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<li>fix rigid command</li>
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<div class="section" id="fix-rigid-command">
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<span id="index-0"></span><h1>fix rigid command</h1>
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</div>
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<div class="section" id="fix-rigid-nve-command">
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<h1>fix rigid/nve command</h1>
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</div>
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<div class="section" id="fix-rigid-nvt-command">
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<h1>fix rigid/nvt command</h1>
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</div>
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<div class="section" id="fix-rigid-npt-command">
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<h1>fix rigid/npt command</h1>
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</div>
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<div class="section" id="fix-rigid-nph-command">
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<h1>fix rigid/nph command</h1>
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</div>
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<div class="section" id="fix-rigid-small-command">
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<h1>fix rigid/small command</h1>
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</div>
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<div class="section" id="fix-rigid-nve-small-command">
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<h1>fix rigid/nve/small command</h1>
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</div>
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<div class="section" id="fix-rigid-nvt-small-command">
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<h1>fix rigid/nvt/small command</h1>
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</div>
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<div class="section" id="fix-rigid-npt-small-command">
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<h1>fix rigid/npt/small command</h1>
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</div>
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<div class="section" id="fix-rigid-nph-small-command">
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<h1>fix rigid/nph/small command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">bodystyle</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
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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"><span class="doc">fix</span></a> command</li>
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<li>style = <em>rigid</em> or <em>rigid/nve</em> or <em>rigid/nvt</em> or <em>rigid/npt</em> or <em>rigid/nph</em> or <em>rigid/small</em> or <em>rigid/nve/small</em> or <em>rigid/nvt/small</em> or <em>rigid/npt/small</em> or <em>rigid/nph/small</em></li>
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<li>bodystyle = <em>single</em> or <em>molecule</em> or <em>group</em></li>
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</ul>
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<pre class="literal-block">
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<em>single</em> args = none
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<em>molecule</em> args = none
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<em>group</em> args = N groupID1 groupID2 ...
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N = # of groups
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groupID1, groupID2, ... = list of N group IDs
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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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<li>keyword = <em>langevin</em> or <em>temp</em> or <em>iso</em> or <em>aniso</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>couple</em> or <em>tparam</em> or <em>pchain</em> or <em>dilate</em> or <em>force</em> or <em>torque</em> or <em>infile</em></li>
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</ul>
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<pre class="literal-block">
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<em>langevin</em> values = Tstart Tstop Tperiod seed
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Tstart,Tstop = desired temperature at start/stop of run (temperature units)
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Tdamp = temperature damping parameter (time units)
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seed = random number seed to use for white noise (positive integer)
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<em>temp</em> values = Tstart Tstop Tdamp
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Tstart,Tstop = desired temperature at start/stop of run (temperature units)
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Tdamp = temperature damping parameter (time units)
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<em>iso</em> or <em>aniso</em> values = Pstart Pstop Pdamp
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Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
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Pdamp = pressure damping parameter (time units)
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<em>x</em> or <em>y</em> or <em>z</em> values = Pstart Pstop Pdamp
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Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
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Pdamp = stress damping parameter (time units)
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<em>couple</em> = <em>none</em> or <em>xyz</em> or <em>xy</em> or <em>yz</em> or <em>xz</em>
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<em>tparam</em> values = Tchain Titer Torder
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Tchain = length of Nose/Hoover thermostat chain
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Titer = number of thermostat iterations performed
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Torder = 3 or 5 = Yoshida-Suzuki integration parameters
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<em>pchain</em> values = Pchain
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Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
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<em>dilate</em> value = dilate-group-ID
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dilate-group-ID = only dilate atoms in this group due to barostat volume changes
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<em>force</em> values = M xflag yflag zflag
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M = which rigid body from 1-Nbody (see asterisk form below)
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xflag,yflag,zflag = off/on if component of center-of-mass force is active
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<em>torque</em> values = M xflag yflag zflag
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M = which rigid body from 1-Nbody (see asterisk form below)
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xflag,yflag,zflag = off/on if component of center-of-mass torque is active
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<em>infile</em> filename
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filename = file with per-body values of mass, center-of-mass, moments of inertia
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<em>mol</em> value = template-ID
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template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command
