Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/html/compute_sna_atom.html
fe49cbe4cc1fefficient_neuronet

Last Change
Raw File

compute_sna_atom.html
View Options

<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>compute sna/atom command &mdash; LAMMPS documentation</title>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type="text/css" />
<link rel="top" title="LAMMPS documentation" href="index.html"/>
<script src="_static/js/modernizr.min.js"></script>
</head>
<body class="wy-body-for-nav" role="document">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="Manual.html" class="icon icon-home"> LAMMPS
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance &amp; scalability</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
</ul>
</div>
&nbsp;
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="Manual.html">LAMMPS</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="Manual.html">Docs</a> &raquo;</li>
<li>compute sna/atom command</li>
<li class="wy-breadcrumbs-aside">
<a href="http://lammps.sandia.gov">Website</a>
<a href="Section_commands.html#comm">Commands</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="compute-sna-atom-command">
<span id="index-0"></span><h1>compute sna/atom command</h1>
</div>
<div class="section" id="compute-snad-atom-command">
<h1>compute snad/atom command</h1>
</div>
<div class="section" id="compute-snav-atom-command">
<h1>compute snav/atom command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">sna</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
<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>
<li>rcutfac = scale factor applied to all cutoff radii (positive real)</li>
<li>rfac0 = parameter in distance to angle conversion (0 &lt; rcutfac &lt; 1)</li>
<li>twojmax = band limit for bispectrum components (non-negative integer)</li>
<li>R_1, R_2,... = list of cutoff radii, one for each type (distance units)</li>
<li>w_1, w_2,... = list of neighbor weights, one for each type</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>diagonal</em> or <em>rmin0</em> or <em>switchflag</em></li>
</ul>
<pre class="literal-block">
<em>diagonal</em> value = <em>0</em> or <em>1</em> or <em>2</em> or <em>3</em>
<em>0</em> = all j1, j2, j &lt;= twojmax, j2 &lt;= j1
<em>1</em> = subset satisfying j1 == j2
<em>2</em> = subset satisfying j1 == j2 == j3
<em>3</em> = subset satisfying j2 &lt;= j1 &lt;= j
<em>rmin0</em> value = parameter in distance to angle conversion (distance units)
<em>switchflag</em> value = <em>0</em> or <em>1</em>
<em>0</em> = do not use switching function
<em>1</em> = use switching function
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">b</span> <span class="nb">all</span> <span class="n">sna</span><span class="o">/</span><span class="n">atom</span> <span class="mf">1.4</span> <span class="mf">0.99363</span> <span class="mi">6</span> <span class="mf">2.0</span> <span class="mf">2.4</span> <span class="mf">0.75</span> <span class="mf">1.0</span> <span class="n">diagonal</span> <span class="mi">3</span> <span class="n">rmin0</span> <span class="mf">0.0</span>
<span class="n">compute</span> <span class="n">db</span> <span class="nb">all</span> <span class="n">sna</span><span class="o">/</span><span class="n">atom</span> <span class="mf">1.4</span> <span class="mf">0.95</span> <span class="mi">6</span> <span class="mf">2.0</span> <span class="mf">1.0</span>
<span class="n">compute</span> <span class="n">vb</span> <span class="nb">all</span> <span class="n">sna</span><span class="o">/</span><span class="n">atom</span> <span class="mf">1.4</span> <span class="mf">0.95</span> <span class="mi">6</span> <span class="mf">2.0</span> <span class="mf">1.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Define a computation that calculates a set of bispectrum components
for each atom in a group.</p>
<p>Bispectrum components of an atom are order parameters characterizing
the radial and angular distribution of neighbor atoms. The detailed
mathematical definition is given in the paper by Thompson et
al. <a class="reference internal" href="pair_snap.html#thompson2014"><span class="std std-ref">(Thompson)</span></a></p>
<p>The position of a neighbor atom <em>i&#8217;</em> relative to a central atom <em>i</em> is
