compute msd command — LAMMPS 15 May 2015 version documentation

# compute msd command

## Syntax

    compute ID group-ID msd keyword values ...

- ID, group-ID are documented in compute command
- msd = 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
    compute 1 upper msd com yes

## Description

Define a computation that calculates the mean-squared displacement (MSD) of the group of atoms, including all effects due to atoms passing thru periodic boundaries. For computation of the non-Gaussian parameter of mean-squared displacement, see the compute msd/nongauss command.

A vector of four quantites is calculated by this compute. The first 3 elements of the vector are the squared dx,dy,dz displacements, summed and averaged over atoms in the group. The 4th element is the total squared displacement, i.e. (dx*dx + dy*dy + dz*dz), summed and averaged over atoms in the group.

The slope of the mean-squared displacement (MSD) versus time is proportional to the diffusion coefficient of the diffusing atoms.

The displacement of an atom is from its original position at the time the compute command was issued. The value of the displacement will be 0.0 for atoms not in the specified compute group.

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 xhe displacment of each atom is calcluated.

Warning

Initial coordinates are stored in “unwrapped” form, by using the image flags associated with each atom. See the dump custom command for a discussion of “unwrapped” coordinates. See the Atoms section of the read_data command for a discussion of image flags and how they are set for each atom. You can reset the image flags (e.g. to 0) before invoking this compute by using the set image command.

Warning

If you want the quantities calculated by this compute to be continuous when running from a restart file, then you should use the same ID for this compute, as in the original run. This is so that the fix this compute creates to store per-atom quantities will also have the same ID, and thus be initialized correctly with time=0 atom coordinates from the restart file.

Output info:

This compute calculates a global vector of length 4, which can be accessed by indices 1-4 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 vector values will be in distance^2 units.

## Restrictions

> none

## Related commands

compute msd/nongauss, compute displace_atom, fix store/state, compute msd/chunk

## Default

The option default is com = no.