Hard Sphere Monte Carlo Simulation

This is my personal project to study Monte-Carlo simulations of monodispersed hard spheres in 3D.

It is not very fast. If you need large scale simulation, maybe you want to use hoomd-blue.

Install

The intended installation flow is now:

pip install .

This builds and installs:

• the Python package hsmc
• the compiled extension module hsmc.chard_sphere
• the bundled assets under workflow
• the helper command hsmc-workflow

After installation, the package should be importable directly:

import hsmc
from hsmc import chard_sphere

The build still requires Eigen to be available for CMake to find during installation.

Bundled Workflows

The workflow templates are shipped with the installed package. List the available workflows with:

hsmc-workflow list

Create a workflow in the current working directory with:

hsmc-workflow create simulate_slit

or:

hsmc-workflow create simulate_slit_v2

You can also choose a destination directory explicitly:

hsmc-workflow create simulate_slit_v2 /path/to/output

General command help is available with:

hsmc-workflow help

For contributor workflow packaging rules, see CONTRIBUTING.md.

Use the Code in Python

The following snippest present the way to start a simulation

from hsmc import chard_sphere
from hsmc.analysis import dump_xyz, TCCOTF
import numpy as np


n_particle = 1000
box = [30, 50, 60]  # box size in X, Y, and Z
is_pbc = [True, True, False]  # no PBC in the z-direction
is_hard = [False, False, True]  # hard walls along z-direction
r_skin = 5.0

# create the system
system = chard_sphere.HSMC(
    n=n_particle, box=box,
    is_pbc=is_pbc, is_hard=is_hard, r_skin=r_skin
)

# randomly fill non-overlapping hard spheres
system.fill_hs()

# reduce the box size slowly to reach desired volume fraction
system.crush(0.50, 0.02)

# print the overview of the system
print(system)


# perform 1000 Monte-Carlo sweeps, collect the configuration every 100 frames

configurations = np.empty((10, n_particle, 3))
for i in range(10):
    for _ in range(100):
        system.sweep()

    # retrieve the positions of the particles
    positions = system.get_positions()
    configurations[i] = positions.T

    # save the positions into an xyz file
    dump_xyz(
        'hard_sphere.xyz', positions.T,
        comment="box:[" + ",".join([  # write box as the comment
            f"{L:.8f} (PBC? {p}; Hard? {h})"
            for L, p, h in zip(system.get_box(), is_pbc, is_hard)
        ]) + "]"
    )