HTML update

doc/html/Section_commands.html

@@ -247,15 +247,15 @@ inside the parenthesis is treated as an “immediate” variable and
 evaluated as an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>.  This is a way
 to use numeric formulas in an input script without having to assign
 them to variable names.  For example, these 3 input script lines:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable X equal (xlo+xhi)/2+sqrt(v_area)
+<pre class="literal-block">
+variable X equal (xlo+xhi)/2+sqrt(v_area)
 region 1 block $X 2 INF INF EDGE EDGE
 variable X delete
-</pre></div>
+</pre>
-</div>
 <p>can be replaced by</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
+<pre class="literal-block">
-</pre></div>
+region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
-</div>
+</pre>
 <p>so that you do not have to define (or discard) a temporary variable X.</p>
 <p>Note that neither the curly-bracket or immediate form of variables can
 contain nested $ characters for other variables to substitute for.

doc/html/Section_example.html

@@ -303,11 +303,11 @@ longer times, e.g. to measure a particular quantity.</p>
 </tbody>
 </table>
 <p>Here is how you can run and visualize one of the sample problems:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">indent</span>
+<pre class="literal-block">
-<span class="n">cp</span> <span class="o">../../</span><span class="n">src</span><span class="o">/</span><span class="n">lmp_linux</span> <span class="o">.</span>           <span class="c1"># copy LAMMPS executable to this dir</span>
+cd indent
-<span class="n">lmp_linux</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">indent</span>            <span class="c1"># run the problem</span>
+cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
-</pre></div>
+lmp_linux -in in.indent            # run the problem
-</div>
+</pre>
 <p>Running the simulation produces the files <em>dump.indent</em> and
 <em>log.lammps</em>.  You can visualize the dump file of snapshots with a
 variety of 3rd-party tools highlighted on the
@@ -321,17 +321,17 @@ ImageMagick or QuickTime or various Windows-based tools.  See the
 <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page for more details.  E.g. this
 Imagemagick command would create a GIF file suitable for viewing in a
 browser.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">convert</span> <span class="o">-</span><span class="n">loop</span> <span class="mi">1</span> <span class="o">*.</span><span class="n">jpg</span> <span class="n">foo</span><span class="o">.</span><span class="n">gif</span>
+<pre class="literal-block">
-</pre></div>
+% convert -loop 1 *.jpg foo.gif
-</div>
+</pre>
 </div>
 <hr class="docutils" />
 <div class="section" id="uppercase-directories">
 <h2>7.2. Uppercase directories</h2>
 <table border="1" class="docutils">
 <colgroup>
-<col width="10%" />
+<col width="11%" />
-<col width="90%" />
+<col width="89%" />
 </colgroup>
 <tbody valign="top">
 <tr class="row-odd"><td>ASPHERE</td>

doc/html/accelerate_opt.html

@@ -139,10 +139,10 @@ follow.</p>
 <span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">opt</span> <span class="o">-</span><span class="n">o</span> <span class="n">mpi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span>   <span class="c1"># or one-line build via Make.py</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">opt</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>                <span class="c1"># run in serial</span>
+<pre class="literal-block">
-<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">opt</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span>   <span class="c1"># run in parallel</span>
+lmp_mpi -sf opt -in in.script                # run in serial
-</pre></div>
+mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel
-</div>
+</pre>
 <p><strong>Required hardware/software:</strong></p>
 <p>None.</p>
 <p><strong>Building LAMMPS with the OPT package:</strong></p>
@@ -159,9 +159,9 @@ The Make.py command will add this automatically.</p>
 <p><strong>Or run with the OPT package by editing an input script:</strong></p>
 <p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix opt</span></a> command, or you can explicitly add an
 &#8220;opt&#8221; suffix to individual styles in your input script, e.g.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">opt</span> <span class="mf">2.5</span>
+<pre class="literal-block">
-</pre></div>
+pair_style lj/cut/opt 2.5
-</div>
+</pre>
 <p><strong>Speed-ups to expect:</strong></p>
 <p>You should see a reduction in the &#8220;Pair time&#8221; value printed at the end
 of a run.  On most machines for reasonable problem sizes, it will be a

doc/html/angle_charmm.html

@@ -137,16 +137,16 @@
 <h1>angle_style charmm/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">charmm</span>
+<pre class="literal-block">
-</pre></div>
+angle_style charmm
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">charmm</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span> <span class="mf">50.0</span> <span class="mf">3.0</span>
+angle_style charmm
-</pre></div>
+angle_coeff 1 300.0 107.0 50.0 3.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_class2.html

@@ -131,18 +131,18 @@
 <h1>angle_style class2/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">class2</span>
+<pre class="literal-block">
-</pre></div>
+angle_style class2
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">class2</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span>
+angle_style class2
-<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="n">bb</span> <span class="mf">10.5872</span> <span class="mf">1.0119</span> <span class="mf">1.5228</span>
+angle_coeff * 75.0
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="n">ba</span> <span class="mf">3.6551</span> <span class="mf">24.895</span> <span class="mf">1.0119</span> <span class="mf">1.5228</span>
+angle_coeff 1 bb 10.5872 1.0119 1.5228
-</pre></div>
+angle_coeff * ba 3.6551 24.895 1.0119 1.5228
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_coeff.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>angle_coeff command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_coeff</span> <span class="n">N</span> <span class="n">args</span>
+<pre class="literal-block">
-</pre></div>
+angle_coeff N args
-</div>
+</pre>
 <ul class="simple">
 <li>N = angle type (see asterisk form below)</li>
 <li>args = coefficients for one or more angle types</li>
@@ -138,11 +138,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">5.0</span>
+angle_coeff 1 300.0 107.0
-<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">10</span> <span class="mf">5.0</span>
+angle_coeff * 5.0
-</pre></div>
+angle_coeff 2*10 5.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -153,7 +153,7 @@ Angle coefficients can also be set in the data file read by the
 <p>N can be specified in one of two ways.  An explicit numeric value can
 be used, as in the 1st example above.  Or a wild-card asterisk can be
 used to set the coefficients for multiple angle types.  This takes the
-form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N = the number of angle types,
+form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N = the number of angle types,
 then an asterisk with no numeric values means all types from 1 to N.  A
 leading asterisk means all types from 1 to n (inclusive).  A trailing
 asterisk means all types from n to N (inclusive).  A middle asterisk
@@ -161,10 +161,10 @@ means all types from m to n (inclusive).</p>
 <p>Note that using an angle_coeff command can override a previous setting
 for the same angle type.  For example, these commands set the coeffs
 for all angle types, then overwrite the coeffs for just angle type 2:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">200.0</span> <span class="mf">107.0</span> <span class="mf">1.2</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="mi">2</span> <span class="mf">50.0</span> <span class="mf">107.0</span>
+angle_coeff * 200.0 107.0 1.2
-</pre></div>
+angle_coeff 2 50.0 107.0
-</div>
+</pre>
 <p>A line in a data file that specifies angle coefficients uses the exact
 same format as the arguments of the angle_coeff command in an input
 script, except that wild-card asterisks should not be used since

doc/html/angle_cosine.html

@@ -131,16 +131,16 @@
 <h1>angle_style cosine/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span>
+<pre class="literal-block">
-</pre></div>
+angle_style cosine
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span>
+angle_style cosine
-</pre></div>
+angle_coeff * 75.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_cosine_delta.html

@@ -131,16 +131,16 @@
 <h1>angle_style cosine/delta/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">delta</span>
+<pre class="literal-block">
-</pre></div>
+angle_style cosine/delta
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">delta</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mf">75.0</span> <span class="mf">100.0</span>
+angle_style cosine/delta
-</pre></div>
+angle_coeff 2*4 75.0 100.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_cosine_periodic.html

@@ -131,16 +131,16 @@
 <h1>angle_style cosine/periodic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">periodic</span>
+<pre class="literal-block">
-</pre></div>
+angle_style cosine/periodic
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">periodic</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span> <span class="mi">1</span> <span class="mi">6</span>
+angle_style cosine/periodic
-</pre></div>
+angle_coeff * 75.0 1 6
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_cosine_shift.html

@@ -131,16 +131,16 @@
 <h1>angle_style cosine/shift/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span>
+<pre class="literal-block">
-</pre></div>
+angle_style cosine/shift
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">45.0</span>
+angle_style cosine/shift
-</pre></div>
+angle_coeff * 10.0 45.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_cosine_shift_exp.html

@@ -131,16 +131,16 @@
 <h1>angle_style cosine/shift/exp/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
+<pre class="literal-block">
-</pre></div>
+angle_style cosine/shift/exp
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">45.0</span> <span class="mf">2.0</span>
+angle_style cosine/shift/exp
-</pre></div>
+angle_coeff * 10.0 45.0 2.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_cosine_squared.html

@@ -131,16 +131,16 @@
 <h1>angle_style cosine/squared/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">squared</span>
+<pre class="literal-block">
-</pre></div>
+angle_style cosine/squared
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">squared</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mf">75.0</span> <span class="mf">100.0</span>
+angle_style cosine/squared
-</pre></div>
+angle_coeff 2*4 75.0 100.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_dipole.html

@@ -131,16 +131,16 @@
 <h1>angle_style dipole/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span>
+<pre class="literal-block">
-</pre></div>
+angle_style dipole
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="mi">6</span> <span class="mf">2.1</span> <span class="mf">180.0</span>
+angle_style dipole
-</pre></div>
+angle_coeff 6 2.1 180.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_fourier.html

@@ -131,9 +131,9 @@
 <h1>angle_style fourier/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">fourier</span>
+<pre class="literal-block">
-</pre></div>
+angle_style fourier
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>

doc/html/angle_fourier_simple.html

@@ -131,9 +131,9 @@
 <h1>angle_style fourier/simple/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">fourier</span><span class="o">/</span><span class="n">simple</span>
+<pre class="literal-block">
-</pre></div>
+angle_style fourier/simple
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>

doc/html/angle_harmonic.html

@@ -137,16 +137,16 @@
 <h1>angle_style harmonic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span>
+<pre class="literal-block">
-</pre></div>
+angle_style harmonic
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span>
+angle_style harmonic
-</pre></div>
+angle_coeff 1 300.0 107.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_hybrid.html

@@ -128,20 +128,20 @@
 <span id="index-0"></span><h1>angle_style hybrid command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">hybrid</span> <span class="n">style1</span> <span class="n">style2</span> <span class="o">...</span>
+<pre class="literal-block">
-</pre></div>
+angle_style hybrid style1 style2 ...
-</div>
+</pre>
 <ul class="simple">
 <li>style1,style2 = list of one or more angle styles</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">cosine</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="n">harmonic</span> <span class="mf">80.0</span> <span class="mf">30.0</span>
+angle_style hybrid harmonic cosine
-<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span> <span class="n">cosine</span> <span class="mf">50.0</span>
+angle_coeff 1 harmonic 80.0 30.0
-</pre></div>
+angle_coeff 2* cosine 50.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_none.html

@@ -128,15 +128,15 @@
 <span id="index-0"></span><h1>angle_style none command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">none</span>
+<pre class="literal-block">
-</pre></div>
+angle_style none
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">none</span>
+<pre class="literal-block">
-</pre></div>
+angle_style none
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_quartic.html

@@ -131,16 +131,16 @@
 <h1>angle_style quartic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span>
+<pre class="literal-block">
-</pre></div>
+angle_style quartic
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">129.1948</span> <span class="mf">56.8726</span> <span class="o">-</span><span class="mf">25.9442</span> <span class="o">-</span><span class="mf">14.2221</span>
+angle_style quartic
-</pre></div>
+angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_sdk.html