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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</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="n">clump</span> <span class="n">rigid</span> <span class="n">single</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">clump</span> <span class="n">rigid</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">clump</span> <span class="n">rigid</span> <span class="n">single</span> <span class="n">force</span> <span class="mi">1</span> <span class="n">off</span> <span class="n">off</span> <span class="n">on</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">428984</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">polychains</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nvt</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">5.0</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">polychains</span> <span class="n">rigid</span> <span class="n">molecule</span> <span class="n">force</span> <span class="mi">1</span><span class="o">*</span><span class="mi">5</span> <span class="n">off</span> <span class="n">off</span> <span class="n">off</span> <span class="n">force</span> <span class="mi">6</span><span class="o">*</span><span class="mi">10</span> <span class="n">off</span> <span class="n">off</span> <span class="n">on</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">polychains</span> <span class="n">rigid</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">428984</span>
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<span class="n">fix</span> <span class="mi">2</span> <span class="n">fluid</span> <span class="n">rigid</span> <span class="n">group</span> <span class="mi">3</span> <span class="n">clump1</span> <span class="n">clump2</span> <span class="n">clump3</span> <span class="n">torque</span> <span class="o">*</span> <span class="n">off</span> <span class="n">off</span> <span class="n">off</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">rods</span> <span class="n">rigid</span><span class="o">/</span><span class="n">npt</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">iso</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">10.0</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">particles</span> <span class="n">rigid</span><span class="o">/</span><span class="n">npt</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">5.0</span> <span class="n">x</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">1.0</span> <span class="n">z</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">1.0</span> <span class="n">couple</span> <span class="n">xz</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">water</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nph</span> <span class="n">molecule</span> <span class="n">iso</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="n">particles</span> <span class="n">rigid</span><span class="o">/</span><span class="n">npt</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">temp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="n">iso</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
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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</h2>
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<p>Treat one or more sets of atoms as independent rigid bodies. This
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means that each timestep the total force and torque on each rigid body
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is computed as the sum of the forces and torques on its constituent
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particles. The coordinates, velocities, and orientations of the atoms
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in each body are then updated so that the body moves and rotates as a
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single entity.</p>
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<p>Examples of large rigid bodies are a colloidal particle, or portions
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of a biomolecule such as a protein.</p>
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<p>Example of small rigid bodies are patchy nanoparticles, such as those
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modeled in <a class="reference internal" href="pair_gran.html#zhang"><span class="std std-ref">this paper</span></a> by Sharon Glotzer’s group, clumps of
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granular particles, lipid molecules consiting of one or more point
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dipoles connected to other spheroids or ellipsoids, irregular
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particles built from line segments (2d) or triangles (3d), and
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coarse-grain models of nano or colloidal particles consisting of a
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small number of constituent particles. Note that the <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a> command can also be used to rigidify small
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molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats
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the constituent atoms as point masses.</p>
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<p>These fixes also update the positions and velocities of the atoms in
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each rigid body via time integration, in the NVE, NVT, NPT, or NPH
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ensemble, as described below.</p>
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<p>There are two main variants of this fix, fix rigid and fix
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rigid/small. The NVE/NVT/NPT/NHT versions belong to one of the two
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variants, as their style names indicate.</p>
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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">Not all of the <em>bodystyle</em> options and keyword/value options are
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available for both the <em>rigid</em> and <em>rigid/small</em> variants. See
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details below.</p>
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</div>
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<p>The <em>rigid</em> variant is typically the best choice for a system with a
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small number of large rigid bodies, each of which can extend across
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the domain of many processors. It operates by creating a single
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global list of rigid bodies, which all processors contribute to.
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MPI_Allreduce operations are performed each timestep to sum the
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contributions from each processor to the force and torque on all the
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bodies. This operation will not scale well in parallel if large
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numbers of rigid bodies are simulated.</p>
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<p>The <em>rigid/small</em> variant is typically best for a system with a large
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number of small rigid bodies. Each body is assigned to the atom
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closest to the geometrical center of the body. The fix operates using
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local lists of rigid bodies owned by each processor and information is
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exchanged and summed via local communication between neighboring
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processors when ghost atom info is accumlated.</p>
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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">To use <em>rigid/small</em> the ghost atom cutoff must be large enough
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to span the distance between the atom that owns the body and every
