr = kwargs.pop('titlestr', '')
if field[0].grid.zdim > 1:
if field[0].grid.gtype in [
GridCode.CurvilinearZGrid, GridCode.RectilinearZGrid
]:
gphrase = 'depth'
depth_or_level = field[0].grid.depth[depth_level]
else:
gphrase = 'level'
depth_or_level = depth_level
depthstr = ' at %s %g ' % (gphrase, depth_or_level)
else:
depthstr = ''
if plottype == 'vector':
ax.set_title(titlestr + 'Velocity field' + depthstr + timestr)
else:
ax.set_title(titlestr + field[0].name + depthstr + timestr)
if not spherical:
ax.set_xlabel('Zonal distance [m]')
ax.set_ylabel('Meridional distance [m]')
plt.draw()
if savefile:
plt.savefig(savefile)
logger.info('Plot saved to ' + savefile + '.png')
plt.close()
return plt, fig, ax, cartopy
def execute(self, pset, endtime, dt, recovery=None, output_file=None, execute_once=False):
"""Execute this Kernel over a ParticleSet for several timesteps"""
particles = pset.data_accessor()
for p in range(pset.size):
particles.set_index(p)
particles.set_state(StateCode.Evaluate)
if abs(dt) < 1e-6 and not execute_once:
logger.warning_once("'dt' is too small, causing numerical accuracy limit problems. Please chose a higher 'dt' and rather scale the 'time' axis of the field accordingly. (related issue #762)")
def remove_deleted(pset):
"""Utility to remove all particles that signalled deletion"""
indices = pset.particle_data['state'] == OperationCode.Delete
if np.count_nonzero(indices) > 0 and output_file is not None:
output_file.write(pset, endtime, deleted_only=indices)
pset.remove_booleanvector(indices)
if recovery is None:
recovery = {}
elif ErrorCode.ErrorOutOfBounds in recovery and ErrorCode.ErrorThroughSurface not in recovery:
recovery[ErrorCode.ErrorThroughSurface] = recovery[ErrorCode.ErrorOutOfBounds]
recovery_map = recovery_base_map.copy()
recovery_map.update(recovery)
if pset.fieldset is not None:
for g in pset.fieldset.gridset.grids:
if len(g.load_chunk) > 0: # not the case if a field in not called in the kernel
g.load_chunk = np.where(g.load_chunk == 2, 3, g.load_chunk)
# Execute the kernel over the particle set
if self.ptype.uses_jit:
self.execute_jit(pset, endtime, dt)
else:
self.execute_python(pset, endtime, dt)
# Remove all particles that signalled deletion
remove_deleted(pset)
# Identify particles that threw errors
error_particles = np.isin(pset.particle_data['state'], [StateCode.Success, StateCode.Evaluate], invert=True)
while np.any(error_particles):
# Apply recovery kernel
for p in np.where(error_particles)[0]:
particles.set_index(p)
if particles.state == OperationCode.StopExecution:
return
if particles.state == OperationCode.Repeat:
particles.set_state(StateCode.Evaluate)
elif particles.state in recovery_map:
recovery_kernel = recovery_map[particles.state]
particles.set_state(StateCode.Success)
recovery_kernel(particles, self.fieldset, particles.time)
if particles.state == StateCode.Success:
particles.set_state(StateCode.Evaluate)
else:
logger.warning_once('Deleting particle because of bug in #749 and #737')
particles.delete()
# Remove all particles that signalled deletion
remove_deleted(pset)
# Execute core loop again to continue interrupted particles
if self.ptype.uses_jit:
self.execute_jit(pset, endtime, dt)
else:
self.execute_python(pset, endtime, dt)
error_particles = np.isin(pset.particle_data['state'], [StateCode.Success, StateCode.Evaluate], invert=True)
def __init__(self, fieldset, ptype, pyfunc=None, funcname=None,
funccode=None, py_ast=None, funcvars=None, c_include="", delete_cfiles=True):
self.fieldset = fieldset
self.ptype = ptype
self._lib = None
self.delete_cfiles = delete_cfiles
self._cleanup_files = None
self._cleanup_lib = None
# Derive meta information from pyfunc, if not given
self.funcname = funcname or pyfunc.__name__
if pyfunc is AdvectionRK4_3D:
warning = False
if isinstance(fieldset.W, Field) and fieldset.W.creation_log != 'from_nemo' and \
fieldset.W._scaling_factor is not None and fieldset.W._scaling_factor > 0:
warning = True
if type(fieldset.W) in [SummedField, NestedField]:
for f in fieldset.W:
if f.creation_log != 'from_nemo' and f._scaling_factor is not None and f._scaling_factor > 0:
warning = True
if warning:
logger.warning_once('Note that in AdvectionRK4_3D, vertical velocity is assumed positive towards increasing z.\n'
' If z increases downward and w is positive upward you can re-orient it downwards by setting fieldset.W.set_scaling_factor(-1.)')