a point within the 3D ball of radius <em>R_ii&#8217; = rcutfac*(R_i + R_i&#8217;)</em></p>
<p>Bartok et al. <a class="reference internal" href="pair_snap.html#bartok2010"><span class="std std-ref">(Bartok)</span></a>, proposed mapping this 3D ball
onto the 3-sphere, the surface of the unit ball in a four-dimensional
space. The radial distance <em>r</em> within <em>R_ii&#8217;</em> is mapped on to a third
polar angle <em>theta0</em> defined by,</p>
<img alt="_images/compute_sna_atom1.jpg" class="align-center" src="_images/compute_sna_atom1.jpg" />
<p>In this way, all possible neighbor positions are mapped on to a subset
of the 3-sphere. Points south of the latitude <em>theta0max=rfac0*Pi</em>
are excluded.</p>
<p>The natural basis for functions on the 3-sphere is formed by the 4D
hyperspherical harmonics <em>U^j_m,m&#8217;(theta, phi, theta0).</em> These
functions are better known as <em>D^j_m,m&#8217;,</em> the elements of the Wigner
<em>D</em>-matrices <a class="reference internal" href="#meremianin2006"><span class="std std-ref">(Meremianin</span></a>,
<a class="reference internal" href="#varshalovich1987"><span class="std std-ref">Varshalovich)</span></a>.</p>
<p>The density of neighbors on the 3-sphere can be written as a sum of
Dirac-delta functions, one for each neighbor, weighted by species and
radial distance. Expanding this density function as a generalized
Fourier series in the basis functions, we can write each Fourier
coefficient as</p>
<img alt="_images/compute_sna_atom2.jpg" class="align-center" src="_images/compute_sna_atom2.jpg" />
<p>The <em>w_i&#8217;</em> neighbor weights are dimensionless numbers that are chosen
to distinguish atoms of different types, while the central atom is
arbitrarily assigned a unit weight. The function <em>fc(r)</em> ensures that
the contribution of each neighbor atom goes smoothly to zero at
<em>R_ii&#8217;</em>:</p>
<img alt="_images/compute_sna_atom4.jpg" class="align-center" src="_images/compute_sna_atom4.jpg" />
<p>The expansion coefficients <em>u^j_m,m&#8217;</em> are complex-valued and they are
not directly useful as descriptors, because they are not invariant
under rotation of the polar coordinate frame. However, the following
scalar triple products of expansion coefficients can be shown to be
real-valued and invariant under rotation <a class="reference internal" href="pair_snap.html#bartok2010"><span class="std std-ref">(Bartok)</span></a>.</p>
<img alt="_images/compute_sna_atom3.jpg" class="align-center" src="_images/compute_sna_atom3.jpg" />
<p>The constants <em>H^jmm&#8217;_j1m1m1&#8217;_j2m2m2&#8217;</em> are coupling coefficients,
analogous to Clebsch-Gordan coefficients for rotations on the
2-sphere. These invariants are the components of the bispectrum and
these are the quantities calculated by the compute <em>sna/atom</em>. They
characterize the strength of density correlations at three points on
the 3-sphere. The j2=0 subset form the power spectrum, which
characterizes the correlations of two points. The lowest-order
components describe the coarsest features of the density function,
while higher-order components reflect finer detail. Note that the
central atom is included in the expansion, so three point-correlations
can be either due to three neighbors, or two neighbors and the central
atom.</p>
<p>Compute <em>snad/atom</em> calculates the derivative of the bispectrum components
summed separately for each atom type:</p>
<img alt="_images/compute_sna_atom5.jpg" class="align-center" src="_images/compute_sna_atom5.jpg" />
<p>The sum is over all atoms <em>i&#8217;</em> of atom type <em>I</em>. For each atom <em>i</em>,
this compute evaluates the above expression for each direction, each
atom type, and each bispectrum component. See section below on output
for a detailed explanation.</p>
<p>Compute <em>snav/atom</em> calculates the virial contribution due to the
derivatives:</p>
<img alt="_images/compute_sna_atom6.jpg" class="align-center" src="_images/compute_sna_atom6.jpg" />
<p>Again, the sum is over all atoms <em>i&#8217;</em> of atom type <em>I</em>. For each atom
<em>i</em>, this compute evaluates the above expression for each of the six
virial components, each atom type, and each bispectrum component. See
