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fix qeq Kokkos bug fix by Stan

This commit is contained in:
Steve Plimpton 2016-09-13 10:54:04 -06:00
parent dd34feb2bd
commit a8081d4507
149 changed files with 2142 additions and 2077 deletions
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2
doc/html/Section_tools.html
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@ -204,7 +204,7 @@ own sub-directories with their own Makefiles.</p>
<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="fix_ipi.html#ipi"><span class="std std-ref">i-pi</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="#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>

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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>
<pre class="literal-block">
angle_style charmm
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">charmm</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style charmm
angle_coeff 1 300.0 107.0 50.0 3.0
</pre>
<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>
</div>
<div class="section" id="description">
<h2>Description</h2>

18
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>
<pre class="literal-block">
angle_style class2
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">class2</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<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 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>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/angle_cosine.html
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@ -131,16 +131,16 @@
<h1>angle_style cosine/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style cosine
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style cosine
angle_coeff * 75.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span>
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/angle_cosine_delta.html
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@ -131,16 +131,16 @@
<h1>angle_style cosine/delta/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style cosine/delta
</pre>
<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></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style cosine/delta
angle_coeff 2*4 75.0 100.0
</pre>
<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>
<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>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/angle_cosine_periodic.html
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@ -131,16 +131,16 @@
<h1>angle_style cosine/periodic/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style cosine/periodic
</pre>
<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></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style cosine/periodic
angle_coeff * 75.0 1 6
</pre>
<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>
<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>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/angle_cosine_shift.html
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@ -131,16 +131,16 @@
<h1>angle_style cosine/shift/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style cosine/shift
</pre>
<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></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style cosine/shift
angle_coeff * 10.0 45.0
</pre>
<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="n">angle_coeff</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">45.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/angle_cosine_shift_exp.html
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@ -131,16 +131,16 @@
<h1>angle_style cosine/shift/exp/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style cosine/shift/exp
</pre>
<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></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style cosine/shift/exp
angle_coeff * 10.0 45.0 2.0
</pre>
<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>
<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>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/angle_cosine_squared.html
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@ -131,16 +131,16 @@
<h1>angle_style cosine/squared/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style cosine/squared
</pre>
<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></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style cosine/squared
angle_coeff 2*4 75.0 100.0
</pre>
<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>
<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>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/angle_dipole.html
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@ -131,16 +131,16 @@
<h1>angle_style dipole/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style dipole
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style dipole
angle_coeff 6 2.1 180.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span>
<span class="n">angle_coeff</span> <span class="mi">6</span> <span class="mf">2.1</span> <span class="mf">180.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

6
doc/html/angle_fourier.html
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@ -131,9 +131,9 @@
<h1>angle_style fourier/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style fourier
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">fourier</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>

6
doc/html/angle_fourier_simple.html
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@ -131,9 +131,9 @@
<h1>angle_style fourier/simple/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style fourier/simple
</pre>
<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></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>

14
doc/html/angle_harmonic.html
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@ -137,16 +137,16 @@
<h1>angle_style harmonic/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style harmonic
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style harmonic
angle_coeff 1 300.0 107.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</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></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/angle_quartic.html
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@ -131,16 +131,16 @@
<h1>angle_style quartic/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style quartic
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style quartic
angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span>
<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>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

20
doc/html/angle_sdk.html
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@ -128,19 +128,19 @@
<span id="index-0"></span><h1>angle_style sdk command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
angle_style sdk
</pre>
<pre class="literal-block">
angle_style sdk/omp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span>
</pre></div>
</div>
<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></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
angle_style sdk
angle_coeff 1 300.0 107.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</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></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/bond_class2.html
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@ -131,16 +131,16 @@
<h1>bond_style class2/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
bond_style class2
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
bond_style class2
bond_coeff 1 1.0 100.0 80.0 80.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span>
<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>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/bond_fene.html
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@ -137,16 +137,16 @@
<h1>bond_style fene/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
bond_style fene
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span>
<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>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/bond_fene_expand.html
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@ -131,16 +131,16 @@
<h1>bond_style fene/expand/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
bond_style fene/expand
</pre>
<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></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
bond_style fene/expand
bond_coeff 1 30.0 1.5 1.0 1.0 0.5
</pre>
<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>
<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>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/bond_harmonic.html
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@ -137,16 +137,16 @@
<h1>bond_style harmonic/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
bond_style harmonic
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
bond_style harmonic
bond_coeff 5 80.0 1.2
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</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></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/bond_harmonic_shift.html
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@ -131,16 +131,16 @@
<h1>bond_style harmonic/shift/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
bond_style harmonic/shift
</pre>
<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></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
bond_style harmonic/shift
bond_coeff 5 10.0 0.5 1.0
</pre>
<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="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>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/bond_harmonic_shift_cut.html
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@ -131,16 +131,16 @@
<h1>bond_style harmonic/shift/cut/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
bond_style harmonic/shift/cut
</pre>
<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></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
bond_style harmonic/shift/cut
bond_coeff 5 10.0 0.5 1.0
</pre>
<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>
<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>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/bond_morse.html
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@ -131,16 +131,16 @@
<h1>bond_style morse/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
bond_style morse
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
bond_style morse
bond_coeff 5 1.0 2.0 1.2
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span>
<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>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

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

22
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@ -131,16 +131,16 @@
<h1>bond_style quartic/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
bond_style quartic
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
bond_style quartic
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span>
<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>
</pre></div>
</div>
</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>
<pre class="literal-block">
delete_bonds all stats
delete_bonds all bond 0 remove
</pre>
<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>
<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>
</pre></div>
</div>
<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.

2
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@ -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 *not* normalized by the square of the lattice
<p>These values are <em>not</em> 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>

10
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@ -164,10 +164,10 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
compute 1 all fep 300 atom charge 2 v_delta
</pre>
<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>
<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>
</pre></div>
</div>
</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;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;. If N =
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 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

10
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@ -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>
<pre class="literal-block">
compute cc1 all chunk/atom molecule
compute myChunk all gyration/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</pre>
<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>
<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>
<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>
</pre></div>
</div>
<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

26
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@ -237,30 +237,29 @@ 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>
<pre class="literal-block">
units real
<div class="highlight-default"><div class="highlight"><pre><span></span>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>
</pre></div>
</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>
<pre class="literal-block">
variable kB equal 1.3806504e-23 # [J/K] Boltzmann
<div class="highlight-default"><div class="highlight"><pre><span></span>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>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># setup problem</span>
</pre></div>
</div>
<pre class="literal-block">
dimension 3
<div class="highlight-default"><div class="highlight"><pre><span></span>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
@ -271,7 +270,8 @@ pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405
timestep ${dt}
thermo $d
</pre>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># equilibration and thermalization</span>
</pre></div>
</div>
@ -287,8 +287,7 @@ run 8000
<span class="c1">#fix NVE all nve</span>
</pre></div>
</div>
<pre class="literal-block">
reset_timestep 0
<div class="highlight-default"><div class="highlight"><pre><span></span>reset_timestep 0
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom NULL virial
@ -306,8 +305,9 @@ 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] &#64; $T K, ${ndens} /A^3&quot;
</pre>
print &quot;average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3&quot;
</pre></div>
</div>
</div>
</div>

14
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@ -141,10 +141,10 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
compute 1 all pressure thermo_temp
compute 1 all pressure NULL pair bond
</pre>
<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>
<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>
</pre></div>
</div>
</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>
<pre class="literal-block">
compute thermo_press all pressure thermo_temp
</pre>
<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></div>
</div>
<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" />

18
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@ -157,14 +157,14 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
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
compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
</pre>
<pre class="literal-block">
fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
fix saed/vtk 1 1 1 c_2 file Ni_000.saed
</pre>
<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>
<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>
</pre></div>
</div>
<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>
<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>
</pre></div>
</div>
</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>*inv(A) along each reciprocal lattice
constructed with spacing <em>c</em><a href="#id1"><span class="problematic" id="id2">*</span></a>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

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@ -134,11 +134,11 @@
<h1>compute snav/atom command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
</pre>
<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>
<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>
<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>
</pre></div>
</div>
<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>
<pre class="literal-block">
for j1 in range(0,twojmax+1):
if(diagonal==2):
print j1/2.,j1/2.,j1/2.
elif(diagonal==1):
for j in range(0,min(twojmax,2*j1)+1,2):
print j1/2.,j1/2.,j/2.
elif(diagonal==0):
for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
print j1/2.,j2/2.,j/2.
elif(diagonal==3):
for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
if (j&gt;=j1): print j1/2.,j2/2.,j/2.
</pre>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
</pre></div>
</div>
<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>

12
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@ -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>
<pre class="literal-block">
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo_style custom step temp etotal press v_press
</pre>
<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>
<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>
<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>
<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>
</pre></div>
</div>
<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

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@ -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>
<pre class="literal-block">
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
fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
</pre>
<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>
<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>
</pre></div>
</div>
</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>*inv(A) along each reciprocal lattice
constructed with spacing <em>c</em><a href="#id1"><span class="problematic" id="id2">*</span></a>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

38
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>create_atoms command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
create_atoms type style args keyword values ...
</pre>
<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></div>
</div>
<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 @@ create_atoms type style args keyword values ...
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
create_atoms 1 box
create_atoms 3 region regsphere basis 2 3
create_atoms 3 single 0 0 5
create_atoms 1 box var v set x xpos set y ypos
</pre>
<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>
<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>
<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>
<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>
</pre></div>
</div>
</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>
<pre class="literal-block">
variable x equal 100
<div class="highlight-default"><div class="highlight"><pre><span></span>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
</pre>
<pre class="literal-block">
variable xx equal 0.0
variable yy equal 0.0
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;
create_atoms 1 box var v set x xx set y yy
</pre>
create_box 1 box
</pre></div>
</div>
<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>
<span class="n">variable</span> <span class="n">yy</span> <span class="n">equal</span> <span class="mf">0.0</span>
<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>
<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>
</pre></div>
</div>
<a class=""
data-lightbox="group-default"
href="_images/sinusoid.jpg"

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

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

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

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

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

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

14
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@ -131,16 +131,16 @@
<h1>dihedral_style nharmonic/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
dihedral_style nharmonic
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">nharmonic</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dihedral_style nharmonic
dihedral_coeff 3 10.0 20.0 30.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">nharmonic</span>
<span class="n">dihedral_coeff</span> <span class="mi">3</span> <span class="mf">10.0</span> <span class="mf">20.0</span> <span class="mf">30.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