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other atom in the body. This distance value is printed out when the
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rigid bodies are defined. If the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> cutoff
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plus neighbor skin does not span this distance, then you should use
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the <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify cutoff</span></a> command with a setting
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epsilon larger than the distance.</p>
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</div>
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<p>Which of the two variants is faster for a particular problem is hard
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to predict. The best way to decide is to perform a short test run.
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Both variants should give identical numerical answers for short runs.
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Long runs should give statistically similar results, but round-off
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differences may accumulate to produce divergent trajectories.</p>
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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">You should not update the atoms in rigid bodies via other
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time-integration fixes (e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>), or you will be integrating
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their motion more than once each timestep. When performing a hybrid
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simulation with some atoms in rigid bodies, and some not, a separate
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time integration fix like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> should be used for the non-rigid particles.</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">These fixes are overkill if you simply want to hold a collection
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of atoms stationary or have them move with a constant velocity. A
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simpler way to hold atoms stationary is to not include those atoms in
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your time integration fix. E.g. use “fix 1 mobile nve” instead of
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“fix 1 all nve”, where “mobile” is the group of atoms that you want to
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move. You can move atoms with a constant velocity by assigning them
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an initial velocity (via the <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a> command),
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setting the force on them to 0.0 (via the <a class="reference internal" href="fix_setforce.html"><span class="doc">fix setforce</span></a> command), and integrating them as usual
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(e.g. via the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command).</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">The aggregate properties of each rigid body are calculated one
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|
time at the start of the first simulation run after this fix is
|
|
specified. The properties include the position and velocity of the
|
|
center-of-mass of the body, its moments of inertia, and its angular
|
|
momentum. This is done using the properties of the constituent atoms
|
|
of the body at that point in time (or see the <em>infile</em> keyword
|
|
option). Thereafter, changing properties of individual atoms in the
|
|
body will have no effect on a rigid body’s dynamics, unless they
|
|
effect the <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> interactions that individual
|
|
particles are part of. For example, you might think you could
|
|
displace the atoms in a body or add a large velocity to each atom in a
|
|
body to make it move in a desired direction before a 2nd run is
|
|
performed, using the <a class="reference internal" href="set.html"><span class="doc">set</span></a> or
|
|
<a class="reference internal" href="displace_atoms.html"><span class="doc">displace_atoms</span></a> or <a class="reference internal" href="velocity.html"><span class="doc">velocity</span></a>
|
|
command. But these commands will not affect the internal attributes
|
|
of the body, and the position and velocity or individual atoms in the
|
|
body will be reset when time integration starts.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>Each rigid body must have two or more atoms. An atom can belong to at
|
|
most one rigid body. Which atoms are in which bodies can be defined
|
|
via several options.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">With fix rigid/small, which requires bodystyle <em>molecule</em>, you
|
|
can define a system that has no rigid bodies initially. This is
|
|
useful when you are using the <em>mol</em> keyword in conjunction with
|
|
another fix that is adding rigid bodies on-the-fly, such as <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a> or <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>.</p>
|
|
</div>
|
|
<p>For bodystyle <em>single</em> the entire fix group of atoms is treated as one
|
|
rigid body. This option is only allowed for fix rigid and its
|
|
sub-styles.</p>
|
|
<p>For bodystyle <em>molecule</em>, each set of atoms in the fix group with a
|
|
different molecule ID is treated as a rigid body. This option is
|
|
allowed for fix rigid and fix rigid/small, and their sub-styles. Note
|
|
that atoms with a molecule ID = 0 will be treated as a single rigid
|
|
body. For a system with atomic solvent (typically this is atoms with
|
|
molecule ID = 0) surrounding rigid bodies, this may not be what you
|
|
want. Thus you should be careful to use a fix group that only
|
|
includes atoms you want to be part of rigid bodies.</p>
|
|
<p>For bodystyle <em>group</em>, each of the listed groups is treated as a
|
|
separate rigid body. Only atoms that are also in the fix group are
|
|
included in each rigid body. This option is only allowed for fix
|
|
rigid and its sub-styles.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">To compute the initial center-of-mass position and other
|
|
properties of each rigid body, the image flags for each atom in the
|
|
body are used to “unwrap” the atom coordinates. Thus you must insure
|
|
that these image flags are consistent so that the unwrapping creates a
|
|
valid rigid body (one where the atoms are close together),
|
|
particularly if the atoms in a single rigid body straddle a periodic
|
|
boundary. This means the input data file or restart file must define
|
|
the image flags for each atom consistently or that you have used the
|
|
<a class="reference internal" href="set.html"><span class="doc">set</span></a> command to specify them correctly. If a dimension is
|
|
non-periodic then the image flag of each atom must be 0 in that
|
|
dimension, else an error is generated.</p>
|
|
</div>
|
|
<p>The <em>force</em> and <em>torque</em> keywords discussed next are only allowed for
|
|
fix rigid and its sub-styles.</p>
|
|
<p>By default, each rigid body is acted on by other atoms which induce an
|
|
external force and torque on its center of mass, causing it to
|
|
translate and rotate. Components of the external center-of-mass force
|
|
and torque can be turned off by the <em>force</em> and <em>torque</em> keywords.
|
|
This may be useful if you wish a body to rotate but not translate, or
|
|
vice versa, or if you wish it to rotate or translate continuously
|
|
unaffected by interactions with other particles. Note that if you
|
|
expect a rigid body not to move or rotate by using these keywords, you
|
|
must insure its initial center-of-mass translational or angular
|
|
velocity is 0.0. Otherwise the initial translational or angular
|
|
momentum the body has will persist.</p>
