doc updates

  <H1></H1><div class="section" id="lammps-documentation">

<h1>LAMMPS Documentation</h1>

<div class="section" id="sep-2016-version">

<h2>7 Sep 2016 version</h2>

<h2>13 Sep 2016 version</h2>

</div>

<div class="section" id="version-info">

<h2>Version info:</h2>

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>

<pre class="literal-block">

variable X equal (xlo+xhi)/2+sqrt(v_area)

<div class="highlight-default"><div class="highlight"><pre><span></span>variable X equal (xlo+xhi)/2+sqrt(v_area)

region 1 block $X 2 INF INF EDGE EDGE

variable X delete

</pre>

</pre></div>

</div>

<p>can be replaced by</p>

<pre class="literal-block">

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

</pre>

<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>

<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.

</tbody>

</table>

<p>Here is how you can run and visualize one of the sample problems:</p>

<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>

<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>

<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>

<pre class="literal-block">

% convert -loop 1 *.jpg foo.gif

</pre>

<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>

</div>

<hr class="docutils" />

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

<h2>7.2. Uppercase directories</h2>

<table border="1" class="docutils">

<colgroup>

<col width="11%" />

<col width="89%" />

<col width="10%" />

<col width="90%" />

</colgroup>

<tbody valign="top">

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

<li><a class="reference internal" href="#eff"><span class="std std-ref">eff</span></a></li>

<li><a class="reference internal" href="#emacs"><span class="std std-ref">emacs</span></a></li>

<li><a class="reference internal" href="#fep"><span class="std std-ref">fep</span></a></li>

<li><a class="reference internal" href="#ipi"><span class="std std-ref">i-pi</span></a></li>

<li><a class="reference internal" href="fix_ipi.html#ipi"><span class="std std-ref">i-pi</span></a></li>

<li><a class="reference internal" href="#ipp"><span class="std std-ref">ipp</span></a></li>

<li><a class="reference internal" href="#kate"><span class="std std-ref">kate</span></a></li>

<li><a class="reference internal" href="#arc"><span class="std std-ref">lmp2arc</span></a></li>

<span id="index-0"></span><h1>atom_modify command</h1>

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

<h2>Syntax</h2>

<pre class="literal-block">

atom_modify keyword values ...

</pre>

<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></div>

</div>

<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>

</div>

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

<h2>Examples</h2>

<pre class="literal-block">

atom_modify map hash

atom_modify map array sort 10000 2.0

atom_modify first colloid

</pre>

<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>

<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>

<span class="n">atom_modify</span> <span class="n">first</span> <span class="n">colloid</span>

</pre></div>

</div>

</div>

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

<h2>Description</h2>