@@ -128,19 +128,19 @@
 <span id="index-0"></span><h1>angle_style sdk command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span>
+<pre class="literal-block">
-</pre></div>
+angle_style sdk
-</div>
+</pre>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span><span class="o">/</span><span class="n">omp</span>
+<pre class="literal-block">
-</pre></div>
+angle_style sdk/omp
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span>
+angle_style sdk
-</pre></div>
+angle_coeff 1 300.0 107.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_style.html

@@ -128,20 +128,20 @@
 <span id="index-0"></span><h1>angle_style command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">style</span>
+<pre class="literal-block">
-</pre></div>
+angle_style style
-</div>
+</pre>
 <ul class="simple">
 <li>style = <em>none</em> or <em>hybrid</em> or <em>charmm</em> or <em>class2</em> or <em>cosine</em> or         <em>cosine/squared</em> or <em>harmonic</em></li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span>
+<pre class="literal-block">
-<span class="n">angle_style</span> <span class="n">charmm</span>
+angle_style harmonic
-<span class="n">angle_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">cosine</span>
+angle_style charmm
-</pre></div>
+angle_style hybrid harmonic cosine
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -207,9 +207,9 @@ package.</p>
 </div>
 <div class="section" id="default">
 <h2>Default</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">none</span>
+<pre class="literal-block">
-</pre></div>
+angle_style none
-</div>
+</pre>
 </div>
 </div>
 

doc/html/angle_table.html

@@ -131,9 +131,9 @@
 <h1>angle_style table/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">table</span> <span class="n">style</span> <span class="n">N</span>
+<pre class="literal-block">
-</pre></div>
+angle_style table style N
-</div>
+</pre>
 <ul class="simple">
 <li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li>
 <li>N = use N values in table</li>
@@ -141,10 +141,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span>
+<pre class="literal-block">
-<span class="n">angle_coeff</span> <span class="mi">3</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span>
+angle_style table linear 1000
-</pre></div>
+angle_coeff 3 file.table ENTRY1
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/angle_zero.html

@@ -134,12 +134,12 @@ angle_style zero <em>nocoeff</em>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">zero</span>
+<pre class="literal-block">
-<span class="n">angle_style</span> <span class="n">zero</span> <span class="n">nocoeff</span>
+angle_style zero
-<span class="n">angle_coeff</span> <span class="o">*</span>
+angle_style zero nocoeff
-<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">120.0</span>
+angle_coeff *
-</pre></div>
+angle_coeff * 120.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/atom_modify.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>atom_modify command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+<pre class="literal-block">
-</pre></div>
+atom_modify keyword values ...
-</div>
+</pre>
 <ul class="simple">
 <li>one or more keyword/value pairs may be appended</li>
 <li>keyword = <em>id</em> or <em>map</em> or <em>first</em> or <em>sort</em></li>
@@ -146,11 +146,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="nb">map</span> <span class="nb">hash</span>
+<pre class="literal-block">
-<span class="n">atom_modify</span> <span class="nb">map</span> <span class="n">array</span> <span class="n">sort</span> <span class="mi">10000</span> <span class="mf">2.0</span>
+atom_modify map hash
-<span class="n">atom_modify</span> <span class="n">first</span> <span class="n">colloid</span>
+atom_modify map array sort 10000 2.0
-</pre></div>
+atom_modify first colloid
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/atom_style.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>atom_style command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">style</span> <span class="n">args</span>
+<pre class="literal-block">
-</pre></div>
+atom_style style args
-</div>
+</pre>
 <ul class="simple">
 <li>style = <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dipole</em> or         <em>dpd</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>meso</em> or        <em>molecular</em> or <em>peri</em> or <em>smd</em> or <em>sphere</em> or <em>tri</em> or         <em>template</em> or <em>hybrid</em></li>
 </ul>
@@ -150,15 +150,15 @@ args = none for any style except the following
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">atomic</span>
+<pre class="literal-block">
-<span class="n">atom_style</span> <span class="n">bond</span>
+atom_style atomic
-<span class="n">atom_style</span> <span class="n">full</span>
+atom_style bond
-<span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">10</span>
+atom_style full
-<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">bond</span>
+atom_style body nparticle 2 10
-<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">5</span>
+atom_style hybrid charge bond
-<span class="n">atom_style</span> <span class="n">template</span> <span class="n">myMols</span>
+atom_style hybrid charge body nparticle 2 5
-</pre></div>
+atom_style template myMols
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/body.html

@@ -247,11 +247,11 @@ mentioned above, the <a class="reference internal" href="fix_rigid.html"><span c
 duplicates its functionality.</p>
 <p>The atom_style body command for this body style takes two additional
 arguments:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
+<pre class="literal-block">
-<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of sub-particles in any body in the system</span>
+atom_style body nparticle Nmin Nmax
-<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of sub-particles in any body in the system</span>
+Nmin = minimum # of sub-particles in any body in the system
-</pre></div>
+Nmax = maximum # of sub-particles in any body in the system
-</div>
+</pre>
 <p>The Nmin and Nmax arguments are used to bound the size of data
 structures used internally by each particle.</p>
 <p>When the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command reads a data file for this
@@ -313,11 +313,11 @@ used for 2d models.  One example use of this body style is for 2d
 discrete element models, as described in <a class="reference internal" href="#fraige"><span class="std std-ref">Fraige</span></a>.  Similar to
 body style <em>nparticle</em>, the atom_style body command for this body
 style takes two additional arguments:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">rounded</span><span class="o">/</span><span class="n">polygon</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
+<pre class="literal-block">
-<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of vertices in any body in the system</span>
+atom_style body rounded/polygon Nmin Nmax
-<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of vertices in any body in the system</span>
+Nmin = minimum # of vertices in any body in the system
-</pre></div>
+Nmax = maximum # of vertices in any body in the system
-</div>
+</pre>
 <p>The Nmin and Nmax arguments are used to bound the size of data
 structures used internally by each particle.</p>
 <p>When the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command reads a data file for this

doc/html/bond_class2.html

@@ -131,16 +131,16 @@
 <h1>bond_style class2/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span>
+<pre class="literal-block">
-</pre></div>
+bond_style class2
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">100.0</span> <span class="mf">80.0</span> <span class="mf">80.0</span>
+bond_style class2
-</pre></div>
+bond_coeff 1 1.0 100.0 80.0 80.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_coeff.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>bond_coeff command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_coeff</span> <span class="n">N</span> <span class="n">args</span>
+<pre class="literal-block">
-</pre></div>
+bond_coeff N args
-</div>
+</pre>
 <ul class="simple">
 <li>N = bond type (see asterisk form below)</li>
 <li>args = coefficients for one or more bond types</li>
@@ -138,12 +138,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">80.0</span> <span class="mf">1.2</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="o">*</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+bond_coeff 5 80.0 1.2
-<span class="n">bond_coeff</span> <span class="mi">1</span><span class="o">*</span><span class="mi">4</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+bond_coeff * 30.0 1.5 1.0 1.0
-<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="n">harmonic</span> <span class="mf">200.0</span> <span class="mf">1.0</span>
+bond_coeff 1*4 30.0 1.5 1.0 1.0
-</pre></div>
+bond_coeff 1 harmonic 200.0 1.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -154,7 +154,7 @@ Bond coefficients can also be set in the data file read by the
 <p>N can be specified in one of two ways.  An explicit numeric value can
 be used, as in the 1st example above.  Or a wild-card asterisk can be
 used to set the coefficients for multiple bond types.  This takes the
-form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N = the number of bond types,
+form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N = the number of bond types,
 then an asterisk with no numeric values means all types from 1 to N.  A
 leading asterisk means all types from 1 to n (inclusive).  A trailing
 asterisk means all types from n to N (inclusive).  A middle asterisk
@@ -162,10 +162,10 @@ means all types from m to n (inclusive).</p>
 <p>Note that using a bond_coeff command can override a previous setting
 for the same bond type.  For example, these commands set the coeffs
 for all bond types, then overwrite the coeffs for just bond type 2:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_coeff</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.2</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mf">200.0</span> <span class="mf">1.2</span>
+bond_coeff * 100.0 1.2
-</pre></div>
+bond_coeff 2 200.0 1.2
-</div>
+</pre>
 <p>A line in a data file that specifies bond coefficients uses the exact
 same format as the arguments of the bond_coeff command in an input
 script, except that wild-card asterisks should not be used since

doc/html/bond_fene.html

@@ -137,16 +137,16 @@
 <h1>bond_style fene/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span>
+<pre class="literal-block">
-</pre></div>
+bond_style fene
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+bond_style fene
-</pre></div>
+bond_coeff 1 30.0 1.5 1.0 1.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_fene_expand.html

@@ -131,16 +131,16 @@
 <h1>bond_style fene/expand/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span><span class="o">/</span><span class="n">expand</span>
+<pre class="literal-block">
-</pre></div>
+bond_style fene/expand
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span><span class="o">/</span><span class="n">expand</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.5</span>
+bond_style fene/expand
-</pre></div>
+bond_coeff 1 30.0 1.5 1.0 1.0 0.5
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_harmonic.html

@@ -137,16 +137,16 @@
 <h1>bond_style harmonic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
+<pre class="literal-block">
-</pre></div>
+bond_style harmonic
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">80.0</span> <span class="mf">1.2</span>
+bond_style harmonic
-</pre></div>
+bond_coeff 5 80.0 1.2
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_harmonic_shift.html

@@ -131,16 +131,16 @@
 <h1>bond_style harmonic/shift/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span>
+<pre class="literal-block">
-</pre></div>
+bond_style harmonic/shift
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">10.0</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
+bond_style harmonic/shift
-</pre></div>
+bond_coeff 5 10.0 0.5 1.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_harmonic_shift_cut.html

@@ -131,16 +131,16 @@
 <h1>bond_style harmonic/shift/cut/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">cut</span>
+<pre class="literal-block">
-</pre></div>
+bond_style harmonic/shift/cut
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">cut</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">10.0</span> <span class="mf">0.5</span> <span class="mf">1.0</span>
+bond_style harmonic/shift/cut
-</pre></div>
+bond_coeff 5 10.0 0.5 1.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_hybrid.html

@@ -128,20 +128,20 @@
 <span id="index-0"></span><h1>bond_style hybrid command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">hybrid</span> <span class="n">style1</span> <span class="n">style2</span> <span class="o">...</span>
+<pre class="literal-block">
-</pre></div>
+bond_style hybrid style1 style2 ...
-</div>
+</pre>
 <ul class="simple">
 <li>style1,style2 = list of one or more bond styles</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">fene</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="n">harmonic</span> <span class="mf">80.0</span> <span class="mf">1.2</span>
+bond_style hybrid harmonic fene
-<span class="n">bond_coeff</span> <span class="mi">2</span><span class="o">*</span> <span class="n">fene</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
+bond_coeff 1 harmonic 80.0 1.2
-</pre></div>
+bond_coeff 2* fene 30.0 1.5 1.0 1.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_morse.html

@@ -131,16 +131,16 @@
 <h1>bond_style morse/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span>
+<pre class="literal-block">
-</pre></div>
+bond_style morse
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">1.0</span> <span class="mf">2.0</span> <span class="mf">1.2</span>
+bond_style morse
-</pre></div>
+bond_coeff 5 1.0 2.0 1.2
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_none.html

@@ -128,15 +128,15 @@
 <span id="index-0"></span><h1>bond_style none command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">none</span>
+<pre class="literal-block">
-</pre></div>
+bond_style none
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">none</span>
+<pre class="literal-block">
-</pre></div>
+bond_style none
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_nonlinear.html

