def execute(self, pset, endtime, dt, recovery=None, output_file=None):
"""Execute this Kernel over a ParticleSet for several timesteps"""
def remove_deleted(pset):
"""Utility to remove all particles that signalled deletion"""
indices = [
i for i, p in enumerate(pset.particles)
if p.state in [ErrorCode.Delete]
]
if len(indices) > 0 and output_file is not None:
output_file.write(pset[indices], endtime, deleted_only=True)
pset.remove(indices)
if recovery is None:
recovery = {}
recovery_map = recovery_base_map.copy()
recovery_map.update(recovery)
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 > 0, 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 = [
p for p in pset.particles if p.state != ErrorCode.Success
]
while len(error_particles) > 0:
# Apply recovery kernel
for p in error_particles:
if p.state == ErrorCode.Repeat:
p.state = ErrorCode.Success
else:
recovery_kernel = recovery_map[p.state]
p.state = ErrorCode.Success
recovery_kernel(p, self.fieldset, p.time)
# 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 = [
p for p in pset.particles if p.state != ErrorCode.Success
]
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(ErrorCode.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'] == ErrorCode.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)
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'],
[ErrorCode.Success, ErrorCode.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 == ErrorCode.StopExecution:
return
if particles.state == ErrorCode.Repeat:
particles.set_state(ErrorCode.Evaluate)
elif particles.state in recovery_map:
recovery_kernel = recovery_map[particles.state]
particles.set_state(ErrorCode.Success)
recovery_kernel(particles, self.fieldset, particles.time)
if particles.state == ErrorCode.Success:
particles.set_state(ErrorCode.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'],
[ErrorCode.Success, ErrorCode.Evaluate],
invert=True)
def execute(self, pset, endtime, dt, recovery=None, output_file=None):
"""Execute this Kernel over a ParticleSet for several timesteps"""
def remove_deleted(pset):
"""Utility to remove all particles that signalled deletion"""
indices = [
i for i, p in enumerate(pset.particles)
if p.state in [ErrorCode.Delete]
]
if len(indices) > 0 and output_file is not None:
output_file.write(pset[indices], endtime, deleted_only=True)
pset.remove(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)
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 = [
p for p in pset.particles if p.state != ErrorCode.Success
]
while len(error_particles) > 0:
# Apply recovery kernel
for p in error_particles:
if p.state == ErrorCode.Repeat:
p.state = ErrorCode.Success
elif p.state in recovery_map: # hotfix for #749, #737 and related issues
recovery_kernel = recovery_map[p.state]
p.state = ErrorCode.Success
recovery_kernel(p, self.fieldset, p.time)
else:
logger.warning_once(
'Deleting particle because of bug in #749 and #737')
p.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 = [
p for p in pset.particles if p.state != ErrorCode.Success
]
