more doc formatting issues triggering errors/warnings in sphinx

doc/html/fix_lb_rigid_pc_sphere.html

@@ -131,26 +131,20 @@
 <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
@@ -176,7 +170,7 @@
 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

doc/html/fix_neb.html

@@ -158,7 +158,7 @@ but those in intermediate replicas do.  During the initial stage of
 NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
 on the atoms of each intermediate replica I is altered, as described
 in the <a class="reference internal" href="neb.html#henkelman1"><span class="std std-ref">(Henkelman1)</span></a> paper, to become:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Fi</span> <span class="o">=</span> <span class="o">-</span><span class="n">Grad</span><span class="p">(</span><span class="n">V</span><span class="p">)</span> <span class="o">+</span> <span class="p">(</span><span class="n">Grad</span><span class="p">(</span><span class="n">V</span><span class="p">)</span> <span class="n">dot</span> <span class="n">That</span><span class="p">)</span> <span class="n">That</span> <span class="o">+</span> <span class="n">Kspring</span> <span class="p">(</span><span class="o">|</span><span class="n">Ri</span><span class="o">+</span><span class="n">i</span> <span class="o">-</span> <span class="n">Ri</span><span class="o">|</span> <span class="o">-</span> <span class="o">|</span><span class="n">Ri</span> <span class="o">-</span> <span class="n">Ri</span><span class="o">-</span><span class="mi">1</span><span class="o">|</span><span class="p">)</span> <span class="n">That</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Fi</span> <span class="o">=</span> <span class="o">-</span><span class="n">Grad</span><span class="p">(</span><span class="n">V</span><span class="p">)</span> <span class="o">+</span> <span class="p">(</span><span class="n">Grad</span><span class="p">(</span><span class="n">V</span><span class="p">)</span> <span class="n">dot</span> <span class="n">That</span><span class="p">)</span> <span class="n">That</span> <span class="o">+</span> <span class="n">Kspring</span> <span class="p">(</span><span class="o">|</span> <span class="n">Ri</span><span class="o">+</span><span class="n">i</span> <span class="o">-</span> <span class="n">Ri</span> <span class="o">|</span> <span class="o">-</span> <span class="o">|</span> <span class="n">Ri</span> <span class="o">-</span> <span class="n">Ri</span><span class="o">-</span><span class="mi">1</span> <span class="o">|</span><span class="p">)</span> <span class="n">That</span>
 </pre></div>
 </div>
 <p>Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
@@ -210,7 +210,7 @@ for more info on packages.</p>
 <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>

doc/html/fix_tune_kspace.html

@@ -206,7 +206,6 @@ called.  Reneighboring is required.</p>
 </div>
 <div class="section" id="default">
 <h2>Default</h2>
-<hr class="docutils" />
 </div>
 </div>
 

doc/html/pair_reax_c.html

@@ -343,9 +343,8 @@ writes into the partial energies file. (default value = 0)</p>
 <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>

doc/src/fix_lb_rigid_pc_sphere.txt

@@ -18,7 +18,7 @@ bodystyle = {single} or {molecule} or {group} :l
   {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

doc/src/fix_neb.txt

@@ -37,7 +37,7 @@ NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting
 on the atoms of each intermediate replica I is altered, as described
 in the "(Henkelman1)"_#Henkelman1 paper, to become:
 
-Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (|Ri+i - Ri| - |Ri - Ri-1|) That :pre
+Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (| Ri+i - Ri | - | Ri - Ri-1 |) That :pre
 
 Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the
 coordinates of its neighbor replicas.  That (t with a hat over it) is

doc/src/fix_tune_kspace.txt

@@ -98,5 +98,3 @@ lj/long/coul/long"_pair_lj_long.html,
 
 [Default:]
 
-:line
-

doc/src/molecule.txt

@@ -44,7 +44,6 @@ molecule CO2 co2.txt boff 3 aoff 2
 molecule 1 mymol.txt offset 6 9 18 23 14 
 molecule objects file.1 scale 1.5 file.1 scale 2.0 file.2 scale 1.3 :pre
 
-:pre
 
 [Description:]
 

doc/src/pair_reax_c.txt

@@ -237,8 +237,8 @@ nbrhood_cutoff: Denotes the near neighbors cutoff (in Angstroms)
 regarding the bonded interactions. (default value = 5.0)
 
 hbond_cutoff: Denotes the cutoff distance (in Angstroms) for hydrogen
-bond interactions.(default value = 7.5. Value of 0.0 turns off hydrogen 
-		bonds)
+bond interactions.(default value = 7.5. Value of 0.0 turns off
+hydrogen bonds)
 
 bond_graph_cutoff: is the threshold used in determining what is a
 physical bond, what is not. Bonds and angles reported in the

doc/src/read_restart.txt

@@ -23,8 +23,6 @@ read_restart restart.*
 read_restart restart.*.mpiio
 read_restart poly.*.% remap :pre
 
-:pre
-
 [Description:]
 
 Read in a previously saved system configuration from a restart file.