|
|
<p>An xflag, yflag, or zflag set to <em>off</em> means turn off the component of
|
|
force of torque in that dimension. A setting of <em>on</em> means turn on
|
|
the component, which is the default. Which rigid body(s) the settings
|
|
apply to is determined by the first argument of the <em>force</em> and
|
|
<em>torque</em> keywords. It can be an integer M from 1 to Nbody, where
|
|
Nbody is the number of rigid bodies defined. A wild-card asterisk can
|
|
be used in place of, or in conjunction with, the M argument to set the
|
|
flags for multiple rigid bodies. This takes the form “*” or “<em>n” or
|
|
“n</em>” or “m*n”. If N = the number of rigid bodies, then an asterisk
|
|
with no numeric values means all bodies from 1 to N. A leading
|
|
asterisk means all bodies from 1 to n (inclusive). A trailing
|
|
asterisk means all bodies from n to N (inclusive). A middle asterisk
|
|
means all types from m to n (inclusive). Note that you can use the
|
|
<em>force</em> or <em>torque</em> keywords as many times as you like. If a
|
|
particular rigid body has its component flags set multiple times, the
|
|
settings from the final keyword are used.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">For computational efficiency, you may wish to turn off pairwise
|
|
and bond interactions within each rigid body, as they no longer
|
|
contribute to the motion. The <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify exclude</span></a> and <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a>
|
|
commands are used to do this. If the rigid bodies have strongly
|
|
overalapping atoms, you may need to turn off these interactions to
|
|
avoid numerical problems due to large equal/opposite intra-body forces
|
|
swamping the contribution of small inter-body forces.</p>
|
|
</div>
|
|
<p>For computational efficiency, you should typically define one fix
|
|
rigid or fix rigid/small command which includes all the desired rigid
|
|
bodies. LAMMPS will allow multiple rigid fixes to be defined, but it
|
|
is more expensive.</p>
|
|
<hr class="docutils" />
|
|
<p>The constituent particles within a rigid body can be point particles
|
|
(the default in LAMMPS) or finite-size particles, such as spheres or
|
|
ellipsoids or line segments or triangles. See the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style sphere and ellipsoid and line and tri</span></a> commands for more
|
|
details on these kinds of particles. Finite-size particles contribute
|
|
differently to the moment of inertia of a rigid body than do point
|
|
particles. Finite-size particles can also experience torque (e.g. due
|
|
to <a class="reference internal" href="pair_gran.html"><span class="doc">frictional granular interactions</span></a>) and have an
|
|
orientation. These contributions are accounted for by these fixes.</p>
|
|
<p>Forces between particles within a body do not contribute to the
|
|
external force or torque on the body. Thus for computational
|
|
efficiency, you may wish to turn off pairwise and bond interactions
|
|
between particles within each rigid body. The <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify exclude</span></a> and <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a>
|
|
commands are used to do this. For finite-size particles this also
|
|
means the particles can be highly overlapped when creating the rigid
|
|
body.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>rigid</em> and <em>rigid/small</em> and <em>rigid/nve</em> styles perform constant
|
|
NVE time integration. The only difference is that the <em>rigid</em> and
|
|
<em>rigid/small</em> styles use an integration technique based on Richardson
|
|
iterations. The <em>rigid/nve</em> style uses the methods described in the
|
|
paper by <a class="reference internal" href="#miller"><span class="std std-ref">Miller</span></a>, which are thought to provide better energy
|
|
conservation than an iterative approach.</p>
|
|
<p>The <em>rigid/nvt</em> and <em>rigid/nvt/small</em> styles performs constant NVT
|
|
integration using a Nose/Hoover thermostat with chains as described
|
|
originally in <a class="reference internal" href="#hoover"><span class="std std-ref">(Hoover)</span></a> and <a class="reference internal" href="#martyna"><span class="std std-ref">(Martyna)</span></a>, which
|
|
thermostats both the translational and rotational degrees of freedom
|
|
of the rigid bodies. The rigid-body algorithm used by <em>rigid/nvt</em>
|
|
is described in the paper by <a class="reference internal" href="#kamberaj"><span class="std std-ref">Kamberaj</span></a>.</p>
|
|
<p>The <em>rigid/npt</em> and <em>rigid/nph</em> (and their /small counterparts) styles
|
|
perform constant NPT or NPH integration using a Nose/Hoover barostat
|
|
with chains. For the NPT case, the same Nose/Hoover thermostat is also
|
|
used as with <em>rigid/nvt</em>.</p>
|
|
<p>The barostat parameters are specified using one or more of the <em>iso</em>,
|
|
<em>aniso</em>, <em>x</em>, <em>y</em>, <em>z</em> and <em>couple</em> keywords. These keywords give you
|
|
the ability to specify 3 diagonal components of the external stress
|
|
tensor, and to couple these components together so that the dimensions
|
|
they represent are varied together during a constant-pressure
|
|
simulation. The effects of these keywords are similar to those
|
|
defined in <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt/nph</span></a></p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Currently the <em>rigid/npt</em> and <em>rigid/nph</em> (and their /small
|
|
counterparts) styles do not support triclinic (non-orthongonal) boxes.</p>
|
|
</div>
|
|
<p>The target pressures for each of the 6 components of the stress tensor
|
|
can be specified independently via the <em>x</em>, <em>y</em>, <em>z</em> keywords, which
|
|
correspond to the 3 simulation box dimensions. For each component,
|
|
the external pressure or tensor component at each timestep is a ramped
|
|
value during the run from <em>Pstart</em> to <em>Pstop</em>. If a target pressure is
|
|
specified for a component, then the corresponding box dimension will
|
|
change during a simulation. For example, if the <em>y</em> keyword is used,
|
|
the y-box length will change. A box dimension will not change if that
|
|
component is not specified, although you have the option to change
|
|
that dimension via the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command.</p>
|
|
<p>For all barostat keywords, the <em>Pdamp</em> parameter operates like the
|
|
<em>Tdamp</em> parameter, determining the time scale on which pressure is
|
|
relaxed. For example, a value of 10.0 means to relax the pressure in
|
|
a timespan of (roughly) 10 time units (e.g. tau or fmsec or psec - see
|
|
the <a class="reference internal" href="units.html"><span class="doc">units</span></a> command).</p>
|
|
<p>Regardless of what atoms are in the fix group (the only atoms which
|
|
are time integrated), a global pressure or stress tensor is computed
|
|
for all atoms. Similarly, when the size of the simulation box is
|
|
changed, all atoms are re-scaled to new positions, unless the keyword
|
|
<em>dilate</em> is specified with a <em>dilate-group-ID</em> for a group that
|
|
represents a subset of the atoms. This can be useful, for example, to
|
|
leave the coordinates of atoms in a solid substrate unchanged and
|
|
controlling the pressure of a surrounding fluid. Another example is a
|
|
system consisting of rigid bodies and point particles where the
|
|
barostat is only coupled with the rigid bodies. This option should be
|
|
used with care, since it can be unphysical to dilate some atoms and
|
|
not others, because it can introduce large, instantaneous
|
|
displacements between a pair of atoms (one dilated, one not) that are
|
|
far from the dilation origin.</p>
|
|
<p>The <em>couple</em> keyword allows two or three of the diagonal components of
|
|
the pressure tensor to be “coupled” together. The value specified
|
|
with the keyword determines which are coupled. For example, <em>xz</em>
|
|
means the <em>Pxx</em> and <em>Pzz</em> components of the stress tensor are coupled.
