Integrator¶

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

Bases:

Molecular dynamics time integration.

Parameters:

dt (float) – Integrator time step size $[\mathrm{time}]$ .
methods (Sequence[hoomd.md.methods.Method]) – Sequence of integration methods. 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. 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) – An object defining the rigid bodies in the simulation.
half_step_hook (hoomd.md.HalfStepHook) – Enables the user to perform arbitrary computations during the half-step of the integration.

Integrator is the top level class that orchestrates the time integration step in molecular dynamics simulations. The integration methods define the equations of motion to integrate under the influence of the given forces and constraints.

Each method applies the given equations of motion to a subset of particles in the simulation state. See the documentation for each method for details on what equations of motion it solves. The intersection of the subsets must be null.

Integrator computes the net force, torque, energy, and virial on each particle as a sum of those applied by hoomd.md.force.Force objects in the forces and constraints lists:

\begin{split} \vec{F}_{\mathrm{net},i} &= \sum_{f \in \mathrm{forces}} \vec{F}_i^f \\ \vec{\tau}_{\mathrm{net},i} &= \sum_{f \in \mathrm{forces}} \vec{\tau}_i^f \\ U_{\mathrm{net},i} &= \sum_{f \in \mathrm{forces}} U_i^f \\ W_{\mathrm{net},i} &= \sum_{f \in \mathrm{forces}} W_i^f \\ \end{split}

Integrator also computes the net additional energy and virial

\begin{split} U_{\mathrm{net},\mathrm{additional}} &= \sum_{f \in \mathrm{forces}} U_\mathrm{additional}^f \\ W_{\mathrm{net},\mathrm{additional}} &= \sum_{f \in \mathrm{forces}} W_\mathrm{additional}^f \\ \end{split}

See md.force.Force for definitions of these terms. Constraints are a special type of force used to enforce specific constraints on the system state, such as distances between particles with hoomd.md.constrain.Distance. Integrator handles rigid bodies as a special case, as it only integrates the degrees of freedom of each body’s center of mass. See hoomd.md.constrain.Rigid for details.

Degrees of freedom

Integrator always integrates the translational degrees of freedom. It optionally integrates one or more rotational degrees of freedom for a given particle i when all the following conditions are met:

The integration method supports rotational degrees of freedom.
integrate_rotational_dof is True.
The moment of inertia is non-zero $I^d_i > 0$ .

Each particle may have zero, one, two, or three rotational degrees of freedom.

Note

By default, integrate_rotational_dof is False. gsd and hoomd.Snapshot also set particle moments of inertia to 0 by default.

Classes

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

Example:

cell = hoomd.md.nlist.Cell(buffer=0.4)
lj = hoomd.md.pair.LJ(nlist=cell)
lj.params[('A', 'A')]  = dict(epsilon=1.0, sigma=1.0)
lj.r_cut[('A', 'A')] = 2.5
nve = hoomd.md.methods.ConstantVolume(
    filter=hoomd.filter.All(),
    thermostat=None,
    )
integrator = hoomd.md.Integrator(dt=0.005,
                                methods=[nve],
                                forces=[lj],
                                )