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### 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 the displacment of each atom is calcluated.

IMPORTANT NOTE: 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.

IMPORTANT NOTE: If an atom is part of a rigid body (see the fix rigid command), it's periodic image flags are altered, and its contribution to the MSD may not reflect its true contribution. See the fix rigid command for details. Thus, to compute the MSD of rigid bodies as they cross periodic boundaries, you will need to post-process a dump file containing coordinates of the atoms in the bodies.

IMPORTANT NOTE: 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 created fix will also have the same ID, and thus be initialized correctly with 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 LIGGGHTS(R)-PUBLIC 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/molecule

Default:

The option default is com = no.