Brownian

class hoomd.md.methods.rattle.Brownian(filter, kT, manifold_constraint, tolerance=1e-06, default_gamma=1.0, default_gamma_r=(1.0, 1.0, 1.0))

Bases: MethodRATTLE

Brownian dynamics with RATTLE constraint.

Parameters:

  • filter (hoomd.filter.filter_like) – Subset of particles to apply this method to.

  • kT (hoomd.variant.variant_like) – Temperature of the simulation \([\mathrm{energy}]\).

  • manifold_constraint (hoomd.md.manifold.Manifold) – Manifold constraint.

  • tolerance (float) – Defines the tolerated error particles are allowed to deviate from the manifold in terms of the implicit function. The units of tolerance match that of the selected manifold’s implicit function. Defaults to 1e-6

  • default_gamma (float) – Default drag coefficient for all particle types \([\mathrm{mass} \cdot \mathrm{time}^{-1}]\).

  • default_gamma_r ([float, float, float]) – Default rotational drag coefficient tensor for all particles \([\mathrm{time}^{-1}]\).

Brownian uses the same integrator as hoomd.md.methods.Brownian, which follows the overdamped Langevin equations of motion with the additional force term \(- \lambda \vec{F}_\mathrm{M}\). The force \(\vec{F}_\mathrm{M}\) keeps the particles on the manifold constraint, where the Lagrange multiplier \(\lambda\) is calculated via the RATTLE algorithm. For more details about Brownian dynamics see hoomd.md.methods.Brownian.

Example

sphere = hoomd.md.manifold.Sphere(r=5)
brownian_rattle = hoomd.md.methods.rattle.Brownian(
    filter=hoomd.filter.All(),
    kT=1.5,
    manifold_constraint=sphere,
    default_gamma=1.0,
    default_gamma_r=(1.0, 1.0, 1.0),
)
simulation.operations.integrator.methods = [brownian_rattle]

Members inherited from AutotunedObject:

property kernel_parameters

Kernel parameters. Read more...

property is_tuning_complete

Check if kernel parameter tuning is complete. Read more...

tune_kernel_parameters()

Start tuning kernel parameters. Read more...

Members inherited from MethodRATTLE:

manifold_constraint

Manifold constraint. Read more...

tolerance

Defines the tolerated error particles are allowed to deviate from the manifold in terms of the implicit function. Read more...

Members defined in Brownian:

filter

Subset of particles to apply this method to.

Type:

hoomd.filter.filter_like

kT

Temperature of the simulation \([\mathrm{energy}]\).

Type:

hoomd.variant.Variant

gamma

The drag coefficient for each particle type \([\mathrm{mass} \cdot \mathrm{time}^{-1}]\).

Type:

TypeParameter[ particle type, float ]

gamma_r

The rotational drag coefficient tensor for each particle type \([\mathrm{time}^{-1}]\).

Type:

TypeParameter[particle type,[float, float , float]]