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@ -137,18 +137,18 @@
<h1>dihedral_style opls/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
dihedral_style opls
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">opls</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dihedral_style opls
dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT
dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC
dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">opls</span>
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">1.740</span> <span class="o">-</span><span class="mf">0.157</span> <span class="mf">0.279</span> <span class="mf">0.00</span> <span class="c1"># CT-CT-CT-CT</span>
<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="mf">0.000</span> <span class="mf">0.000</span> <span class="mf">0.366</span> <span class="mf">0.000</span> <span class="c1"># CT-CT-CT-HC</span>
<span class="n">dihedral_coeff</span> <span class="mi">3</span> <span class="mf">0.000</span> <span class="mf">0.000</span> <span class="mf">0.318</span> <span class="mf">0.000</span> <span class="c1"># HC-CT-CT-HC</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>dihedral_style quadratic/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
dihedral_style quadratic
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">quadratic</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dihedral_style quadratic
dihedral_coeff 100.0 80.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">quadratic</span>
<span class="n">dihedral_coeff</span> <span class="mf">100.0</span> <span class="mf">80.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

18
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@ -128,18 +128,18 @@
<span id="index-0"></span><h1>dihedral_style spherical command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
dihedral_style spherical
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">spherical</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0
dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 &amp;
17.3 0 0.0 0 1 158 1 0 0.0 0 &amp;
15.1 0 0.0 0 0 0.0 0 1 167.3 1
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">286.1</span> <span class="mi">1</span> <span class="mi">124</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span>
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">3</span> <span class="mf">286.1</span> <span class="mi">1</span> <span class="mi">114</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">90</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span> <span class="o">&amp;</span>
<span class="mf">17.3</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">158</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="o">&amp;</span>
<span class="mf">15.1</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">167.3</span> <span class="mi">1</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

16
doc/html/dihedral_style.html
View File

@ -128,20 +128,20 @@
<span id="index-0"></span><h1>dihedral_style command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
dihedral_style style
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">style</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>none</em> or <em>hybrid</em> or <em>charmm</em> or <em>class2</em> or <em>harmonic</em> or <em>helix</em> or <em>multi/harmonic</em> or <em>opls</em></li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dihedral_style harmonic
dihedral_style multi/harmonic
dihedral_style hybrid harmonic charmm
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">harmonic</span>
<span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span>
<span class="n">dihedral_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">charmm</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

4
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View File

@ -432,8 +432,10 @@ will be duplicate nodes in the list.</p>
rectangle for each processor (1 to 4).</p>
<p>For a 3d problem, the syntax is similar with 8 vertices listed for
each processor, instead of 4, and &#8220;SQUARES&#8221; replaced by &#8220;CUBES&#8221;.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes a global scalar which is the imbalance factor

6
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@ -229,9 +229,9 @@ quantities or the printing of unwrapped coordinates to a dump file.</p>
<p>This fix computes a temperature each time it is invoked for use by the
Boltzmann criterion. To do this, the fix creates its own compute of
style <em>temp</em>, as if this command had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp all temp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details. Note
that the ID of the new compute is the fix-ID with underscore + &#8220;temp&#8221;
appended and the group for the new compute is &#8220;all&#8221;, so that the

24
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@ -371,10 +371,10 @@ temperature is used to compute the kinetic contribution to the
pressure, even though this is subsequently ignored by default. To do
this, the fix creates its own computes of style &#8220;temp&#8221; and &#8220;pressure&#8221;,
as if these commands had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp virial
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">virial</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
+ underscore + &#8220;press&#8221;, and the group for the new computes is the same
@ -388,8 +388,10 @@ fix&#8217;s temperature or pressure via the
or pressure during thermodynamic output via the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command using the appropriate compute-ID.
It also means that changing attributes of <em>thermo_temp</em> or
<em>thermo_press</em> will have no effect on this fix.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> and <em>press</em> options are
supported by this fix. You can use them to assign a
@ -423,12 +425,12 @@ potential energy. This fix does not support the
because that would result in double-counting of the fix energy in the
minimization energy. Instead, the fix energy can be explicitly
added to the potential energy using one of these two variants:</p>
<pre class="literal-block">
variable emin equal pe+f_1
</pre>
<pre class="literal-block">
variable emin equal pe+f_1/atoms
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">emin</span> <span class="n">equal</span> <span class="n">pe</span><span class="o">+</span><span class="n">f_1</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">emin</span> <span class="n">equal</span> <span class="n">pe</span><span class="o">+</span><span class="n">f_1</span><span class="o">/</span><span class="n">atoms</span>
</pre></div>
</div>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
<p>This fix is invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>, but

36
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View File

@ -141,13 +141,13 @@
<li>Kd = derivative gain in PID equation (unitless)</li>
<li>pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or v_name</li>
</ul>
<pre class="literal-block">
c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID
f_ID = global scalar calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID
v_name = value calculated by an equal-style variable with name
</pre>
<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">scalar</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="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">component</span> <span class="n">of</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>
<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</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="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">component</span> <span class="n">of</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>
<span class="n">v_name</span> <span class="o">=</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</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>
</pre></div>
</div>
<ul class="simple">
<li>setpoint = desired value of process variable (same units as process variable)</li>
<li>cvar = name of control variable</li>
@ -155,11 +155,11 @@ v_name = value calculated by an equal-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol
fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall
fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol
</pre>
<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">controller</span> <span class="mi">100</span> <span class="mf">1.0</span> <span class="mf">0.5</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">c_thermo_temp</span> <span class="mf">1.5</span> <span class="n">tcontrol</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">controller</span> <span class="mi">100</span> <span class="mf">0.2</span> <span class="mf">0.5</span> <span class="mi">0</span> <span class="mf">100.0</span> <span class="n">v_pxxwall</span> <span class="mf">1.01325</span> <span class="n">xwall</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">controller</span> <span class="mi">10000</span> <span class="mf">0.2</span> <span class="mf">0.5</span> <span class="mi">0</span> <span class="mi">2000</span> <span class="n">v_avpe</span> <span class="o">-</span><span class="mf">3.785</span> <span class="n">tcontrol</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -269,14 +269,14 @@ because the value of <em>e_n-1</em> is not yet defined.</p>
<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> or the evaluation of a
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a>. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity.</p>
<p>If <em>pvar</em> begins with &#8220;c_&#8221;, a compute ID must follow which has been
<p>If <em>pvar</em> begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
previously defined in the input script and which generates a global
scalar or vector. 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 scalar
calculated by the compute is used. If a bracketed integer is
appended, the Ith value of the vector 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 <em>pvar</em> begins with &#8220;f_&#8221;, a fix ID must follow which has been
<p>If <em>pvar</em> begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
previously defined in the input script and which generates a global
scalar or vector. 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
@ -285,7 +285,7 @@ references the values, or else an error results. If no bracketed integer
is appended, the scalar calculated by the fix is used. If a bracketed
integer is appended, the Ith value of the vector 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 <em>pvar</em> begins with &#8220;v_&#8221;, a variable name must follow which has been
<p>If <em>pvar</em> begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has been
previously defined in the input script. Only equal-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>equal</em> define a formula which
@ -296,12 +296,14 @@ variable.</p>
<p>The target value <em>setpoint</em> for the process variable must be a numeric
value, in whatever units <em>pvar</em> is defined for.</p>
<p>The control variable <em>cvar</em> must be the name of an <a class="reference internal" href="variable.html"><span class="doc">internal-style variable</span></a> previously defined in the input script. Note
that it is not specified with a &#8220;v_&#8221; prefix, just the name of the
that it is not specified with a &#8220;<a href="#id7"><span class="problematic" id="id8">v_</span></a>&#8221; prefix, just the name of the
variable. It must be an internal-style variable, because this fix
updates its value directly. Note that other commands can use an
equal-style versus internal-style variable interchangeably.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Currenlty, no information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix produces a global vector with 3 values which can be accessed

4
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@ -262,8 +262,10 @@ be on the order of <span class="math">\(10^{-7}\)</span> for relatively large
temperature gradients. A higher precision can be achieved by
decreasing the timestep.</p>
</div>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of

6
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix gld command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">gld</span> <span class="n">Tstart</span> <span class="n">Tstop</span> <span class="n">N_k</span> <span class="n">seed</span> <span class="n">series</span> <span class="n">c_1</span> <span class="n">tau_1</span> <span class="o">...</span> <span class="n">c_N_k</span> <span class="n">tau_N_k</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>gld = style name of this fix command</li>

4
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@ -374,8 +374,10 @@ screen every N timesteps.</p>
test runs, see <a class="reference internal" href="#fluid-mackay"><span class="std std-ref">Mackay et al.</span></a>. Please include a citation to
this paper if the lb_fluid fix is used in work contributing to
published research.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Due to the large size of the fluid data, this fix writes it&#8217;s own
binary restart files, if requested, independent of the main LAMMPS
<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>; no information about <em>lb_fluid</em>

26
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@ -158,9 +158,9 @@
<h1>fix nph/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID style_name keyword value ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style_name</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>style_name = <em>nvt</em> or <em>npt</em> or <em>nph</em></li>
@ -508,14 +508,14 @@ thermostatting and barostatting.</p>
<p>These fixes compute a temperature and pressure each timestep. To do
this, the fix creates its own computes of style &#8220;temp&#8221; and &#8220;pressure&#8221;,
as if one of these two sets of commands had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp
</pre>
<pre class="literal-block">
compute fix-ID_temp all temp
compute fix-ID_press all pressure fix-ID_temp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
+ underscore + &#8220;press&#8221;. For fix nvt, the group for the new computes
@ -606,8 +606,10 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>These fixes writes the state of all the thermostat and barostat
variables to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify

22
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@ -229,14 +229,14 @@ controlled by another fix - e.g. by <a class="reference internal" href="fix_nh.h
<p>This fix computes a temperature and pressure at each timestep. To do
this, the fix creates its own computes of style &#8220;temp&#8221; and &#8220;pressure&#8221;,
as if one of these two sets of commands had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp
</pre>
<pre class="literal-block">
compute fix-ID_temp all temp
compute fix-ID_press all pressure fix-ID_temp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
+ underscore + &#8220;press&#8221;. The group for
@ -266,8 +266,10 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the values of E0, V0, and P0, as well as the
state of all the thermostat and barostat
variables to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the
@ -291,7 +293,7 @@ compute temperature on a subset of atoms.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by these
fixes to add the energy change induced by Nose/Hoover thermostatting
and barostatting to the system&#8217;s potential energy as part of
<a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>. Either way, this energy is *not*
<a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>. Either way, this energy is <em>not</em>
included in the definition of internal energy E when calculating the value
of Delta in the above equation.</p>
<p>These fixes compute a global scalar and a global vector of quantities,

4
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@ -232,7 +232,9 @@ symmetry, so the list must include one from each pair of
equal-and-opposite neighbors. A pair of orientation files for a
Sigma=5 tilt boundary are shown below. A tutorial that can help for
writing the orientation files is given in <a class="reference internal" href="#wicaksono2"><span class="std std-ref">(Wicaksono2)</span></a></p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the potential energy of atom interactions with the grain

