Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
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.
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)
CHANGELOG.rst contains the full change log.
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.
HOOMD-blue is available under the 3-clause BSD license.