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:
1) Extend the fieldset with a small 'halo'
2) Add a periodic boundary kernel to the
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
But before we apply the halo, we first define two new fieldset constants
halo_west. They store the original zonal extend of the grid (so before adding the halo) and will be used later in the
Note that some hydrodynamic data, such as the global ORCA grid used in NEMO, already has a halo. In these cases, do not extent the fieldset with the halo but only add the periodic boundary kernel, where you use the explicit values for halo_east and halo_west
fieldset.add_constant('halo_west', fieldset.U.grid.lon) fieldset.add_constant('halo_east', fieldset.U.grid.lon[-1]) 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
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
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.