glotzerlab/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-blue discussion board: Ask the HOOMD-blue user community for help.
• HOOMD-blue website: Additional information and publications.
• HOOMD-blue benchmark scripts: Scripts to evaluate the performance of HOOMD-blue simulations.
• HOOMD-blue validation tests: Scripts to validate that HOOMD-blue performs accurate simulations.

Related tools

• hoomd-rs: Infinitely customizable MC/MD simulations and order parameter computations in Rust. Faster than HOOMD-blue in most benchmarks.

• freud: Analyze HOOMD-blue simulation results with the freud Python library.

• signac: Manage your workflow with signac.

• Molecular Simulation Design Framework (MoSDeF) tools:

  • mbuild: Assemble reusable components into complex molecular systems.
  • foyer: Perform atom-typing and define classical molecular modeling force fields.
  • gmso: A flexible and mutable data structure for chemical topologies that writes HOOMD-blue formats.

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(buffer=0.4)
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)
bussi = hoomd.md.methods.thermostats.Bussi(kT=1.5)
nvt = hoomd.md.methods.ConstantVolume(filter=hoomd.filter.All(), thermostat=bussi)
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)

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

HOOMD-blue is available under the 3-clause BSD license.