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displace_atoms command
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LAMMPS 15 May 2015 version documentation
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displace_atoms command
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<div
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<span
id=
"index-0"
></span><h1>
displace_atoms command
<a
class=
"headerlink"
href=
"#displace-atoms-command"
title=
"Permalink to this headline"
>
¶
</a></h1>
<div
class=
"section"
id=
"syntax"
>
<h2>
Syntax
<a
class=
"headerlink"
href=
"#syntax"
title=
"Permalink to this headline"
>
¶
</a></h2>
<div
class=
"highlight-python"
><div
class=
"highlight"
><pre>
displace_atoms group-ID style args keyword value ...
</pre></div>
</div>
<ul
class=
"simple"
>
<li>
group-ID = ID of group of atoms to displace
</li>
<li>
style =
<em>
move
</em>
or
<em>
ramp
</em>
or
<em>
random
</em>
or
<em>
rotate
</em></li>
</ul>
<pre
class=
"literal-block"
>
<em>
move
</em>
args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units)
<em>
ramp
</em>
args = ddim dlo dhi dim clo chi
ddim =
<em>
x
</em>
or
<em>
y
</em>
or
<em>
z
</em>
dlo,dhi = displacement distance between dlo and dhi (distance units)
dim =
<em>
x
</em>
or
<em>
y
</em>
or
<em>
z
</em>
clo,chi = lower and upper bound of domain to displace (distance units)
<em>
random
</em>
args = dx dy dz seed
dx,dy,dz = random displacement magnitude in each dimension (distance units)
seed = random # seed (positive integer)
<em>
rotate
</em>
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)
</pre>
<ul
class=
"simple"
>
<li>
zero or more keyword/value pairs may be appended
</li>
</ul>
<pre
class=
"literal-block"
>
keyword =
<em>
units
</em>
value =
<em>
box
</em>
or
<em>
lattice
</em>
</pre>
</div>
<div
class=
"section"
id=
"examples"
>
<h2>
Examples
<a
class=
"headerlink"
href=
"#examples"
title=
"Permalink to this headline"
>
¶
</a></h2>
<div
class=
"highlight-python"
><div
class=
"highlight"
><pre>
displace_atoms top move 0 -5 0 units box
displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5
</pre></div>
</div>
</div>
<div
class=
"section"
id=
"description"
>
<h2>
Description
<a
class=
"headerlink"
href=
"#description"
title=
"Permalink to this headline"
>
¶
</a></h2>
<p>
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.
</p>
<p>
The
<em>
move
</em>
style displaces the group of atoms by the specified 3d
distance.
</p>
<p>
The
<em>
ramp
</em>
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.
</p>
<p>
The
<em>
random
</em>
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.
</p>
<p>
The
<em>
rotate
</em>
style rotates each atom in the group by the angle
<em>
theta
</em>
around a rotation axis
<em>
R
</em>
= (Rx,Ry,Rz) that goes thru a point
<em>
P
</em>
=
(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
<em>
R
</em>
, then your fingers wrap around the
axis in the direction of positive theta.
</p>
<p>
Distance units for displacements and the origin point of the
<em>
rotate
</em>
style are determined by the setting of
<em>
box
</em>
or
<em>
lattice
</em>
for the
<em>
units
</em>
keyword.
<em>
Box
</em>
means distance units as defined by the
<a
class=
"reference internal"
href=
"units.html"
><em>
units
</em></a>
command - e.g. Angstroms for
<em>
real
</em>
units.
<em>
Lattice
</em>
means distance units are in lattice spacings. The
<a
class=
"reference internal"
href=
"lattice.html"
><em>
lattice
</em></a>
command must have been previously used to
define the lattice spacing.
</p>
<hr
class=
"docutils"
/>
<div
class=
"admonition warning"
>
<p
class=
"first admonition-title"
>
Warning
</p>
<p
class=
"last"
>
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
<a
class=
"reference internal"
href=
"boundary.html"
><em>
boundary
</em></a>
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
<a
class=
"reference internal"
href=
"change_box.html"
><em>
change_box
</em></a>
command if that effect is desired.
</p>
</div>
<div
class=
"admonition warning"
>
<p
class=
"first admonition-title"
>
Warning
</p>
<p
class=
"last"
>
Atoms can be moved arbitrarily long distances by this
command. If the simulation box is non-periodic and shrink-wrapped
(see the
<a
class=
"reference internal"
href=
"boundary.html"
><em>
boundary
</em></a>
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
<a
class=
"reference internal"
href=
"processors.html"
><em>
processors
</em></a>
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.
</p>
</div>
</div>
<hr
class=
"docutils"
/>
<div
class=
"section"
id=
"restrictions"
>
<h2>
Restrictions
<a
class=
"headerlink"
href=
"#restrictions"
title=
"Permalink to this headline"
>
¶
</a></h2>
<p>
You cannot rotate around any rotation vector except the z-axis for a
2d simulation.
</p>
</div>
<div
class=
"section"
id=
"related-commands"
>
<h2>
Related commands
<a
class=
"headerlink"
href=
"#related-commands"
title=
"Permalink to this headline"
>
¶
</a></h2>
<p><a
class=
"reference internal"
href=
"lattice.html"
><em>
lattice
</em></a>
,
<a
class=
"reference internal"
href=
"change_box.html"
><em>
change_box
</em></a>
,
<a
class=
"reference internal"
href=
"fix_move.html"
><em>
fix_move
</em></a></p>
</div>
<div
class=
"section"
id=
"default"
>
<h2>
Default
<a
class=
"headerlink"
href=
"#default"
title=
"Permalink to this headline"
>
¶
</a></h2>
<p>
The option defaults are units = lattice.
</p>
</div>
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