@@ -131,16 +131,16 @@
 <h1>bond_style nonlinear/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">nonlinear</span>
+<pre class="literal-block">
-</pre></div>
+bond_style nonlinear
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">nonlinear</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mf">100.0</span> <span class="mf">1.1</span> <span class="mf">1.4</span>
+bond_style nonlinear
-</pre></div>
+bond_coeff 2 100.0 1.1 1.4
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_quartic.html

@@ -131,16 +131,16 @@
 <h1>bond_style quartic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span>
+<pre class="literal-block">
-</pre></div>
+bond_style quartic
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mi">1200</span> <span class="o">-</span><span class="mf">0.55</span> <span class="mf">0.25</span> <span class="mf">1.3</span> <span class="mf">34.6878</span>
+bond_style quartic
-</pre></div>
+bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -184,10 +184,10 @@ to 1,1,1, as indicated as a restriction below.</p>
 <p>Note that when bonds are dumped to a file via the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command, bonds with type 0 are not included.  The
 <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command can also be used to query the
 status of broken bonds or permanently delete them, e.g.:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">stats</span>
+<pre class="literal-block">
-<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">bond</span> <span class="mi">0</span> <span class="n">remove</span>
+delete_bonds all stats
-</pre></div>
+delete_bonds all bond 0 remove
-</div>
+</pre>
 <hr class="docutils" />
 <p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
 functionally the same as the corresponding style without the suffix.

doc/html/bond_style.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>bond_style command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">style</span> <span class="n">args</span>
+<pre class="literal-block">
-</pre></div>
+bond_style style args
-</div>
+</pre>
 <ul class="simple">
 <li>style = <em>none</em> or <em>hybrid</em> or <em>class2</em> or <em>fene</em> or <em>fene/expand</em> or         <em>harmonic</em> or <em>morse</em> or <em>nonlinear</em> or <em>quartic</em></li>
 </ul>
@@ -141,11 +141,11 @@ args = none for any style except <em>hybrid</em>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
+<pre class="literal-block">
-<span class="n">bond_style</span> <span class="n">fene</span>
+bond_style harmonic
-<span class="n">bond_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">fene</span>
+bond_style fene
-</pre></div>
+bond_style hybrid harmonic fene
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_table.html

@@ -131,9 +131,9 @@
 <h1>bond_style table/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">table</span> <span class="n">style</span> <span class="n">N</span>
+<pre class="literal-block">
-</pre></div>
+bond_style table style N
-</div>
+</pre>
 <ul class="simple">
 <li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li>
 <li>N = use N values in table</li>
@@ -141,10 +141,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span>
+<pre class="literal-block">
-<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">ENTRY1</span>
+bond_style table linear 1000
-</pre></div>
+bond_coeff 1 file.table ENTRY1
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_write.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>bond_write command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_write</span> <span class="n">btype</span> <span class="n">N</span> <span class="n">inner</span> <span class="n">outer</span> <span class="n">file</span> <span class="n">keyword</span> <span class="n">itype</span> <span class="n">jtype</span>
+<pre class="literal-block">
-</pre></div>
+bond_write btype N inner outer file keyword itype jtype
-</div>
+</pre>
 <ul class="simple">
 <li>btype = bond types</li>
 <li>N = # of values</li>
@@ -143,10 +143,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_write</span> <span class="mi">1</span> <span class="mi">500</span> <span class="mf">0.5</span> <span class="mf">3.5</span> <span class="n">table</span><span class="o">.</span><span class="n">txt</span> <span class="n">Harmonic_1</span>
+<pre class="literal-block">
-<span class="n">bond_write</span> <span class="mi">3</span> <span class="mi">1000</span> <span class="mf">0.1</span> <span class="mf">6.0</span> <span class="n">table</span><span class="o">.</span><span class="n">txt</span> <span class="n">Morse</span>
+bond_write 1 500 0.5 3.5 table.txt Harmonic_1
-</pre></div>
+bond_write 3 1000 0.1 6.0 table.txt Morse
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/bond_zero.html

@@ -134,12 +134,12 @@ bond_style zero <em>nocoeff</em>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">zero</span>
+<pre class="literal-block">
-<span class="n">bond_style</span> <span class="n">zero</span> <span class="n">nocoeff</span>
+bond_style zero
-<span class="n">bond_coeff</span> <span class="o">*</span>
+bond_style zero nocoeff
-<span class="n">bond_coeff</span> <span class="o">*</span> <span class="mf">2.14</span>
+bond_coeff *
-</pre></div>
+bond_coeff * 2.14
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/change_box.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>change_box command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">parameter</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
+<pre class="literal-block">
-</pre></div>
+change_box group-ID parameter args ... keyword args ...
-</div>
+</pre>
 <ul class="simple">
 <li>group-ID = ID of group of atoms to (optionally) displace</li>
 <li>one or more parameter/arg pairs may be appended</li>
@@ -175,10 +175,10 @@ parameter = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>xz</em>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">xy</span> <span class="n">final</span> <span class="o">-</span><span class="mf">2.0</span> <span class="n">z</span> <span class="n">final</span> <span class="mf">0.0</span> <span class="mf">5.0</span> <span class="n">boundary</span> <span class="n">p</span> <span class="n">p</span> <span class="n">f</span> <span class="n">remap</span> <span class="n">units</span> <span class="n">box</span>
+<pre class="literal-block">
-<span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">remap</span>
+change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
-</pre></div>
+change_box all x scale 1.1 y volume z volume remap
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -223,15 +223,15 @@ will be re-shrink-wrapped before the change_box command completes.
 Instead you could do something like this, assuming the simulation box
 is non-periodic and atoms extend from 0 to 20 in all dimensions:</p>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span>
+<pre class="literal-block">
-<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span>   <span class="c1"># this will fail to insert an atom</span>
+change_box all x final -10 20
-</pre></div>
+create_atoms 1 single -5 5 5   # this will fail to insert an atom
-</div>
+</pre>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span> <span class="n">boundary</span> <span class="n">f</span> <span class="n">s</span> <span class="n">s</span>
+<pre class="literal-block">
-<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span>
+change_box all x final -10 20 boundary f s s
-<span class="n">change_box</span> <span class="n">boundary</span> <span class="n">s</span> <span class="n">s</span> <span class="n">s</span>      <span class="c1"># this will work</span>
+create_atoms 1 single -5 5 5
-</pre></div>
+change_box boundary s s s      # this will work
-</div>
+</pre>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">Unlike the earlier &#8220;displace_box&#8221; version of this command, atom
@@ -295,30 +295,30 @@ used following a keyword that changed the volume, which is any of the
 <em>x</em>, <em>y</em>, <em>z</em> keywords.  If the preceding keyword &#8220;key&#8221; had a <em>volume</em>
 style, then both it and the current keyword apply to the keyword
 preceding &#8220;key&#8221;.  I.e. this sequence of keywords is allowed:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span>
+<pre class="literal-block">
-</pre></div>
+change_box all x scale 1.1 y volume z volume
-</div>
+</pre>
 <p>The <em>volume</em> style changes the associated dimension so that the
 overall box volume is unchanged relative to its value before the
 preceding keyword was invoked.</p>
 <p>If the following command is used, then the z box length will shrink by
 the same 1.1 factor the x box length was increased by:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
+<pre class="literal-block">
-</pre></div>
+change_box all x scale 1.1 z volume
-</div>
+</pre>
 <p>If the following command is used, then the y,z box lengths will each
 shrink by sqrt(1.1) to keep the volume constant.  In this case, the
 y,z box lengths shrink so as to keep their relative aspect ratio
 constant:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span><span class="s2">&quot;x scale 1.1 y volume z volume</span>
+<pre class="literal-block">
-</pre></div>
+change_box all&quot;x scale 1.1 y volume z volume
-</div>
+</pre>
 <p>If the following command is used, then the final box will be a factor
 of 10% larger in x and y, and a factor of 21% smaller in z, so as to
 keep the volume constant:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">y</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
+<pre class="literal-block">
-</pre></div>
+change_box all x scale 1.1 z volume y scale 1.1 z volume
-</div>
+</pre>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">For solids or liquids, when one dimension of the box is

doc/html/comm_style.html

@@ -128,19 +128,19 @@
 <span id="index-0"></span><h1>comm_style command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_style</span> <span class="n">style</span>
+<pre class="literal-block">
-</pre></div>
+comm_style style
-</div>
+</pre>
 <ul class="simple">
 <li>style = <em>brick</em> or <em>tiled</em></li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_style</span> <span class="n">brick</span>
+<pre class="literal-block">
-<span class="n">comm_style</span> <span class="n">tiled</span>
+comm_style brick
-</pre></div>
+comm_style tiled
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/compute_angle_local.html

@@ -174,11 +174,11 @@ For example, angle output from the <a class="reference internal" href="compute_p
 with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
 command in a consistent way.</p>
 <p>Here is an example of how to do this:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">atype</span> <span class="n">aatom1</span> <span class="n">aatom2</span> <span class="n">aatom3</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">angle</span><span class="o">/</span><span class="n">local</span> <span class="n">theta</span> <span class="n">eng</span>
+compute 1 all property/local atype aatom1 aatom2 aatom3
-<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
+compute 2 all angle/local theta eng
-</pre></div>
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_2[1] c_2[2]
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a local vector or local array depending on the
 number of keywords.  The length of the vector or number of rows in the

doc/html/compute_angmom_chunk.html

@@ -178,11 +178,11 @@ how they are set for each atom.  You can reset the image flags
 <p>The simplest way to output the results of the compute angmom/chunk
 calculation 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">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">angmom</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+compute cc1 all chunk/atom molecule
-<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_myChunk</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">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk all angmom/chunk cc1
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =

doc/html/compute_body_local.html

@@ -183,10 +183,10 @@ details of the different styles.</p>
 body sub-particles are x,y,z coordinates, then the dump file will be
 formatted similar to the output of a <a class="reference internal" href="dump.html"><span class="doc">dump atom or custom</span></a>
 command.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">body</span><span class="o">/</span><span class="n">local</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span>
+<pre class="literal-block">
-<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
+compute 1 all body/local type 1 2 3
-</pre></div>
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4]
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a local vector or local array depending on the
 number of keywords.  The length of the vector or number of rows in the

doc/html/compute_centro_atom.html

@@ -234,7 +234,7 @@ simulation into gold (FCC).  These were provided by Jon Zimmerman
 <span class="n">Free</span> <span class="n">surface</span> <span class="o">~</span> <span class="mf">23.0</span>
 </pre></div>
 </div>
-<p>These values are <em>not</em> normalized by the square of the lattice
+<p>These values are *not* normalized by the square of the lattice
 parameter.  If they were, normalized values would be:</p>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Bulk</span> <span class="n">lattice</span> <span class="o">=</span> <span class="mi">0</span>
 <span class="n">Dislocation</span> <span class="n">core</span> <span class="o">~</span> <span class="mf">0.06</span> <span class="p">(</span><span class="mf">0.03</span> <span class="n">to</span> <span class="mf">0.075</span><span class="p">)</span>

doc/html/compute_chunk_atom.html

@@ -361,13 +361,13 @@ is assigned to the atom.  If the integer value is > 0, it becomes the
 chunk ID to the atom.  <em>Nchunk</em> is set to the largest chunk ID.  Note
 that this excludes atoms which are not in the specified group or
 optional region.</p>
-<p>If the style begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
+<p>If the style begins with &#8220;c_&#8221;, a compute ID must follow which has been
 previously defined in the input script.  If no bracketed integer is
 appended, the per-atom vector calculated by the compute is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
 calculated by the compute is used.  Users can also write code for
 their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If the style begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
+<p>If the style begins with &#8220;f_&#8221;, a fix ID must follow which has been
 previously defined in the input script.  If no bracketed integer is
 appended, the per-atom vector calculated by the fix is used.  If a
 bracketed integer is appended, the Ith column of the per-atom array
@@ -375,7 +375,7 @@ calculated by the fix is used.  Note that some fixes only produce
 their values on certain timesteps, which must be compatible with the
 timestep on which this compute accesses the fix, else an error
 results.  Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name for an <em>atom</em> or
+<p>If a value begins with &#8220;v_&#8221;, a variable name for an <em>atom</em> or
 <em>atomfile</em> style <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> must follow which has been
 previously defined in the input script.  Variables of style <em>atom</em> can
 reference thermodynamic keywords and various per-atom attributes, or