|
|
<em>Xyz</em> means all 3 diagonal components are coupled. Coupling means two
|
|
things: the instantaneous stress will be computed as an average of the
|
|
corresponding diagonal components, and the coupled box dimensions will
|
|
be changed together in lockstep, meaning coupled dimensions will be
|
|
dilated or contracted by the same percentage every timestep. The
|
|
<em>Pstart</em>, <em>Pstop</em>, <em>Pdamp</em> parameters for any coupled dimensions must
|
|
be identical. <em>Couple xyz</em> can be used for a 2d simulation; the <em>z</em>
|
|
dimension is simply ignored.</p>
|
|
<p>The <em>iso</em> and <em>aniso</em> keywords are simply shortcuts that are
|
|
equivalent to specifying several other keywords together.</p>
|
|
<p>The keyword <em>iso</em> means couple all 3 diagonal components together when
|
|
pressure is computed (hydrostatic pressure), and dilate/contract the
|
|
dimensions together. Using “iso Pstart Pstop Pdamp” is the same as
|
|
specifying these 4 keywords:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
|
|
<span class="n">y</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
|
|
<span class="n">z</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
|
|
<span class="n">couple</span> <span class="n">xyz</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>The keyword <em>aniso</em> means <em>x</em>, <em>y</em>, and <em>z</em> dimensions are controlled
|
|
independently using the <em>Pxx</em>, <em>Pyy</em>, and <em>Pzz</em> components of the
|
|
stress tensor as the driving forces, and the specified scalar external
|
|
pressure. Using “aniso Pstart Pstop Pdamp” is the same as specifying
|
|
these 4 keywords:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
|
|
<span class="n">y</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
|
|
<span class="n">z</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
|
|
<span class="n">couple</span> <span class="n">none</span>
|
|
</pre></div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>The keyword/value option pairs are used in the following ways.</p>
|
|
<p>The <em>langevin</em> and <em>temp</em> and <em>tparam</em> keywords perform thermostatting
|
|
of the rigid bodies, altering both their translational and rotational
|
|
degrees of freedom. What is meant by “temperature” of a collection of
|
|
rigid bodies and how it can be monitored via the fix output is
|
|
discussed below.</p>
|
|
<p>The <em>langevin</em> keyword applies a Langevin thermostat to the constant
|
|
NVE time integration performed by either the <em>rigid</em> or <em>rigid/small</em>
|
|
or <em>rigid/nve</em> styles. It cannot be used with the <em>rigid/nvt</em> style.
|
|
The desired temperature at each timestep is a ramped value during the
|
|
run from <em>Tstart</em> to <em>Tstop</em>. The <em>Tdamp</em> parameter is specified in
|
|
time units and determines how rapidly the temperature is relaxed. For
|
|
example, a value of 100.0 means to relax the temperature in a timespan
|
|
of (roughly) 100 time units (tau or fmsec or psec - see the
|
|
<a class="reference internal" href="units.html"><span class="doc">units</span></a> command). The random # <em>seed</em> must be a positive
|
|
integer.</p>
|
|
<p>The way that Langevin thermostatting operates is explained on the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> doc page. If you wish to simply viscously
|
|
damp the rotational motion without thermostatting, you can set
|
|
<em>Tstart</em> and <em>Tstop</em> to 0.0, which means only the viscous drag term in
|
|
the Langevin thermostat will be applied. See the discussion on the
|
|
<a class="reference internal" href="fix_viscous.html"><span class="doc">fix viscous</span></a> doc page for details.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">When the <em>langevin</em> keyword is used with fix rigid versus fix
|
|
rigid/small, different dynamics will result for parallel runs. This
|
|
is because of the way random numbers are used in the two cases. The
|
|
dynamics for the two cases should be statistically similar, but will
|
|
not be identical, even for a single timestep.</p>
|
|
</div>
|
|
<p>The <em>temp</em> and <em>tparam</em> keywords apply a Nose/Hoover thermostat to the
|
|
NVT time integration performed by the <em>rigid/nvt</em> style. They cannot
|
|
be used with the <em>rigid</em> or <em>rigid/small</em> or <em>rigid/nve</em> styles. The
|
|
desired temperature at each timestep is a ramped value during the run
|
|
from <em>Tstart</em> to <em>Tstop</em>. The <em>Tdamp</em> parameter is specified in time
|
|
units and determines how rapidly the temperature is relaxed. For
|
|
example, a value of 100.0 means to relax the temperature in a timespan
|
|
of (roughly) 100 time units (tau or fmsec or psec - see the
|
|
<a class="reference internal" href="units.html"><span class="doc">units</span></a> command).</p>
|
|
<p>Nose/Hoover chains are used in conjunction with this thermostat. The
|
|
<em>tparam</em> keyword can optionally be used to change the chain settings
|
|
used. <em>Tchain</em> is the number of thermostats in the Nose Hoover chain.
|
|
This value, along with <em>Tdamp</em> can be varied to dampen undesirable
|
|
oscillations in temperature that can occur in a simulation. As a rule
|
|
of thumb, increasing the chain length should lead to smaller
|
|
oscillations. The keyword <em>pchain</em> specifies the number of
|
|
thermostats in the chain thermostatting the barostat degrees of
|
|
freedom.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">There are alternate ways to thermostat a system of rigid bodies.
