Removing particles from the simulation (iPython)

10 bodies, and assign them unique hashes so we can keep track of them (see UniquelyIdentifyingParticlesWithHashes.html).

import rebound
import numpy as np

sim = rebound.Simulation()
sim.add(m=1., hash=0)
for i in range(1,10):
    sim.add(a=i, hash=i)
sim.move_to_com()

print("Particle hashes:{0}".format([sim.particles[i].hash for i in range(sim.N)]))
Particle hashes:[c_uint(0), c_uint(1), c_uint(2), c_uint(3), c_uint(4), c_uint(5), c_uint(6), c_uint(7), c_uint(8), c_uint(9)]

Let us add one more particle, this time with a custom name:

sim.add(a=10, hash="Saturn")
print("Particle hashes:{0}".format([sim.particles[i].hash for i in range(sim.N)]))
Particle hashes:[c_uint(0), c_uint(1), c_uint(2), c_uint(3), c_uint(4), c_uint(5), c_uint(6), c_uint(7), c_uint(8), c_uint(9), c_uint(4066125545)]

Now let us run perform a short integration to isolate the particles that interest us for a longer simulation:

Noutputs = 1000
xs = np.zeros((sim.N, Noutputs))
ys = np.zeros((sim.N, Noutputs))
times = np.linspace(0.,50*2.*np.pi, Noutputs, endpoint=False)
for i, time in enumerate(times):
    sim.integrate(time)
    xs[:,i] = [sim.particles[j].x for j in range(sim.N)]
    ys[:,i] = [sim.particles[j].y for j in range(sim.N)]
%matplotlib inline
import matplotlib.pyplot as plt
fig,ax = plt.subplots(figsize=(15,5))
for i in range(sim.N):
    plt.plot(xs[i,:], ys[i,:])
ax.set_aspect('equal')
../_images/RemovingParticlesFromSimulation_5_0.png

At this stage, we might be interested in particles that remained within some semimajor axis range, particles that were in resonance with a particular planet, etc. Let’s imagine a simple (albeit arbitrary) case where we only want to keep particles that had \(x < 0\) at the end of the preliminary integration. Let’s first print out the particle hashes and x positions.

print("Hash\t\tx")
for i in range(sim.N):
    print("{0}\t{1}".format(sim.particles[i].hash, xs[i,-1]))
Hash                x
c_uint(0)   0.0
c_uint(1)   0.9510565162930091
c_uint(2)   -1.0717399536588612
c_uint(3)   -2.2765351809117464
c_uint(4)   0.15703926303973234
c_uint(5)   -4.897155109586999
c_uint(6)   -4.824394540939856
c_uint(7)   -2.2862837234997975
c_uint(8)   2.111033731282993
c_uint(9)   5.290067270630363
c_uint(4066125545)  -8.776421396714463

Note that 4066125545 is the hash corresponding to the string “Saturn” we added above. We can use the remove() function to filter out particles. As an argument, we pass the corresponding index in the particles array.

for i in reversed(range(1,sim.N)):
    if xs[i,-1] > 0:
        sim.remove(i)
print("Number of particles after cut = {0}".format(sim.N))
print("Hashes of remaining particles = {0}".format([p.hash for p in sim.particles]))
Number of particles after cut = 7
Hashes of remaining particles = [c_uint(0), c_uint(2), c_uint(3), c_uint(5), c_uint(6), c_uint(7), c_uint(4066125545)]

By default, the remove() function removes the i-th particle from the particles array, and shifts all particles with higher indices down by 1. This ensures that the original order in the particles array is preserved. Note that this is helpful for example if you use an integrator such as WHFast which uses Jacobi coordinates.

By running through the planets in reverse order, we are guaranteed that when a particle with index i gets removed, the particle replacing it doesn’t need to also be removed (we already checked it).

If you have many particles and many removals (or you don’t care about the ordering), you can save the reshuffling of all particles with higher indices with the flag keepSorted=0:

sim.remove(2, keepSorted=0)
print("Number of particles after cut = {0}".format(sim.N))
print("Hashes of remaining particles = {0}".format([p.hash for p in sim.particles]))
Number of particles after cut = 6
Hashes of remaining particles = [c_uint(0), c_uint(2), c_uint(4066125545), c_uint(5), c_uint(6), c_uint(7)]

We see that the order of the particles array has changed.

Because in general particles can change positions in the particles array, a more robust way of referring to particles (rather than through their index) is through their hash, which won’t change. You can pass sim.remove either the hash directly, or if you pass a string, it will be automatically converted to its corresponding hash:

sim.remove(hash="Saturn")
print("Number of particles after cut = {0}".format(sim.N))
print("Hashes of remaining particles = {0}".format([p.hash for p in sim.particles]))
Number of particles after cut = 5
Hashes of remaining particles = [c_uint(0), c_uint(2), c_uint(5), c_uint(6), c_uint(7)]

If you try to remove a particle with an invalid index or hash, an exception is thrown, which might be catch using the standard python syntax:

try:
    sim.remove(hash="Planet 9")
except RuntimeError as e:
    print("A runtime error occured: {0}".format(e))
A runtime error occured: Particle to be removed not found in simulation.  Did not remove particle.