doc/html/compute_com_chunk.html

@@ -176,11 +176,11 @@ and how they are set for each atom.  You can reset the image flags
 <p>The simplest way to output the results of the compute com/chunk
 calculation 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">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+compute cc1 all chunk/atom molecule
-<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_myChunk</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">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk all com/chunk cc1
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =

doc/html/compute_coord_atom.html

@@ -140,11 +140,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">coord</span><span class="o">/</span><span class="n">atom</span> <span class="mf">2.0</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">coord</span><span class="o">/</span><span class="n">atom</span> <span class="mf">6.0</span> <span class="mi">1</span> <span class="mi">2</span>
+compute 1 all coord/atom 2.0
-<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">coord</span><span class="o">/</span><span class="n">atom</span> <span class="mf">6.0</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mi">5</span><span class="o">*</span><span class="mi">8</span> <span class="o">*</span>
+compute 1 all coord/atom 6.0 1 2
-</pre></div>
+compute 1 all coord/atom 6.0 2*4 5*8 *
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -162,7 +162,7 @@ atoms of all types (same as the &#8220;*&#8221; format, see below).</p>
 <p>The <em>typeN</em> keywords can be specified in one of two ways.  An explicit
 numeric value can be used, as in the 2nd example above.  Or a
 wild-card asterisk can be used to specify a range of atom types.  This
-takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N = the number of
+takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N = the number of
 atom types, then an asterisk with no numeric values means all types
 from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A trailing asterisk means all types from n to N

doc/html/compute_dihedral_local.html

@@ -168,11 +168,11 @@ For example, dihedral output from the <a class="reference internal" href="comput
 with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
 command in a consistent way.</p>
 <p>Here is an example of how to do this:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">dtype</span> <span class="n">datom1</span> <span class="n">datom2</span> <span class="n">datom3</span> <span class="n">datom4</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">dihedral</span><span class="o">/</span><span class="n">local</span> <span class="n">phi</span>
+compute 1 all property/local dtype datom1 datom2 datom3 datom4
-<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+compute 2 all dihedral/local phi
-</pre></div>
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a local vector or local array depending on the
 number of keywords.  The length of the vector or number of rows in the

doc/html/compute_dipole_chunk.html

@@ -181,11 +181,11 @@ and how they are set for each atom.  You can reset the image flags
 <p>The simplest way to output the results of the compute com/chunk
 calculation 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">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">dipole</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+compute cc1 all chunk/atom molecule
-<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_myChunk</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">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk all dipole/chunk cc1
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =

doc/html/compute_fep.html

@@ -164,10 +164,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">fep</span> <span class="mi">298</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">epsilon</span> <span class="mi">1</span> <span class="o">*</span> <span class="n">v_delta</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">sigma</span> <span class="mi">1</span> <span class="o">*</span> <span class="n">v_delta</span> <span class="n">volume</span> <span class="n">yes</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">fep</span> <span class="mi">300</span> <span class="n">atom</span> <span class="n">charge</span> <span class="mi">2</span> <span class="n">v_delta</span>
+compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
-</pre></div>
+compute 1 all fep 300 atom charge 2 v_delta
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -307,7 +307,7 @@ each, as in the 1st example above.  I &lt;= J is required.  LAMMPS sets
 the coefficients for the symmetric J,I interaction to the same
 values. A wild-card asterisk can be used in place of or in conjunction
 with the I,J arguments to set the coefficients for multiple pairs of
-atom types.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N =
+atom types.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N =
 the number of atom types, then an asterisk with no numeric values
 means all types from 1 to N.  A leading asterisk means all types from
 1 to n (inclusive).  A trailing asterisk means all types from n to N

doc/html/compute_gyration_chunk.html

@@ -193,11 +193,11 @@ using the <a class="reference internal" href="set.html"><span class="doc">set im
 <p>The simplest way to output the results of the compute gyration/chunk
 calculation 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">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">gyration</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+compute cc1 all chunk/atom molecule
-<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_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk all gyration/chunk cc1
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global vector if the <em>tensor</em> keyword is not
 specified and a global array if it is.  The length of the vector or

doc/html/compute_heat_flux.html

@@ -237,29 +237,30 @@ energy/area/time <a class="reference internal" href="units.html"><span class="do
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Sample LAMMPS input script for thermal conductivity of solid Ar</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>units       real
+<pre class="literal-block">
+units       real
 variable    T equal 70
 variable    V equal vol
 variable    dt equal 4.0
 variable    p equal 200     # correlation length
 variable    s equal 10      # sample interval
 variable    d equal $p*$s   # dump interval
-</pre></div>
+</pre>
-</div>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># convert from LAMMPS real units to SI</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable    kB equal 1.3806504e-23    # [J/K] Boltzmann
+<pre class="literal-block">
+variable    kB equal 1.3806504e-23    # [J/K] Boltzmann
 variable    kCal2J equal 4186.0/6.02214e23
 variable    A2m equal 1.0e-10
 variable    fs2s equal 1.0e-15
 variable    convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}
-</pre></div>
+</pre>
-</div>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># setup problem</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>dimension    3
+<pre class="literal-block">
+dimension    3
 boundary     p p p
 lattice      fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
 region       box block 0 4 0 4 0 4
@@ -270,8 +271,7 @@ pair_style   lj/cut 13.0
 pair_coeff   * * 0.2381 3.405
 timestep     ${dt}
 thermo            $d
-</pre></div>
+</pre>
-</div>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># equilibration and thermalization</span>
 </pre></div>
 </div>
@@ -287,7 +287,8 @@ run          8000
 <span class="c1">#fix         NVE all nve</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span>reset_timestep 0
+<pre class="literal-block">
+reset_timestep 0
 compute      myKE all ke/atom
 compute      myPE all pe/atom
 compute      myStress all stress/atom NULL virial
@@ -305,9 +306,8 @@ thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
 run          100000
 variable     k equal (v_k11+v_k22+v_k33)/3.0
 variable     ndens equal count(all)/vol
-print        &quot;average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3&quot;
+print        &quot;average conductivity: $k[W/mK] &#64; $T K, ${ndens} /A^3&quot;
-</pre></div>
+</pre>
-</div>
 </div>
 </div>
 

doc/html/compute_improper_local.html

@@ -169,11 +169,11 @@ For example, improper output from the <a class="reference internal" href="comput
 with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
 command in a consistent way.</p>
 <p>Here is an example of how to do this:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">itype</span> <span class="n">iatom1</span> <span class="n">iatom2</span> <span class="n">iatom3</span> <span class="n">iatom4</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">improper</span><span class="o">/</span><span class="n">local</span> <span class="n">chi</span>
+compute 1 all property/local itype iatom1 iatom2 iatom3 iatom4
-<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+compute 2 all improper/local chi
-</pre></div>
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a local vector or local array depending on the
 number of keywords.  The length of the vector or number of rows in the

doc/html/compute_inertia_chunk.html

@@ -177,11 +177,11 @@ how they are set for each atom.  You can reset the image flags
 <p>The simplest way to output the results of the compute inertia/chunk
 calculation 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">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">inertia</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+compute cc1 all chunk/atom molecule
-<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_myChunk</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">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk all inertia/chunk cc1
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =

doc/html/compute_ke_atom_eff.html

@@ -168,11 +168,11 @@ eFF.</p>
 thermodynamic output by using the <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a>
 command, as shown in the following example:</p>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>         <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
+<pre class="literal-block">
-<span class="n">thermo_style</span>    <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
+compute         effTemp all temp/eff
-<span class="n">thermo_modify</span>   <span class="n">temp</span> <span class="n">effTemp</span>
+thermo_style    custom step etotal pe ke temp press
-</pre></div>
+thermo_modify   temp effTemp
-</div>
+</pre>
 <p>The value of the kinetic energy will be 0.0 for atoms (nuclei or
 electrons) not in the specified compute group.</p>
 <p><strong>Output info:</strong></p>

doc/html/compute_ke_eff.html

@@ -169,11 +169,11 @@ the <a class="reference internal" href="compute_temp_eff.html"><span class="doc"
 printed with thermodynamic output by using the
 <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
 example:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>         <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
+<pre class="literal-block">
-<span class="n">thermo_style</span>    <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
+compute         effTemp all temp/eff
-<span class="n">thermo_modify</span>   <span class="n">temp</span> <span class="n">effTemp</span>
+thermo_style    custom step etotal pe ke temp press
-</pre></div>
+thermo_modify   temp effTemp
-</div>
+</pre>
 <p>See <a class="reference internal" href="compute_temp_eff.html"><span class="doc">compute temp/eff</span></a>.</p>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global scalar (the KE).  This value can be

doc/html/compute_meso_t_atom.html

@@ -149,7 +149,7 @@ for each atom in a group.</p>
 <p>The internal temperature is the ratio of internal energy over the heat
 capacity associated with the internal degrees of freedom of a mesoscopic
 particles, e.g. a Smooth-Particle Hydrodynamics particle.</p>
-<p><a href="#id1"><span class="problematic" id="id2">T_</span></a><em>int</em> = <a href="#id3"><span class="problematic" id="id4">E_</span></a><em>int</em> / <a href="#id5"><span class="problematic" id="id6">C_</span></a><em>V, int</em></p>
+<p>T_<em>int</em> = E_<em>int</em> / C_<em>V, int</em></p>
 <p>See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in
 LAMMPS.</p>
 <p>The value of the internal energy will be 0.0 for atoms not in the

doc/html/compute_modify.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>compute_modify command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">compute</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
+<pre class="literal-block">
-</pre></div>
+compute_modify compute-ID keyword value ...
-</div>
+</pre>
 <ul class="simple">
 <li>compute-ID = ID of the compute to modify</li>
 <li>one or more keyword/value pairs may be listed</li>
@@ -145,10 +145,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">myTemp</span> <span class="n">extra</span> <span class="mi">0</span>
+<pre class="literal-block">
-<span class="n">compute_modify</span> <span class="n">newtemp</span> <span class="n">dynamic</span> <span class="n">yes</span> <span class="n">extra</span> <span class="mi">600</span>
+compute_modify myTemp extra 0
-</pre></div>
+compute_modify newtemp dynamic yes extra 600
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/compute_msd_chunk.html