|
|
You can use <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> to treat the individual
|
|
particles in the rigid bodies as effectively immersed in an implicit
|
|
solvent, e.g. a Brownian dynamics model. For hybrid systems with both
|
|
rigid bodies and solvent particles, you can thermostat only the
|
|
solvent particles that surround one or more rigid bodies by
|
|
appropriate choice of groups in the compute and fix commands for
|
|
temperature and thermostatting. The solvent interactions with the
|
|
rigid bodies should then effectively thermostat the rigid body
|
|
temperature as well without use of the Langevin or Nose/Hoover options
|
|
associated with the fix rigid commands.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>The <em>mol</em> keyword can only be used with fix rigid/small. It must be
|
|
used when other commands, such as <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a> or
|
|
<a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>, add rigid bodies on-the-fly during a
|
|
simulation. You specify a <em>template-ID</em> previously defined using the
|
|
<a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command, which reads a file that defines the
|
|
molecule. You must use the same <em>template-ID</em> that the other fix
|
|
which is adding rigid bodies uses. The coordinates, atom types, atom
|
|
diameters, center-of-mass, and moments of inertia can be specified in
|
|
the molecule file. See the <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command for
|
|
details. The only settings required to be in this file are the
|
|
coordinates and types of atoms in the molecule, in which case the
|
|
molecule command calculates the other quantities itself.</p>
|
|
<p>Note that these other fixes create new rigid bodies, in addition to
|
|
those defined initially by this fix via the <em>bodystyle</em> setting.</p>
|
|
<p>Also note that when using the <em>mol</em> keyword, extra restart information
|
|
about all rigid bodies is written out whenever a restart file is
|
|
written out. See the NOTE in the next section for details.</p>
|
|
<hr class="docutils" />
|
|
<p>The <em>infile</em> keyword allows a file of rigid body attributes to be read
|
|
in from a file, rather then having LAMMPS compute them. There are 5
|
|
such attributes: the total mass of the rigid body, its center-of-mass
|
|
position, its 6 moments of inertia, its center-of-mass velocity, and
|
|
the 3 image flags of the center-of-mass position. For rigid bodies
|
|
consisting of point particles or non-overlapping finite-size
|
|
particles, LAMMPS can compute these values accurately. However, for
|
|
rigid bodies consisting of finite-size particles which overlap each
|
|
other, LAMMPS will ignore the overlaps when computing these 4
|
|
attributes. The amount of error this induces depends on the amount of
|
|
overlap. To avoid this issue, the values can be pre-computed
|
|
(e.g. using Monte Carlo integration).</p>
|
|
<p>The format of the file is as follows. Note that the file does not
|
|
have to list attributes for every rigid body integrated by fix rigid.
|
|
Only bodies which the file specifies will have their computed
|
|
attributes overridden. The file can contain initial blank lines or
|
|
comment lines starting with “#” which are ignored. The first
|
|
non-blank, non-comment line should list N = the number of lines to
|
|
follow. The N successive lines contain the following information:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">ID1</span> <span class="n">masstotal</span> <span class="n">xcm</span> <span class="n">ycm</span> <span class="n">zcm</span> <span class="n">ixx</span> <span class="n">iyy</span> <span class="n">izz</span> <span class="n">ixy</span> <span class="n">ixz</span> <span class="n">iyz</span> <span class="n">vxcm</span> <span class="n">vycm</span> <span class="n">vzcm</span> <span class="n">lx</span> <span class="n">ly</span> <span class="n">lz</span> <span class="n">ixcm</span> <span class="n">iycm</span> <span class="n">izcm</span>
|
|
<span class="n">ID2</span> <span class="n">masstotal</span> <span class="n">xcm</span> <span class="n">ycm</span> <span class="n">zcm</span> <span class="n">ixx</span> <span class="n">iyy</span> <span class="n">izz</span> <span class="n">ixy</span> <span class="n">ixz</span> <span class="n">iyz</span> <span class="n">vxcm</span> <span class="n">vycm</span> <span class="n">vzcm</span> <span class="n">lx</span> <span class="n">ly</span> <span class="n">lz</span> <span class="n">ixcm</span> <span class="n">iycm</span> <span class="n">izcm</span>
|
|
<span class="o">...</span>
|
|
<span class="n">IDN</span> <span class="n">masstotal</span> <span class="n">xcm</span> <span class="n">ycm</span> <span class="n">zcm</span> <span class="n">ixx</span> <span class="n">iyy</span> <span class="n">izz</span> <span class="n">ixy</span> <span class="n">ixz</span> <span class="n">iyz</span> <span class="n">vxcm</span> <span class="n">vycm</span> <span class="n">vzcm</span> <span class="n">lx</span> <span class="n">ly</span> <span class="n">lz</span> <span class="n">ixcm</span> <span class="n">iycm</span> <span class="n">izcm</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>The rigid body IDs are all positive integers. For the <em>single</em>
|
|
bodystyle, only an ID of 1 can be used. For the <em>group</em> bodystyle,
|
|
IDs from 1 to Ng can be used where Ng is the number of specified
|
|
groups. For the <em>molecule</em> bodystyle, use the molecule ID for the
|
|
atoms in a specific rigid body as the rigid body ID.</p>
|
|
<p>The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are
|
|
self-explanatory. The center-of-mass should be consistent with what
|
|
is calculated for the position of the rigid body with all its atoms
|
|
unwrapped by their respective image flags. If this produces a
|
|
center-of-mass that is outside the simulation box, LAMMPS wraps it
|
|
back into the box.</p>
|
|
<p>The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
|
|
values consistent with the current orientation of the rigid body
|
|
around its center of mass. The values are with respect to the
|
|
simulation box XYZ axes, not with respect to the prinicpal axes of the
|
|
rigid body itself. LAMMPS performs the latter calculation internally.</p>
|
|
<p>The (vxcm,vycm,vzcm) values are the velocity of the center of mass.
