atomistics.workflows.langevin.LangevinWorkflow

atomistics.workflows.langevin.LangevinWorkflow#

class atomistics.workflows.langevin.LangevinWorkflow(structure: Atoms, temperature: float = 1000.0, overheat_fraction: float = 2.0, damping_timescale: float = 100.0, time_step: int = 1, seed: int | None = None)[source]#

Bases: Workflow

LangevinWorkflow class represents a workflow for performing Langevin dynamics simulation.

Parameters:

  • structure (ase.Atoms) – The atomic structure.

  • temperature (float, optional) – The temperature in Kelvin. Default is 1000.0.

  • overheat_fraction (float, optional) – The fraction by which to overheat the system. Default is 2.0.

  • damping_timescale (float, optional) – The damping timescale in fs. Default is 100.0.

  • time_step (int, optional) – The time step in fs. Default is 1.

  • seed (int, optional) – Seed for the random number generator, for reproducible trajectories. Default is None, which uses non-deterministic entropy.

structure#

The atomic structure.

Type:

ase.Atoms

temperature#

The temperature in Kelvin.

Type:

float

overheat_fraction#

The fraction by which the system is overheated.

Type:

float

damping_timescale#

The damping timescale in fs.

Type:

float

time_step#

The time step in fs.

Type:

int

masses#

The masses of the atoms.

Type:

numpy.ndarray

positions#

The positions of the atoms.

Type:

numpy.ndarray

velocities#

The velocities of the atoms.

Type:

numpy.ndarray

gamma#

The damping coefficients of the atoms.

Type:

numpy.ndarray

forces#

The forces on the atoms.

Type:

numpy.ndarray

generate_structures()[source]#

Generates the structures for the Langevin dynamics simulation.

analyse_structures()[source]#

Analyzes the structures generated in the Langevin dynamics simulation.

__init__(structure: Atoms, temperature: float = 1000.0, overheat_fraction: float = 2.0, damping_timescale: float = 100.0, time_step: int = 1, seed: int | None = None)[source]#

Methods

__init__(structure[, temperature, ...])

analyse_structures(output_dict)

Analyzes the structures generated in the Langevin dynamics simulation.

generate_structures()

Generates the structures for the Langevin dynamics simulation.
analyse_structures(output_dict: dict[str, dict[int, Any]])[source]#

Analyzes the structures generated in the Langevin dynamics simulation.

Parameters:

output_dict (dict) – A dictionary containing the output structures.

Returns:

A tuple containing the potential energy and kinetic energy.

Return type:

tuple

generate_structures() → dict[str, dict[int, Atoms]][source]#

Generates the structures for the Langevin dynamics simulation.

Returns:

A dictionary containing the generated structures.

Return type:

dict