@@ -213,11 +213,11 @@ correctly with chunk reference positions from the restart file.</p>
 <p>The simplest way to output the results of the compute com/msd
 calculation 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">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">msd</span> <span class="n">cc1</span>
+compute cc1 all chunk/atom molecule
-<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_myChunk</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">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk all com/msd cc1
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =

doc/html/compute_omega_chunk.html

@@ -178,11 +178,11 @@ how they are set for each atom.  You can reset the image flags
 <p>The simplest way to output the results of the compute omega/chunk
 calculation 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">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">omega</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+compute cc1 all chunk/atom molecule
-<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_myChunk</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">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk all omega/chunk cc1
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =

doc/html/compute_pair_local.html

@@ -206,11 +206,11 @@ For example, pair output from the <a class="reference internal" href="compute_pr
 with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
 command in a consistent way.</p>
 <p>Here is an example of how to do this:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">patom1</span> <span class="n">patom2</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">pair</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span> <span class="n">eng</span> <span class="n">force</span>
+compute 1 all property/local patom1 patom2
-<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+compute 2 all pair/local dist eng force
-</pre></div>
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_2[1] c_2[2] c_2[3]
-</div>
+</pre>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4

doc/html/compute_pe.html

@@ -173,9 +173,9 @@ specified if a fix is to contribute potential energy to this command.</p>
 </div>
 <p>A compute of this style with the ID of &#8220;thermo_pe&#8221; is created when
 LAMMPS starts up, as if this command were in the input script:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_pe</span> <span class="nb">all</span> <span class="n">pe</span>
+<pre class="literal-block">
-</pre></div>
+compute thermo_pe all pe
-</div>
+</pre>
 <p>See the &#8220;thermo_style&#8221; command for more details.</p>
 <hr class="docutils" />
 <p><strong>Output info:</strong></p>

doc/html/compute_pe_atom.html

@@ -185,11 +185,11 @@ command.</p>
 <p>As an example of per-atom potential energy compared to total potential
 energy, these lines in an input script should yield the same result
 in the last 2 columns of thermo output:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>              <span class="n">peratom</span> <span class="nb">all</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span>
+<pre class="literal-block">
-<span class="n">compute</span>              <span class="n">pe</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_peratom</span>
+compute              peratom all pe/atom
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">pe</span> <span class="n">c_pe</span>
+compute              pe all reduce sum c_peratom
-</pre></div>
+thermo_style        custom step temp etotal press pe c_pe
-</div>
+</pre>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">The per-atom energy does not any Lennard-Jones tail corrections

doc/html/compute_pressure.html

@@ -141,10 +141,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">NULL</span> <span class="n">pair</span> <span class="n">bond</span>
+compute 1 all pressure thermo_temp
-</pre></div>
+compute 1 all pressure NULL pair bond
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -196,9 +196,9 @@ degrees-of-freedom divided by d = dimensionality, where the DOF value
 is calcluated by the temperature compute.  See the various <a class="reference internal" href="compute.html"><span class="doc">compute temperature</span></a> styles for details.</p>
 <p>A compute of this style with the ID of &#8220;thermo_press&#8221; is created when
 LAMMPS starts up, as if this command were in the input script:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span>
+<pre class="literal-block">
-</pre></div>
+compute thermo_press all pressure thermo_temp
-</div>
+</pre>
 <p>where &#8220;thermo_temp&#8221; is the ID of a similarly defined compute of style
 &#8220;temp&#8221;.  See the &#8220;thermo_style&#8221; command for more details.</p>
 <hr class="docutils" />

doc/html/compute_property_atom.html

@@ -136,25 +136,25 @@
 <li>property/atom = style name of this compute command</li>
 <li>input = one or more atom attributes</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">possible</span> <span class="n">attributes</span> <span class="o">=</span> <span class="nb">id</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">proc</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span>
+<pre class="literal-block">
-                   <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">xs</span><span class="p">,</span> <span class="n">ys</span><span class="p">,</span> <span class="n">zs</span><span class="p">,</span> <span class="n">xu</span><span class="p">,</span> <span class="n">yu</span><span class="p">,</span> <span class="n">zu</span><span class="p">,</span> <span class="n">ix</span><span class="p">,</span> <span class="n">iy</span><span class="p">,</span> <span class="n">iz</span><span class="p">,</span>
+possible attributes = id, mol, proc, type, mass,
-                   <span class="n">vx</span><span class="p">,</span> <span class="n">vy</span><span class="p">,</span> <span class="n">vz</span><span class="p">,</span> <span class="n">fx</span><span class="p">,</span> <span class="n">fy</span><span class="p">,</span> <span class="n">fz</span><span class="p">,</span>
+                   x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
-                      <span class="n">q</span><span class="p">,</span> <span class="n">mux</span><span class="p">,</span> <span class="n">muy</span><span class="p">,</span> <span class="n">muz</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span>
+                   vx, vy, vz, fx, fy, fz,
-                      <span class="n">radius</span><span class="p">,</span> <span class="n">diameter</span><span class="p">,</span> <span class="n">omegax</span><span class="p">,</span> <span class="n">omegay</span><span class="p">,</span> <span class="n">omegaz</span><span class="p">,</span>
+                      q, mux, muy, muz, mu,
-                   <span class="n">angmomx</span><span class="p">,</span> <span class="n">angmomy</span><span class="p">,</span> <span class="n">angmomz</span><span class="p">,</span>
+                      radius, diameter, omegax, omegay, omegaz,
-                   <span class="n">shapex</span><span class="p">,</span><span class="n">shapey</span><span class="p">,</span> <span class="n">shapez</span><span class="p">,</span>
+                   angmomx, angmomy, angmomz,
-                   <span class="n">quatw</span><span class="p">,</span> <span class="n">quati</span><span class="p">,</span> <span class="n">quatj</span><span class="p">,</span> <span class="n">quatk</span><span class="p">,</span> <span class="n">tqx</span><span class="p">,</span> <span class="n">tqy</span><span class="p">,</span> <span class="n">tqz</span><span class="p">,</span>
+                   shapex,shapey, shapez,
-                   <span class="n">end1x</span><span class="p">,</span> <span class="n">end1y</span><span class="p">,</span> <span class="n">end1z</span><span class="p">,</span> <span class="n">end2x</span><span class="p">,</span> <span class="n">end2y</span><span class="p">,</span> <span class="n">end2z</span><span class="p">,</span>
+                   quatw, quati, quatj, quatk, tqx, tqy, tqz,
-                   <span class="n">corner1x</span><span class="p">,</span> <span class="n">corner1y</span><span class="p">,</span> <span class="n">corner1z</span><span class="p">,</span>
+                   end1x, end1y, end1z, end2x, end2y, end2z,
-                   <span class="n">corner2x</span><span class="p">,</span> <span class="n">corner2y</span><span class="p">,</span> <span class="n">corner2z</span><span class="p">,</span>
+                   corner1x, corner1y, corner1z,
-                   <span class="n">corner3x</span><span class="p">,</span> <span class="n">corner3y</span><span class="p">,</span> <span class="n">corner3z</span><span class="p">,</span>
+                   corner2x, corner2y, corner2z,
-                   <span class="n">nbonds</span><span class="p">,</span>
+                   corner3x, corner3y, corner3z,
-                      <span class="n">vfrac</span><span class="p">,</span> <span class="n">s0</span><span class="p">,</span>
+                   nbonds,
-                   <span class="n">spin</span><span class="p">,</span> <span class="n">eradius</span><span class="p">,</span> <span class="n">ervel</span><span class="p">,</span> <span class="n">erforce</span><span class="p">,</span>
+                      vfrac, s0,
-                      <span class="n">rho</span><span class="p">,</span> <span class="n">drho</span><span class="p">,</span> <span class="n">e</span><span class="p">,</span> <span class="n">de</span><span class="p">,</span> <span class="n">cv</span><span class="p">,</span>
+                   spin, eradius, ervel, erforce,
-                      <span class="n">i_name</span><span class="p">,</span> <span class="n">d_name</span>
+                      rho, drho, e, de, cv,
-</pre></div>
+                      i_name, d_name
-</div>
+</pre>
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">id</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span>
 <span class="n">mol</span> <span class="o">=</span> <span class="n">molecule</span> <span class="n">ID</span>
 <span class="n">proc</span> <span class="o">=</span> <span class="n">ID</span> <span class="n">of</span> <span class="n">processor</span> <span class="n">that</span> <span class="n">owns</span> <span class="n">atom</span>

doc/html/compute_property_chunk.html

@@ -192,12 +192,12 @@ will be in unitless reduced units (0-1).</p>
 <p>The simplest way to output the results of the compute property/chunk
 calculation 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">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span> <span class="n">count</span>
+compute cc1 all chunk/atom molecule
-<span class="n">compute</span> <span class="n">myChunk2</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+compute myChunk1 all property/chunk cc1 count
-<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_myChunk1</span> <span class="n">c_myChunk2</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">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk2 all com/chunk cc1
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global vector or global array depending on
 the number of input values.  The length of the vector or number of

doc/html/compute_reduce.html

@@ -148,14 +148,14 @@
 <li>one or more inputs can be listed</li>
 <li>input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
+<pre class="literal-block">
-<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
-<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+c_ID = per-atom or local vector calculated by a compute with ID
-<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
-<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
+f_ID = per-atom or local vector calculated by a fix with ID
-<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
+f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
-</pre></div>
+v_name = per-atom vector calculated by an atom-style variable with name
-</div>
+</pre>
 <ul class="simple">
 <li>zero or more keyword/args pairs may be appended</li>
 <li>keyword = <em>replace</em></li>
@@ -168,13 +168,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_force</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">reduce</span><span class="o">/</span><span class="n">region</span> <span class="n">subbox</span> <span class="nb">sum</span> <span class="n">c_force</span>
+compute 1 all reduce sum c_force
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">c_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">f_ave</span> <span class="n">v_myKE</span>
+compute 1 all reduce/region subbox sum c_force
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">c_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">f_ave</span> <span class="n">v_myKE</span>
+compute 2 all reduce min c_press[2] f_ave v_myKE
-<span class="n">compute</span> <span class="mi">3</span> <span class="n">fluid</span> <span class="n">reduce</span> <span class="nb">max</span> <span class="n">c_index</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_index</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_dist</span> <span class="n">replace</span> <span class="mi">1</span> <span class="mi">3</span> <span class="n">replace</span> <span class="mi">2</span> <span class="mi">3</span>
+compute 2 all reduce min c_press[*] f_ave v_myKE
-</pre></div>
+compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -211,7 +211,7 @@ component) or can be the result of a <a class="reference internal" href="compute
 <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.</p>
 <p>Note that for values from a compute or fix, the bracketed index I can
 be specified using a wildcard asterisk with the index to effectively
-specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
+specify multiple values.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
 &#8220;m*n&#8221;.  If N = the size of the vector (for <em>mode</em> = scalar) or the
 number of columns in the array (for <em>mode</em> = vector), then an asterisk
 with no numeric values means all indices from 1 to N.  A leading
@@ -222,18 +222,18 @@ means all indices from m to n (inclusive).</p>
 had been listed one by one.  E.g. these 2 compute reduce commands are
 equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
 command creates a per-atom array with 6 columns:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
+compute myPress all stress/atom NULL
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
+compute 2 all reduce min myPress[*]
-                         <span class="n">myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
+compute 2 all reduce min myPress[1] myPress[2] myPress[3] &amp;
-</pre></div>
+                         myPress[4] myPress[5] myPress[6]
-</div>
+</pre>
 <hr class="docutils" />
 <p>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
 self-explanatory.  Note that other atom attributes can be used as
 inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command and then specifying
 an input value from that compute.</p>
-<p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
+<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
 previously defined in the input script.  Computes can generate
 per-atom or local quantities.  See the individual
 <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> doc page for details.  If no bracketed integer
@@ -243,7 +243,7 @@ by the compute is used.  Users can also write code for their own
 compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.  See the
 discussion above for how I can be specified with a wildcard asterisk
 to effectively specify multiple values.</p>
-<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
+<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
 previously defined in the input script.  Fixes can generate per-atom
 or local quantities.  See the individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> doc page for
 details.  Note that some fixes only produce their values on certain
@@ -254,7 +254,7 @@ integer is appended, the Ith column of the array calculated by the fix
 is used.  Users can also write code for their own fix style and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.  See the discussion above for how
 I can be specified with a wildcard asterisk to effectively specify
 multiple values.</p>
-<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
+<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
 been previously defined in the input script.  It must be an
 <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>.  Atom-style variables can
 reference thermodynamic keywords and various per-atom attributes, or
@@ -271,12 +271,12 @@ Then, instead of performing a min/max on the <em>vec1</em> input vector, the
 stored index is used to select the Nth element of the <em>vec1</em> vector.</p>
 <p>Thus, for example, if you wish to use this compute to find the bond
 with maximum stretch, you can do it as follows:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span>
+<pre class="literal-block">
-<span class="n">compute</span>      <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span>
+compute 1 all property/local batom1 batom2
-<span class="n">compute</span>      <span class="mi">3</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">max</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_2</span> <span class="n">replace</span> <span class="mi">1</span> <span class="mi">3</span> <span class="n">replace</span> <span class="mi">2</span> <span class="mi">3</span>
+compute      2 all bond/local dist
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+compute      3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
-</pre></div>
+thermo_style custom step temp c_3[1] c_3[2] c_3[3]
-</div>
+</pre>
 <p>The first two input values in the compute reduce command are vectors
 with the IDs of the 2 atoms in each bond, using the <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a> command.  The last input
 value is bond distance, using the <a class="reference internal" href="compute_bond_local.html"><span class="doc">compute bond/local</span></a> command.  Instead of taking the