12
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@ -232,9 +232,9 @@ ring.</p>
<p>To run a PIMD simulation with M quasi-beads in each ring polymer using
N MPI tasks for each partition&#8217;s domain-decomposition, you would use P
= MxN processors (cores) and run the simulation as follows:</p>
<pre class="literal-block">
mpirun -np P lmp_mpi -partition MxN -in script
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="n">P</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">partition</span> <span class="n">MxN</span> <span class="o">-</span><span class="ow">in</span> <span class="n">script</span>
</pre></div>
</div>
<p>Note that in the LAMMPS input script for a multi-partition simulation,
it is often very useful to define a <a class="reference internal" href="variable.html"><span class="doc">uloop-style variable</span></a> such as</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">ibead</span> <span class="n">uloop</span> <span class="n">M</span> <span class="n">pad</span>
@ -243,11 +243,11 @@ it is often very useful to define a <a class="reference internal" href="variable
<p>where M is the number of quasi-beads (partitions) used in the
calculation. The uloop variable can then be used to manage I/O
related tasks for each of the partitions, e.g.</p>
<pre class="literal-block">
dump dcd all dcd 10 system_${ibead}.dcd
<div class="highlight-default"><div class="highlight"><pre><span></span>dump dcd all dcd 10 system_${ibead}.dcd
restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
read_restart system_${ibead}.restart2
</pre>
</pre></div>
</div>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>

32
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@ -157,10 +157,10 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units)
fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units)
</pre>
<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">qbmsst</span> <span class="n">z</span> <span class="mf">0.122</span> <span class="n">q</span> <span class="mi">25</span> <span class="n">mu</span> <span class="mf">0.9</span> <span class="n">tscale</span> <span class="mf">0.01</span> <span class="n">damp</span> <span class="mi">200</span> <span class="n">seed</span> <span class="mi">35082</span> <span class="n">f_max</span> <span class="mf">0.3</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="n">eta</span> <span class="mi">1</span> <span class="n">beta</span> <span class="mi">400</span> <span class="n">T_init</span> <span class="mi">110</span> <span class="p">(</span><span class="n">liquid</span> <span class="n">methane</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">REAX</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">real</span> <span class="n">units</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">qbmsst</span> <span class="n">z</span> <span class="mi">72</span> <span class="n">q</span> <span class="mi">40</span> <span class="n">tscale</span> <span class="mf">0.05</span> <span class="n">damp</span> <span class="mi">1</span> <span class="n">seed</span> <span class="mi">47508</span> <span class="n">f_max</span> <span class="mf">120.0</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="n">eta</span> <span class="mf">1.0</span> <span class="n">beta</span> <span class="mi">500</span> <span class="n">T_init</span> <span class="mi">300</span> <span class="p">(</span><span class="n">quartz</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">BKS</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">metal</span> <span class="n">units</span><span class="p">)</span>
</pre></div>
</div>
<p>Two example input scripts are given, including shocked alpha quartz
and shocked liquid methane. The input script first equilibrate an
initial state with the quantum thermal bath at the target temperature
@ -242,8 +242,10 @@ thermal bath and the system before shock loading.</p>
<p>For all pressure styles, the simulation box stays orthorhombic in
shape. Parrinello-Rahman boundary conditions (tilted box) are
supported by LAMMPS, but are not implemented for QBMSST.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Because the state of the random number generator is not written to
<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, this fix cannot be restarted
&#8220;exactly&#8221; in an uninterrupted fashion. However, in a statistical
@ -269,16 +271,16 @@ headers, the following LAMMPS commands are suggested. Here the
<a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> energy command is also enabled to allow
the thermo keyword <em>etotal</em> to print the quantity &lt;i&gt;etot&lt;/i&gt;. See
also the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command.</p>
<pre class="literal-block">
fix fix_id all msst z
fix_modify fix_id energy yes
variable dhug equal f_fix_id[1]
variable dray equal f_fix_id[2]
variable lgr_vel equal f_fix_id[3]
variable lgr_pos equal f_fix_id[4]
variable T_qm equal f_fix_id[5]
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">fix_id</span> <span class="nb">all</span> <span class="n">msst</span> <span class="n">z</span>
<span class="n">fix_modify</span> <span class="n">fix_id</span> <span class="n">energy</span> <span class="n">yes</span>
<span class="n">variable</span> <span class="n">dhug</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">dray</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">lgr_vel</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">lgr_pos</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">T_qm</span> <span class="n">equal</span> <span class="n">f_fix_id</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">ke</span> <span class="n">pe</span> <span class="n">lz</span> <span class="n">pzz</span> <span class="n">etotal</span> <span class="n">v_dhug</span> <span class="n">v_dray</span> <span class="n">v_lgr_vel</span> <span class="n">v_lgr_pos</span> <span class="n">v_T_qm</span> <span class="n">f_fix_id</span>
</pre></div>
</div>
<p>The global scalar under the entry f_fix_id is the quantity of thermo
energy as an extra part of &lt;i&gt;etot&lt;/i&gt;. This global scalar and the
vector of 5 quantities can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. It is worth noting that the

26
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@ -165,15 +165,27 @@ fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5
<h2>Description</h2>
<p>Restrain the motion of the specified sets of atoms by making them part
of a bond or angle or dihedral interaction whose strength can vary
over time during a simulation. This is functionally equivalent to
over time during a simulation. This is functionally similar to
creating a bond or angle or dihedral for the same atoms in a data
file, as specified by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command, albeit
with a time-varying pre-factor coefficient. For the purpose of
forcefield parameter-fitting or mapping a molecular potential energy
surface, this fix reduces the hassle and risk associated with
modifying data files. In other words, use this fix to temporarily
force a molecule to adopt a particular conformation. To create a
permanent bond or angle or dihedral, you should modify the data file.</p>
with a time-varying pre-factor coefficient, and except for exclusion
rules, as explained below.</p>
<p>For the purpose of forcefield parameter-fitting or mapping a molecular
potential energy surface, this fix reduces the hassle and risk
associated with modifying data files. In other words, use this fix to
temporarily force a molecule to adopt a particular conformation. To
create a permanent bond or angle or dihedral, you should modify the
data file.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Adding a bond/angle/dihedral with this command does not apply
the exclusion rules and weighting factors specified by the
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command to atoms in the restraint
that are now bonded (1-2,1-3,1-4 neighbors) as a result. If they are
close enough to interact in a <a class="reference internal" href="pair_style.html"><span class="doc">pair_style</span></a> sense
(non-bonded interaction), then the bond/angle/dihedral restraint
interaction will simply be superposed on top of that interaction.</p>
</div>
<p>The group-ID specified by this fix is ignored.</p>
<p>The second example above applies a restraint to hold the dihedral
angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant

16
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@ -147,13 +147,13 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all rx kinetics.rx none dense lammps_rk4
fix 1 all rx kinetics.rx none sparse lammps_rk4 1
fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10
fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8
fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1
</pre>
<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">rx</span> <span class="n">kinetics</span><span class="o">.</span><span class="n">rx</span> <span class="n">none</span> <span class="n">dense</span> <span class="n">lammps_rk4</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rx</span> <span class="n">kinetics</span><span class="o">.</span><span class="n">rx</span> <span class="n">none</span> <span class="n">sparse</span> <span class="n">lammps_rk4</span> <span class="mi">1</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rx</span> <span class="n">kinetics</span><span class="o">.</span><span class="n">rx</span> <span class="n">lucy</span> <span class="n">sparse</span> <span class="n">lammps_rk4</span> <span class="mi">10</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rx</span> <span class="n">kinetics</span><span class="o">.</span><span class="n">rx</span> <span class="n">none</span> <span class="n">dense</span> <span class="n">rkf45</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">6</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">8</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rx</span> <span class="n">kinetics</span><span class="o">.</span><span class="n">rx</span> <span class="n">none</span> <span class="n">dense</span> <span class="n">rkf45</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">6</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">8</span> <span class="o">-</span><span class="mi">1</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -271,7 +271,7 @@ temperature exponent <em>n</em>, and the activation energy <em>Ea</em>.</p>
are used by the <a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> command to
define the thermodynamic properties of each species. Furthermore, the
number of species molecules (i.e., concentration) can be specified
either with the <a class="reference internal" href="set.html"><span class="doc">set</span></a> command using the &#8220;d_&#8221; prefix or by
either with the <a class="reference internal" href="set.html"><span class="doc">set</span></a> command using the &#8220;<a href="#id3"><span class="problematic" id="id4">d_</span></a>&#8221; prefix or by
reading directly the concentrations from a data file. For the latter
case, the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command with the fix keyword
should be specified, where the fix-ID will be the &#8220;fix rx`ID with a &lt;SPECIES&#8221;&gt;`_ suffix, e.g.</p>

4
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@ -289,8 +289,10 @@ the RATTLE constraints. You can check whether the constraints work
correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp
to 1 and recompiling LAMMPS.</p>
</div>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about these fixes is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to these fixes. No global or per-atom quantities are
stored by these fixes for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of these fixes

4
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@ -166,7 +166,9 @@ the mass of the entire group. Note that K is thus a force constant
for the aggregate force on the group of atoms, not a per-atom force.</p>
<p>If RG0 is specified as NULL, then the RG of the group is computed at
the time the fix is specified, and that value is used as the target.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

10
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix ti/rs command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">ti</span><span class="o">/</span><span class="n">rs</span> <span class="n">lambda_initial</span> <span class="n">lambda_final</span> <span class="n">t_switch</span> <span class="n">t_equil</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>ti/rs = style name of this fix command</li>
@ -198,7 +198,9 @@ scaling is faster at temperatures closer to the initial temperature of
the procedure.</p>
<p>An example script using this command is provided in the
examples/USER/misc/ti directory.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>This fix computes a global vector quantitie which can be accessed by
various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The vector has

10
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix ti/spring command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID ti/spring K t_switch t_equil keyword value ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">ti</span><span class="o">/</span><span class="n">spring</span> <span class="n">K</span> <span class="n">t_switch</span> <span class="n">t_equil</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>ti/spring = style name of this fix command</li>
@ -205,7 +205,9 @@ issues with the canonical sampling of harmonic degrees of freedom
(notice that the <em>chain</em> option will NOT solve this problem). The
Langevin thermostat (<a class="reference external" href="fix_langevin.html&quot;">fix langevin</a>) works fine.</p>
</div>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the original coordinates of tethered atoms to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so that the spring effect will be the
same in a restarted simulation. See the <a class="reference internal" href="read_restart.html"><span class="doc">read restart</span></a> command for info on how to re-specify a fix
in an input script that reads a restart file, so that the operation of

