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### compute displace/atom command

Syntax:

    compute ID group-ID displace/atom

- ID, group-ID are documented in compute command
- displace/atom = style name of this compute command

Examples:

    compute 1 all displace/atom

Description:

Define a computation that calculates the current displacement of each atom in the group from its original coordinates, including all effects due to atoms passing thru periodic boundaries.

A vector of four quantites per atom is calculated by this compute. The first 3 elements of the vector are the dx,dy,dz displacements. The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy + dz*dz).

The displacement of an atom is from its original position at the time the compute command was issued. To store the original coordinates, the compute creates its own fix of style "store/state", as if this command had been issued:

    fix compute-ID_store_state group-ID store/state xu yu zu

See the fix store/state command for details. Note that the ID of the new fix is the compute-ID + underscore + "store/state", and the group for the new fix is the same as the compute group.

The value of the displacement will be 0.0 for atoms not in the specified compute group.

IMPORTANT NOTE: Fix store/state stores the initial coordinates 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 the computed displacement may not reflect its true displacement. See the fix rigid command for details. Thus, to compute the displacement 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 per-atom array with 4 columns, which can be accessed by indices 1-4 by any command that uses per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output options.

The per-atom array values will be in distance units.

Restrictions: none

Related commands:

compute msd, dump custom, fix store/state

Default: none