elif pyfunc is AdvectionAnalytical:
if ptype.uses_jit:
raise NotImplementedError('Analytical Advection only works in Scipy mode')
if fieldset.U.interp_method != 'cgrid_velocity':
raise NotImplementedError('Analytical Advection only works with C-grids')
if fieldset.U.grid.gtype not in [GridCode.CurvilinearZGrid, GridCode.RectilinearZGrid]:
raise NotImplementedError('Analytical Advection only works with Z-grids in the vertical')
if funcvars is not None:
self.funcvars = funcvars
elif hasattr(pyfunc, '__code__'):
self.funcvars = list(pyfunc.__code__.co_varnames)
else:
self.funcvars = None
self.funccode = funccode or inspect.getsource(pyfunc.__code__)
# Parse AST if it is not provided explicitly
self.py_ast = py_ast or parse(fix_indentation(self.funccode)).body[0]
if pyfunc is None:
# Extract user context by inspecting the call stack
stack = inspect.stack()
try:
user_ctx = stack[-1][0].f_globals
user_ctx['math'] = globals()['math']
user_ctx['ParcelsRandom'] = globals()['ParcelsRandom']
user_ctx['random'] = globals()['random']
user_ctx['StateCode'] = globals()['StateCode']
user_ctx['OperationCode'] = globals()['OperationCode']
user_ctx['ErrorCode'] = globals()['ErrorCode']
except:
logger.warning("Could not access user context when merging kernels")
user_ctx = globals()
finally:
del stack # Remove cyclic references
# Compile and generate Python function from AST
py_mod = parse("")
py_mod.body = [self.py_ast]
exec(compile(py_mod, "<ast>", "exec"), user_ctx)
self.pyfunc = user_ctx[self.funcname]
else:
self.pyfunc = pyfunc
if version_info[0] < 3:
numkernelargs = len(inspect.getargspec(self.pyfunc).args)
else:
numkernelargs = len(inspect.getfullargspec(self.pyfunc).args)
assert numkernelargs == 3, \
'Since Parcels v2.0, kernels do only take 3 arguments: particle, fieldset, time !! AND !! Argument order in field interpolation is time, depth, lat, lon.'
self.name = "%s%s" % (ptype.name, self.funcname)
# Generate the kernel function and add the outer loop
if self.ptype.uses_jit:
kernelgen = KernelGenerator(fieldset, ptype)
kernel_ccode = kernelgen.generate(deepcopy(self.py_ast),
self.funcvars)
self.field_args = kernelgen.field_args
self.vector_field_args = kernelgen.vector_field_args
fieldset = self.fieldset
for f in self.vector_field_args.values():
Wname = f.W.ccode_name if f.W else 'not_defined'
for sF_name, sF_component in zip([f.U.ccode_name, f.V.ccode_name, Wname], ['U', 'V', 'W']):
if sF_name not in self.field_args:
if sF_name != 'not_defined':
self.field_args[sF_name] = getattr(f, sF_component)
self.const_args = kernelgen.const_args
loopgen = LoopGenerator(fieldset, ptype)
if path.isfile(c_include):
with open(c_include, 'r') as f:
c_include_str = f.read()
else:
c_include_str = c_include
self.ccode = loopgen.generate(self.funcname, self.field_args, self.const_args,
kernel_ccode, c_include_str)
if MPI:
mpi_comm = MPI.COMM_WORLD
mpi_rank = mpi_comm.Get_rank()
basename = path.join(get_cache_dir(), self._cache_key) if mpi_rank == 0 else None
basename = mpi_comm.bcast(basename, root=0)
basename = basename + "_%d" % mpi_rank
else:
basename = path.join(get_cache_dir(), "%s_0" % self._cache_key)
self.src_file = "%s.c" % basename
self.lib_file = "%s.%s" % (basename, 'dll' if platform == 'win32' else 'so')
self.log_file = "%s.log" % basename
def execute(self,
pyfunc=AdvectionRK4,
endtime=None,
runtime=None,
dt=1.,
moviedt=None,
recovery=None,
output_file=None,
movie_background_field=None,
verbose_progress=None,
postIterationCallbacks=None,
callbackdt=None):
"""Execute a given kernel function over the particle set for
multiple timesteps. Optionally also provide sub-timestepping
for particle output.