|
|
The (lx,ly,lz) values are the angular momentum of the body. The
|
|
(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you
|
|
wish the body to have no initial motion.</p>
|
|
<p>The (ixcm,iycm,izcm) values are the image flags of the center of mass
|
|
of the body. For periodic dimensions, they specify which image of the
|
|
simulation box the body is considered to be in. An image of 0 means
|
|
it is inside the box as defined. A value of 2 means add 2 box lengths
|
|
to get the true value. A value of -1 means subtract 1 box length to
|
|
get the true value. LAMMPS updates these flags as the rigid bodies
|
|
cross periodic boundaries during the simulation.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">If you use the <em>infile</em> or <em>mol</em> keywords and write restart
|
|
files during a simulation, then each time a restart file is written,
|
|
the fix also write an auxiliary restart file with the name
|
|
rfile.rigid, where “rfile” is the name of the restart file,
|
|
e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary
|
|
file is in the same format described above. Thus it can be used in a
|
|
new input script that restarts the run and re-specifies a rigid fix
|
|
using an <em>infile</em> keyword and the appropriate filename. Note that the
|
|
auxiliary file will contain one line for every rigid body, even if the
|
|
original file only listed a subset of the rigid bodies.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p>If you use a <a class="reference internal" href="compute.html"><span class="doc">temperature compute</span></a> with a group that
|
|
includes particles in rigid bodies, the degrees-of-freedom removed by
|
|
each rigid body are accounted for in the temperature (and pressure)
|
|
computation, but only if the temperature group includes all the
|
|
particles in a particular rigid body.</p>
|
|
<p>A 3d rigid body has 6 degrees of freedom (3 translational, 3
|
|
rotational), except for a collection of point particles lying on a
|
|
straight line, which has only 5, e.g a dimer. A 2d rigid body has 3
|
|
degrees of freedom (2 translational, 1 rotational).</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">You may wish to explicitly subtract additional
|
|
degrees-of-freedom if you use the <em>force</em> and <em>torque</em> keywords to
|
|
eliminate certain motions of one or more rigid bodies. LAMMPS does
|
|
not do this automatically.</p>
|
|
</div>
|
|
<p>The rigid body contribution to the pressure of the system (virial) is
|
|
also accounted for by this fix.</p>
|
|
<hr class="docutils" />
|
|
<p>If your simlulation is a hybrid model with a mixture of rigid bodies
|
|
and non-rigid particles (e.g. solvent) there are several ways these
|
|
rigid fixes can be used in tandem with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, and <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
|
|
<p>If you wish to perform NVE dynamics (no thermostatting or
|
|
barostatting), use fix rigid or fix rigid/nve to integrate the rigid
|
|
bodies, and <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to integrate the non-rigid
|
|
particles.</p>
|
|
<p>If you wish to perform NVT dynamics (thermostatting, but no
|
|
barostatting), you can use fix rigid/nvt for the rigid bodies, and any
|
|
thermostatting fix for the non-rigid particles (<a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>,
|
|
<a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, <a class="reference internal" href="fix_temp_berendsen.html"><span class="doc">fix temp/berendsen</span></a>). You can also use fix rigid
|
|
or fix rigid/nve for the rigid bodies and thermostat them using <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> on the group that contains all the
|
|
particles in the rigid bodies. The net force added by <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> to each rigid body effectively thermostats
|
|
its translational center-of-mass motion. Not sure how well it does at
|
|
thermostatting its rotational motion.</p>
|
|
<p>If you with to perform NPT or NPH dynamics (barostatting), you cannot
|
|
use both <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> and fix rigid/npt (or the nph
|
|
variants). This is because there can only be one fix which monitors
|
|
the global pressure and changes the simulation box dimensions. So you
|
|
have 3 choices:</p>
|
|
<ul class="simple">
|
|
<li>Use fix rigid/npt for the rigid bodies. Use the <em>dilate</em> all option
|
|
so that it will dilate the positions of the non-rigid particles as
|
|
well. Use <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> (or any other thermostat) for the
|
|
non-rigid particles.</li>
|
|
<li>Use <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> for the group of non-rigid particles. Use
|
|
the <em>dilate</em> all option so that it will dilate the center-of-mass
|
|
positions of the rigid bodies as well. Use fix rigid/nvt for the
|
|
rigid bodies.</li>
|
|
<li>Use <a class="reference internal" href="fix_press_berendsen.html"><span class="doc">fix press/berendsen</span></a> to compute the
|
|
pressure and change the box dimensions. Use fix rigid/nvt for the
|
|
rigid bodies. Use <a class="reference external" href="fix_nh.thml">fix nvt</a> (or any other thermostat) for
|
|
the non-rigid particles.</li>
|
|
</ul>
|
|
<p>In all case, the rigid bodies and non-rigid particles both contribute
|
|
to the global pressure and the box is scaled the same by any of the
|
|
barostatting fixes.</p>
|
|
<p>You could even use the 2nd and 3rd options for a non-hybrid simulation
|
|
consisting of only rigid bodies, assuming you give <a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> an empty group, though it’s an odd thing to do. The
|
|
barostatting fixes (<a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a> and <a class="reference internal" href="fix_press_berendsen.html"><span class="doc">fix press/berensen</span></a>) will monitor the pressure
|
|
and change the box dimensions, but not time integrate any particles.
|
|
The integration of the rigid bodies will be performed by fix
|
|
rigid/nvt.</p>
|
|
<hr class="docutils" />
|
|
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
|
|
functionally the same as the corresponding style without the suffix.
