facade

Module containing an abstract base class for MD engine facades

class MDMC.MD.engine_facades.facade.MDEngine

Abstract base class for MD engine facades

clear() → None

Deletes all atoms of the MD engine, restores all settings to their default values, and frees all memory.

abstract convert_trajectory(start: int = 0, stop: int = None, step: int = 1, **settings: dict) → CompactTrajectory

Parses the trajectory from the MDEngine format into MDMC format

Parameters:

• start (int) – The index of the first trajectory, inclusive.

• stop (int) – The index of the last trajectory, exclusive.

• step (int) – The step size between trajectories.

• **settings –

  scaled_positions (bool)

  If the trajectory_file has scaled positions

  atom_IDs (list)

  LAMMPS ID of the atoms which should be included. If not passed then all atoms are included in the converted trajectory.

Returns:

The CompactTrajectory from the most recent production simulation

Return type:

CompactTrajectory

abstract eval(variable: str) → Any

Evaluates some simulation variable.

abstract minimize(n_steps: int, minimize_every: int = 10, **settings: dict) → None

Minimizes the simulation energy

Parameters:

• n_steps (int) – Maximum number of MD steps during the energy minimization.

• minimize_every (int, optional, default 10) – Number of MD steps between two consecutive minimizations.

property parent_simulation: Simulation

Get or set the simulation that created this engine facade

Returns:

The Simulation object that created this engine facade

Return type:

Simulation

abstract reset_config() → None

Resets the configuration of the simulation to that in saved_config

abstract run(n_steps: int, equilibration: bool) → None

Runs a simulation. Must follow a call to setup_universe() and setup_simulation().

Parameters:

• n_steps (int) – Number of steps for the time integrator.

• equilibration (bool) – If True, run is equilibration which does not store the trajectory. Otherwise run is prodution.

abstract save_config() → None

Sets self.saved_config to the current configuration

abstract property saved_config: Configuration

Get the saved configuration of the atomic positions

Returns:

The atomic positions

Return type:

Configuration

abstract setup_simulation(**settings: dict) → None

Sets the options required to perform a simulation on a setup Universe. Must follow a call to setup_universe().

Parameters:

• universe (Universe) – A molecular dynamics Universe which will be simulated in the MDEngine.

• settings** – The majority of these are generic but some are specific to the MDEngine that is being used.

abstract setup_universe(universe: str, **settings: dict) → None

Creates a Universe.configuration and populates with Structure

Parameters:

• universe (Universe) – A molecular dynamics Universe which will be setup in the MDEngine.

• **settings – The majority of these are generic but some are specific to the MDEngine that is being used.

property time_step: float

Get the simulation time step in fs from the parent simulation

Returns:

Simulation time step in fs

Return type:

float

property traj_step: int

Get the number of simulation steps between saving the CompactTrajectory from the parent simulation

Returns:

Number of simulation steps that elapse between the CompactTrajectory being stored

Return type:

int

abstract update_parameters() → None

Updates the MDEngine force field Parameter objects from the Universe

exception MDMC.MD.engine_facades.facade.MDEngineError

Raised when MD engine raises an exception from a run command