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@ -131,50 +131,50 @@
<h1>fix ttm/mod command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile
fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">ttm</span> <span class="n">seed</span> <span class="n">C_e</span> <span class="n">rho_e</span> <span class="n">kappa_e</span> <span class="n">gamma_p</span> <span class="n">gamma_s</span> <span class="n">v_0</span> <span class="n">Nx</span> <span class="n">Ny</span> <span class="n">Nz</span> <span class="n">T_infile</span> <span class="n">N</span> <span class="n">T_outfile</span>
<span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">ttm</span><span class="o">/</span><span class="n">mod</span> <span class="n">seed</span> <span class="n">init_file</span> <span class="n">Nx</span> <span class="n">Ny</span> <span class="n">Nz</span> <span class="n">T_infile</span> <span class="n">N</span> <span class="n">T_outfile</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>style = <em>ttm</em> or <em>ttm_mod</em></li>
<li>seed = random number seed to use for white noise (positive integer)</li>
<li>remaining arguments for fix ttm:</li>
</ul>
<pre class="literal-block">
C_e = electronic specific heat (energy/(electron*temperature) units)
rho_e = electronic density (electrons/volume units)
kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units)
gamma_p = friction coefficient due to electron-ion interactions (mass/time units)
gamma_s = friction coefficient due to electronic stopping (mass/time units)
v_0 = electronic stopping critical velocity (velocity units)
Nx = number of thermal solve grid points in the x-direction (positive integer)
Ny = number of thermal solve grid points in the y-direction (positive integer)
Nz = number of thermal solve grid points in the z-direction (positive integer)
T_infile = filename to read initial electronic temperature from
N = dump TTM temperatures every this many timesteps, 0 = no dump
T_outfile = filename to write TTM temperatures to (only needed if N &gt; 0)
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">C_e</span> <span class="o">=</span> <span class="n">electronic</span> <span class="n">specific</span> <span class="n">heat</span> <span class="p">(</span><span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">electron</span><span class="o">*</span><span class="n">temperature</span><span class="p">)</span> <span class="n">units</span><span class="p">)</span>
<span class="n">rho_e</span> <span class="o">=</span> <span class="n">electronic</span> <span class="n">density</span> <span class="p">(</span><span class="n">electrons</span><span class="o">/</span><span class="n">volume</span> <span class="n">units</span><span class="p">)</span>
<span class="n">kappa_e</span> <span class="o">=</span> <span class="n">electronic</span> <span class="n">thermal</span> <span class="n">conductivity</span> <span class="p">(</span><span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">time</span><span class="o">*</span><span class="n">distance</span><span class="o">*</span><span class="n">temperature</span><span class="p">)</span> <span class="n">units</span><span class="p">)</span>
<span class="n">gamma_p</span> <span class="o">=</span> <span class="n">friction</span> <span class="n">coefficient</span> <span class="n">due</span> <span class="n">to</span> <span class="n">electron</span><span class="o">-</span><span class="n">ion</span> <span class="n">interactions</span> <span class="p">(</span><span class="n">mass</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span><span class="p">)</span>
<span class="n">gamma_s</span> <span class="o">=</span> <span class="n">friction</span> <span class="n">coefficient</span> <span class="n">due</span> <span class="n">to</span> <span class="n">electronic</span> <span class="n">stopping</span> <span class="p">(</span><span class="n">mass</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span><span class="p">)</span>
<span class="n">v_0</span> <span class="o">=</span> <span class="n">electronic</span> <span class="n">stopping</span> <span class="n">critical</span> <span class="n">velocity</span> <span class="p">(</span><span class="n">velocity</span> <span class="n">units</span><span class="p">)</span>
<span class="n">Nx</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">x</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
<span class="n">Ny</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">y</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
<span class="n">Nz</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">z</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
<span class="n">T_infile</span> <span class="o">=</span> <span class="n">filename</span> <span class="n">to</span> <span class="n">read</span> <span class="n">initial</span> <span class="n">electronic</span> <span class="n">temperature</span> <span class="kn">from</span>
<span class="nn">N</span> <span class="o">=</span> <span class="n">dump</span> <span class="n">TTM</span> <span class="n">temperatures</span> <span class="n">every</span> <span class="n">this</span> <span class="n">many</span> <span class="n">timesteps</span><span class="p">,</span> <span class="mi">0</span> <span class="o">=</span> <span class="n">no</span> <span class="n">dump</span>
<span class="n">T_outfile</span> <span class="o">=</span> <span class="n">filename</span> <span class="n">to</span> <span class="n">write</span> <span class="n">TTM</span> <span class="n">temperatures</span> <span class="n">to</span> <span class="p">(</span><span class="n">only</span> <span class="n">needed</span> <span class="k">if</span> <span class="n">N</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span>
</pre></div>
</div>
<ul class="simple">
<li>remaining arguments for fix ttm/mod:</li>
</ul>
<pre class="literal-block">
init_file = file with the parameters to TTM
Nx = number of thermal solve grid points in the x-direction (positive integer)
Ny = number of thermal solve grid points in the y-direction (positive integer)
Nz = number of thermal solve grid points in the z-direction (positive integer)
T_infile = filename to read initial electronic temperature from
N = dump TTM temperatures every this many timesteps, 0 = no dump
T_outfile = filename to write TTM temperatures to (only needed if N &gt; 0)
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">init_file</span> <span class="o">=</span> <span class="n">file</span> <span class="k">with</span> <span class="n">the</span> <span class="n">parameters</span> <span class="n">to</span> <span class="n">TTM</span>
<span class="n">Nx</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">x</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
<span class="n">Ny</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">y</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
<span class="n">Nz</span> <span class="o">=</span> <span class="n">number</span> <span class="n">of</span> <span class="n">thermal</span> <span class="n">solve</span> <span class="n">grid</span> <span class="n">points</span> <span class="ow">in</span> <span class="n">the</span> <span class="n">z</span><span class="o">-</span><span class="n">direction</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
<span class="n">T_infile</span> <span class="o">=</span> <span class="n">filename</span> <span class="n">to</span> <span class="n">read</span> <span class="n">initial</span> <span class="n">electronic</span> <span class="n">temperature</span> <span class="kn">from</span>
<span class="nn">N</span> <span class="o">=</span> <span class="n">dump</span> <span class="n">TTM</span> <span class="n">temperatures</span> <span class="n">every</span> <span class="n">this</span> <span class="n">many</span> <span class="n">timesteps</span><span class="p">,</span> <span class="mi">0</span> <span class="o">=</span> <span class="n">no</span> <span class="n">dump</span>
<span class="n">T_outfile</span> <span class="o">=</span> <span class="n">filename</span> <span class="n">to</span> <span class="n">write</span> <span class="n">TTM</span> <span class="n">temperatures</span> <span class="n">to</span> <span class="p">(</span><span class="n">only</span> <span class="n">needed</span> <span class="k">if</span> <span class="n">N</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out
fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out
fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ttm</span> <span class="mi">699489</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">10</span> <span class="mf">0.1</span> <span class="mf">0.0</span> <span class="mf">2.0</span> <span class="mi">1</span> <span class="mi">12</span> <span class="mi">1</span> <span class="n">initialTs</span> <span class="mi">1000</span> <span class="n">T</span><span class="o">.</span><span class="n">out</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ttm</span> <span class="mi">123456</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">5.0</span> <span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span> <span class="n">Te</span><span class="o">.</span><span class="ow">in</span> <span class="mi">1</span> <span class="n">Te</span><span class="o">.</span><span class="n">out</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ttm</span><span class="o">/</span><span class="n">mod</span> <span class="mi">34277</span> <span class="n">parameters</span><span class="o">.</span><span class="n">txt</span> <span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span> <span class="n">T_init</span> <span class="mi">10</span> <span class="n">T_out</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -330,32 +330,34 @@ is calculated as</p>
<p>The fix ttm/mod parameter file <em>init_file</em> has the following syntax/
Every line with the odd number is considered as a comment and
ignored. The lines with the even numbers are treated as follows:</p>
<pre class="literal-block">
a_0, energy/(temperature*electron) units
a_1, energy/(temperature^2*electron) units
a_2, energy/(temperature^3*electron) units
a_3, energy/(temperature^4*electron) units
a_4, energy/(temperature^5*electron) units
C_0, energy/(temperature*electron) units
A, 1/temperature units
rho_e, electrons/volume units
D_e, length^2/time units
gamma_p, mass/time units
gamma_s, mass/time units
v_0, length/time units
I_0, energy/(time*length^2) units
lsurface, electron grid units (positive integer)
rsurface, electron grid units (positive integer)
l_skin, length units
tau, time units
B, dimensionless
lambda, length units
n_ion, ions/volume units
surface_movement: 0 to disable tracking of surface motion, 1 to enable
T_e_min, temperature units
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">a_0</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
<span class="n">a_1</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">^</span><span class="mi">2</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
<span class="n">a_2</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">^</span><span class="mi">3</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
<span class="n">a_3</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">^</span><span class="mi">4</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
<span class="n">a_4</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">^</span><span class="mi">5</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
<span class="n">C_0</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">temperature</span><span class="o">*</span><span class="n">electron</span><span class="p">)</span> <span class="n">units</span>
<span class="n">A</span><span class="p">,</span> <span class="mi">1</span><span class="o">/</span><span class="n">temperature</span> <span class="n">units</span>
<span class="n">rho_e</span><span class="p">,</span> <span class="n">electrons</span><span class="o">/</span><span class="n">volume</span> <span class="n">units</span>
<span class="n">D_e</span><span class="p">,</span> <span class="n">length</span><span class="o">^</span><span class="mi">2</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span>
<span class="n">gamma_p</span><span class="p">,</span> <span class="n">mass</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span>
<span class="n">gamma_s</span><span class="p">,</span> <span class="n">mass</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span>
<span class="n">v_0</span><span class="p">,</span> <span class="n">length</span><span class="o">/</span><span class="n">time</span> <span class="n">units</span>
<span class="n">I_0</span><span class="p">,</span> <span class="n">energy</span><span class="o">/</span><span class="p">(</span><span class="n">time</span><span class="o">*</span><span class="n">length</span><span class="o">^</span><span class="mi">2</span><span class="p">)</span> <span class="n">units</span>
<span class="n">lsurface</span><span class="p">,</span> <span class="n">electron</span> <span class="n">grid</span> <span class="n">units</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
<span class="n">rsurface</span><span class="p">,</span> <span class="n">electron</span> <span class="n">grid</span> <span class="n">units</span> <span class="p">(</span><span class="n">positive</span> <span class="n">integer</span><span class="p">)</span>
<span class="n">l_skin</span><span class="p">,</span> <span class="n">length</span> <span class="n">units</span>
<span class="n">tau</span><span class="p">,</span> <span class="n">time</span> <span class="n">units</span>
<span class="n">B</span><span class="p">,</span> <span class="n">dimensionless</span>
<span class="k">lambda</span><span class="p">,</span> <span class="n">length</span> <span class="n">units</span>
<span class="n">n_ion</span><span class="p">,</span> <span class="n">ions</span><span class="o">/</span><span class="n">volume</span> <span class="n">units</span>
<span class="n">surface_movement</span><span class="p">:</span> <span class="mi">0</span> <span class="n">to</span> <span class="n">disable</span> <span class="n">tracking</span> <span class="n">of</span> <span class="n">surface</span> <span class="n">motion</span><span class="p">,</span> <span class="mi">1</span> <span class="n">to</span> <span class="n">enable</span>
<span class="n">T_e_min</span><span class="p">,</span> <span class="n">temperature</span> <span class="n">units</span>
</pre></div>
</div>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>These fixes write the state of the electronic subsystem and the energy
exchange between the subsystems to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command
for info on how to re-specify a fix in an input script that reads a