section below on output for a detailed explanation.</p>
<p>The value of all bispectrum components will be zero for atoms not in
the group. Neighbor atoms not in the group do not contribute to the
bispectrum of atoms in the group.</p>
<p>The neighbor list needed to compute this quantity is constructed each
time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.</p>
<p>The argument <em>rcutfac</em> is a scale factor that controls the ratio of
atomic radius to radial cutoff distance.</p>
<p>The argument <em>rfac0</em> and the optional keyword <em>rmin0</em> define the
linear mapping from radial distance to polar angle <em>theta0</em> on the
3-sphere.</p>
<p>The argument <em>twojmax</em> and the keyword <em>diagonal</em> define which
bispectrum components are generated. See section below on output for a
detailed explanation of the number of bispectrum components and the
ordered in which they are listed</p>
<p>The keyword <em>switchflag</em> can be used to turn off the switching
function.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you have a bonded system, then the settings of
<a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a>
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the calculation. One way to get
around this, is to write a dump file, and use the <a class="reference internal" href="rerun.html"><span class="doc">rerun</span></a>
command to compute the bispectrum components for snapshots in the dump
file. The rerun script can use a <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a>
command that includes all pairs in the neighbor list.</p>
</div>
<p>;line</p>
<p><strong>Output info:</strong></p>
<p>Compute <em>sna/atom</em> calculates a per-atom array, each column
corresponding to a particular bispectrum component. The total number
of columns and the identities of the bispectrum component contained in
each column depend on the values of <em>twojmax</em> and <em>diagonal</em>, as
described by the following piece of python code:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">j1</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">twojmax</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
<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>
components of the atom position. Each of these sub-blocks contains
one column for each bispectrum component, the same as for compute
<em>sna/atom</em></p>
<p>Compute <em>snav/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 six sub-blocks corresponding to the <em>xx</em>, <em>yy</em>, <em>zz</em>,
<em>yz</em>, <em>xz</em>, and <em>xy</em> components of the virial tensor in Voigt
notation. Each of these sub-blocks contains one column for each
bispectrum component, the same as for compute <em>sna/atom</em></p>
<p>These values can be accessed by any command that uses per-atom values
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">Section_howto 15</span></a> for an overview of LAMMPS output
options.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>These computes are part of the SNAP package. They are only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="pair_snap.html"><span class="doc">pair_style snap</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The optional keyword defaults are <em>diagonal</em> = 0, <em>rmin0</em> = 0,
<em>switchflag</em> = 1.</p>
<hr class="docutils" />
<p id="thompson2014"><strong>(Thompson)</strong> Thompson, Swiler, Trott, Foiles, Tucker, under review, preprint
available at <a class="reference external" href="http://arxiv.org/abs/1409.3880">arXiv:1409.3880</a></p>
<p id="bartok2010"><strong>(Bartok)</strong> Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).</p>
<p id="meremianin2006"><strong>(Meremianin)</strong> Meremianin, J. Phys. A, 39, 3099 (2006).</p>
<p id="varshalovich1987"><strong>(Varshalovich)</strong> Varshalovich, Moskalev, Khersonskii, Quantum Theory
of Angular Momentum, World Scientific, Singapore (1987).</p>
</div>
</div>
</div>
</div>
<footer>
<hr/>
<div role="contentinfo">
<p>
&copy; Copyright 2013 Sandia Corporation.
</p>
</div>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js"></script>
<script type="text/javascript" src="_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
</script>
</body>
</html>
c4science · Help