pysages.methods.harmonic_bias¶

Overview

`pysages.methods.harmonic_bias.HarmonicBiasState`(xi, ...)	Description of a state biased by a harmonic potential for a CV.
`pysages.methods.harmonic_bias.HarmonicBias`(...)	Harmonic bias method class.

Details

Harmonic bias method.

Biasing a simulation towards a value of a collective variable is the foundation of a number of advanced sampling methods - umbrella integration, WHAM, string method to name a few. This method implements such a bias.

The Hamiltonian is amended with a term \(\mathcal{H} = \mathcal{H}_0 + \mathcal{H}_\mathrm{HB}(\xi)\) where \(\mathcal{H}_\mathrm{HB}(\xi) = \boldsymbol{K}/2 (\xi_0 - \xi)^2\) biases the simulations around the collective variable \(\xi_0\).

class pysages.methods.harmonic_bias.HarmonicBiasState(xi: Array, bias: Array, ncalls: int)¶

Description of a state biased by a harmonic potential for a CV.

xi: JaxArray: Collective variable value of the last simulation step.
bias: JaxArray: Array with harmonic biasing forces for each particle in the simulation.

xi: Array¶: Alias for field number 0

bias: Array¶: Alias for field number 1

ncalls: int¶: Alias for field number 2

class pysages.methods.harmonic_bias.HarmonicBias(cvs, kspring, center, **kwargs)¶

Harmonic bias method class.

property kspring¶: Retrieve the spring constant.