pysages.methods.metad¶

Overview

`pysages.methods.metad.MetadynamicsState`(xi, ...)	Metadynamics helper state
`pysages.methods.metad.PartialMetadynamicsState`(xi, ...)	Helper intermediate Metadynamics state
`pysages.methods.metad.Metadynamics`(cvs, ...)	Implementation of Standard and Well-tempered Metadynamics as described in [PNAS 99.20, 12562-6 (2002)](https://doi.org/10.1073/pnas.202427399) and [Phys.

Details

Implementation of Standard and Well-tempered Metadynamics both with optional support for grids.

class pysages.methods.metad.MetadynamicsState(xi: Array, bias: Array, heights: Array, centers: Array, sigmas: Array, grid_potential: Array | None, grid_gradient: Array | None, idx: int, ncalls: int)¶

Metadynamics helper state

Parameters:

xi (JaxArray) – Collective variable value in the last simulation step.
bias (JaxArray) – Array of Metadynamics bias forces for each particle in the simulation.
heights (JaxArray) – Height values for all accumulated Gaussians (zeros for not yet added Gaussians).
centers (JaxArray) – Centers of the accumulated Gaussians.
sigmas (JaxArray) – Widths of the accumulated Gaussians.
grid_potential (Optional[JaxArray]) – Array of Metadynamics bias potentials stored on a grid.
grid_gradient (Optional[JaxArray]) – Array of Metadynamics bias gradients evaluated on a grid.
idx (int) – Index of the next Gaussian to be deposited.
ncalls (int) – Counts the number of times method.update has been called.

xi: Array¶: Alias for field number 0

bias: Array¶: Alias for field number 1

heights: Array¶: Alias for field number 2

centers: Array¶: Alias for field number 3

sigmas: Array¶: Alias for field number 4

grid_potential: Array | None¶: Alias for field number 5

grid_gradient: Array | None¶: Alias for field number 6

idx: int¶: Alias for field number 7

ncalls: int¶: Alias for field number 8

class pysages.methods.metad.PartialMetadynamicsState(xi: Array, heights: Array, centers: Array, sigmas: Array, grid_potential: Array | None, grid_gradient: Array | None, idx: int, grid_idx: Array | None)¶

Helper intermediate Metadynamics state

xi: Array¶: Alias for field number 0

heights: Array¶: Alias for field number 1

centers: Array¶: Alias for field number 2

sigmas: Array¶: Alias for field number 3

grid_potential: Array | None¶: Alias for field number 4

grid_gradient: Array | None¶: Alias for field number 5

idx: int¶: Alias for field number 6

grid_idx: Array | None¶: Alias for field number 7

class pysages.methods.metad.Metadynamics(cvs, height, sigma, stride, ngaussians, deltaT=None, **kwargs)¶: Implementation of Standard and Well-tempered Metadynamics as described in [PNAS 99.20, 12562-6 (2002)](https://doi.org/10.1073/pnas.202427399) and [Phys. Rev. Lett. 100, 020603 (2008)](https://doi.org/10.1103/PhysRevLett.100.020603)

pysages.methods.metad.build_gaussian_accumulator(method: Metadynamics)¶: Returns a function that given a MetadynamicsState, and the value of the CV, stores the next Gaussian that is added to the biasing potential.

pysages.methods.metad.build_bias_grad_evaluator(method: Metadynamics)¶: Returns a function that given the deposited Gaussians parameters, computes the gradient of the biasing potential with respect to the CVs.

pysages.methods.metad.sum_of_gaussians(xi, heights, centers, sigmas, periods)¶: Sum of n-dimensional Gaussians potential.