State

Overview

Details

class msibi.state.State(name: str, kT: float, traj_file: str, n_frames: int, sampling_stride: int = 1, alpha0: float = 1.0, alpha_form: str = 'constant', _dir=None)

A single state point used as part of a multistate optimization.

Parameters:

  • name (str) – State name used in creating state directory space and output files.

  • kT ((Union[float, int])) – Unitless heat energy (product of Boltzmann’s constant and temperature).

  • traj_file (path to a gsd.hoomd file) – The target gsd trajectory associated with this state. This trajectory calcualtes the target distributions used during optimization.

  • n_frames (int) – The number of frames to use when calculating distributions. When calculating distributions, the last n_frames of the trajectory will be used.

  • sampling_stride (int, default=1) – The stride step-size used when iterating through the last n_frames of the query simulation trajectory.

  • alpha0 ((Union[float, int]), default=1.0) – The base alpha value used to scale the weight of this state.

  • alpha_form (str, optional, default='constant') – Alpha can be a constant number that is applied to the potential at all independent values (x), or it can be a linear function that approaches zero as x approaches x_cut. Available options are ‘constant’ and ‘linear’.

property n_frames: int

The number of frames used in calculating distributions.

property sampling_stride: int

The stride step size used to calcualte distributions when iterating through n_frames.

property alpha0: int | float

State point base weighting value.

alpha(pot_x_range: ndarray = None, dx: float = None) → float | ndarray

State point weighting value, also known as alpha.

Note

This method is called in msibi.forces.Force when performing the potential update between iterations. To change the alpha value for a state point use the alpha0 setter.

Parameters:

pot_x_range (np.ndarray, optional, default=None) – The x value range for the potential being optimized. This is used to generate an array of alpha values, so must be defined when msibi.State.alpha_form is “linear”.