IMLCV.base.bias

Module Contents

Classes

EnergyResult
BC	base class for biased Energy of MD simulation.
Energy	base class for biased Energy of MD simulation.
PlumedEnerg	base class for biased Energy of MD simulation.
Bias	base class for biased MD runs.
CompositeBias	Class that combines several biases in one single bias.
BiasF	Bias according to CV.
NoneBias	dummy bias.

Functions

plot_app(bias, outputs[, n, vmin, vmax, map, ...])

class IMLCV.base.bias.EnergyResult

energy: float

gpos: Array | None

vtens: Array | None

__post_init__()

__add__(other) → EnergyResult

__str__() → EnergyResult.__str__.str

Return str(self).

class IMLCV.base.bias.BC

base class for biased Energy of MD simulation.

save(filename: str | Path)

static load(filename) → BC

exception IMLCV.base.bias.EnergyError

Bases: Exception

Common base class for all non-exit exceptions.

class IMLCV.base.bias.Energy

Bases: BC

base class for biased Energy of MD simulation.

abstract property cell

abstract property coordinates

property sp: IMLCV.base.CV.SystemParams

static load(filename) → Energy

abstract _compute_coor(gpos=False, vir=False) → EnergyResult

_handle_exception()

compute_from_system_params(gpos=False, vir=False, sp: SystemParams | None = None, nl: NeighbourList | None = None) → EnergyResult

class IMLCV.base.bias.PlumedEnerg

Bases: Energy

base class for biased Energy of MD simulation.

exception IMLCV.base.bias.BiasError

Bases: Exception

Common base class for all non-exit exceptions.

class IMLCV.base.bias.Bias(collective_variable: IMLCV.base.CV.CollectiveVariable, start=None, step=None)

Bases: BC, abc.ABC

base class for biased MD runs.

update_bias(md: IMLCV.base.MdEngine.MDEngine)

update the bias.

Can only change the properties from _get_args

_update_bias()

update the bias.

Can only change the properties from _get_args

compute_from_system_params(sp: IMLCV.base.CV.SystemParams, gpos=False, vir=False, nl: NeighbourList | None = None, jit=True) → tuple[IMLCV.base.CV.CV, EnergyResult]

Computes the bias, the gradient of the bias wrt the coordinates and the virial.

compute_from_cv(cvs: IMLCV.base.CV.CV, diff=False, jit=True) → IMLCV.base.CV.CV

compute the energy and derivative.

If map==False, the cvs are assumed to be already mapped

abstract _compute(cvs, *args)

function that calculates the bias potential. CVs live in mapped space

abstract get_args()

function that return dictionary with kwargs of _compute.

finalize()

Should be called at end of metadynamics simulation.

Optimises compute

static load(filename) → Bias

plot(name, x_unit: str | None = None, y_unit: str | None = None, n=50, traj: list[CV] | None = None, vmin=0, vmax=100 * kjmol, map=False, inverted=False, margin=None, x_lim=None, y_lim=None, bins=None)

plot bias.

IMLCV.base.bias.plot_app(bias: Bias, outputs: list[parsl.data_provider.files.File], n: int = 50, vmin: float = 0, vmax: float = 100 * kjmol, map: bool = True, inverted=False, traj: list[CV] | None = None, margin=None, x_unit=None, y_unit=None, x_lim=None, y_lim=None, bins=None)

class IMLCV.base.bias.CompositeBias(biases: collections.abc.Iterable[Bias], fun=jnp.sum)

Bases: Bias

Class that combines several biases in one single bias.

_append_bias(b: Bias)

_compute(cvs, *args)

function that calculates the bias potential. CVs live in mapped space

finalize()

Should be called at end of metadynamics simulation.

Optimises compute

update_bias(md: IMLCV.base.MdEngine.MDEngine)

update the bias.

Can only change the properties from _get_args

get_args()

function that return dictionary with kwargs of _compute.

class IMLCV.base.bias.BiasF(cvs: IMLCV.base.CV.CollectiveVariable, g=None)

Bases: Bias

Bias according to CV.

_compute(cvs)

function that calculates the bias potential. CVs live in mapped space

get_args()

function that return dictionary with kwargs of _compute.

class IMLCV.base.bias.NoneBias(cvs: IMLCV.base.CV.CollectiveVariable)

Bases: BiasF

dummy bias.