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<title>fix recenter command — LAMMPS 15 May 2015 version documentation</title>
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<li>fix recenter command</li>
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<div class="section" id="fix-recenter-command">
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<span id="index-0"></span><h1>fix recenter command<a class="headerlink" href="#fix-recenter-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>fix ID group-ID recenter x y z 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>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
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<li>recenter = style name of this fix command</li>
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<li>x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below)</li>
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>shift</em> or <em>units</em></li>
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</ul>
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<pre class="literal-block">
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<em>shift</em> value = group-ID
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group-ID = group of atoms whose coords are shifted
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<em>units</em> value = <em>box</em> or <em>lattice</em> or <em>fraction</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>fix 1 all recenter 0.0 0.5 0.0
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fix 1 all recenter INIT INIT NULL
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fix 1 all recenter INIT 0.0 0.0 units box
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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>Constrain the center-of-mass position of a group of atoms by adjusting
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the coordinates of the atoms every timestep. This is simply a small
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shift that does not alter the dynamics of the system or change the
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relative coordinates of any pair of atoms in the group. This can be
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used to insure the entire collection of atoms (or a portion of them)
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do not drift during the simulation due to random perturbations
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(e.g. <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a> thermostatting).</p>
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<p>Distance units for the x,y,z values are determined by the setting of
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the <em>units</em> keyword, as discussed below. One or more x,y,z values can
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also be specified as NULL, which means exclude that dimension from
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this operation. Or it can be specified as INIT which means to
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constrain the center-of-mass to its initial value at the beginning of
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the run.</p>
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<p>The center-of-mass (COM) is computed for the group specified by the
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fix. If the current COM is different than the specified x,y,z, then a
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group of atoms has their coordinates shifted by the difference. By
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default the shifted group is also the group specified by the fix. A
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different group can be shifted by using the <em>shift</em> keyword. For
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example, the COM could be computed on a protein to keep it in the
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center of the simulation box. But the entire system (protein + water)
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could be shifted.</p>
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<p>If the <em>units</em> keyword is set to <em>box</em>, then the distance units of
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x,y,z are defined by the <a class="reference internal" href="units.html"><em>units</em></a> command - e.g. Angstroms
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for <em>real</em> units. A <em>lattice</em> value means the distance units are in
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lattice spacings. The <a class="reference internal" href="lattice.html"><em>lattice</em></a> command must have been
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previously used to define the lattice spacing. A <em>fraction</em> value
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means a fractional distance between the lo/hi box boundaries, e.g. 0.5
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= middle of the box. The default is to use lattice units.</p>
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<p>Note that the <a class="reference internal" href="velocity.html"><em>velocity</em></a> command can be used to create
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velocities with zero aggregate linear and/or angular momentum.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">This fix performs its operations at the same point in
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the timestep as other time integration fixes, such as <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>, or <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>.
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Thus fix recenter should normally be the last such fix specified in
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the input script, since the adjustments it makes to atom coordinates
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should come after the changes made by time integration. LAMMPS will
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warn you if your fixes are not ordered this way.</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">If you use this fix on a small group of atoms (e.g. a
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molecule in solvent) without using the <em>shift</em> keyword to adjust the
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positions of all atoms in the system, then the results can be
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unpredictable. For example, if the molecule is pushed in one
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direction by the solvent, its velocity will increase. But its
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coordinates will be recentered, meaning it is pushed back towards the
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force. Thus over time, the velocity and temperature of the molecule
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could become very large (though it won’t appear to be moving due to
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the recentering). If you are thermostatting the entire system, then
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the solvent would be cooled to compensate. A better solution for this
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simulation scenario is to use the <a class="reference internal" href="fix_spring.html"><em>fix spring</em></a> command
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to tether the molecule in place.</p>
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</div>
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</div>
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<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
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<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
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are relevant to this fix.</p>
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<p>This fix computes a global scalar which can be accessed by various
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<a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The scalar is the
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distance the group is moved by fix recenter.</p>
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<p>This fix also computes global 3-vector which can be accessed by
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various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The 3
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quantities in the vector are xyz components of displacement applied to
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the group of atoms by the fix.</p>
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<p>The scalar and vector values calculated by this fix are “extensive”.</p>
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<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
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the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
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</div>
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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>This fix should not be used with an x,y,z setting that causes a large
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shift in the system on the 1st timestep, due to the requested COM
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being very different from the initial COM. This could cause atoms to
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be lost, especially in parallel. Instead, use the
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<a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a> command, which can be used to
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move atoms a large distance.</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="fix_momentum.html"><em>fix momentum</em></a>, <a class="reference internal" href="velocity.html"><em>velocity</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 shift = fix group-ID, and units = lattice.</p>
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