.. index:: displace_atoms

displace_atoms command
======================

Syntax
""""""

.. parsed-literal::

   displace_atoms group-ID style args keyword value ...

* group-ID = ID of group of atoms to displace
* style = *move* or *ramp* or *random* or *rotate*
.. parsed-literal::

     *move* args = delx dely delz
       delx,dely,delz = distance to displace in each dimension (distance units)
     *ramp* args = ddim dlo dhi dim clo chi
       ddim = *x* or *y* or *z*
       dlo,dhi = displacement distance between dlo and dhi (distance units)
       dim = *x* or *y* or *z*
       clo,chi = lower and upper bound of domain to displace (distance units)
     *random* args = dx dy dz seed
       dx,dy,dz = random displacement magnitude in each dimension (distance units)
       seed = random # seed (prime number greater 10000)
     *rotate* args = Px Py Pz Rx Ry Rz theta
       Px,Py,Pz = origin point of axis of rotation (distance units)
       Rx,Ry,Rz = axis of rotation vector
       theta = angle of rotation (degrees)

* zero or more keyword/value pairs may be appended
.. parsed-literal::

     keyword = *units*
       value = *box* or *lattice*



Examples
""""""""

.. parsed-literal::

   displace_atoms top move 0 -5 0 units box
   displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5

Description
"""""""""""

Displace a group of atoms.  This can be used to move atoms a large
distance before beginning a simulation or to randomize atoms initially
on a lattice.  For example, in a shear simulation, an initial strain
can be imposed on the system.  Or two groups of atoms can be brought
into closer proximity.

The *move* style displaces the group of atoms by the specified 3d
distance.

The *ramp* style displaces atoms a variable amount in one dimension
depending on the atom's coordinate in a (possibly) different
dimension.  For example, the second example command displaces atoms in
the x-direction an amount between 0.0 and 5.0 distance units.  Each
atom's displacement depends on the fractional distance its y
coordinate is between 2.0 and 20.5.  Atoms with y-coordinates outside
those bounds will be moved the minimum (0.0) or maximum (5.0) amount.

The *random* style independently moves each atom in the group by a
random displacement, uniformly sampled from a value between -dx and
+dx in the x dimension, and similarly for y and z.  Random numbers are
used in such a way that the displacement of a particular atom is the
same, regardless of how many processors are being used.

The *rotate* style rotates each atom in the group by the angle *theta*
around a rotation axis *R* = (Rx,Ry,Rz) that goes thru a point *P* =
(Px,Py,Pz).  The direction of rotation for the atoms around the
rotation axis is consistent with the right-hand rule: if your
right-hand's thumb points along *R*, then your fingers wrap around the
axis in the direction of positive theta.

Distance units for displacements and the origin point of the *rotate*
style are determined by the setting of *box* or *lattice* for the
*units* keyword.  *Box* means distance units as defined by the
:doc:`units <units>` command - e.g. Angstroms for *real* units.
*Lattice* means distance units are in lattice spacings.  The
:doc:`lattice <lattice>` command must have been previously used to
define the lattice spacing.


----------


.. warning::

   Care should be taken not to move atoms on top of other
   atoms.  After the move, atoms are remapped into the periodic
   simulation box if needed, and any shrink-wrap boundary conditions (see
   the :doc:`boundary <boundary>` command) are enforced which may change
   the box size.  Other than this effect, this command does not change
   the size or shape of the simulation box.  See the
   :doc:`change_box <change_box>` command if that effect is desired.

.. warning::

   Atoms can be moved arbitrarily long distances by this
   command.  If the simulation box is non-periodic and shrink-wrapped
   (see the :doc:`boundary <boundary>` command), this can change its size
   or shape.  This is not a problem, except that the mapping of
   processors to the simulation box is not changed by this command from
   its initial 3d configuration; see the :doc:`processors <processors>`
   command.  Thus, if the box size/shape changes dramatically, the
   mapping of processors to the simulation box may not end up as optimal
   as the initial mapping attempted to be.


----------


Restrictions
""""""""""""


You cannot rotate around any rotation vector except the z-axis for a
2d simulation.

Related commands
""""""""""""""""

:doc:`lattice <lattice>`, :doc:`change_box <change_box>`,
:doc:`fix_move <fix_move>`

Default
"""""""

The option defaults are units = lattice.


.. _liws: http://www.cfdem.com
.. _ld: Manual.html
.. _lc: Section_commands.html#comm