HOOMD-blue

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HOOMD-blue is a Python package that runs simulations of particle systems on CPUs and GPUs. It performs hard particle Monte Carlo simulations of a variety of shape classes and molecular dynamics simulations of particles with a range of pair, bond, angle, and other potentials. Many features are targeted at the soft matter research community, though the code is general and capable of many types of particle simulations.

Resources

Example scripts

These examples demonstrate some of the Python API.

Hard particle Monte Carlo:

import hoomd

mc = hoomd.hpmc.integrate.ConvexPolyhedron()
mc.shape['octahedron'] = dict(vertices=[
    (-0.5, 0, 0),
    (0.5, 0, 0),
    (0, -0.5, 0),
    (0, 0.5, 0),
    (0, 0, -0.5),
    (0, 0, 0.5),
])

cpu = hoomd.device.CPU()
sim = hoomd.Simulation(device=cpu, seed=20)
sim.operations.integrator = mc
# The tutorial describes how to construct an initial configuration 'init.gsd'.
sim.create_state_from_gsd(filename='init.gsd')

sim.run(1e5)

Molecular dynamics:

import hoomd

cell = hoomd.md.nlist.Cell()
lj = hoomd.md.pair.LJ(nlist=cell)
lj.params[('A', 'A')] = dict(epsilon=1, sigma=1)
lj.r_cut[('A', 'A')] = 2.5

integrator = hoomd.md.Integrator(dt=0.005)
integrator.forces.append(lj)
nvt = hoomd.md.methods.NVT(kT=1.5, filter=hoomd.filter.All(), tau=1.0)
integrator.methods.append(nvt)

gpu = hoomd.device.GPU()
sim = hoomd.Simulation(device=gpu)
sim.operations.integrator = integrator
# The tutorial describes how to construct an initial configuration 'init.gsd'.
sim.create_state_from_gsd(filename='init.gsd')
sim.state.thermalize_particle_momenta(filter=hoomd.filter.All(), kT=1.5)

sim.run(1e5)

Getting started

Tutorials

How to guides

Python API

Developer guide

Reference