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.
Related tools
- freud: Analyze HOOMD-blue simulation results with the freud Python library.
- signac: Manage your workflow with signac.
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
HOOMD-blue is available under the 3-clause BSD license.