HPMC simulation of spherocylinders

[edwinb-ai]

Hello, I have tried to do simulations of spherocylinders on HOOMD-blue, and according to the documentation, a two-vertex ConvexSpheropolyhedron corresponds to a spherocylinder, and I have the following code:

import itertools
import math

import gsd.hoomd
import hoomd
import numpy as np

m = 4
N_particles = m**3

spacing = 4.0
K = math.ceil(N_particles ** (1 / 3))
L = K * spacing

x = np.linspace(-L / 2, L / 2, K, endpoint=False)
position = list(itertools.product(x, repeat=3))
position = position[0:N_particles]
orientation = [(1, 0, 0, 0)] * N_particles

frame = gsd.hoomd.Frame()
frame.particles.N = N_particles
frame.particles.position = position
frame.particles.orientation = orientation
frame.particles.typeid = [0] * N_particles
frame.particles.types = ["spherocylinder"]
frame.configuration.box = [L, L, L, 0, 0, 0]

with gsd.hoomd.open(name="lattice.gsd", mode="w") as f:
    f.append(frame)

cpu = hoomd.device.CPU()
simulation = hoomd.Simulation(device=cpu, seed=12)

mc = hoomd.hpmc.integrate.ConvexSpheropolyhedron(default_d=0.1, default_a=0.1)
mc.shape["spherocylinder"] = dict(
    vertices=[
        (0, 0, -2),
        (0, 0, 2),
    ],
    sweep_radius=0.5,
)

simulation.operations.integrator = mc
simulation.create_state_from_gsd(filename="lattice.gsd")

simulation.run(0)

print(mc.type_shapes)

logger = hoomd.logging.Logger()
logger.add(mc, quantities=["type_shapes"])
hoomd.write.GSD.write(
    state=simulation.state, mode="wb", filename="random.gsd", logger=logger
)

Now, when I print the shape type, I get the following.

[{'type': 'ConvexPolyhedron', 'rounding_radius': 0.5, 'vertices': [[0, 0, -2], [0, 0, 2]]}]

I wonder if it's really doing the correct overlap check if it's not the ConvexSpheropolyhedron type that's being printed. Additionally, I cannot visualize this in OVITO because it expects a shape with four vertices because it assumes that the particle types are actually ConvexPolyhedron.

[joaander]

Yes, a two vertex convex spheropolyhedron is a sphereocylinder because the support function computation will sweep a sphere across the line connecting the points. The GSD type_shapes schema does not differentiate between spheropolyhedra and convex polyhedra with only sharp edges: https://gsd.readthedocs.io/en/v3.4.2/shapes.html#convex-polyhedra

Have you tried the latest version of OVITO? It recently added support for the two vertex case: glotzerlab/gsd#310 (comment)

[edwinb-ai]

Thank you for the reply. Also, using the current version of OVITO works correctly.