60
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View File

@ -179,12 +179,12 @@ args = coord epsilon sigma cutoff
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box
fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5
fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5
fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj93</span> <span class="n">xlo</span> <span class="o">-</span><span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="n">units</span> <span class="n">box</span>
<span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj93</span> <span class="n">xhi</span> <span class="n">EDGE</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
<span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj126</span> <span class="n">v_wiggle</span> <span class="mf">23.2</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
<span class="n">fix</span> <span class="n">zwalls</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">colloid</span> <span class="n">zlo</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.858</span> <span class="n">zhi</span> <span class="mf">40.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.858</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -321,22 +321,22 @@ want.</p>
in a time-dependent fashion using equal-style
<a class="reference internal" href="variable.html"><span class="doc">variables</span></a>. The wall interaction parameters (epsilon,
sigma) could be varied with additional variable definitions.</p>
<pre class="literal-block">
variable ramp equal ramp(0,10)
fix 1 all wall xlo v_ramp 1.0 1.0 2.5
</pre>
<pre class="literal-block">
variable linear equal vdisplace(0,20)
fix 1 all wall xlo v_linear 1.0 1.0 2.5
</pre>
<pre class="literal-block">
variable wiggle equal swiggle(0.0,5.0,3.0)
fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
</pre>
<pre class="literal-block">
variable wiggle equal cwiggle(0.0,5.0,3.0)
fix 1 all wall xlo v_wiggle 1.0 1.0 2.5
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">ramp</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_ramp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">linear</span> <span class="n">equal</span> <span class="n">vdisplace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">20</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_linear</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">swiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_wiggle</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">cwiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_wiggle</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
</pre></div>
</div>
<p>The ramp(lo,hi) function adjusts the wall position linearly from lo to
hi over the course of a run. The vdisplace(c0,velocity) function does
something similar using the equation position = c0 + velocity*delta,
@ -344,18 +344,20 @@ where delta is the elapsed time.</p>
<p>The swiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, where omega = 2 PI
/ period:</p>
<pre class="literal-block">
position = c0 + A sin(omega*delta)
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">)</span>
</pre></div>
</div>
<p>The cwiggle(c0,A,period) function causes the wall position to
oscillate sinusoidally according to this equation, which will have an
initial wall velocity of 0.0, and thus may impose a gentler
perturbation on the particles:</p>
<pre class="literal-block">
position = c0 + A (1 - cos(omega*delta))
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">cos</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">))</span>
</pre></div>
</div>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the energy of interaction between atoms and each wall to

4
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@ -280,7 +280,9 @@ and does not blow up as r -&gt; 0, but you must use a large enough
<em>epsilon</em> that particles always reamin on the correct side of the
region surface (r &gt; 0).</p>
</div>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the energy of interaction between atoms and the wall to the

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File diff suppressed because it is too large Load Diff

16
doc/html/improper_class2.html
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@ -131,17 +131,17 @@
<h1>improper_style class2/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
improper_style class2
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">class2</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
improper_style class2
improper_coeff 1 100.0 0
improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">class2</span>
<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mi">0</span>
<span class="n">improper_coeff</span> <span class="o">*</span> <span class="n">aa</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">115.06</span> <span class="mf">130.01</span> <span class="mf">115.06</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/improper_cossq.html
View File

@ -131,16 +131,16 @@
<h1>improper_style cossq/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
improper_style cossq
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">cossq</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
improper_style cossq
improper_coeff 1 4.0 0.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">cossq</span>
<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">4.0</span> <span class="mf">0.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/improper_cvff.html
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@ -134,16 +134,16 @@
<h1>improper_style cvff/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
improper_style cvff
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">cvff</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
improper_style cvff
improper_coeff 1 80.0 -1 4
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">cvff</span>
<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="o">-</span><span class="mi">1</span> <span class="mi">4</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

8
doc/html/improper_distance.html
View File

@ -132,10 +132,10 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
improper_style distance
improper_coeff 1 80.0 100.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">distance</span>
<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="mf">100.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/improper_fourier.html
View File

@ -131,16 +131,16 @@
<h1>improper_style fourier/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
improper_style fourier
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">fourier</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
improper_style fourier
improper_coeff 1 100.0 180.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">fourier</span>
<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">180.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

14
doc/html/improper_harmonic.html
View File

@ -137,16 +137,16 @@
<h1>improper_style harmonic/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
improper_style harmonic
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">harmonic</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
improper_style harmonic
improper_coeff 1 100.0 0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">harmonic</span>
<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mi">0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

18
doc/html/improper_ring.html
View File

@ -131,16 +131,16 @@
<h1>improper_style ring/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
improper_style ring
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">ring</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
improper_style ring
improper_coeff 1 8000 70.5
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">ring</span>
<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mi">8000</span> <span class="mf">70.5</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -150,8 +150,8 @@ improper_coeff 1 8000 70.5
specified by (i,j,k,l) indices and theta0 its equilibrium value.</p>
<p>If the 4 atoms in an improper quadruplet (listed in the data file read
by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command) are ordered i,j,k,l then
theta_<em>ijl</em> is the angle between atoms i,j and l, theta_<em>ijk</em> is the
angle between atoms i,j and k, theta_<em>kjl</em> is the angle between atoms
<a href="#id1"><span class="problematic" id="id2">theta_</span></a><em>ijl</em> is the angle between atoms i,j and l, <a href="#id3"><span class="problematic" id="id4">theta_</span></a><em>ijk</em> is the
angle between atoms i,j and k, <a href="#id5"><span class="problematic" id="id6">theta_</span></a><em>kjl</em> is the angle between atoms
j,k, and l.</p>
<p>The &#8220;ring&#8221; improper style implements the improper potential introduced
by Destree et al., in Equation (9) of <a class="reference internal" href="#destree"><span class="std std-ref">(Destree)</span></a>. This

14
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@ -131,16 +131,16 @@
<h1>improper_style umbrella/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
improper_style umbrella
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">umbrella</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
improper_style umbrella
improper_coeff 1 100.0 180.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">improper_style</span> <span class="n">umbrella</span>
<span class="n">improper_coeff</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">180.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

22
doc/html/pair_adp.html
View File

@ -131,17 +131,17 @@
<h1>pair_style adp/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style adp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">adp</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style adp
pair_coeff * * Ta.adp Ta
pair_coeff * * ../potentials/AlCu.adp Al Al Cu
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">adp</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ta</span><span class="o">.</span><span class="n">adp</span> <span class="n">Ta</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">AlCu</span><span class="o">.</span><span class="n">adp</span> <span class="n">Al</span> <span class="n">Al</span> <span class="n">Cu</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -188,9 +188,9 @@ file which has tabulated ADP values for w elements and their alloy
interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types
and you want the 1st 3 to be Al, and the 4th to be Cu, you would use
the following pair_coeff command:</p>
<pre class="literal-block">
pair_coeff * * AlCu.adp Al Al Al Cu
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">AlCu</span><span class="o">.</span><span class="n">adp</span> <span class="n">Al</span> <span class="n">Al</span> <span class="n">Al</span> <span class="n">Cu</span>
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Al arguments map LAMMPS atom types 1,2,3 to the Al
element in the extended <em>setfl</em> file. The final Cu argument maps

52
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@ -143,9 +143,9 @@
<h1>pair_style rebo/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style style cutoff LJ_flag TORSION_flag
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">cutoff</span> <span class="n">LJ_flag</span> <span class="n">TORSION_flag</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>airebo</em> or <em>airebo/morse</em> or <em>rebo</em></li>
<li>cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only)</li>
@ -155,19 +155,19 @@ pair_style style cutoff LJ_flag TORSION_flag
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style airebo 3.0
pair_style airebo 2.5 1 0
pair_coeff * * ../potentials/CH.airebo H C
</pre>
<pre class="literal-block">
pair_style airebo/morse 3.0
pair_coeff * * ../potentials/CH.airebo-m H C
</pre>
<pre class="literal-block">
pair_style rebo
pair_coeff * * ../potentials/CH.airebo H C
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">airebo</span> <span class="mf">3.0</span>
<span class="n">pair_style</span> <span class="n">airebo</span> <span class="mf">2.5</span> <span class="mi">1</span> <span class="mi">0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">H</span> <span class="n">C</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">airebo</span><span class="o">/</span><span class="n">morse</span> <span class="mf">3.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span><span class="o">-</span><span class="n">m</span> <span class="n">H</span> <span class="n">C</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">rebo</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">H</span> <span class="n">C</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -242,9 +242,9 @@ to specify the path for the potential file.</p>
<p>As an example, if your LAMMPS simulation has 4 atom types and you want
the 1st 3 to be C, and the 4th to be H, you would use the following
pair_coeff command:</p>
<pre class="literal-block">
pair_coeff * * CH.airebo C C C H
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">CH</span><span class="o">.</span><span class="n">airebo</span> <span class="n">C</span> <span class="n">C</span> <span class="n">C</span> <span class="n">H</span>
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three C arguments map LAMMPS atom types 1,2,3 to the C
element in the AIREBO file. The final H argument maps LAMMPS atom
@ -273,13 +273,13 @@ The 3 values correspond to the following sub-categories:</p>
</ol>
<p>To print these quantities to the log file (with descriptive column
headings) the following commands could be included in an input script:</p>
<pre class="literal-block">
compute 0 all pair airebo
variable REBO equal c_0[1]
variable LJ equal c_0[2]
variable TORSION equal c_0[3]
thermo_style custom step temp epair v_REBO v_LJ v_TORSION
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">0</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">airebo</span>
<span class="n">variable</span> <span class="n">REBO</span> <span class="n">equal</span> <span class="n">c_0</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">LJ</span> <span class="n">equal</span> <span class="n">c_0</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">TORSION</span> <span class="n">equal</span> <span class="n">c_0</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_REBO</span> <span class="n">v_LJ</span> <span class="n">v_TORSION</span>
</pre></div>
</div>
<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.

