This tutorial will show how to implement Periodic boundary conditions (where particles that leave the domain on one side enter again on the other side) can be implemented in Parcels
The idea in Parcels is to do two things:
.execute
We'll start by importing the relevant modules
from parcels import FieldSet, ParticleSet, JITParticle, plotTrajectoriesFile
from parcels import AdvectionRK4
from datetime import timedelta as delta
import math
We import the Peninsula fieldset; note that we need to set allow_time_extrapolation
because the Peninsula fieldset has only one time snapshot.
fieldset = FieldSet.from_parcels('Peninsula_data/peninsula', allow_time_extrapolation=True)
Extending the fieldset with a halo is very simply done using the add_periodic_halo()
method. Halos can be added either in the zonal direction, the meridional direction, or both, by setting zonal
and/or meridional
to True
fieldset.add_periodic_halo(zonal=True)
The other item we need is a custom Kernel that can move the particle from one side of the domain to the other.
def periodicBC(particle, fieldset, time, dt):
if particle.lon < fieldset.halo_west:
particle.lon += fieldset.halo_east - fieldset.halo_west
elif particle.lon > fieldset.halo_east:
particle.lon -= fieldset.halo_east - fieldset.halo_west
The fieldset constants halo_east
and halo_west
in the kernel above were set during the call to add_periodic_halo()
, and store the original zonal extent of the fieldset. If we would have also used meridional=True
in add_periodic_halo()
, fieldset.halo_north
and fieldset.halo_south
would also have been added.
Now define a particle set and execute it as usual
pset = ParticleSet.from_line(fieldset, pclass=JITParticle,
size=10, start=(0.7, 0.1), finish=(0.7, 0.4))
output_file = pset.ParticleFile(name="PeriodicParticle", outputdt=delta(hours=1))
pset.execute(AdvectionRK4 + pset.Kernel(periodicBC),
runtime=delta(hours=24), dt=delta(minutes=5),
output_file=output_file)
Compiled JITParticleAdvectionRK4periodicBC ==> /var/folders/r2/8593q8z93kd7t4j9kbb_f7p00000gn/T/parcels-501/e314053eec65b2ef80b5495b2134f745.so
And finally plot the particle trajectories
plotTrajectoriesFile('PeriodicParticle.nc')
We can see that the particles start at 0.7E, move eastward, and once they hit the boundary at 0.895428E, they jump to the other side of the domain (the horizontal lines). So we have periodic boundary conditions!
As a note, one may ask why we need the halo. Why can't we use simply the PeriodicBC
kernel? This is because, if the particle is close to the edge of the fieldset (but still in it), AdvectionRK4
will need to interpolate velocities that may lay outside the fieldset domain. With the halo, we make sure AdvectionRK4
can access these values.