:param pyfunc: Kernel function to execute. This can be the name of a
defined Python function or a :class:`parcels.kernel.Kernel` object.
Kernels can be concatenated using the + operator
:param endtime: End time for the timestepping loop.
It is either a datetime object or a positive double.
:param runtime: Length of the timestepping loop. Use instead of endtime.
It is either a timedelta object or a positive double.
:param dt: Timestep interval to be passed to the kernel.
It is either a timedelta object or a double.
Use a negative value for a backward-in-time simulation.
:param moviedt: Interval for inner sub-timestepping (leap), which dictates
the update frequency of animation.
It is either a timedelta object or a positive double.
None value means no animation.
:param output_file: :mod:`parcels.particlefile.ParticleFile` object for particle output
:param recovery: Dictionary with additional `:mod:parcels.tools.error`
recovery kernels to allow custom recovery behaviour in case of
kernel errors.
:param movie_background_field: field plotted as background in the movie if moviedt is set.
'vector' shows the velocity as a vector field.
:param verbose_progress: Boolean for providing a progress bar for the kernel execution loop.
:param postIterationCallbacks: (Optional) Array of functions that are to be called after each iteration (post-process, non-Kernel)
:param callbackdt: (Optional, in conjecture with 'postIterationCallbacks) timestep inverval to (latestly) interrupt the running kernel and invoke post-iteration callbacks from 'postIterationCallbacks'
"""
# check if pyfunc has changed since last compile. If so, recompile
if self.kernel is None or (self.kernel.pyfunc is not pyfunc
and self.kernel is not pyfunc):
# Generate and store Kernel
if isinstance(pyfunc, Kernel):
self.kernel = pyfunc
else:
self.kernel = self.Kernel(pyfunc)
# Prepare JIT kernel execution
if self.ptype.uses_jit:
self.kernel.remove_lib()
cppargs = ['-DDOUBLE_COORD_VARIABLES'
] if self.lonlatdepth_dtype == np.float64 else None
self.kernel.compile(compiler=GNUCompiler(cppargs=cppargs))
self.kernel.load_lib()
# Convert all time variables to seconds
if isinstance(endtime, delta):
raise RuntimeError('endtime must be either a datetime or a double')
if isinstance(endtime, datetime):
endtime = np.datetime64(endtime)
if isinstance(endtime, np.datetime64):
if self.time_origin.calendar is None:
raise NotImplementedError(
'If fieldset.time_origin is not a date, execution endtime must be a double'
)
endtime = self.time_origin.reltime(endtime)
if isinstance(runtime, delta):
runtime = runtime.total_seconds()
if isinstance(dt, delta):
dt = dt.total_seconds()
outputdt = output_file.outputdt if output_file else np.infty
if isinstance(outputdt, delta):
outputdt = outputdt.total_seconds()
if isinstance(moviedt, delta):
moviedt = moviedt.total_seconds()
if isinstance(callbackdt, delta):
callbackdt = callbackdt.total_seconds()
assert runtime is None or runtime >= 0, 'runtime must be positive'
assert outputdt is None or outputdt >= 0, 'outputdt must be positive'
assert moviedt is None or moviedt >= 0, 'moviedt must be positive'
mintime, maxtime = self.fieldset.gridset.dimrange(
'time_full') if self.fieldset is not None else (0, 1)
if np.any(np.isnan(self.particle_data['time'])):
self.particle_data['time'][np.isnan(
self.particle_data['time'])] = mintime if dt >= 0 else maxtime
# Derive _starttime and endtime from arguments or fieldset defaults
if runtime is not None and endtime is not None:
raise RuntimeError(
'Only one of (endtime, runtime) can be specified')
_starttime = self.particle_data['time'].min(
) if dt >= 0 else self.particle_data['time'].max()
if self.repeatdt is not None and self.repeat_starttime is None:
