Bias

class mlptrain.sampling.bias.Bias(zeta_func: ReactionCoordinate, kappa: float, reference: float)

Bases: ASEConstraint, Function

Modifies the forces and energy of a set of ASE atoms under a bias

__call__(atoms)

Value of the bias for set of atom pairs in atoms

__init__(zeta_func: ReactionCoordinate, kappa: float, reference: float)

Bias that modifies the forces and energy of a set of atoms under a harmonic bias function.

Harmonic biasing potential: ω = κ/2 (ζ(r) - ζ_ref)^2

e.g. bias = mlt.bias.Bias(to_average=[[0, 1]], reference=2, kappa=10)

Parameters:

• kappa – Value of the spring constant, κ

• reference – Reference value of the reaction coordinate, ζ_ref

adjust_forces(atoms, forces)

Adjust the forces of a set of atoms in place using the gradient of the bias function:

F = -∇E -∇B

where ∇E is the gradient of the energy with respect to the coordinates and B is the bias.

adjust_positions(atoms, newpositions)

Method required for ASE but not used in mlp-train

adjust_potential_energy(atoms)

Adjust the energy of a set of atoms using the bias function

grad(atoms)

Gradient of the biasing potential a set of atom pairs in atoms