Commit 717e719b authored by Steve Plimpton's avatar Steve Plimpton
Browse files

HTML update

parent 10b4411d

doc/html/Section_commands.html

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@@ -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>

</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.

doc/html/Section_example.html

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@@ -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>

<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
@@ -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></div>

</div>

<pre class="literal-block">

% convert -loop 1 *.jpg foo.gif

</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="90%" />

<col width="11%" />

<col width="89%" />

</colgroup>

<tbody valign="top">

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

doc/html/accelerate_opt.html

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@@ -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>

<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>

</pre></div>

</div>

<pre class="literal-block">

lmp_mpi -sf opt -in in.script                # run in serial

mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel

</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></div>

</div>

<pre class="literal-block">

pair_style lj/cut/opt 2.5

</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

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@@ -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></div>

</div>

<pre class="literal-block">

angle_style charmm

</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>

<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>

</pre></div>

</div>

<pre class="literal-block">

angle_style charmm

angle_coeff 1 300.0 107.0 50.0 3.0

</pre>

</div>

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

<h2>Description</h2>

doc/html/angle_class2.html

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@@ -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></div>

</div>

<pre class="literal-block">

angle_style class2

</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>

<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span>

<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>

<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>

</pre></div>

</div>

<pre class="literal-block">

angle_style class2

angle_coeff * 75.0

angle_coeff 1 bb 10.5872 1.0119 1.5228

angle_coeff * ba 3.6551 24.895 1.0119 1.5228

</pre>

</div>

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

<h2>Description</h2>

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