mass = 1
radius = 0.1
dynamics = m.Overdamped
style = {'color': 'dodgerblue'}
class Big(m.Particle):
mass = 1
radius = 8
frozen = True
style = {'color': 'orange'}
# simple harmonic potential to pull particles
pot = m.Potential.harmonic(k=1, r0=0.1, max=3)
# make big cell in the middle
Big(m.Universe.center)
#Big.style.visible = False
# create a uniform mesh of particles and bonds on the surface of a sphere
parts, bonds = m.bind_sphere(pot,
type=Blue,
n=5,
phi=(0.6 * np.pi, 0.8 * np.pi),
radius=Big.radius + Blue.radius)
# run the model
m.show()
r = m.forces.random(0, 5)
m.bind(r, Cell)
#m.bind(r, Actin)
# make a yolk at the center of the simulation domain
yolk = Yolk(m.Universe.center)
# create the initial cell positions
cell_positions = m.random_points(m.SolidSphere, 6000, dr=dr, phi=(0, epiboly_percent * np.pi)) \
* ((1 + dr/2) * Yolk.radius) + yolk.position
# create an actin mesh that covers a section of a sphere.
parts, bonds = m.bind_sphere(p_actin, type=Actin, n=4, \
phi=(0.9 * epiboly_percent * np.pi, \
(epiboly_percent + actin_percent * (1 - epiboly_percent)) * np.pi), \
radius = Yolk.radius + Actin.radius)
# create the initial cell cells
[Cell(p) for p in cell_positions]
#m.bind_pairwise(h, c.neighbors(2* Cell.radius), cutoff=2*Cell.radius, pairs=[(Cell,Actin)])
# set visiblity on the different objects
Yolk.style.visible = True
Actin.style.visible = True
#Cell.style.visible = False
# display function to write out values, any code can go here.
#m.bind(pb, B, B)
#m.bind(pab, A, B)
r = m.forces.random(0, 5)
m.bind(r, A)
#m.bind(r, B)
c = C(m.Universe.center)
pos_a = m.random_points(m.SolidSphere, 3000, dr=0.25, phi=(0, 0.60 * np.pi)) \
* ((1 + 0.25/2) * C.radius) + m.Universe.center
parts, bonds = m.bind_sphere(h,
type=B,
n=4,
phi=(0.6 * np.pi, np.pi),
radius=C.radius + B.radius)
[A(p) for p in pos_a]
# grab a vertical slice of the neighbors of the yolk:
slice_parts = [p for p in c.neighbors() if p.spherical()[1] > 0]
m.bind_pairwise(pab, slice_parts, cutoff=5 * A.radius, pairs=[(A, B)])
#A.style.visible = False
C.style.visible = False
B.style.visible = False
#A.style.visible = False
#pb= m.Potential.glj(e=0.00001, r0=0.1, m=3, min=0.01, max=Blue.radius*3)
pb = m.Potential.coulomb(q=0.01, min=0.01, max=3)
# potential between the small and big particles
pot = m.Potential.glj(e=1, m=2, max=5)
Big(m.Universe.center)
Big.style.visible = False
m.bind(pot, Big, Blue)
m.bind(pb, Blue, Blue)
parts, bonds = m.bind_sphere(h, type=Blue, n=4, phi=(0.55 * np.pi, 1 * np.pi), radius = Big.radius + Blue.radius)
#for b in bonds:
# print("energy(", b.id, "): ", b.energy())
#print("parts: ", parts)
#parts[0].destroy()
#parts[3].destroy()
#parts[7].destroy()