more doc formatting issues triggering errors/warnings in sphinx

<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">lb</span><span class="o">/</span><span class="n">rigid</span><span class="o">/</span><span class="n">pc</span><span class="o">/</span><span class="n">sphere</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>

</pre></div>

</div>

<ul>

<li><p class="first">ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</p>

</li>

<li><p class="first">lb/rigid/pc/sphere = style name of this fix command</p>

</li>

<li><p class="first">bodystyle = <em>single</em> or <em>molecule</em> or <em>group</em></p>

</li>

<li><dl class="first docutils">

<dt><em>single</em> args = none</dt>

<dd><p class="first"><em>molecule</em> args = none

<em>group</em> args = N groupID1 groupID2 ...</p>

<blockquote class="last">

<div><p>N = # of groups</p>

</div></blockquote>

</dd>

</dl>

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

</li>

<li><p class="first">keyword = <em>force</em> or <em>torque</em> or <em>innerNodes</em></p>

</li>

<ul class="simple">

<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>

<li>lb/rigid/pc/sphere = style name of this fix command</li>

<li>bodystyle = <em>single</em> or <em>molecule</em> or <em>group</em></li>

</ul>

<pre class="literal-block">

<em>single</em> args = none

<em>molecule</em> args = none

<em>group</em> args = N groupID1 groupID2 ...

  N = # of groups

</pre>

<ul class="simple">

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

<li>keyword = <em>force</em> or <em>torque</em> or <em>innerNodes</em></li>

</ul>

<pre class="literal-block">

<em>force</em> values = M xflag yflag zflag

created to be used in place of that fix, to integrate the equations of

motion of spherical rigid bodies when a lattice-Boltzmann fluid is

present with a user-specified value of the force-coupling constant.

The fix uses the integration algorithm described in <a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a> to update the positions, velocities, and orientations of

The fix uses the integration algorithm described in <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a> to update the positions, velocities, and orientations of

a set of spherical rigid bodies experiencing velocity dependent

hydrodynamic forces.  The spherical bodies are assumed to rotate as

solid, uniform density spheres, with moments of inertia calculated

<p><a class="reference internal" href="neb.html"><span class="doc">neb</span></a></p>

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

<p id="henkelman"><strong>(Henkelman1)</strong> Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).</p>

<p id="id1"><strong>(Henkelman2)</strong> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,

<p id="id3"><strong>(Henkelman2)</strong> Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,

9901-9904 (2000).</p>

</div>

</div>

</div>

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

<h2>Default</h2>

<hr class="docutils" />

</div>

</div>

<p>nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)

regarding the bonded interactions. (default value = 5.0)</p>

<p>hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen

bond interactions.(default value = 7.5. Value of 0.0 turns off hydrogen</p>

<blockquote>

<div>bonds)</div></blockquote>

bond interactions.(default value = 7.5. Value of 0.0 turns off

hydrogen bonds)</p>

<p>bond_graph_cutoff: is the threshold used in determining what is a

physical bond, what is not. Bonds and angles reported in the

trajectory file rely on this cutoff. (default value = 0.3)</p>

  {single} args = none

  {molecule} args = none

  {group} args = N groupID1 groupID2 ...

    N = # of groups

    N = # of groups :pre

zero or more keyword/value pairs may be appended :l

keyword = {force} or {torque} or {innerNodes} :l

  {force} values = M xflag yflag zflag