doc/html/compute_rigid_local.html

@@ -202,10 +202,10 @@ there will be no consistent ordering of the entries within the local
 vector or array from one timestep to the next.</p>
 <p>Here is an example of how to use this compute to dump rigid body info
 to a file:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rigid</span><span class="o">/</span><span class="n">local</span> <span class="n">myRigid</span> <span class="n">mol</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span>
+<pre class="literal-block">
-<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span>
+compute 1 all rigid/local myRigid mol x y z fx fy fz
-</pre></div>
+dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]
-</div>
+</pre>
 <hr class="docutils" />
 <p>This section explains the rigid body attributes that can be specified.</p>
 <p>The <em>id</em> attribute is the atomID of the atom which owns the rigid body, which is

doc/html/compute_saed.html

@@ -157,14 +157,14 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Al</span> <span class="n">O</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="n">dR_Ewald</span> <span class="mf">0.01</span> <span class="n">c</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">0.5</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Ni</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="n">c</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="n">manual</span> <span class="n">echo</span>
+compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
-</pre></div>
+compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
-</div>
+</pre>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_1</span> <span class="n">file</span> <span class="n">Al2O3_001</span><span class="o">.</span><span class="n">saed</span>
+<pre class="literal-block">
-<span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_2</span> <span class="n">file</span> <span class="n">Ni_000</span><span class="o">.</span><span class="n">saed</span>
+fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
-</pre></div>
+fix saed/vtk 1 1 1 c_2 file Ni_000.saed
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -193,7 +193,7 @@ shown in the 2D diagram below.</p>
                      height="auto"
                      alt=""/>
                 </a><p>For a mesh defined by the simulation domain, a rectilinear grid is
-constructed with spacing <em>c</em><a href="#id1"><span class="problematic" id="id2">*</span></a>inv(A) along each reciprocal lattice
+constructed with spacing <em>c</em>*inv(A) along each reciprocal lattice
 axis. Where A are the vectors corresponding to the edges of the
 simulation cell. If one or two directions has non-periodic boundary
 conditions, then the spacing in these directions is defined from the

doc/html/compute_slice.html

@@ -139,20 +139,20 @@
 <li>Nskip = extract every Nskip elements from input vector(s)</li>
 <li>input = c_ID, c_ID[N], f_ID, f_ID[N]</li>
 </ul>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+<pre class="literal-block">
-<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="k">global</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
+c_ID = global vector calculated by a compute with ID
-<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+c_ID[I] = Ith column of global array calculated by a compute with ID
-<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="k">global</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
+f_ID = global vector calculated by a fix with ID
-<span class="n">v_name</span> <span class="o">=</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
+f_ID[I] = Ith column of global array calculated by a fix with ID
-</pre></div>
+v_name = vector calculated by an vector-style variable with name
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">slice</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">10</span> <span class="n">c_msdmol</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">slice</span> <span class="mi">301</span> <span class="mi">400</span> <span class="mi">1</span> <span class="n">c_msdmol</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">v_myVec</span>
+compute 1 all slice 1 100 10 c_msdmol[4]
-</pre></div>
+compute 1 all slice 301 400 1 c_msdmol[4] v_myVec
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -172,14 +172,14 @@ vector, which is typically shorter than the input vector.</p>
 vector.  Each listed input must be a global vector or column of a
 global array calculated by another <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> or
 <a class="reference internal" href="fix.html"><span class="doc">fix</span></a>.</p>
-<p>If an input value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has
+<p>If an input value begins with &#8220;c_&#8221;, a compute ID must follow which has
 been previously defined in the input script and which generates a
 global vector or array.  See the individual <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> doc
 page for details.  If no bracketed integer is appended, the vector
 calculated by the compute is used.  If a bracketed integer is
 appended, the Ith column of the array calculated by the compute is
 used.  Users can also write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
+<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
 previously defined in the input script and which generates a global
 vector or array.  See the individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> doc page for
 details.  Note that some fixes only produce their values on certain
@@ -188,7 +188,7 @@ the values, else an error results.  If no bracketed integer is
 appended, the vector calculated by the fix is used.  If a bracketed
 integer is appended, the Ith column of the array calculated by the fix
 is used.  Users can also write code for their own fix style and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
-<p>If an input value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which
+<p>If an input value begins with &#8220;v_&#8221;, a variable name must follow which
 has been previously defined in the input script.  Only vector-style
 variables can be referenced.  See the <a class="reference internal" href="variable.html"><span class="doc">variable</span></a> command
 for details.  Note that variables of style <em>vector</em> define a formula

doc/html/compute_smd_triangle_mesh_vertices.html

@@ -145,7 +145,7 @@
 <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 href="#id4"><span class="problematic" id="id5">`fix smd/wall\_surface &lt;ls_&gt;`_</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>
@@ -157,7 +157,7 @@ for an overview of LAMMPS output options.</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 href="#id6"><span class="problematic" id="id7">`fix smd/wall\_surface &lt;ls_&gt;`_</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
 visualization purposes.</p>

doc/html/compute_sna_atom.html

@@ -134,11 +134,11 @@
 <h1>compute snav/atom command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">sna</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">snad</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-<span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">snav</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-</pre></div>
+compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-</div>
+</pre>
 <ul class="simple">
 <li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
 <li>sna/atom = style name of this compute command</li>
@@ -276,22 +276,22 @@ corresponding to a particular bispectrum component.  The total number
 of columns and the identities of the bispectrum component contained in
 each column depend on the values of <em>twojmax</em> and <em>diagonal</em>, as
 described by the following piece of python code:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">j1</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">twojmax</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
+<pre class="literal-block">
-    <span class="k">if</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">2</span><span class="p">):</span>
+for j1 in range(0,twojmax+1):
-        <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span>
+    if(diagonal==2):
-    <span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">1</span><span class="p">):</span>
+        print j1/2.,j1/2.,j1/2.
-        <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="mi">2</span><span class="o">*</span><span class="n">j1</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
+    elif(diagonal==1):
-            <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
+        for j in range(0,min(twojmax,2*j1)+1,2):
-    <span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">0</span><span class="p">):</span>
+            print j1/2.,j1/2.,j/2.
-        <span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
+    elif(diagonal==0):
-            <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
+        for j2 in range(0,j1+1):
-                <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
+            for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
-    <span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">3</span><span class="p">):</span>
+                print j1/2.,j2/2.,j/2.
-        <span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
+    elif(diagonal==3):
-            <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
+        for j2 in range(0,j1+1):
-                <span class="k">if</span> <span class="p">(</span><span class="n">j</span><span class="o">&gt;=</span><span class="n">j1</span><span class="p">):</span> <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
+            for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
-</pre></div>
+                if (j&gt;=j1): print j1/2.,j2/2.,j/2.
-</div>
+</pre>
 <p>Compute <em>snad/atom</em> evaluates a per-atom array. The columns are
 arranged into <em>ntypes</em> blocks, listed in order of atom type <em>I</em>.  Each
 block contains three sub-blocks corresponding to the <em>x</em>, <em>y</em>, and <em>z</em>

doc/html/compute_stress_atom.html

@@ -234,12 +234,12 @@ d = dimension and V is the volume of the system, the result should be
 -P, where P is the total pressure of the system.</p>
 <p>These lines in an input script for a 3d system should yield that
 result.  I.e. the last 2 columns of thermo output will be the same:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>              <span class="n">peratom</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
+<pre class="literal-block">
-<span class="n">compute</span>              <span class="n">p</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+compute              peratom all stress/atom NULL
-<span class="n">variable</span>     <span class="n">press</span> <span class="n">equal</span> <span class="o">-</span><span class="p">(</span><span class="n">c_p</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">c_p</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">+</span><span class="n">c_p</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span><span class="o">/</span><span class="p">(</span><span class="mi">3</span><span class="o">*</span><span class="n">vol</span><span class="p">)</span>
+compute              p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
-<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">v_press</span>
+variable     press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
-</pre></div>
+thermo_style        custom step temp etotal press v_press
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a per-atom array with 6 columns, which can be
 accessed by indices 1-6 by any command that uses per-atom values from

doc/html/compute_temp.html

@@ -172,9 +172,9 @@ needed, the subtracted degrees-of-freedom can be altered using the
 <em>extra</em> option of the <a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command.</p>
 <p>A compute of this style with the ID of &#8220;thermo_temp&#8221; is created when
 LAMMPS starts up, as if this command were in the input script:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_temp</span> <span class="nb">all</span> <span class="n">temp</span>
+<pre class="literal-block">
-</pre></div>
+compute thermo_temp all temp
-</div>
+</pre>
 <p>See the &#8220;thermo_style&#8221; command for more details.</p>
 <p>See <a class="reference internal" href="Section_howto.html#howto-16"><span class="std std-ref">this howto section</span></a> of the manual for
 a discussion of different ways to compute temperature and perform

doc/html/compute_temp_chunk.html

@@ -254,11 +254,11 @@ IDs.</p>
 </div>
 <p>The simplest way to output the per-chunk results of the compute
 temp/chunk calculation 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">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span> <span class="n">temp</span>
+compute cc1 all chunk/atom molecule
-<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_myChunk</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk all temp/chunk cc1 temp
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
-</div>
+</pre>
 <hr class="docutils" />
 <p>The keyword/value option pairs are used in the following ways.</p>
 <p>The <em>com</em> keyword can be used with a value of <em>yes</em> to subtract the

doc/html/compute_temp_cs.html

@@ -140,10 +140,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">oxygen_c</span><span class="o">-</span><span class="n">s</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">O_core</span> <span class="n">O_shell</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">core_shells</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">cores</span> <span class="n">shells</span>
+compute oxygen_c-s all temp/cs O_core O_shell
-</pre></div>
+compute core_shells all temp/cs cores shells
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/compute_temp_eff.html

