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<title>angle_style mesocnt command — LAMMPS documentation</title>
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<li class="toctree-l2"><a class="reference internal" href="angle_amoeba.html">angle_style amoeba command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_charmm.html">angle_style charmm command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_class2.html">angle_style class2 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_class2.html#angle-style-class2-p6-command">angle_style class2/p6 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_cosine.html">angle_style cosine command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_cosine_buck6d.html">angle_style cosine/buck6d command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_cosine_delta.html">angle_style cosine/delta command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_cosine_periodic.html">angle_style cosine/periodic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_cosine_shift.html">angle_style cosine/shift command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_cosine_shift_exp.html">angle_style cosine/shift/exp command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_cosine_squared.html">angle_style cosine/squared command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_cosine_squared_restricted.html">angle_style cosine/squared/restricted command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_cross.html">angle_style cross command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_dipole.html">angle_style dipole command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_fourier.html">angle_style fourier command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_fourier_simple.html">angle_style fourier/simple command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_gaussian.html">angle_style gaussian command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_harmonic.html">angle_style harmonic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_hybrid.html">angle_style hybrid command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_lepton.html">angle_style lepton command</a></li>
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<li class="toctree-l2 current"><a class="current reference internal" href="#">angle_style mesocnt command</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#related-commands">Related commands</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
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</ul>
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</li>
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<li class="toctree-l2"><a class="reference internal" href="angle_mm3.html">angle_style mm3 command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_none.html">angle_style none command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_quartic.html">angle_style quartic command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_spica.html">angle_style spica command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_table.html">angle_style table command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="angle_zero.html">angle_style zero command</a></li>
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</ul>
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<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
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<li class="breadcrumb-item active">angle_style mesocnt command</li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="angle-style-mesocnt-command">
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<span id="index-0"></span><h1>angle_style mesocnt command<a class="headerlink" href="#angle-style-mesocnt-command" title="Link to this heading"></a></h1>
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<section id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Link to this heading"></a></h2>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">angle_style</span><span class="w"> </span><span class="n">mesocnt</span>
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</pre></div>
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</div>
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</section>
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<section id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Link to this heading"></a></h2>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">angle_style</span><span class="w"> </span><span class="n">mesocnt</span>
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<span class="k">angle_coeff</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">buckling</span><span class="w"> </span><span class="n">C</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">20.0</span>
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<span class="k">angle_coeff</span><span class="w"> </span><span class="m">4</span><span class="w"> </span><span class="n">harmonic</span><span class="w"> </span><span class="n">C</span><span class="w"> </span><span class="m">8</span><span class="w"> </span><span class="m">4</span><span class="w"> </span><span class="m">10.0</span>
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<span class="k">angle_coeff</span><span class="w"> </span><span class="m">2</span><span class="w"> </span><span class="n">buckling</span><span class="w"> </span><span class="n">custom</span><span class="w"> </span><span class="m">400.0</span><span class="w"> </span><span class="m">50.0</span><span class="w"> </span><span class="m">5.0</span>
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<span class="k">angle_coeff</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">harmonic</span><span class="w"> </span><span class="n">custom</span><span class="w"> </span><span class="m">300.0</span>
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</pre></div>
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</div>
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</section>
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<section id="description">
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<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
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<div class="versionadded">
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<p><span class="versionmodified added">Added in version 15Sep2022.</span></p>
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</div>
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<p>The <em>mesocnt</em> angle style uses the potential</p>
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<div class="math notranslate nohighlight">
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\[\begin{split}E = K_\text{H} \Delta \theta^2, \qquad |\Delta \theta| < \Delta
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\theta_\text{B} \\
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E = K_\text{H} \Delta \theta_\text{B}^2 +
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K_\text{B} (\Delta \theta - \Delta \theta_\text{B}), \qquad |\Delta
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\theta| \geq \Delta \theta_\text{B}\end{split}\]</div>
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<p>where <span class="math notranslate nohighlight">\(\Delta \theta = \theta - \pi\)</span> is the bending angle of the
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nanotube, <span class="math notranslate nohighlight">\(K_\text{H}\)</span> and <span class="math notranslate nohighlight">\(K_\text{B}\)</span> are prefactors for
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the harmonic and linear regime respectively and <span class="math notranslate nohighlight">\(\Delta
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\theta_\text{B}\)</span> is the buckling angle. Note that the usual 1/2 factor
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for the harmonic potential is included in <span class="math notranslate nohighlight">\(K_\text{H}\)</span>.</p>
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<p>The style implements parameterization presets of <span class="math notranslate nohighlight">\(K_\text{H}\)</span>,
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<span class="math notranslate nohighlight">\(K_\text{B}\)</span> and <span class="math notranslate nohighlight">\(\Delta \theta_\text{B}\)</span> for mesoscopic
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simulations of carbon nanotubes based on the atomistic simulations of
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<a class="reference internal" href="#srivastava-2"><span class="std std-ref">(Srivastava)</span></a> and buckling considerations of
