md.alchemy.methods

Overview

Alchemostat	Alchemostat base class.
NVT	Alchemical NVT integration.

Details

Alchemical MD integration methods.

class hoomd.md.alchemy.methods.Alchemostat(alchemical_dof)

Alchemostat base class.

Note

Alchemostat is the base class for all alchemical integration methods. Users should use the subclasses and not instantiate Alchemostat directly.

New in version 3.1.0.

property alchemical_dof

List of alchemical degrees of freedom.

Type:

list [hoomd.md.alchemy.pair.AlchemicalDOF ]

class hoomd.md.alchemy.methods.NVT(alchemical_kT, alchemical_dof, period=1)

Alchemical NVT integration.

Implements molecular dynamics simulations of an extended statistical mechanical ensemble that includes alchemical degrees of freedom describing particle attributes as thermodynamic variables.

Parameters:

• alchemical_kT (hoomd.variant.variant_like) – Temperature set point for the alchemostat \([\mathrm{energy}]\).

• alchemical_dof (list [hoomd.md.alchemy.pair.AlchemicalDOF]) – List of alchemical degrees of freedom.

• period (int) – Timesteps between applications of the alchemostat.

Attention

hoomd.md.alchemy.methods.NVT does not support execution on GPUs.

Attention

hoomd.md.alchemy.methods.NVT does not support MPI parallel simulations.

Attention

hoomd.md.alchemy.methods.NVT objects are not picklable.

Danger

NVT must be the first item in the hoomd.md.Integrator.methods list.

See also

Zhou et al. 2019.

New in version 3.1.0.

alchemical_kT

Temperature set point for the alchemostat \([\mathrm{energy}]\).

Type:

hoomd.variant.Variant

alchemical_dof

List of alchemical degrees of freedom.

Type:

list [hoomd.md.alchemy.pair.AlchemicalDOF]

period

Timesteps between applications of the alchemostat.

Type:

int