diff --git a/doc/html/Section_packages.html b/doc/html/Section_packages.html
index f882ee234b79dd950c663dcd562776ff97eeb72f..fedd3cc1aeab1bf60be2ef8a243874f7da2d40d4 100644
--- a/doc/html/Section_packages.html
+++ b/doc/html/Section_packages.html
@@ -493,7 +493,7 @@ name links to a sub-section below with more details.</p>
 <td>python</td>
 <td>lib/python</td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="Section_tools.html#reax"><span class="std std-ref">REAX</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="#reax"><span class="std std-ref">REAX</span></a></td>
 <td>ReaxFF potential</td>
 <td>Aidan Thompson (Sandia)</td>
 <td><a class="reference internal" href="pair_reax.html"><span class="doc">pair_style reax</span></a></td>
diff --git a/doc/html/compute_rdf.html b/doc/html/compute_rdf.html
index c8d486553f81b8529974235193cac096a5a90746..ef1d1d8cfc7491e2b640f3f7e9a03f2a98bdaaf4 100644
--- a/doc/html/compute_rdf.html
+++ b/doc/html/compute_rdf.html
@@ -227,7 +227,7 @@ atoms of type jtypeN.</p>
 to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a> command, for
 example:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myRDF</span> <span class="nb">all</span> <span class="n">rdf</span> <span class="mi">50</span>
-<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myRDF</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">rdf</span> <span class="n">mode</span> <span class="n">vector</span>
+<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">rdf</span> <span class="n">mode</span> <span class="n">vector</span>
 </pre></div>
 </div>
 <p><strong>Output info:</strong></p>
diff --git a/doc/html/fix_lb_pc.html b/doc/html/fix_lb_pc.html
index 8a5281c6c339b5078347caf8b1accde74127f9da..4fe4f72ced796e7ad662779a4479b2c96b8a22a4 100644
--- a/doc/html/fix_lb_pc.html
+++ b/doc/html/fix_lb_pc.html
@@ -146,7 +146,7 @@
 <h2>Description</h2>
 <p>Update the positions and velocities of the individual particles
 described by <em>group-ID</em>, experiencing velocity-dependent hydrodynamic
-forces, using 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>.  This integration algorithm should only be used if a
+forces, using the integration algorithm described in <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a>.  This integration algorithm should only be used if a
 user-specified value for the force-coupling constant used in <a class="reference internal" href="fix_lb_fluid.html"><span class="doc">fix lb/fluid</span></a> has been set; do not use this integration
 algorithm if the force coupling constant has been set by default.</p>
 </div>
diff --git a/doc/html/pair_thole.html b/doc/html/pair_thole.html
index b2742247f9f2b3e44caf95d97b9e7bc2c705ccc6..e3a5f8b9cb117efd9bcbd87cff9f12285b63b1db 100644
--- a/doc/html/pair_thole.html
+++ b/doc/html/pair_thole.html
@@ -189,8 +189,8 @@ short distances by a function</p>
 \frac{s_{ij} r_{ij} }{2} \right)
 \exp \left( - s_{ij} r_{ij} \right) \end{equation}\]</div>
 <p>This function results from an adaptation to point charges
-<a class="reference internal" href="tutorial_drude.html#noskov"><span class="std std-ref">(Noskov)</span></a> of the dipole screening scheme originally proposed
-by <a class="reference internal" href="tutorial_drude.html#thole"><span class="std std-ref">Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
+<a class="reference internal" href="#noskov"><span class="std std-ref">(Noskov)</span></a> of the dipole screening scheme originally proposed
+by <a class="reference internal" href="#thole"><span class="std std-ref">Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
 by the polarizability of the atoms, <span class="math">\(\alpha_i\)</span>, and by a Thole
 damping parameter <span class="math">\(a\)</span>.  This Thole damping parameter usually takes
 a value of 2.6, but in certain force fields the value can depend upon