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<a class="reference internal" href="#zhigilei1-1"><span class="std std-ref">(Zhigilei)</span></a>.</p>
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<p>The following coefficients must be defined for each angle type via the
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<a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a> command as in the examples above, or
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in the data file or restart files read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> commands:</p>
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<ul class="simple">
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<li><p>mode = <em>buckling</em> or <em>harmonic</em></p></li>
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<li><p>preset = <em>C</em> or <em>custom</em></p></li>
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<li><p>additional parameters depending on preset</p></li>
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</ul>
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<p>If mode <em>harmonic</em> is chosen, the potential is simply harmonic and
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does not switch to the linear term when the buckling angle is
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reached. In <em>buckling</em> mode, the full piecewise potential is used.</p>
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<p>Preset <em>C</em> is for carbon nanotubes, and the additional parameters are:</p>
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<ul class="simple">
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<li><p>chiral index <span class="math notranslate nohighlight">\(n\)</span> (unitless)</p></li>
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<li><p>chiral index <span class="math notranslate nohighlight">\(m\)</span> (unitless)</p></li>
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<li><p><span class="math notranslate nohighlight">\(r_0\)</span> (distance)</p></li>
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</ul>
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<p>Here, <span class="math notranslate nohighlight">\(r_0\)</span> is the equilibrium distance of the bonds included in
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the angle, see <a class="reference internal" href="bond_mesocnt.html"><span class="doc">bond_style mesocnt</span></a>.</p>
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<p>In harmonic mode with preset <em>custom</em>, the additional parameter is:</p>
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<ul class="simple">
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<li><p><span class="math notranslate nohighlight">\(K_\text{H}\)</span> (energy)</p></li>
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</ul>
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<p>Hence, this setting is simply a wrapper for <a class="reference internal" href="bond_harmonic.html"><span class="doc">bond_style harmonic</span></a> with an equilibrium angle of 180 degrees.</p>
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<p>In harmonic mode with preset <em>custom</em>, the additional parameters are:</p>
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<ul class="simple">
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<li><p><span class="math notranslate nohighlight">\(K_\text{H}\)</span> (energy)</p></li>
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<li><p><span class="math notranslate nohighlight">\(K_\text{B}\)</span> (energy)</p></li>
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<li><p><span class="math notranslate nohighlight">\(\Delta \theta_\text{B}\)</span> (degrees)</p></li>
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</ul>
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<p><span class="math notranslate nohighlight">\(\Delta \theta_\text{B}\)</span> is specified in degrees, but LAMMPS
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converts it to radians internally; hence <span class="math notranslate nohighlight">\(K_\text{H}\)</span> is
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effectively energy per radian^2 and <span class="math notranslate nohighlight">\(K_\text{B}\)</span> is energy per
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radian.</p>
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<hr class="docutils" />
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<p>In <em>buckling</em> mode, this angle style adds the <em>buckled</em> property to
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all atoms in the simulation, which is an integer flag indicating
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whether the bending angle at a given atom has exceeded <span class="math notranslate nohighlight">\(\Delta
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\theta_\text{B}\)</span>. It can be accessed as an atomic variable, e.g. for
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custom dump commands, as <em>i_buckled</em>.</p>
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<div class="admonition note">
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<p class="admonition-title">Note</p>
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<p>If the initial state of the simulation contains buckled nanotubes
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and <a class="reference internal" href="pair_mesocnt.html"><span class="doc">pair_style mesocnt</span></a> is used, the
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<em>i_buckled</em> atomic variable needs to be initialized before the
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pair_style is defined by doing a <em>run 0</em> command straight after the
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angle_style command. See below for an example.</p>
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</div>
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<p>If CNTs are already buckled at the start of the simulation, this
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script will correctly initialize <em>i_buckled</em>:</p>
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<div class="highlight-LAMMPS notranslate"><div class="highlight"><pre><span></span><span class="k">angle_style</span><span class="w"> </span><span class="n">mesocnt</span>
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<span class="k">angle_coeff</span><span class="w"> </span><span class="m">1</span><span class="w"> </span><span class="n">buckling</span><span class="w"> </span><span class="n">C</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">10</span><span class="w"> </span><span class="m">20.0</span>
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<span class="k">run</span><span class="w"> </span><span class="m">0</span>
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<span class="k">pair_style</span><span class="w"> </span><span class="n">mesocnt</span><span class="w"> </span><span class="m">60.0</span>
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<span class="k">pair_coeff</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="n">C_10_10.mesocnt</span><span class="w"> </span><span class="m">1</span>
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</pre></div>
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</div>
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</section>
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|
<section id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Link to this heading"></a></h2>
|
|
<p>This angle style can only be used if LAMMPS was built with the
|
|
MOLECULE and MESONT packages. See the <a class="reference internal" href="Build_package.html"><span class="doc">Build package</span></a> doc page for more info.</p>
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</section>
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|
<section id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Link to this heading"></a></h2>
|
|
<p><a class="reference internal" href="angle_coeff.html"><span class="doc">angle_coeff</span></a></p>
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</section>
|
|
<section id="default">
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<h2>Default<a class="headerlink" href="#default" title="Link to this heading"></a></h2>
|
|
<p>none</p>
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|
<hr class="docutils" />
|
|
<p id="srivastava-2"><strong>(Srivastava)</strong> Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417
|
|
(2005).</p>
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<p id="zhigilei1-1"><strong>(Zhigilei)</strong> Volkov and Zhigilei, ACS Nano 4, 6187 (2010).</p>
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