lammps/doc/compute_displace_atom.txt

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compute displace/atom command :h3

[Syntax:]

compute ID group-ID displace/atom :pre

ID, group-ID are documented in "compute"_compute.html command
displace/atom = style name of this compute command :ul

[Examples:]

compute 1 all displace/atom :pre

[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 are calculated by this compute.
The first 3 elements of the cector are the dx,dy,dz displacements.
The 4th component is the total displacement, i.e. sqrt(dx*dx + dy*dy +
dz*dz).

To store the original coordinates at the time this compute is issued,
the compute creates its own fix of style "coord/original", as if this
command had been issued:

fix compute-ID_coord_original group-ID coord/original :pre

See the "fix coord/original"_fix_coord_original.html command for
details.  Note that the ID of the new fix is the compute-ID +
underscore + "coord_original", 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 coord/original stores the initial coordinates in
"unwrapped" form, by using the image flags associated with each atom.
See the "dump custom"_dump.html command for a discussion of
"unwrapped" coordinates.  See the Atoms section of the
"read_data"_read_data.html 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"_set.html command.

IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix
rigid"_fix_rigid.html command), it's periodic image flags are altered,
and the computed MSD will not reflect its true displacement.  See the
"fix rigid"_fix_rigid.html 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"_dump.html 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"_read_restart.html,
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 vector of length 4 for each atom, which can
be accessed by indices 1-4 by any command that uses per-atom computes
as input.  See "this section"_Section_howto.html#4_15 for an overview
of LAMMPS output options.

[Restrictions:] none

[Related commands:]

"compute msd"_compute_msd.html, "dump custom"_dump.html, "fix
coord/original"_fix_coord_original.html

[Default:] none