@@ -170,11 +170,11 @@ reported by LAMMPS in the thermodynamic quantities reported via the
 <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
 example:</p>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>         <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
+<pre class="literal-block">
-<span class="n">thermo_style</span>    <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
+compute         effTemp all temp/eff
-<span class="n">thermo_modify</span>   <span class="n">temp</span> <span class="n">effTemp</span>
+thermo_style    custom step etotal pe ke temp press
-</pre></div>
+thermo_modify   temp effTemp
-</div>
+</pre>
 <p>A 6-component kinetic energy tensor is also calculated by this compute
 for use in the computation of a pressure tensor.  The formula for the
 components of the tensor is the same as the above formula, except that

doc/html/compute_ti.html

@@ -154,10 +154,10 @@ pair style args = atype v_name1 v_name2
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ti</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span> <span class="n">v_lj</span> <span class="n">v_dlj</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mi">2</span> <span class="n">v_c</span> <span class="n">v_dc</span> <span class="n">kspace</span> <span class="mi">1</span> <span class="n">v_ks</span> <span class="n">v_dks</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ti</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="n">v_lj</span> <span class="n">v_dlj</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="o">*</span> <span class="n">v_c</span> <span class="n">v_dc</span> <span class="n">kspace</span> <span class="o">*</span> <span class="n">v_ks</span> <span class="n">v_dks</span>
+compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
-</pre></div>
+compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -192,7 +192,7 @@ with respect to <em>lambda</em>.</p>
 numeric values can be used, as in the 1st example above.  Or a
 wildcard asterisk can be used in place of or in conjunction with the
 <em>atype</em> argument to select multiple atom types.  This takes the form
-&#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N = the number of atom types, then
+&#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N = the number of atom types, then
 an asterisk with no numeric values means all types from 1 to N.  A
 leading asterisk means all types from 1 to n (inclusive).  A trailing
 asterisk means all types from n to N (inclusive).  A middle asterisk

doc/html/compute_torque_chunk.html

@@ -177,11 +177,11 @@ how they are set for each atom.  You can reset the image flags
 <p>The simplest way to output the results of the compute torque/chunk
 calculation 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">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">torque</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+compute cc1 all chunk/atom molecule
-<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_myChunk</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">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk all torque/chunk cc1
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =

doc/html/compute_vacf.html

@@ -159,12 +159,12 @@ averaged over atoms in the group.</p>
 <p>The integral of the VACF versus time is proportional to the diffusion
 coefficient of the diffusing atoms.  This can be computed in the
 following manner, using the <a class="reference internal" href="variable.html"><span class="doc">variable trap()</span></a> function:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span>         <span class="mi">2</span> <span class="nb">all</span> <span class="n">vacf</span>
+<pre class="literal-block">
-<span class="n">fix</span>             <span class="mi">5</span> <span class="nb">all</span> <span class="n">vector</span> <span class="mi">1</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
+compute         2 all vacf
-<span class="n">variable</span>        <span class="n">diff</span> <span class="n">equal</span> <span class="n">dt</span><span class="o">*</span><span class="n">trap</span><span class="p">(</span><span class="n">f_5</span><span class="p">)</span>
+fix             5 all vector 1 c_2[4]
-<span class="n">thermo_style</span>    <span class="n">custom</span> <span class="n">step</span> <span class="n">v_diff</span>
+variable        diff equal dt*trap(f_5)
-</pre></div>
+thermo_style    custom step v_diff
-</div>
+</pre>
 <div class="admonition note">
 <p class="first admonition-title">Note</p>
 <p class="last">If you want the quantities calculated by this compute to be

doc/html/compute_vcm_chunk.html

@@ -167,11 +167,11 @@ non-zero chunk IDs.</p>
 <p>The simplest way to output the results of the compute vcm/chunk
 calculation 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">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">vcm</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
+compute cc1 all chunk/atom molecule
-<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_myChunk</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">out</span> <span class="n">mode</span> <span class="n">vector</span>
+compute myChunk all vcm/chunk cc1
-</pre></div>
+fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
-</div>
+</pre>
 <p><strong>Output info:</strong></p>
 <p>This compute calculates a global array where the number of rows = the
 number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command.  The number of columns =

doc/html/compute_voronoi_atom.html

@@ -158,14 +158,14 @@ or <em>face_threshold</em> or <em>neighbors</em> or <em>peratom</em></li>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="mi">2</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">surface</span> <span class="n">matrix</span>
+compute 1 all voronoi/atom
-<span class="n">compute</span> <span class="mi">3</span><span class="n">b</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">radius</span> <span class="n">v_r</span>
+compute 2 precipitate voronoi/atom surface matrix
-<span class="n">compute</span> <span class="mi">4</span> <span class="n">solute</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">only_group</span>
+compute 3b precipitate voronoi/atom radius v_r
-<span class="n">compute</span> <span class="mi">5</span> <span class="n">defects</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">occupation</span>
+compute 4 solute voronoi/atom only_group
-<span class="n">compute</span> <span class="mi">6</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">neighbors</span> <span class="n">yes</span>
+compute 5 defects voronoi/atom occupation
-</pre></div>
+compute 6 all voronoi/atom neighbors yes
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -199,11 +199,11 @@ can be obtained by running a &#8220;reduce sum&#8221; compute on c_2[3]</p>
 <p>If the <em>radius</em> keyword is specified with an atom style variable as
 the argument, a poly-disperse Voronoi tessellation is
 performed. Examples for radius variables are</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">r1</span> <span class="n">atom</span> <span class="p">(</span><span class="nb">type</span><span class="o">==</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="mf">0.1</span><span class="o">+</span><span class="p">(</span><span class="nb">type</span><span class="o">==</span><span class="mi">2</span><span class="p">)</span><span class="o">*</span><span class="mf">0.4</span>
+<pre class="literal-block">
-<span class="n">compute</span> <span class="n">radius</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">radius</span>
+variable r1 atom (type==1)*0.1+(type==2)*0.4
-<span class="n">variable</span> <span class="n">r2</span> <span class="n">atom</span> <span class="n">c_radius</span>
+compute radius all property/atom radius
-</pre></div>
+variable r2 atom c_radius
-</div>
+</pre>
 <p>Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms
 and 0.4 units for type 2 atoms, and v_r2 accesses the radius property
 present in atom_style sphere for granular models.</p>
@@ -247,10 +247,10 @@ uses local values from a compute as input.  See <a class="reference internal" hr
 options. More specifically, the array can be accessed by a
 <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command to write a file containing
 all the Voronoi neighbors in a system:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">6</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">neighbors</span> <span class="n">yes</span>
+<pre class="literal-block">
-<span class="n">dump</span> <span class="n">d2</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1</span> <span class="n">dump</span><span class="o">.</span><span class="n">neighbors</span> <span class="n">index</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
+compute 6 all voronoi/atom neighbors yes
-</pre></div>
+dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
-</div>
+</pre>
 <p>If the <em>face_threshold</em> keyword is used, then only faces
 with areas greater than the threshold are stored.</p>
 <hr class="docutils" />

doc/html/compute_xrd.html

@@ -159,10 +159,10 @@
 <span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">xrd</span> <span class="mf">1.541838</span> <span class="n">Al</span> <span class="n">O</span> <span class="mi">2</span><span class="n">Theta</span> <span class="mi">10</span> <span class="mi">100</span> <span class="n">c</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="n">LP</span> <span class="mi">1</span> <span class="n">manual</span>
 </pre></div>
 </div>
-<div class="highlight-default"><div class="highlight"><pre><span></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">histo</span><span class="o">/</span><span class="n">weight</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">0.087</span> <span class="mf">0.87</span> <span class="mi">250</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">file</span> <span class="n">Rad2Theta</span><span class="o">.</span><span class="n">xrd</span>
+<pre class="literal-block">
-<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span><span class="o">/</span><span class="n">weight</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">250</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">file</span> <span class="n">Deg2Theta</span><span class="o">.</span><span class="n">xrd</span>
+fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
-</pre></div>
+fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -196,7 +196,7 @@ shown in the 2D diagram below.</p>
                      height="auto"
                      alt=""/>
                 </a><p>For a mesh defined by the simulation domain, a rectilinear grid is
-constructed with spacing <em>c</em><a href="#id1"><span class="problematic" id="id2">*</span></a>inv(A) along each reciprocal lattice
+constructed with spacing <em>c</em>*inv(A) along each reciprocal lattice
 axis. Where A are the vectors corresponding to the edges of the
 simulation cell. If one or two directions has non-periodic boundary
 conditions, then the spacing in these directions is defined from the

doc/html/create_atoms.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>create_atoms command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_atoms</span> <span class="nb">type</span> <span class="n">style</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
+<pre class="literal-block">
-</pre></div>
+create_atoms type style args keyword values ...
-</div>
+</pre>
 <ul class="simple">
 <li>type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</li>
 <li>style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></li>
@@ -172,12 +172,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span>
+<pre class="literal-block">
-<span class="n">create_atoms</span> <span class="mi">3</span> <span class="n">region</span> <span class="n">regsphere</span> <span class="n">basis</span> <span class="mi">2</span> <span class="mi">3</span>
+create_atoms 1 box
-<span class="n">create_atoms</span> <span class="mi">3</span> <span class="n">single</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">5</span>
+create_atoms 3 region regsphere basis 2 3
-<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">var</span> <span class="n">v</span> <span class="nb">set</span> <span class="n">x</span> <span class="n">xpos</span> <span class="nb">set</span> <span class="n">y</span> <span class="n">ypos</span>
+create_atoms 3 single 0 0 5
-</pre></div>
+create_atoms 1 box var v set x xpos set y ypos
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -328,19 +328,19 @@ the sinusoid would appear to be &#8220;smoother&#8221;.  Also note the use of th
 &#8220;xlat&#8221; and &#8220;ylat&#8221; <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> keywords which
 converts lattice spacings to distance.  Click on the image for a
 larger version.</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span>variable        x equal 100
+<pre class="literal-block">
+variable        x equal 100
 variable        y equal 25
 lattice              hex 0.8442
 region               box block 0 $x 0 $y -0.5 0.5
-create_box   1 box
+create_box  1 box
-</pre></div>
+</pre>
-</div>
+<pre class="literal-block">
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span>        <span class="n">xx</span> <span class="n">equal</span> <span class="mf">0.0</span>
+variable        xx equal 0.0
-<span class="n">variable</span>        <span class="n">yy</span> <span class="n">equal</span> <span class="mf">0.0</span>
+variable        yy equal 0.0
-<span class="n">variable</span>        <span class="n">v</span> <span class="n">equal</span> <span class="s2">&quot;(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) &gt; 0.0&quot;</span>
+variable        v equal &quot;(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) &gt; 0.0&quot;
-<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">var</span> <span class="n">v</span> <span class="nb">set</span> <span class="n">x</span> <span class="n">xx</span> <span class="nb">set</span> <span class="n">y</span> <span class="n">yy</span>
+create_atoms        1 box var v set x xx set y yy
-</pre></div>
+</pre>
-</div>
 <a class=""
                data-lightbox="group-default"
                href="_images/sinusoid.jpg"