self.repeat_starttime = _starttime
if runtime is not None:
endtime = _starttime + runtime * np.sign(dt)
elif endtime is None:
mintime, maxtime = self.fieldset.gridset.dimrange('time_full')
endtime = maxtime if dt >= 0 else mintime
execute_once = False
if abs(endtime - _starttime) < 1e-5 or dt == 0 or runtime == 0:
dt = 0
runtime = 0
endtime = _starttime
logger.warning_once(
"dt or runtime are zero, or endtime is equal to Particle.time. "
"The kernels will be executed once, without incrementing time")
execute_once = True
self.particle_data['dt'][:] = dt
# First write output_file, because particles could have been added
if output_file:
output_file.write(self, _starttime)
if moviedt:
self.show(field=movie_background_field,
show_time=_starttime,
animation=True)
if moviedt is None:
moviedt = np.infty
if callbackdt is None:
interupt_dts = [np.infty, moviedt, outputdt]
if self.repeatdt is not None:
interupt_dts.append(self.repeatdt)
callbackdt = np.min(np.array(interupt_dts))
time = _starttime
if self.repeatdt:
next_prelease = self.repeat_starttime + (
abs(time - self.repeat_starttime) // self.repeatdt +
1) * self.repeatdt * np.sign(dt)
else:
next_prelease = np.infty if dt > 0 else -np.infty
next_output = time + outputdt if dt > 0 else time - outputdt
next_movie = time + moviedt if dt > 0 else time - moviedt
next_callback = time + callbackdt if dt > 0 else time - callbackdt
next_input = self.fieldset.computeTimeChunk(
time, np.sign(dt)) if self.fieldset is not None else np.inf
tol = 1e-12
if verbose_progress is None:
walltime_start = time_module.time()
if verbose_progress:
pbar = self.__create_progressbar(_starttime, endtime)
while (time < endtime and dt > 0) or (time > endtime
and dt < 0) or dt == 0:
if verbose_progress is None and time_module.time(
) - walltime_start > 10:
# Showing progressbar if runtime > 10 seconds
if output_file:
logger.info('Temporary output files are stored in %s.' %
output_file.tempwritedir_base)
logger.info(
'You can use "parcels_convert_npydir_to_netcdf %s" to convert these '
'to a NetCDF file during the run.' %
output_file.tempwritedir_base)
pbar = self.__create_progressbar(_starttime, endtime)
verbose_progress = True
if dt > 0:
time = min(next_prelease, next_input, next_output, next_movie,
next_callback, endtime)
else:
time = max(next_prelease, next_input, next_output, next_movie,
next_callback, endtime)
self.kernel.execute(self,
endtime=time,
dt=dt,
recovery=recovery,
output_file=output_file,
execute_once=execute_once)
if abs(time - next_prelease) < tol:
pset_new = ParticleSet(
fieldset=self.fieldset,
time=time,
lon=self.repeatlon,
lat=self.repeatlat,
depth=self.repeatdepth,
pclass=self.repeatpclass,
lonlatdepth_dtype=self.lonlatdepth_dtype,
partitions=False,
pid_orig=self.repeatpid,
**self.repeatkwargs)
p = pset_new.data_accessor()
for i in range(pset_new.size):
p.set_index(i)
p.dt = dt
self.add(pset_new)
next_prelease += self.repeatdt * np.sign(dt)
if abs(time - next_output) < tol:
if output_file:
output_file.write(self, time)
next_output += outputdt * np.sign(dt)
if abs(time - next_movie) < tol:
self.show(field=movie_background_field,
show_time=time,
animation=True)
next_movie += moviedt * np.sign(dt)
# ==== insert post-process here to also allow for memory clean-up via external func ==== #
if abs(time - next_callback) < tol:
if postIterationCallbacks is not None:
for extFunc in postIterationCallbacks:
extFunc()
next_callback += callbackdt * np.sign(dt)
if time != endtime:
next_input = self.fieldset.computeTimeChunk(time, dt)
if dt == 0:
break
if verbose_progress:
pbar.update(abs(time - _starttime))
if output_file:
output_file.write(self, time)
if verbose_progress:
pbar.finish()