hoomd.md

Details

Molecular Dynamics.

Perform Molecular Dynamics simulations with HOOMD-blue.

class hoomd.md.Integrator(dt, integrate_rotational_dof=False, forces=None, constraints=None, methods=None, rigid=None)

Enables a variety of standard integration methods.

Parameters

dt (float) – Integrator time step size \([\mathrm{time}]\).
methods (Sequence[hoomd.md.methods.Method]) – Sequence of integration methods. Each integration method can be applied to only a specific subset of particles. The intersection of the subsets must be null. The default value of None initializes an empty list.
forces (Sequence[hoomd.md.force.Force]) – Sequence of forces applied to the particles in the system. All the forces are summed together. The default value of None initializes an empty list.
integrate_rotational_dof (bool) – When True, integrate rotational degrees of freedom.
constraints (Sequence[hoomd.md.constrain.Constraint]) – Sequence of constraint forces applied to the particles in the system. The default value of None initializes an empty list. Rigid body objects (i.e. hoomd.md.constrain.Rigid) are not allowed in the list.
rigid (hoomd.md.constrain.Rigid) – A rigid bodies object defining the rigid bodies in the simulation.

Classes of the following modules can be used as elements in methods:

The classes of following modules can be used as elements in forces

The classes of the following module can be used as elements in constraints

hoomd.md.constrain

Examples:

nlist = hoomd.md.nlist.Cell()
lj = hoomd.md.pair.LJ(nlist=nlist)
lj.params.default = dict(epsilon=1.0, sigma=1.0)
lj.r_cut[('A', 'A')] = 2**(1/6)
nve = hoomd.md.methods.NVE(filter=hoomd.filter.All())
integrator = hoomd.md.Integrator(dt=0.001, methods=[nve], forces=[lj])
sim.operations.integrator = integrator