doc/html/create_bonds.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>create_bonds command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_bonds</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">group2</span><span class="o">-</span><span class="n">ID</span> <span class="n">btype</span> <span class="n">rmin</span> <span class="n">rmax</span>
+<pre class="literal-block">
-</pre></div>
+create_bonds group-ID group2-ID btype rmin rmax
-</div>
+</pre>
 <ul class="simple">
 <li>group-ID = ID of first group</li>
 <li>group2-ID = ID of second group, bonds will be between atoms in the 2 groups</li>
@@ -141,10 +141,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_bonds</span> <span class="nb">all</span> <span class="nb">all</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.2</span>
+<pre class="literal-block">
-<span class="n">create_bonds</span> <span class="n">surf</span> <span class="n">solvent</span> <span class="mi">3</span> <span class="mf">2.0</span> <span class="mf">2.4</span>
+create_bonds all all 1 1.0 1.2
-</pre></div>
+create_bonds surf solvent 3 2.0 2.4
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/create_box.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>create_box command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_box</span> <span class="n">N</span> <span class="n">region</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
+<pre class="literal-block">
-</pre></div>
+create_box N region-ID keyword value ...
-</div>
+</pre>
 <ul class="simple">
 <li>N = # of atom types to use in this simulation</li>
 <li>region-ID = ID of region to use as simulation domain</li>
@@ -151,10 +151,10 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_box</span> <span class="mi">2</span> <span class="n">mybox</span>
+<pre class="literal-block">
-<span class="n">create_box</span> <span class="mi">2</span> <span class="n">mybox</span> <span class="n">bond</span><span class="o">/</span><span class="n">types</span> <span class="mi">2</span> <span class="n">extra</span><span class="o">/</span><span class="n">bond</span><span class="o">/</span><span class="n">per</span><span class="o">/</span><span class="n">atom</span> <span class="mi">1</span>
+create_box 2 mybox
-</pre></div>
+create_box 2 mybox bond/types 2 extra/bond/per/atom 1
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/delete_atoms.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>delete_atoms command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_atoms</span> <span class="n">style</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
+<pre class="literal-block">
-</pre></div>
+delete_atoms style args keyword value ...
-</div>
+</pre>
 <ul class="simple">
 <li>style = <em>group</em> or <em>region</em> or <em>overlap</em> or <em>porosity</em></li>
 </ul>
@@ -158,13 +158,13 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_atoms</span> <span class="n">group</span> <span class="n">edge</span>
+<pre class="literal-block">
-<span class="n">delete_atoms</span> <span class="n">region</span> <span class="n">sphere</span> <span class="n">compress</span> <span class="n">no</span>
+delete_atoms group edge
-<span class="n">delete_atoms</span> <span class="n">overlap</span> <span class="mf">0.3</span> <span class="nb">all</span> <span class="nb">all</span>
+delete_atoms region sphere compress no
-<span class="n">delete_atoms</span> <span class="n">overlap</span> <span class="mf">0.5</span> <span class="n">solvent</span> <span class="n">colloid</span>
+delete_atoms overlap 0.3 all all
-<span class="n">delete_atoms</span> <span class="n">porosity</span> <span class="n">cube</span> <span class="mf">0.1</span> <span class="mi">482793</span> <span class="n">bond</span> <span class="n">yes</span>
+delete_atoms overlap 0.5 solvent colloid
-</pre></div>
+delete_atoms porosity cube 0.1 482793 bond yes
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/delete_bonds.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>delete_bonds command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">arg</span> <span class="n">keyword</span> <span class="o">...</span>
+<pre class="literal-block">
-</pre></div>
+delete_bonds group-ID style arg keyword ...
-</div>
+</pre>
 <ul>
 <li><p class="first">group-ID = group ID</p>
 </li>
@@ -157,12 +157,12 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="n">frozen</span> <span class="n">multi</span> <span class="n">remove</span>
+<pre class="literal-block">
-<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">4</span> <span class="n">special</span>
+delete_bonds frozen multi remove
-<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">bond</span> <span class="mi">0</span><span class="o">*</span><span class="mi">3</span> <span class="n">special</span>
+delete_bonds all atom 4 special
-<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">stats</span>
+delete_bonds all bond 0*3 special
-</pre></div>
+delete_bonds all stats
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -183,7 +183,7 @@ be an integer from 0 to N, where N is the number of relevant types
 (atom types, bond types, etc).  A value of 0 is only relevant for
 style <em>bond</em>; see details below.  In all cases, a wildcard asterisk
 can be used in place of or in conjunction with the <em>type</em> argument to
-specify a range of types.  This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
+specify a range of types.  This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
 &#8220;m*n&#8221;.  If N = the number of types, then an asterisk with no numeric
 values means all types from 0 to N.  A leading asterisk means all
 types from 0 to n (inclusive).  A trailing asterisk means all types

doc/html/dihedral_charmm.html

@@ -137,18 +137,18 @@
 <h1>dihedral_style charmm/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">charmm</span>
+<pre class="literal-block">
-</pre></div>
+dihedral_style charmm
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">charmm</span>
+<pre class="literal-block">
-<span class="n">dihedral_coeff</span>  <span class="mi">1</span> <span class="mf">0.2</span> <span class="mi">1</span> <span class="mi">180</span> <span class="mf">1.0</span>
+dihedral_style charmm
-<span class="n">dihedral_coeff</span>  <span class="mi">2</span> <span class="mf">1.8</span> <span class="mi">1</span>   <span class="mi">0</span> <span class="mf">1.0</span>
+dihedral_coeff  1 0.2 1 180 1.0
-<span class="n">dihedral_coeff</span>  <span class="mi">1</span> <span class="mf">3.1</span> <span class="mi">2</span> <span class="mi">180</span> <span class="mf">0.5</span>
+dihedral_coeff  2 1.8 1   0 1.0
-</pre></div>
+dihedral_coeff  1 3.1 2 180 0.5
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/dihedral_class2.html

@@ -131,21 +131,21 @@
 <h1>dihedral_style class2/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">class2</span>
+<pre class="literal-block">
-</pre></div>
+dihedral_style class2
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">class2</span>
+<pre class="literal-block">
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">75</span> <span class="mi">100</span> <span class="mi">70</span> <span class="mi">80</span> <span class="mi">60</span>
+dihedral_style class2
-<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">mbt</span> <span class="mf">3.5945</span> <span class="mf">0.1704</span> <span class="o">-</span><span class="mf">0.5490</span> <span class="mf">1.5228</span>
+dihedral_coeff 1 100 75 100 70 80 60
-<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">ebt</span> <span class="mf">0.3417</span> <span class="mf">0.3264</span> <span class="o">-</span><span class="mf">0.9036</span> <span class="mf">0.1368</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.8080</span> <span class="mf">1.0119</span> <span class="mf">1.1010</span>
+dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
-<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="n">at</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.1850</span> <span class="o">-</span><span class="mf">0.7963</span> <span class="o">-</span><span class="mf">2.0220</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.3991</span> <span class="mf">110.2453</span> <span class="mf">105.1270</span>
+dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
-<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">aat</span> <span class="o">-</span><span class="mf">13.5271</span> <span class="mf">110.2453</span> <span class="mf">105.1270</span>
+dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
-<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">bb13</span> <span class="mf">0.0</span> <span class="mf">1.0119</span> <span class="mf">1.1010</span>
+dihedral_coeff * aat -13.5271 110.2453 105.1270
-</pre></div>
+dihedral_coeff * bb13 0.0 1.0119 1.1010
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/dihedral_coeff.html

@@ -128,9 +128,9 @@
 <span id="index-0"></span><h1>dihedral_coeff command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_coeff</span> <span class="n">N</span> <span class="n">args</span>
+<pre class="literal-block">
-</pre></div>
+dihedral_coeff N args
-</div>
+</pre>
 <ul class="simple">
 <li>N = dihedral type (see asterisk form below)</li>
 <li>args = coefficients for one or more dihedral types</li>
@@ -138,11 +138,11 @@
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="mi">1</span> <span class="mi">3</span>
+<pre class="literal-block">
-<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="mf">80.0</span> <span class="mi">1</span> <span class="mi">3</span> <span class="mf">0.5</span>
+dihedral_coeff 1 80.0 1 3
-<span class="n">dihedral_coeff</span> <span class="mi">2</span><span class="o">*</span> <span class="mf">80.0</span> <span class="mi">1</span> <span class="mi">3</span> <span class="mf">0.5</span>
+dihedral_coeff * 80.0 1 3 0.5
-</pre></div>
+dihedral_coeff 2* 80.0 1 3 0.5
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>
@@ -154,7 +154,7 @@ Dihedral coefficients can also be set in the data file read by the
 <p>N can be specified in one of two ways.  An explicit numeric value can
 be used, as in the 1st example above.  Or a wild-card asterisk can be
 used to set the coefficients for multiple dihedral types.  This takes the
-form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;.  If N = the number of dihedral types,
+form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;.  If N = the number of dihedral types,
 then an asterisk with no numeric values means all types from 1 to N.  A
 leading asterisk means all types from 1 to n (inclusive).  A trailing
 asterisk means all types from n to N (inclusive).  A middle asterisk
@@ -162,10 +162,10 @@ means all types from m to n (inclusive).</p>
 <p>Note that using a dihedral_coeff command can override a previous setting
 for the same dihedral type.  For example, these commands set the coeffs
 for all dihedral types, then overwrite the coeffs for just dihedral type 2:</p>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="mf">80.0</span> <span class="mi">1</span> <span class="mi">3</span>
+<pre class="literal-block">
-<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="mf">200.0</span> <span class="mi">1</span> <span class="mi">3</span>
+dihedral_coeff * 80.0 1 3
-</pre></div>
+dihedral_coeff 2 200.0 1 3
-</div>
+</pre>
 <p>A line in a data file that specifies dihedral coefficients uses the exact
 same format as the arguments of the dihedral_coeff command in an input
 script, except that wild-card asterisks should not be used since

doc/html/dihedral_cosine_shift_exp.html

@@ -131,16 +131,16 @@
 <h1>dihedral_style cosine/shift/exp/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
+<pre class="literal-block">
-</pre></div>
+dihedral_style cosine/shift/exp
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span>
+<pre class="literal-block">
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">10.0</span> <span class="mf">45.0</span> <span class="mf">2.0</span>
+dihedral_style cosine/shift/exp
-</pre></div>
+dihedral_coeff 1 10.0 45.0 2.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/dihedral_fourier.html

@@ -131,16 +131,16 @@
 <h1>dihedral_style fourier/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">fourier</span>
+<pre class="literal-block">
-</pre></div>
+dihedral_style fourier
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">fourier</span>
+<pre class="literal-block">
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">3</span> <span class="o">-</span><span class="mf">0.846200</span> <span class="mi">3</span> <span class="mf">0.0</span> <span class="mf">7.578800</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mf">0.138000</span> <span class="mi">2</span> <span class="o">-</span><span class="mf">180.0</span>
+dihedral_style fourier
-</pre></div>
+dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/dihedral_helix.html

@@ -131,16 +131,16 @@
 <h1>dihedral_style helix/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">helix</span>
+<pre class="literal-block">
-</pre></div>
+dihedral_style helix
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">helix</span>
+<pre class="literal-block">
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="mf">100.0</span> <span class="mf">40.0</span>
+dihedral_style helix
-</pre></div>
+dihedral_coeff 1 80.0 100.0 40.0
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/dihedral_hybrid.html

@@ -128,20 +128,20 @@
 <span id="index-0"></span><h1>dihedral_style hybrid command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">hybrid</span> <span class="n">style1</span> <span class="n">style2</span> <span class="o">...</span>
+<pre class="literal-block">
-</pre></div>
+dihedral_style hybrid style1 style2 ...
-</div>
+</pre>
 <ul class="simple">
 <li>style1,style2 = list of one or more dihedral styles</li>
 </ul>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">helix</span>
+<pre class="literal-block">
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="n">harmonic</span> <span class="mf">6.0</span> <span class="mi">1</span> <span class="mi">3</span>
+dihedral_style hybrid harmonic helix
-<span class="n">dihedral_coeff</span> <span class="mi">2</span><span class="o">*</span> <span class="n">helix</span> <span class="mi">10</span> <span class="mi">10</span> <span class="mi">10</span>
+dihedral_coeff 1 harmonic 6.0 1 3
-</pre></div>
+dihedral_coeff 2* helix 10 10 10
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>

doc/html/dihedral_multi_harmonic.html

@@ -131,16 +131,16 @@
 <h1>dihedral_style multi/harmonic/omp command</h1>
 <div class="section" id="syntax">
 <h2>Syntax</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span>
+<pre class="literal-block">
-</pre></div>
+dihedral_style multi/harmonic
-</div>
+</pre>
 </div>
 <div class="section" id="examples">
 <h2>Examples</h2>
-<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span>
+<pre class="literal-block">
-<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span>
+dihedral_style multi/harmonic
-</pre></div>
+dihedral_coeff 1 20 20 20 20 20
-</div>
+</pre>
 </div>
 <div class="section" id="description">
 <h2>Description</h2>