compute msd/nongauss command

Syntax

compute ID group-ID msd/nongauss keyword values ...
  • ID, group-ID are documented in compute command

  • msd/nongauss = style name of this compute command

  • zero or more keyword/value pairs may be appended

  • keyword = com

    com value = yes or no
    

Examples

compute 1 all msd/nongauss
compute 1 upper msd/nongauss com yes

Description

Define a computation that calculates the mean-squared displacement (MSD) and non-Gaussian parameter (NGP) of the group of atoms, including all effects due to atoms passing thru periodic boundaries.

A vector of three quantities is calculated by this compute. The first element of the vector is the total squared dx,dy,dz displacements drsquared = (dx*dx + dy*dy + dz*dz) of atoms, and the second is the fourth power of these displacements drfourth = (dx*dx + dy*dy + dz*dz)*(dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the group. The 3rd component is the nonGaussian diffusion parameter NGP = 3*drfourth/(5*drsquared*drsquared), i.e.

_images/compute_msd_nongauss.jpg

The NGP is a commonly used quantity in studies of dynamical heterogeneity. Its minimum theoretical value (-0.4) occurs when all atoms have the same displacement magnitude. NGP=0 for Brownian diffusion, while NGP > 0 when some mobile atoms move faster than others.

If the com option is set to yes then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the displacment of each atom is calculated.

See the compute msd doc page for further important NOTEs, which also apply to this compute.

Output info:

This compute calculates a global vector of length 3, which can be accessed by indices 1-3 by any command that uses global vector values from a compute as input. See this section for an overview of LAMMPS output options.

The vector values are “intensive”. The first vector value will be in distance^2 units, the second is in distance^4 units, and the 3rd is dimensionless.

Restrictions

This compute is part of the MISC package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

Default

The option default is com = no.