16
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View File

@ -134,20 +134,20 @@
<h1>pair_style beck/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style beck Rc
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">beck</span> <span class="n">Rc</span>
</pre></div>
</div>
<ul class="simple">
<li>Rc = cutoff for interactions (distance units)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style beck 8.0
pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746
pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">beck</span> <span class="mf">8.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">399.671876712</span> <span class="mf">0.0000867636112694</span> <span class="mf">0.675</span> <span class="mf">4.390</span> <span class="mf">0.0003746</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">399.671876712</span> <span class="mf">0.0000867636112694</span> <span class="mf">0.675</span> <span class="mf">4.390</span> <span class="mf">0.0003746</span> <span class="mf">6.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

16
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View File

@ -128,18 +128,18 @@
<span id="index-0"></span><h1>pair_style body command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style body cutoff
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">body</span> <span class="n">cutoff</span>
</pre></div>
</div>
<p>cutoff = global cutoff for interactions (distance units)</p>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style body 3.0
pair_coeff * * 1.0 1.0
pair_coeff 1 1 1.0 1.5 2.5
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">body</span> <span class="mf">3.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.5</span> <span class="mf">2.5</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

56
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View File

@ -161,9 +161,9 @@
<h1>pair_style born/coul/wolf/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style style args
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>born</em> or <em>born/coul/long</em> or <em>born/coul/long/cs</em> or <em>born/coul/msm</em> or <em>born/coul/wolf</em></li>
<li>args = list of arguments for a particular style</li>
@ -185,31 +185,31 @@ pair_style style args
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style born 10.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</pre>
<pre class="literal-block">
pair_style born/coul/long 10.0
pair_style born/coul/long/cs 10.0
pair_style born/coul/long 10.0 8.0
pair_style born/coul/long/cs 10.0 8.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</pre>
<pre class="literal-block">
pair_style born/coul/msm 10.0
pair_style born/coul/msm 10.0 8.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</pre>
<pre class="literal-block">
pair_style born/coul/wolf 0.25 10.0
pair_style born/coul/wolf 0.25 10.0 9.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
<span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">wolf</span> <span class="mf">0.25</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">wolf</span> <span class="mf">0.25</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

58
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View File

@ -179,9 +179,9 @@
<h1>pair_style buck/coul/msm/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style style args
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>buck</em> or <em>buck/coul/cut</em> or <em>buck/coul/long</em> or <em>buck/coul/long/cs</em> or <em>buck/coul/msm</em></li>
<li>args = list of arguments for a particular style</li>
@ -202,32 +202,32 @@ pair_style style args
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style buck 2.5
pair_coeff * * 100.0 1.5 200.0
pair_coeff * * 100.0 1.5 200.0 3.0
</pre>
<pre class="literal-block">
pair_style buck/coul/cut 10.0
pair_style buck/coul/cut 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0
</pre>
<pre class="literal-block">
pair_style buck/coul/long 10.0
pair_style buck/coul/long/cs 10.0
pair_style buck/coul/long 10.0 8.0
pair_style buck/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
</pre>
<pre class="literal-block">
pair_style buck/coul/msm 10.0
pair_style buck/coul/msm 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span> <span class="mf">2.5</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">3.0</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">9.0</span> <span class="mf">8.0</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">9.0</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">9.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

54
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@ -158,9 +158,9 @@
<h1>pair_style lj/charmm/coul/msm/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style style args
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/charmm/coul/charmm</em> or <em>lj/charmm/coul/charmm/implicit</em> or <em>lj/charmm/coul/long</em> or <em>lj/charmm/coul/msm</em></li>
<li>args = list of arguments for a particular style</li>
@ -182,30 +182,30 @@ pair_style style args
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style lj/charmm/coul/charmm 8.0 10.0
pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</pre>
<pre class="literal-block">
pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</pre>
<pre class="literal-block">
pair_style lj/charmm/coul/long 8.0 10.0
pair_style lj/charmm/coul/long 8.0 10.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</pre>
<pre class="literal-block">
pair_style lj/charmm/coul/msm 8.0 10.0
pair_style lj/charmm/coul/msm 8.0 10.0 9.0
pair_coeff * * 100.0 2.0
pair_coeff 1 1 100.0 2.0 150.0 3.5
</pre>
<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">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">7.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
</pre></div>
</div>
<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">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">implicit</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">implicit</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">7.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
</pre></div>
</div>
<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">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
</pre></div>
</div>
<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">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">charmm</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">150.0</span> <span class="mf">3.5</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

42
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@ -158,9 +158,9 @@
<h1>pair_style lj/class2/coul/long/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style style args
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/class2</em> or <em>lj/class2/coul/cut</em> or <em>lj/class2/coul/long</em></li>
<li>args = list of arguments for a particular style</li>
@ -178,24 +178,24 @@ pair_style style args
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style lj/class2 10.0
pair_coeff * * 100.0 2.5
pair_coeff 1 2* 100.0 2.5 9.0
</pre>
<pre class="literal-block">
pair_style lj/class2/coul/cut 10.0
pair_style lj/class2/coul/cut 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
pair_coeff 1 1 100.0 3.5 9.0 9.0
</pre>
<pre class="literal-block">
pair_style lj/class2/coul/long 10.0
pair_style lj/class2/coul/long 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</pre>
<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">class2</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.5</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span><span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.5</span> <span class="mf">9.0</span>
</pre></div>
</div>
<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">class2</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">class2</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">3.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span> <span class="mf">9.0</span>
</pre></div>
</div>
<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">class2</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">class2</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">3.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">3.5</span> <span class="mf">9.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

20
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@ -134,22 +134,22 @@
<h1>pair_style colloid/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style colloid cutoff
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">colloid</span> <span class="n">cutoff</span>
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for colloidal interactions (distance units)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style colloid 10.0
pair_coeff * * 25 1.0 10.0 10.0
pair_coeff 1 1 144 1.0 0.0 0.0 3.0
pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0
pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">colloid</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mi">25</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">144</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">3.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mf">75.398</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">10.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">39.478</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mf">10.0</span> <span class="mf">25.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

32
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@ -134,10 +134,10 @@
<h1>pair_style comb3 command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style comb
pair_style comb3 keyword
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">comb</span>
<span class="n">pair_style</span> <span class="n">comb3</span> <span class="n">keyword</span>
</pre></div>
</div>
<pre class="literal-block">
keyword = <em>polar</em>
<em>polar</em> value = <em>polar_on</em> or <em>polar_off</em> = whether or not to include atomic polarization
@ -145,15 +145,15 @@ keyword = <em>polar</em>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style comb
pair_coeff * * ../potentials/ffield.comb Si
pair_coeff * * ../potentials/ffield.comb Hf Si O
</pre>
<pre class="literal-block">
pair_style comb3 polar_off
pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">comb</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb</span> <span class="n">Si</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb</span> <span class="n">Hf</span> <span class="n">Si</span> <span class="n">O</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">comb3</span> <span class="n">polar_off</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb3</span> <span class="n">O</span> <span class="n">Cu</span> <span class="n">N</span> <span class="n">C</span> <span class="n">O</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -191,9 +191,9 @@ command, where N is the number of LAMMPS atom types.</p>
HfO&lt;sub&gt;2&lt;/sub&gt; interface has 4 atom types, and you want the 1st and
last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
use the following pair_coeff command:</p>
<pre class="literal-block">
pair_coeff * * ../potentials/ffield.comb Si Hf O Si
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">comb</span> <span class="n">Si</span> <span class="n">Hf</span> <span class="n">O</span> <span class="n">Si</span>
</pre></div>
</div>
<p>The first two arguments must be * * so as to span all LAMMPS atom
types. The first and last Si arguments map LAMMPS atom types 1 and 4
to the Si element in the <em>ffield.comb</em> file. The second Hf argument

124
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@ -206,18 +206,18 @@
<h1>pair_style tip4p/long/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style coul/cut cutoff
pair_style coul/debye kappa cutoff
pair_style coul/dsf alpha cutoff
pair_style coul/long cutoff
pair_style coul/long/cs cutoff
pair_style coul/long/gpu cutoff
pair_style coul/wolf alpha cutoff
pair_style coul/streitz cutoff keyword alpha
pair_style tip4p/cut otype htype btype atype qdist cutoff
pair_style tip4p/long otype htype btype atype qdist cutoff
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span>
<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">debye</span> <span class="n">kappa</span> <span class="n">cutoff</span>
<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">dsf</span> <span class="n">alpha</span> <span class="n">cutoff</span>
<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="n">cutoff</span>
<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="n">cutoff</span>
<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">gpu</span> <span class="n">cutoff</span>
<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">wolf</span> <span class="n">alpha</span> <span class="n">cutoff</span>
<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="n">cutoff</span> <span class="n">keyword</span> <span class="n">alpha</span>
<span class="n">pair_style</span> <span class="n">tip4p</span><span class="o">/</span><span class="n">cut</span> <span class="n">otype</span> <span class="n">htype</span> <span class="n">btype</span> <span class="n">atype</span> <span class="n">qdist</span> <span class="n">cutoff</span>
<span class="n">pair_style</span> <span class="n">tip4p</span><span class="o">/</span><span class="n">long</span> <span class="n">otype</span> <span class="n">htype</span> <span class="n">btype</span> <span class="n">atype</span> <span class="n">qdist</span> <span class="n">cutoff</span>
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for Coulombic interactions</li>
<li>kappa = Debye length (inverse distance units)</li>
@ -226,46 +226,46 @@ pair_style tip4p/long otype htype btype atype qdist cutoff
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style coul/cut 2.5
pair_coeff * *
pair_coeff 2 2 3.5
</pre>
<pre class="literal-block">
pair_style coul/debye 1.4 3.0
pair_coeff * *
pair_coeff 2 2 3.5
</pre>
<pre class="literal-block">
pair_style coul/dsf 0.05 10.0
pair_coeff * *
</pre>
<pre class="literal-block">
pair_style coul/long 10.0
pair_style coul/long/cs 10.0
pair_coeff * *
</pre>
<pre class="literal-block">
pair_style coul/msm 10.0
pair_coeff * *
</pre>
<pre class="literal-block">
pair_style coul/wolf 0.2 9.0
pair_coeff * *
</pre>
<pre class="literal-block">
pair_style coul/streitz 12.0 ewald
pair_style coul/streitz 12.0 wolf 0.30
pair_coeff * * AlO.streitz Al O
</pre>
<pre class="literal-block">
pair_style tip4p/cut 1 2 7 8 0.15 12.0
pair_coeff * *
</pre>
<pre class="literal-block">
pair_style tip4p/long 1 2 7 8 0.15 10.0
pair_coeff * *
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="mf">2.5</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">3.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">debye</span> <span class="mf">1.4</span> <span class="mf">3.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">3.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">dsf</span> <span class="mf">0.05</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">msm</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">wolf</span> <span class="mf">0.2</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="mf">12.0</span> <span class="n">ewald</span>
<span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="mf">12.0</span> <span class="n">wolf</span> <span class="mf">0.30</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">AlO</span><span class="o">.</span><span class="n">streitz</span> <span class="n">Al</span> <span class="n">O</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tip4p</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">12.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">tip4p</span><span class="o">/</span><span class="n">long</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mf">0.15</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -317,21 +317,21 @@ used with <a class="reference internal" href="pair_eam.html"><span class="doc">p
short-range potential that has been parameterized appropriately) via
the <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid/overlay</span></a> command. Likewise,
charge equilibration must be performed via the <a class="reference internal" href="fix_qeq.html"><span class="doc">fix qeq/slater</span></a> command. For example:</p>
<pre class="literal-block">
pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy
pair_coeff * * coul/streitz AlO.streitz Al O
pair_coeff * * eam/alloy AlO.eam.alloy Al O
fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="mf">12.0</span> <span class="n">wolf</span> <span class="mf">0.31</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="n">AlO</span><span class="o">.</span><span class="n">streitz</span> <span class="n">Al</span> <span class="n">O</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span> <span class="n">AlO</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">alloy</span> <span class="n">Al</span> <span class="n">O</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">slater</span> <span class="mi">1</span> <span class="mf">12.0</span> <span class="mf">1.0e-6</span> <span class="mi">100</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span>
</pre></div>
</div>
<p>The keyword <em>wolf</em> in the coul/streitz command denotes computing
Coulombic interactions via Wolf summation. An additional damping
parameter is required for the Wolf summation, as described for the
coul/wolf potential above. Alternatively, Coulombic interactions can
be computed via an Ewald summation. For example:</p>
<pre class="literal-block">
pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy
kspace_style ewald 1e-6
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">coul</span><span class="o">/</span><span class="n">streitz</span> <span class="mf">12.0</span> <span class="n">ewald</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span>
<span class="n">kspace_style</span> <span class="n">ewald</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">6</span>
</pre></div>
</div>
<p>Keyword <em>ewald</em> does not need a damping parameter, but a
<a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> must be defined, which can be style
<em>ewald</em> or <em>pppm</em>. The Ewald method was used in Streitz and

