regenerate html pages with new txt2rst tool

listed above:</p>

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<tr class="row-odd"><td>build the accelerator library</td>

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>

</div>

</pre>

<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></div>

</div>

<pre class="literal-block">

region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE

</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.

<dt><em>Bad TIP4P bond type for PPPMDisp/TIP4P</em></dt>

<dd>Specified bond type is not valid.</dd>

<dt><em>Bad fix ID in fix append/atoms command</em></dt>

<dd>The value of the fix_id for keyword spatial must start with &#8216;<a href="#id6"><span class="problematic" id="id7">f_</span></a>&#8216;.</dd>

<dd>The value of the fix_id for keyword spatial must start with &#8216;f_&#8217;.</dd>

<dt><em>Bad grid of processors</em></dt>

<dd>The 3d grid of processors defined by the processors command does not

match the number of processors LAMMPS is being run on.</dd>

have fully consistent image flags, since some bonds will cross

periodic boundaries and connect two atoms with the same image

flag.</dd>

<dt><em>KIM Model does not provide `energy&#8217;; Potential energy will be zero</em></dt>

<dt><em>KIM Model does not provide &#8216;energy&#8217;; Potential energy will be zero</em></dt>

<dd>Self-explanatory.</dd>

<dt><em>KIM Model does not provide `forces&#8217;; Forces will be zero</em></dt>

<dt><em>KIM Model does not provide &#8216;forces&#8217;; Forces will be zero</em></dt>

<dd>Self-explanatory.</dd>

<dt><em>KIM Model does not provide `particleEnergy&#8217;; energy per atom will be zero</em></dt>

<dt><em>KIM Model does not provide &#8216;particleEnergy&#8217;; energy per atom will be zero</em></dt>

<dd>Self-explanatory.</dd>

<dt><em>KIM Model does not provide `particleVirial&#8217;; virial per atom will be zero</em></dt>

<dt><em>KIM Model does not provide &#8216;particleVirial&#8217;; virial per atom will be zero</em></dt>

<dd>Self-explanatory.</dd>

<dt><em>Kspace_modify slab param &lt; 2.0 may cause unphysical behavior</em></dt>

<dd>The kspace_modify slab parameter should be larger to insure periodic

</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>

<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>

<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>

</pre></div>

</div>

<pre class="literal-block">

cd indent

cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir

lmp_linux -in in.indent            # run the problem

</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

<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></div>

</div>

<pre class="literal-block">

% convert -loop 1 *.jpg foo.gif

</pre>

</div>

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<div class="section" id="uppercase-directories">

<h2>7.2. Uppercase directories</h2>

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<tr class="row-odd"><td>ASPHERE</td>