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displace_atoms.txt
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.. 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)
any of delx,dely,delz can be a variable (see below)
*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 (positive integer)
*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
displacement vector. Any of the 3 quantities defining the vector
components can be specified as an equal-style or atom-style
:doc:`variable <variable>`. If the value is a variable, it should be
specified as v_name, where name is the variable name. In this case,
the variable will be evaluated, and its value(s) used for the
displacement(s). The scale factor implied by the *units* keyword will
also be applied to the variable result.
Equal-style variables can specify formulas with various mathematical
functions, and include :doc:`thermo_style <thermo_style>` command
keywords for the simulation box parameters and timestep and elapsed
time. Atom-style variables can specify the same formulas as
equal-style variables but can also include per-atom values, such as
atom coordinates or per-atom values read from a file. Note that if
the variable references other :doc:`compute <compute>` or :doc:`fix <fix>`
commands, those values must be up-to-date for the current timestep.
See the "Variable Accuracy" section of the :doc:`variable <variable>`
doc page for more details.
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 thumb points along *R*, then your fingers wrap around the
axis in the direction of positive theta.
If the defined :doc:`atom_style <atom_style>` assigns an orientation to
each atom (:doc:`atom styles <atom_style>` ellipsoid, line, tri, body),
then that property is also updated appropriately to correspond to the
atom's rotation.
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.
----------
.. note::
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.
.. note::
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.
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm
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