14
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@ -131,17 +131,17 @@
<h1>pair_style coul/diel/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style coul/diel cutoff
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">diel</span> <span class="n">cutoff</span>
</pre></div>
</div>
<p>cutoff = global cutoff (distance units)</p>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style coul/diel 3.5
pair_coeff 1 4 78. 1.375 0.112
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">coul</span><span class="o">/</span><span class="n">diel</span> <span class="mf">3.5</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">4</span> <span class="mf">78.</span> <span class="mf">1.375</span> <span class="mf">0.112</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

26
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@ -131,9 +131,9 @@
<h1>pair_style buck/coul/long/cs command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style style args
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>born/coul/long/cs</em> or <em>buck/coul/long/cs</em></li>
<li>args = list of arguments for a particular style</li>
@ -149,16 +149,16 @@ pair_style style args
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style born/coul/long/cs 10.0 8.0
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</pre>
<pre class="literal-block">
pair_style buck/coul/long/cs 10.0
pair_style buck/coul/long/cs 10.0 8.0
pair_coeff * * 100.0 1.5 200.0
pair_coeff 1 1 100.0 1.5 200.0 9.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">6.08</span> <span class="mf">0.317</span> <span class="mf">2.340</span> <span class="mf">24.18</span> <span class="mf">11.51</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span>
<span class="n">pair_style</span> <span class="n">buck</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">10.0</span> <span class="mf">8.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">100.0</span> <span class="mf">1.5</span> <span class="mf">200.0</span> <span class="mf">9.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

52
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View File

@ -149,12 +149,12 @@
<h1>pair_style lj/long/dipole/long command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style lj/cut/dipole/cut cutoff (cutoff2)
pair_style lj/sf/dipole/sf cutoff (cutoff2)
pair_style lj/cut/dipole/long cutoff (cutoff2)
pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2)
</pre>
<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">dipole</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">sf</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">sf</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</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">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">flag_lj</span> <span class="n">flag_coul</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units)</li>
<li>cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units)</li>
@ -175,26 +175,26 @@ pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2)
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style lj/cut/dipole/cut 10.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
</pre>
<pre class="literal-block">
pair_style lj/sf/dipole/sf 9.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
</pre>
<pre class="literal-block">
pair_style lj/cut/dipole/long 10.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
</pre>
<pre class="literal-block">
pair_style lj/long/dipole/long long long 3.5 10.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0
</pre>
<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">dipole</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
</pre></div>
</div>
<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">sf</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">sf</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
</pre></div>
</div>
<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">dipole</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
</pre></div>
</div>
<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">long</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">long</span> <span class="n">long</span> <span class="mf">3.5</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

28
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@ -143,10 +143,10 @@
<h1>pair_style dpd/tstat/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style dpd T cutoff seed
pair_style dpd/tstat Tstart Tstop cutoff seed
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dpd</span> <span class="n">T</span> <span class="n">cutoff</span> <span class="n">seed</span>
<span class="n">pair_style</span> <span class="n">dpd</span><span class="o">/</span><span class="n">tstat</span> <span class="n">Tstart</span> <span class="n">Tstop</span> <span class="n">cutoff</span> <span class="n">seed</span>
</pre></div>
</div>
<ul class="simple">
<li>T = temperature (temperature units)</li>
<li>Tstart,Tstop = desired temperature at start/end of run (temperature units)</li>
@ -156,16 +156,16 @@ pair_style dpd/tstat Tstart Tstop cutoff seed
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style dpd 1.0 2.5 34387
pair_coeff * * 3.0 1.0
pair_coeff 1 1 3.0 1.0 1.0
</pre>
<pre class="literal-block">
pair_style dpd/tstat 1.0 1.0 2.5 34387
pair_coeff * * 1.0
pair_coeff 1 1 1.0 1.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dpd</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mi">34387</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">3.0</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">3.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dpd</span><span class="o">/</span><span class="n">tstat</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mi">34387</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

22
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@ -131,9 +131,9 @@
<h1>pair_style dpd/fdt/energy command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style style args
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>dpd/fdt</em> or <em>dpd/fdt/energy</em></li>
<li>args = list of arguments for a particular style</li>
@ -150,14 +150,14 @@ pair_style style args
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style dpd/fdt 300.0 2.5 34387
pair_coeff * * 3.0 1.0 2.5
</pre>
<pre class="literal-block">
pair_style dpd/fdt/energy 2.5 34387
pair_coeff * * 3.0 1.0 0.1 2.5
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dpd</span><span class="o">/</span><span class="n">fdt</span> <span class="mf">300.0</span> <span class="mf">2.5</span> <span class="mi">34387</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">3.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">dpd</span><span class="o">/</span><span class="n">fdt</span><span class="o">/</span><span class="n">energy</span> <span class="mf">2.5</span> <span class="mi">34387</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">3.0</span> <span class="mf">1.0</span> <span class="mf">0.1</span> <span class="mf">2.5</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

64
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@ -176,32 +176,32 @@
<h1>pair_style eam/fs/opt command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style style
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>eam</em> or <em>eam/alloy</em> or <em>eam/cd</em> or <em>eam/fs</em></li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style eam
pair_coeff * * cuu3
pair_coeff 1*3 1*3 niu3.eam
</pre>
<pre class="literal-block">
pair_style eam/alloy
pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni
</pre>
<pre class="literal-block">
pair_style eam/cd
pair_coeff * * ../potentials/FeCr.cdeam Fe Cr
</pre>
<pre class="literal-block">
pair_style eam/fs
pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">cuu3</span>
<span class="n">pair_coeff</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="n">niu3</span><span class="o">.</span><span class="n">eam</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span><span class="o">/</span><span class="n">alloy</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">alloy</span> <span class="n">Ni</span> <span class="n">Al</span> <span class="n">Ni</span> <span class="n">Ni</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span><span class="o">/</span><span class="n">cd</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">FeCr</span><span class="o">.</span><span class="n">cdeam</span> <span class="n">Fe</span> <span class="n">Cr</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eam</span><span class="o">/</span><span class="n">fs</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">fs</span> <span class="n">Ni</span> <span class="n">Al</span> <span class="n">Ni</span> <span class="n">Ni</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -270,9 +270,9 @@ single argument:</p>
<li>filename</li>
</ul>
<p>Thus the following command</p>
<pre class="literal-block">
pair_coeff *2 1*2 cuu3.eam
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span><span class="mi">2</span> <span class="mi">1</span><span class="o">*</span><span class="mi">2</span> <span class="n">cuu3</span><span class="o">.</span><span class="n">eam</span>
</pre></div>
</div>
<p>will read the cuu3 potential file and use the tabulated Cu values for
F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs
1,2 and 2,1 are ignored). See the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> doc
@ -315,9 +315,9 @@ density). The units for the effective charge Z are &#8220;atomic charge&#8221;
sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used
by LAMMPS to compute the pair potential term in the EAM energy
expression as r*phi, in units of eV-Angstroms, via the formula</p>
<pre class="literal-block">
r*phi = 27.2 * 0.529 * Zi * Zj
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">r</span><span class="o">*</span><span class="n">phi</span> <span class="o">=</span> <span class="mf">27.2</span> <span class="o">*</span> <span class="mf">0.529</span> <span class="o">*</span> <span class="n">Zi</span> <span class="o">*</span> <span class="n">Zj</span>
</pre></div>
</div>
<p>where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms.</p>
<hr class="docutils" />
<p>Style <em>eam/alloy</em> computes pairwise interactions using the same
@ -350,9 +350,9 @@ page for alternate ways to specify the path for the potential file.
If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to
be Ni, and the 4th to be Al, you would use the following pair_coeff
command:</p>
<pre class="literal-block">
pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">alloy</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Al</span>
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni
element in the <em>setfl</em> file. The final Al argument maps LAMMPS atom
@ -446,9 +446,9 @@ require that; the user can tabulate any functional form desired in the
FS potential files.</p>
<p>For style <em>eam/fs</em>, the form of the pair_coeff command is exactly the
same as for style <em>eam/alloy</em>, e.g.</p>
<pre class="literal-block">
pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">NiAlH_jea</span><span class="o">.</span><span class="n">eam</span><span class="o">.</span><span class="n">fs</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Ni</span> <span class="n">Al</span>
</pre></div>
</div>
<p>where there are N additional arguments after the filename, where N is
the number of LAMMPS atom types. See the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>
doc page for alternate ways to specify the path for the potential

