HOOMD-blue

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

Documentation: Tutorial, full Python API description, and usage information.
Citing HOOMD-blue How to cite the code.
Installation guide: Instructions for installing HOOMD-blue binaries.
Compilation guide: Instructions for compiling HOOMD-blue.
hoomd-users mailing list: Send messages to the HOOMD-blue user community.
HOOMD-blue website: Additional information and publications.
HOOMD-blue benchmark scripts: Scripts to evaluate the performance of HOOMD-blue simulations.

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
# See HOOMD tutorial for 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
# See HOOMD tutorial for 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)

Change log

CHANGELOG.rst contains the full change log.

Contributing to HOOMD-blue

Contributions are welcomed via pull requests. Please report bugs and suggest feature enhancements via the issue tracker. See CONTRIBUTING.rst and ARCHITECTURE.md for more information.

License