HyperdynamicsPositionDistortion

class HyperdynamicsPositionDistortion(atom_tag, maximum_radius=None)

Class for calculating position distortions used in a hyperdynamics simulation.

Parameters:

• atom_tag (str) – The tag of the atoms to distort from their positions.

• maximum_radius (PhysicalQuantity of type length) – The distance from the equilibrium position to the transition state.

atomTag()

Returns:

The tag of the atoms that have a positional acceleration.

Return type:

str

maximumRadius()

Returns:

The maximum radius of the position distortion.

Return type:

PhysicalQuantity of type length

numberOfVariables()

Returns:

The number of variables that are being accelerated.

Return type:

int

uniqueString()

Return a unique string representing the state of the object.

Usage Examples

General

Notes

The HyperdynamicsPositionDistortion implements a distortion based on atomic position. This distortion can be used in either a StaticHyperdynamics or CollectiveVariableHyperdynamics simulation.

The atoms whose positions are used to define the distortions are given with a configuration tag using the atom_tag argument. A maximum radius of the distance between the atomic position and the transition state is also given with the max_radius argument. When the distortion is reset the current atomic position is recorded. The distortion \(\chi\) is then given as:

\[\begin{split}\chi = \begin{cases} \frac{|\mathbf{r} - \mathbf{r}_0|}{r_{max}} & |\mathbf{r} - \mathbf{r}_0| \leq r_{max} \\ 1 & |\mathbf{r} - \mathbf{r}_0| > r_{max} \\ \end{cases}\end{split}\]

Here \(\mathbf{r}\) is the current atomic position, \(\mathbf{r}_0\) is the reference atomic position and \(r_{max}\) is the maximum distance between the atomic position and the transition state. The distortion ranges from 0 to 1 and is limited to 1 once the atom moves outside the maximum radius.

This type of distortion is most useful for simulations in crystalline materials. Here the crystal lattice gives the atomic position a well defined reference point. In amorphous materials it is likely more efficient to use distortions which do not rely on a well defined reference point, such as the HyperdynamicsBondDistortion.