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<title>fix poems — LAMMPS 15 May 2015 version documentation</title>
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<div class="section" id="fix-poems">
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<h1>fix poems<a class="headerlink" href="#fix-poems" title="Permalink to this headline">¶</a></h1>
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<p>Syntax:</p>
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<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID poems keyword values
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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>poems = style name of this fix command</li>
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<li>keyword = <em>group</em> or <em>file</em> or <em>molecule</em></li>
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</ul>
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<pre class="literal-block">
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<em>group</em> values = list of group IDs
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<em>molecule</em> values = none
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<em>file</em> values = filename
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</pre>
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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 3 fluid poems group clump1 clump2 clump3
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fix 3 fluid poems file cluster.list
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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>Treats one or more sets of atoms as coupled rigid bodies. This means
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that each timestep the total force and torque on each rigid body is
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computed and the coordinates and velocities of the atoms are updated
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so that the collection of bodies move as a coupled set. This can be
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useful for treating a large biomolecule as a collection of connected,
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coarse-grained particles.</p>
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<p>The coupling, associated motion constraints, and time integration is
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performed by the software package <a class="reference external" href="http://www.rpi.edu/~anderk5/lab">Parallelizable Open source Efficient Multibody Software (POEMS)</a> which computes the
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constrained rigid-body motion of articulated (jointed) multibody
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systems <a class="reference internal" href="#anderson"><span>(Anderson)</span></a>. POEMS was written and is distributed
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by Prof Kurt Anderson, his graduate student Rudranarayan Mukherjee,
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and other members of his group at Rensselaer Polytechnic Institute
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(RPI). Rudranarayan developed the LAMMPS/POEMS interface. For
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copyright information on POEMS and other details, please refer to the
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documents in the poems directory distributed with LAMMPS.</p>
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<p>This fix updates the positions and velocities of the rigid atoms with
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a constant-energy time integration, so you should not update the same
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atoms via other fixes (e.g. nve, nvt, npt, temp/rescale, langevin).</p>
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<p>Each body must have a non-degenerate inertia tensor, which means if
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must contain at least 3 non-collinear atoms. Which atoms are in which
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bodies can be defined via several options.</p>
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<p>For option <em>group</em>, each of the listed groups is treated as a rigid
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body. Note that only atoms that are also in the fix group are
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included in each rigid body.</p>
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<p>For option <em>molecule</em>, each set of atoms in the group with a different
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molecule ID is treated as a rigid body.</p>
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<p>For option <em>file</em>, sets of atoms are read from the specified file and
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each set is treated as a rigid body. Each line of the file specifies
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a rigid body in the following format:</p>
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<p>ID type atom1-ID atom2-ID atom3-ID ...</p>
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<p>ID as an integer from 1 to M (the number of rigid bodies). Type is
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any integer; it is not used by the fix poems command. The remaining
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arguments are IDs of atoms in the rigid body, each typically from 1 to
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N (the number of atoms in the system). Only atoms that are also in
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the fix group are included in each rigid body. Blank lines and lines
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that begin with ‘#’ are skipped.</p>
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<p>A connection between a pair of rigid bodies is inferred if one atom is
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common to both bodies. The POEMS solver treats that atom as a
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spherical joint with 3 degrees of freedom. Currently, a collection of
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bodies can only be connected by joints as a linear chain. The entire
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collection of rigid bodies can represent one or more chains. Other
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connection topologies (tree, ring) are not allowed, but will be added
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later. Note that if no joints exist, it is more efficient to use the
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<a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command to simulate the system.</p>
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<p>When the poems fix is defined, it will print out statistics on the
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total # of clusters, bodies, joints, atoms involved. A cluster in
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this context means a set of rigid bodies connected by joints.</p>
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<p>For computational efficiency, you should turn off pairwise and bond
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interactions within each rigid body, as they no longer contribute to
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the motion. The “neigh_modify exclude” and “delete_bonds” commands
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can be used to do this if each rigid body is a group.</p>
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<p>For computational efficiency, you should only define one fix poems
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which includes all the desired rigid bodies. LAMMPS will allow
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multiple poems fixes to be defined, but it is more expensive.</p>
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<p>The degrees-of-freedom removed by coupled rigid bodies are accounted
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for in temperature and pressure computations. Similarly, the rigid
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body contribution to the pressure virial is also accounted for. The
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latter is only correct if forces within the bodies have been turned
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off, and there is only a single fix poems defined.</p>
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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. No global or per-atom quantities are stored
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by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. No parameter of this fix can
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be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command.
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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 is part of the POEMS package. It is only enabled if LAMMPS
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was built with that package, which also requires the POEMS library be
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built and linked with LAMMPS. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</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_rigid.html"><em>fix rigid</em></a>, <a class="reference internal" href="delete_bonds.html"><em>delete_bonds</em></a>,
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<a class="reference internal" href="neigh_modify.html"><em>neigh_modify</em></a> exclude</p>
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<p><strong>Default:</strong> none</p>
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<hr class="docutils" />
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<p id="anderson"><strong>(Anderson)</strong> Anderson, Mukherjee, Critchley, Ziegler, and Lipton
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“POEMS: Parallelizable Open-source Efficient Multibody Software ”,
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Engineering With Computers (2006). (<a class="reference external" href="http://dx.doi.org/10.1007/s00366-006-0026-x">link to paper</a>)</p>
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