more typesetting corrections in docs indicated by sphinx warnings

<li><a class="reference internal" href="#eff"><span class="std std-ref">eff</span></a></li>

<li><a class="reference internal" href="#emacs"><span class="std std-ref">emacs</span></a></li>

<li><a class="reference internal" href="#fep"><span class="std std-ref">fep</span></a></li>

<li><a class="reference internal" href="fix_ipi.html#ipi"><span class="std std-ref">i-pi</span></a></li>

<li><a class="reference internal" href="#ipi"><span class="std std-ref">i-pi</span></a></li>

<li><a class="reference internal" href="#ipp"><span class="std std-ref">ipp</span></a></li>

<li><a class="reference internal" href="#kate"><span class="std std-ref">kate</span></a></li>

<li><a class="reference internal" href="#arc"><span class="std std-ref">lmp2arc</span></a></li>

<div class="section" id="description">

<h2>Description</h2>

<p>Define a computation that returns the coordinates of the vertices

corresponding to the triangle-elements of a mesh created by the <a href="#id4"><span class="problematic" id="id5">`fix smd/wall\_surface &lt;ls_&gt;`_</span></a>.</p>

corresponding to the triangle-elements of a mesh created by the <a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">fix smd/wall_surface</span></a>.</p>

<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth

Mach Dynamics in LAMMPS.</p>

<p><strong>Output info:</strong></p>

(x3/y3/z3) corresponding to the first, second, and third vertex of

each triangle.</p>

<p>It is only meaningful to use this compute for a group of particles

which is created via the <a href="#id6"><span class="problematic" id="id7">`fix smd/wall\_surface &lt;ls_&gt;`_</span></a> command.</p>

which is created via the <a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">fix smd/wall_surface</span></a> command.</p>

<p>The output of this compute can be used with the dump2vtk_tris tool to

generate a VTK representation of the smd/wall_surace mesh for

generate a VTK representation of the smd/wall_surface mesh for

visualization purposes.</p>

<p>The values will be given in <a class="reference internal" href="units.html"><span class="doc">units</span></a> of distance.</p>

</div>

</div>

<div class="section" id="related-commands">

<h2>Related commands</h2>

<p><a class="reference internal" href="fix_smd_move_triangulated_surface.html"><span class="doc">compute smd/move/tri/surf</span></a>,

<a href="#id8"><span class="problematic" id="id9">`compute smd/wall/surface &lt;ls_&gt;`_</span></a></p>

<p><a class="reference internal" href="fix_smd_move_triangulated_surface.html"><span class="doc">fix smd/move/tri/surf</span></a>,

<a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">fix smd/wall_surface</span></a></p>

<p><strong>Default:</strong> none</p>

</div>

</div>

</div>

<div class="section" id="description">

<h2>Description</h2>

<hr class="docutils" />

<p>Specify the dihedral force field coefficients for one or more dihedral types.

The number and meaning of the coefficients depends on the dihedral style.

Dihedral coefficients can also be set in the data file read by the

<li>seed = random number seed to use for generating noise (positive integer)</li>

<li>zero or more keyword/value pairs may be appended</li>

</ul>

<dl class="docutils">

<dt>keyword = <em>noneq</em> and/or <em>every</em></dt>

<dd><p class="first"><em>noneq</em> Cmatrix  = file to read the non-equilibrium covariance matrix from

<em>every</em> stride   = apply the GLE once every time steps. Reduces the accuracy</p>

<blockquote class="last">

<div>of the integration of the GLE, but has *no effect* on the accuracy of equilibrium

sampling. It might change sampling properties when used together with <em>noneq</em>.</div></blockquote>

</dd>

</dl>

<pre class="literal-block">

keyword = <em>noneq</em> or <em>every</em>

  <em>noneq</em> Cmatrix  = file to read the non-equilibrium covariance matrix from

  <em>every</em> stride   = apply the GLE once every time steps. Reduces the accuracy

      of the integration of the GLE, but has *no effect* on the accuracy of equilibrium

      sampling. It might change sampling properties when used together with <em>noneq</em>.

</pre>

</div>

<div class="section" id="examples">

<h2>Examples</h2>

<p>fix 3 boundary gle 6 300 300 31415 smart.A

fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C</p>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">3</span> <span class="n">boundary</span> <span class="n">gle</span> <span class="mi">6</span> <span class="mi">300</span> <span class="mi">300</span> <span class="mi">31415</span> <span class="n">smart</span><span class="o">.</span><span class="n">A</span>

<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gle</span> <span class="mi">6</span> <span class="mi">300</span> <span class="mi">300</span> <span class="mi">31415</span> <span class="n">qt</span><span class="o">-</span><span class="mi">300</span><span class="n">k</span><span class="o">.</span><span class="n">A</span> <span class="n">noneq</span> <span class="n">qt</span><span class="o">-</span><span class="mi">300</span><span class="n">k</span><span class="o">.</span><span class="n">C</span>

</pre></div>

</div>

</div>

<div class="section" id="description">

<h2>Description</h2>

<p>Each degree of freedom in the thermostatted group is supplemented

with Ns additional degrees of freedom s, and the equations of motion

become</p>

<p>dq/dt=p/m

d(p,s)/dt=(F,0) - A(p,s) + B dW/dt</p>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dq</span><span class="o">/</span><span class="n">dt</span><span class="o">=</span><span class="n">p</span><span class="o">/</span><span class="n">m</span>

<span class="n">d</span><span class="p">(</span><span class="n">p</span><span class="p">,</span><span class="n">s</span><span class="p">)</span><span class="o">/</span><span class="n">dt</span><span class="o">=</span><span class="p">(</span><span class="n">F</span><span class="p">,</span><span class="mi">0</span><span class="p">)</span> <span class="o">-</span> <span class="n">A</span><span class="p">(</span><span class="n">p</span><span class="p">,</span><span class="n">s</span><span class="p">)</span> <span class="o">+</span> <span class="n">B</span> <span class="n">dW</span><span class="o">/</span><span class="n">dt</span>

</pre></div>

</div>

<p>where F is the physical force, A is the drift matrix (that generalizes

the friction in Langevin dynamics), B is the diffusion term and dW/dt

un-correlated Gaussian random forces. The A matrix couples the physical

<div class="section" id="description">

<h2>Description</h2>

<p>This fix enables LAMMPS to be run as a client for the i-PI Python

wrapper <a class="reference internal" href="#ipi"><span class="std std-ref">(IPI)</span></a> for performing a path integral molecular dynamics

wrapper <a class="reference internal" href="#ipihome"><span class="std std-ref">(IPI)</span></a> for performing a path integral molecular dynamics

(PIMD) simulation.  The philosophy behind i-PI is described in the

following publication <a class="reference internal" href="#ipicpc"><span class="std std-ref">(IPI-CPC)</span></a>.</p>

<p>A version of the i-PI package, containing only files needed for use

<hr class="docutils" />

<p id="ipicpc"><strong>(IPI-CPC)</strong> Ceriotti, More and Manolopoulos, Comp Phys Comm, 185,

1019-1026 (2014).</p>

<p id="ipi"><strong>(IPI)</strong>

<p id="ipihome"><strong>(IPI)</strong>

<a class="reference external" href="http://epfl-cosmo.github.io/gle4md/index.html?page=ipi">http://epfl-cosmo.github.io/gle4md/index.html?page=ipi</a></p>

</div>

</div>