|
|
They have been optimized to run faster, depending on your available
|
|
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a>
|
|
of the manual. The accelerated styles take the same arguments and
|
|
should produce the same results, except for round-off and precision
|
|
issues.</p>
|
|
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
|
|
KOKKOS, USER-OMP and OPT packages, respectively. They are only
|
|
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
|
<p>You can specify the accelerated styles explicitly in your input script
|
|
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
|
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
|
|
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
|
|
more instructions on how to use the accelerated styles effectively.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
|
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
|
<p>No information about the <em>rigid</em> and <em>rigid/small</em> and <em>rigid/nve</em>
|
|
fixes are written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. The
|
|
exception is if the <em>infile</em> or <em>mol</em> keyword is used, in which case
|
|
an auxiliary file is written out with rigid body information each time
|
|
a restart file is written, as explained above for the <em>infile</em>
|
|
keyword. For style <em>rigid/nvt</em> the state of the Nose/Hoover
|
|
thermostat is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the
|
|
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify
|
|
a fix in an input script that reads a restart file, so that the
|
|
operation of the fix continues in an uninterrupted fashion.</p>
|
|
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by the
|
|
rigid/nvt fix to add the energy change induced by the thermostatting
|
|
to the system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
|
|
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> and <em>press</em> options are
|
|
supported by the rigid/npt and rigid/nph fixes to change the computes used
|
|
to calculate the instantaneous pressure tensor. Note that the rigid/nvt fix
|
|
does not use any external compute to compute instantaneous temperature.</p>
|
|
<p>The <em>rigid</em> and <em>rigid/small</em> and <em>rigid/nve</em> fixes compute a global
|
|
scalar which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar value calculated by
|
|
these fixes is “intensive”. The scalar is the current temperature of
|
|
the collection of rigid bodies. This is averaged over all rigid
|
|
bodies and their translational and rotational degrees of freedom. The
|
|
translational energy of a rigid body is 1/2 m v^2, where m = total
|
|
mass of the body and v = the velocity of its center of mass. The
|
|
rotational energy of a rigid body is 1/2 I w^2, where I = the moment
|
|
of inertia tensor of the body and w = its angular velocity. Degrees
|
|
of freedom constrained by the <em>force</em> and <em>torque</em> keywords are
|
|
removed from this calculation, but only for the <em>rigid</em> and
|
|
<em>rigid/nve</em> fixes.</p>
|
|
<p>The <em>rigid/nvt</em>, <em>rigid/npt</em>, and <em>rigid/nph</em> fixes compute a global
|
|
scalar which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar value calculated by
|
|
these fixes is “extensive”. The scalar is the cumulative energy
|
|
change due to the thermostatting and barostatting the fix performs.</p>
|
|
<p>All of the <em>rigid</em> fixes except <em>rigid/small</em> compute a global array
|
|
of values which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The number of rows in the
|
|
array is equal to the number of rigid bodies. The number of columns
|
|
is 15. Thus for each rigid body, 15 values are stored: the xyz coords
|
|
of the center of mass (COM), the xyz components of the COM velocity,
|
|
the xyz components of the force acting on the COM, the xyz components
|
|
of the torque acting on the COM, and the xyz image flags of the COM.</p>
|
|
<p>The center of mass (COM) for each body is similar to unwrapped
|
|
coordinates written to a dump file. It will always be inside (or
|
|
slightly outside) the simulation box. The image flags have the same
|
|
meaning as image flags for atom positions (see the “dump” command).
|
|
This means you can calculate the unwrapped COM by applying the image
|
|
flags to the COM, the same as when unwrapped coordinates are written
|
|
to a dump file.</p>
|
|
<p>The force and torque values in the array are not affected by the
|
|
<em>force</em> and <em>torque</em> keywords in the fix rigid command; they reflect
|
|
values before any changes are made by those keywords.</p>
|
|
<p>The ordering of the rigid bodies (by row in the array) is as follows.
|
|
For the <em>single</em> keyword there is just one rigid body. For the
|
|
<em>molecule</em> keyword, the bodies are ordered by ascending molecule ID.
|
|
For the <em>group</em> keyword, the list of group IDs determines the ordering
|
|
of bodies.</p>
|
|
<p>The array values calculated by these fixes are “intensive”, meaning
|
|
they are independent of the number of atoms in the simulation.</p>
|
|
<p>No parameter of these fixes can be used with the <em>start/stop</em> keywords
|
|
of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. These fixes are not invoked during
|
|
<a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>These fixes are all part of the RIGID package. It is only enabled if
|
|
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
|
<p>Assigning a temperature via the <a class="reference internal" href="velocity.html"><span class="doc">velocity create</span></a>
|
|
command to a system with <a class="reference internal" href="#"><span class="doc">rigid bodies</span></a> may not have
|
|
the desired outcome for two reasons. First, the velocity command can
|
|
be invoked before the rigid-body fix is invoked or initialized and the
|
|
number of adjusted degrees of freedom (DOFs) is known. Thus it is not
|
|
possible to compute the target temperature correctly. Second, the
|
|
assigned velocities may be partially canceled when constraints are
|
|
first enforced, leading to a different temperature than desired. A
|
|
workaround for this is to perform a <a class="reference internal" href="run.html"><span class="doc">run 0</span></a> command, which
|
|
insures all DOFs are accounted for properly, and then rescale the
|
|
temperature to the desired value before performing a simulation. For
|
|
example:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">velocity</span> <span class="nb">all</span> <span class="n">create</span> <span class="mf">300.0</span> <span class="mi">12345</span>
|
|
<span class="n">run</span> <span class="mi">0</span> <span class="c1"># temperature may not be 300K</span>
|
|
<span class="n">velocity</span> <span class="nb">all</span> <span class="n">scale</span> <span class="mf">300.0</span> <span class="c1"># now it should be</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a>, <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify</span></a>
|
|
exclude, <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are force * on on on and torque * on on on,
|
|
meaning all rigid bodies are acted on by center-of-mass force and
|
|
torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3.</p>
|
|
<hr class="docutils" />
|
|
<p id="hoover"><strong>(Hoover)</strong> Hoover, Phys Rev A, 31, 1695 (1985).</p>
|
|
<p id="kamberaj"><strong>(Kamberaj)</strong> Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).</p>
|
|
<p id="martyna"><strong>(Martyna)</strong> Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992);
|
|
Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.</p>
|
|
<p id="miller"><strong>(Miller)</strong> Miller, Eleftheriou, Pattnaik, Ndirango, and Newns,
|
|
J Chem Phys, 116, 8649 (2002).</p>
|
|
<p id="zhang"><strong>(Zhang)</strong> Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
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