Calculate local entropy pro — OVITO User Manual 3.16.0 documentation

# Calculate local entropy pro

Distribution of per-atom local entropy values in a nanocrystalline palladium microstructure

This is a Python-based modifier function computing the local pair entropy fingerprint of each particle as described in:

> P.M. Piaggi and M. Parrinello,
> Entropy based fingerprint for local crystalline order,
> J. Chem. Phys. 147, 114112 (2017)
> https://doi.org/10.1063/1.4998408

The modifier function stores the computed pair entropy values, which are always negative, in the output particle property `Entropy`. Lower entropy values correspond to more ordered structural environments. The modifier function does not take into account the types of the input particles; it assumes the model is a single-component system.

The calculation algorithm follows closely the C++ implementation of the compute entropy/atom command of the LAMMPS MD code. The meaning of the input parameters of the modifier is the same as for the LAMMPS command.

## Parameters

Cutoff

  Cutoff distance for the \(g(r)\) calculation.

Sigma

  Width of Gaussians used in the \(g(r)\) smoothing.

Use local density

  Use the local density around each atom to normalize the \(g(r)\).

Compute average

  Average the pair entropy values over neighbors.

Average cutoff

  Cutoff distance for the averaging over neighbors.

See also

Source code of this modifier function