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< title > displace_atoms command — LAMMPS 15 May 2015 version documentation< / title >
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
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< li > displace_atoms command< / li >
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< div class = "section" id = "displace-atoms-command" >
< 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 >
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< 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
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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)
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< / pre >
< ul class = "simple" >
< li > zero or more keyword/value pairs may be appended< / li >
< / ul >
< pre class = "literal-block" >
keyword = < em > units< / em >
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value = < em > box< / em > or < em > lattice< / em >
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< / pre >
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< 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
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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
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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
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dimension. For example, the second example command displaces atoms in
the x-direction an amount between 0.0 and 5.0 distance units. Each
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atom’ s displacement depends on the fractional distance its y
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coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside
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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
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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
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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 > =
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(Px,Py,Pz). The direction of rotation for the atoms around the
rotation axis is consistent with the right-hand rule: if your
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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
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atoms. After the move, atoms are remapped into the periodic
simulation box if needed, and any shrink-wrap boundary conditions (see
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the < a class = "reference internal" href = "boundary.html" > < em > boundary< / em > < / a > command) are enforced which may change
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the box size. Other than this effect, this command does not change
the size or shape of the simulation box. See the
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< 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
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command. If the simulation box is non-periodic and shrink-wrapped
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(see the < a class = "reference internal" href = "boundary.html" > < em > boundary< / em > < / a > command), this can change its size
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or shape. This is not a problem, except that the mapping of
processors to the simulation box is not changed by this command from
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its initial 3d configuration; see the < a class = "reference internal" href = "processors.html" > < em > processors< / em > < / a >
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command. Thus, if the box size/shape changes dramatically, the
mapping of processors to the simulation box may not end up as optimal
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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 >
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