12
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View File

@ -128,12 +128,12 @@
<span id="index-0"></span><h1>pair_style edip command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style edip
</pre>
<pre class="literal-block">
pair_style edip/omp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">edip</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">edip</span><span class="o">/</span><span class="n">omp</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>

26
doc/html/pair_eff.html
View File

@ -128,9 +128,9 @@
<span id="index-0"></span><h1>pair_style eff/cut command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style eff/cut cutoff keyword args ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for Coulombic interactions</li>
<li>zero or more keyword/value pairs may be appended</li>
@ -146,16 +146,16 @@ keyword = <em>limit/eradius</em> or <em>pressure/evirials</em> or <em>ecp</em>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style eff/cut 39.7
pair_style eff/cut 40.0 limit/eradius
pair_style eff/cut 40.0 limit/eradius pressure/evirials
pair_style eff/cut 40.0 ecp 1 Si 3 C
pair_coeff * *
pair_coeff 2 2 20.0
pair_coeff 1 s 0.320852 2.283269 0.814857
pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">39.7</span>
<span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">40.0</span> <span class="n">limit</span><span class="o">/</span><span class="n">eradius</span>
<span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">40.0</span> <span class="n">limit</span><span class="o">/</span><span class="n">eradius</span> <span class="n">pressure</span><span class="o">/</span><span class="n">evirials</span>
<span class="n">pair_style</span> <span class="n">eff</span><span class="o">/</span><span class="n">cut</span> <span class="mf">40.0</span> <span class="n">ecp</span> <span class="mi">1</span> <span class="n">Si</span> <span class="mi">3</span> <span class="n">C</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">20.0</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="n">s</span> <span class="mf">0.320852</span> <span class="mf">2.283269</span> <span class="mf">0.814857</span>
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="n">p</span> <span class="mf">22.721015</span> <span class="mf">0.728733</span> <span class="mf">1.103199</span> <span class="mf">17.695345</span> <span class="mf">6.693621</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

24
doc/html/pair_eim.html
View File

@ -131,21 +131,21 @@
<h1>pair_style eim/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style style
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>eim</em></li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style eim
pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl
pair_coeff * * Na Cl ffield.eim Na Na Na Cl
pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">eim</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">eim</span> <span class="n">Na</span> <span class="n">Cl</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="n">ffield</span><span class="o">.</span><span class="n">eim</span> <span class="n">Na</span> <span class="n">Na</span> <span class="n">Na</span> <span class="n">Cl</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="o">../</span><span class="n">potentials</span><span class="o">/</span><span class="n">ffield</span><span class="o">.</span><span class="n">eim</span> <span class="n">Cl</span> <span class="n">NULL</span> <span class="n">Na</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -207,9 +207,9 @@ to specify the path for the potential file.</p>
system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms
types and you want the 1st 3 to be Na, and the 4th to be Cl, you would
use the following pair_coeff command:</p>
<pre class="literal-block">
pair_coeff * * Na Cl ffield.eim Na Na Na Cl
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Na</span> <span class="n">Cl</span> <span class="n">ffield</span><span class="o">.</span><span class="n">eim</span> <span class="n">Na</span> <span class="n">Na</span> <span class="n">Na</span> <span class="n">Cl</span>
</pre></div>
</div>
<p>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
The filename is the EIM potential file. The Na and Cl arguments
(before the file name) are the two elements for which info will be

18
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View File

@ -128,21 +128,21 @@
<span id="index-0"></span><h1>pair_style exp6/rx command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style exp6/rx cutoff
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">exp6</span><span class="o">/</span><span class="n">rx</span> <span class="n">cutoff</span>
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for DPD interactions (distance units)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style exp6/rx 10.0
pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0
pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0
pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">exp6</span><span class="o">/</span><span class="n">rx</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="n">h2o</span> <span class="n">h2o</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="n">h2o</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">exp6</span><span class="o">.</span><span class="n">params</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mi">1</span><span class="n">fluid</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

36
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View File

@ -140,25 +140,25 @@
<h1>pair_style gauss/cut/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style gauss cutoff
pair_style gauss/cut cutoff
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">gauss</span> <span class="n">cutoff</span>
<span class="n">pair_style</span> <span class="n">gauss</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span>
</pre></div>
</div>
<ul class="simple">
<li>cutoff = global cutoff for Gauss interactions (distance units)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style gauss 12.0
pair_coeff * * 1.0 0.9
pair_coeff 1 4 1.0 0.9 10.0
</pre>
<pre class="literal-block">
pair_style gauss/cut 3.5
pair_coeff 1 4 0.2805 1.45 0.112
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">gauss</span> <span class="mf">12.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">0.9</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">4</span> <span class="mf">1.0</span> <span class="mf">0.9</span> <span class="mf">10.0</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">gauss</span><span class="o">/</span><span class="n">cut</span> <span class="mf">3.5</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">4</span> <span class="mf">0.2805</span> <span class="mf">1.45</span> <span class="mf">0.112</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -239,11 +239,11 @@ sites have an atom within the distance at which the force is a maximum
= sqrt(0.5/b). This quantity can be accessed via the <a class="reference internal" href="compute_pair.html"><span class="doc">compute pair</span></a> command as a vector of values of length 1.</p>
<p>To print this quantity to the log file (with a descriptive column
heading) the following commands could be included in an input script:</p>
<pre class="literal-block">
compute gauss all pair gauss
variable occ equal c_gauss[1]
thermo_style custom step temp epair v_occ
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">gauss</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">gauss</span>
<span class="n">variable</span> <span class="n">occ</span> <span class="n">equal</span> <span class="n">c_gauss</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_occ</span>
</pre></div>
</div>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">

14
doc/html/pair_gayberne.html
View File

@ -137,9 +137,9 @@
<h1>pair_style gayberne/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style gayberne gamma upsilon mu cutoff
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">gayberne</span> <span class="n">gamma</span> <span class="n">upsilon</span> <span class="n">mu</span> <span class="n">cutoff</span>
</pre></div>
</div>
<ul class="simple">
<li>gamma = shift for potential minimum (typically 1)</li>
<li>upsilon = exponent for eta orientation-dependent energy function</li>
@ -149,10 +149,10 @@ pair_style gayberne gamma upsilon mu cutoff
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style gayberne 1.0 1.0 1.0 10.0
pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">gayberne</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.7</span> <span class="mf">1.7</span> <span class="mf">3.4</span> <span class="mf">3.4</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

26
doc/html/pair_gromacs.html
View File

@ -140,9 +140,9 @@
<h1>pair_style lj/gromacs/coul/gromacs/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style style args
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>lj/gromacs</em> or <em>lj/gromacs/coul/gromacs</em></li>
<li>args = list of arguments for a particular style</li>
@ -157,16 +157,16 @@ pair_style style args
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style lj/gromacs 9.0 12.0
pair_coeff * * 100.0 2.0
pair_coeff 2 2 100.0 2.0 8.0 10.0
</pre>
<pre class="literal-block">
pair_style lj/gromacs/coul/gromacs 9.0 12.0
pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
pair_coeff * * 100.0 2.0
</pre>
<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">gromacs</span> <span class="mf">9.0</span> <span class="mf">12.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mf">100.0</span> <span class="mf">2.0</span> <span class="mf">8.0</span> <span class="mf">10.0</span>
</pre></div>
</div>
<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">gromacs</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">gromacs</span> <span class="mf">9.0</span> <span class="mf">12.0</span>
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">gromacs</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">gromacs</span> <span class="mf">8.0</span> <span class="mf">10.0</span> <span class="mf">7.0</span> <span class="mf">9.0</span>
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">100.0</span> <span class="mf">2.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

36
doc/html/pair_hbond_dreiding.html
View File

@ -137,9 +137,9 @@
<h1>pair_style hbond/dreiding/morse/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">style</span> <span class="n">N</span> <span class="n">inner_distance_cutoff</span> <span class="n">outer_distance_cutoff</span> <span class="n">angle_cutof</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>hbond/dreiding/lj</em> or <em>hbond/dreiding/morse</em></li>
<li>n = cosine angle periodicity</li>
@ -151,14 +151,14 @@ pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
</pre>
<pre class="literal-block">
pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">lj</span> <span class="mi">4</span> <span class="mf">9.0</span> <span class="mf">11.0</span> <span class="mi">90</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">lj</span> <span class="mi">3</span> <span class="n">i</span> <span class="mf">9.5</span> <span class="mf">2.75</span> <span class="mi">4</span> <span class="mf">9.0</span> <span class="mf">11.0</span> <span class="mf">90.0</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">hybrid</span><span class="o">/</span><span class="n">overlay</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">morse</span> <span class="mi">2</span> <span class="mf">9.0</span> <span class="mf">11.0</span> <span class="mi">90</span>
<span class="n">pair_coeff</span> <span class="mi">1</span> <span class="mi">2</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">morse</span> <span class="mi">3</span> <span class="n">i</span> <span class="mf">3.88</span> <span class="mf">1.7241379</span> <span class="mf">2.9</span> <span class="mi">2</span> <span class="mi">9</span> <span class="mi">11</span> <span class="mi">90</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -265,7 +265,7 @@ follows:</p>
<p>A single hydrogen atom type K can be specified, or a wild-card
asterisk can be used in place of or in conjunction with the K
arguments to select multiple types as hydrogens. This takes the form
&#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;. See the <a class="reference external" href="pair_coeff">pair_coeff</a> command
&#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. See the <a class="reference external" href="pair_coeff">pair_coeff</a> command
doc page for details.</p>
<p>If the donor flag is <em>i</em>, then the atom of type I in the pair_coeff
command is treated as the donor, and J is the acceptor. If the donor
@ -321,12 +321,12 @@ quantities can be accessed via the <a class="reference internal" href="compute_p
command as a vector of values of length 2.</p>
<p>To print these quantities to the log file (with a descriptive column
heading) the following commands could be included in an input script:</p>
<pre class="literal-block">
compute hb all pair hbond/dreiding/lj
variable n_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom step temp epair v_E_hbond
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">hb</span> <span class="nb">all</span> <span class="n">pair</span> <span class="n">hbond</span><span class="o">/</span><span class="n">dreiding</span><span class="o">/</span><span class="n">lj</span>
<span class="n">variable</span> <span class="n">n_hbond</span> <span class="n">equal</span> <span class="n">c_hb</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="c1">#number hbonds</span>
<span class="n">variable</span> <span class="n">E_hbond</span> <span class="n">equal</span> <span class="n">c_hb</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="c1">#hbond energy</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">epair</span> <span class="n">v_E_hbond</span>
</pre></div>
</div>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">

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