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<li>displace_atoms command</li>
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<div class="section" id="displace-atoms-command">
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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>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>displace_atoms group-ID style args keyword value ...
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</pre></div>
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</div>
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<ul class="simple">
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<li>group-ID = ID of group of atoms to displace</li>
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<li>style = <em>move</em> or <em>ramp</em> or <em>random</em> or <em>rotate</em></li>
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</ul>
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<pre class="literal-block">
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<em>move</em> args = delx dely delz
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delx,dely,delz = distance to displace in each dimension (distance units)
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any of delx,dely,delz can be a variable (see below)
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<em>ramp</em> args = ddim dlo dhi dim clo chi
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ddim = <em>x</em> or <em>y</em> or <em>z</em>
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dlo,dhi = displacement distance between dlo and dhi (distance units)
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dim = <em>x</em> or <em>y</em> or <em>z</em>
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clo,chi = lower and upper bound of domain to displace (distance units)
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<em>random</em> args = dx dy dz seed
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dx,dy,dz = random displacement magnitude in each dimension (distance units)
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seed = random # seed (positive integer)
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<em>rotate</em> args = Px Py Pz Rx Ry Rz theta
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Px,Py,Pz = origin point of axis of rotation (distance units)
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Rx,Ry,Rz = axis of rotation vector
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theta = angle of rotation (degrees)
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</pre>
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<ul class="simple">
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<li>zero or more keyword/value pairs may be appended</li>
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</ul>
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<pre class="literal-block">
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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>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>displace_atoms top move 0 -5 0 units box
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displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<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
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on a lattice. For example, in a shear simulation, an initial strain
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can be imposed on the system. Or two groups of atoms can be brought
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into closer proximity.</p>
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<p>The <em>move</em> style displaces the group of atoms by the specified 3d
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displacement vector. Any of the 3 quantities defining the vector
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components can be specified as an equal-style or atom-style
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<a class="reference internal" href="variable.html"><em>variable</em></a>. If the value is a variable, it should be
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specified as v_name, where name is the variable name. In this case,
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the variable will be evaluated, and its value(s) used for the
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displacement(s). The scale factor implied by the <em>units</em> keyword will
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also be applied to the variable result.</p>
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<p>Equal-style variables can specify formulas with various mathematical
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functions, and include <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command
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keywords for the simulation box parameters and timestep and elapsed
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time. Atom-style variables can specify the same formulas as
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equal-style variables but can also include per-atom values, such as
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atom coordinates or per-atom values read from a file. Note that if
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the variable references other <a class="reference internal" href="compute.html"><em>compute</em></a> or <a class="reference internal" href="fix.html"><em>fix</em></a>
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commands, those values must be up-to-date for the current timestep.
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See the “Variable Accuracy” section of the <a class="reference internal" href="variable.html"><em>variable</em></a>
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doc page for more details.</p>
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<p>The <em>ramp</em> style displaces atoms a variable amount in one dimension
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depending on the atom’s coordinate in a (possibly) different
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dimension. For example, the second example command displaces atoms in
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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>
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<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
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+dx in the x dimension, and similarly for y and z. Random numbers are
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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>
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<p>The <em>rotate</em> style rotates each atom in the group by the angle <em>theta</em>
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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
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rotation axis is consistent with the right-hand rule: if your
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right-hand thumb points along <em>R</em>, then your fingers wrap around the
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axis in the direction of positive theta.</p>
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<p>If the defined <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> assigns an orientation to
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each atom (<a class="reference internal" href="atom_style.html"><em>atom styles</em></a> ellipsoid, line, tri, body),
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then that property is also updated appropriately to correspond to the
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atom’s rotation.</p>
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<p>Distance units for displacements and the origin point of the <em>rotate</em>
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style are determined by the setting of <em>box</em> or <em>lattice</em> for the
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<em>units</em> keyword. <em>Box</em> means distance units as defined by the
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<a class="reference internal" href="units.html"><em>units</em></a> command - e.g. Angstroms for <em>real</em> units.
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<em>Lattice</em> means distance units are in lattice spacings. The
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<a class="reference internal" href="lattice.html"><em>lattice</em></a> command must have been previously used to
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define the lattice spacing.</p>
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<hr class="docutils" />
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Care should be taken not to move atoms on top of other atoms.
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After the move, atoms are remapped into the periodic simulation box if
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needed, and any shrink-wrap boundary conditions (see the
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<a class="reference internal" href="boundary.html"><em>boundary</em></a> command) are enforced which may change the
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box size. Other than this effect, this command does not change the
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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>
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</div>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Atoms can be moved arbitrarily long distances by this command.
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If the simulation box is non-periodic and shrink-wrapped (see the
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<a class="reference internal" href="boundary.html"><em>boundary</em></a> command), this can change its size or shape.
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This is not a problem, except that the mapping of processors to the
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simulation box is not changed by this command from its initial 3d
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configuration; see the <a class="reference internal" href="processors.html"><em>processors</em></a> command. Thus, if
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the box size/shape changes dramatically, the mapping of processors to
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the simulation box may not end up as optimal as the initial mapping
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attempted to be.</p>
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</div>
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</div>
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<hr class="docutils" />
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>You cannot rotate around any rotation vector except the z-axis for a
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2d simulation.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<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>,
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<a class="reference internal" href="fix_move.html"><em>fix_move</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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<p>The option defaults are units = lattice.</p>
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