Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/_sources/compute_displace_atom.txt
9cf43f2a0b7flammm-master

Last Change
Raw File

compute_displace_atom.txt
View Options

.. index:: compute displace/atom
compute displace/atom command
=============================
Syntax
""""""
.. parsed-literal::
compute ID group-ID displace/atom
* ID, group-ID are documented in :doc:`compute <compute>` command
* displace/atom = style name of this compute command
Examples
""""""""
.. parsed-literal::
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. The value of the displacement will be
0.0 for atoms not in the specified compute group.
.. note::
Initial coordinates are stored in "unwrapped" form, by using the
image flags associated with each atom. See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
See the Atoms section of the :doc:`read_data <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 :doc:`set image <set>` command.
.. note::
If you want the quantities calculated by this compute to be
continuous when running from a :doc:`restart file <read_restart>`, 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 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 :ref:`Section_howto 15 <howto_15>` for an overview of LAMMPS output
options.
The per-atom array values will be in distance :doc:`units <units>`.
Restrictions
""""""""""""
none
Related commands
""""""""""""""""
:doc:`compute msd <compute_msd>`, :doc:`dump custom <dump>`, :doc:`fix store/state <fix_store_state>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
c4science · Help