Advanced Epiboly With Clusters and Events

We can write a much more detailed model of epiboly using clusters and events:

import mechanica as m
import numpy as np

# dimensions of universe
dim=np.array([30., 30., 30.])
center = dim / 2

m.Simulator(
  dim=dim,
  cutoff=12,
  integrator=m.FORWARD_EULER,
  dt=0.0005)

class C(m.Cluster):
  radius=2.3

  class B(m.Particle):
    radius=0.25
    dynamics = m.Overdamped
    mass=15
    style={"color":"skyblue"}

  def split(self, event):
    print("C.split(" + str(self) + ", event: " + str(event) + ")")
    axis = self.position - C.yolk_pos
    print("axis: " + str(axis))
    m.Cluster.split(self, axis=axis)

  events = [m.on_time(split,
                      period=0.2,
                      predicate="largest")]

class Yolk(m.Particle):
  radius = 10
  mass = 1000000
  dynamics=m.Overdamped
  style={"color":"gold"}

total_height = 2 * Yolk.radius + 2 * C.radius
yshift = total_height/2 - Yolk.radius
cshift = total_height/2 - C.radius - 1

yolk = Yolk(position=center-[0., 0., yshift])

c = C(position=center+[0., 0., cshift])

C.yolk_pos = yolk.position

c.B(4000)

pb  = m.Potential.soft_sphere(kappa=300, epsilon=6, r0=0.5, \
                              eta=2, tol = 0.05, min=0, max=3)

pub = m.Potential.soft_sphere(kappa=400, epsilon=0, r0=0.5, \
                              eta=2, tol = 0.05, min=0.001, max=1.5)

py = m.Potential.soft_sphere(kappa=300, epsilon=25, r0=1, \
                             eta=2, tol = 0.04, min=0, \
                             max=10, shift=True)

rforce = m.forces.random(0, 1)

m.bind(rforce, C.B)
m.bind(pb, C.B, C.B, bound=True)
m.bind(pub, C.B, C.B, bound=False)
m.bind(py, Yolk, C.B)

m.Simulator.irun()

The complete simulation script is here, and can be downloaded here:

Download: this example script: