Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/doc/html/compute_saed.html
1d3f94fbb20cefficient_neuronet

Last Change
Raw File

compute_saed.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 saed 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 saed 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-saed-command">
<span id="index-0"></span><h1>compute saed 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">saed</span> <span class="k">lambda</span> <span class="n">type1</span> <span class="n">type2</span> <span class="o">...</span> <span class="n">typeN</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="compute.html"><span class="doc">compute</span></a> command</li>
<li>saed = style name of this compute command</li>
<li>lambda = wavelength of incident radiation (length units)</li>
<li>type1 type2 ... typeN = chemical symbol of each atom type (see valid options below)</li>
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>Kmax</em> or <em>Zone</em> or <em>dR_Ewald</em> or <em>c</em> or <em>manual</em> or <em>echo</em></li>
</ul>
<pre class="literal-block">
<em>Kmax</em> value = Maximum distance explored from reciprocal space origin
(inverse length units)
<em>Zone</em> values = z1 z2 z3
z1,z2,z3 = Zone axis of incident radiation. If z1=z2=z3=0 all
reciprocal space will be meshed up to <em>Kmax</em>
<em>dR_Ewald</em> value = Thickness of Ewald sphere slice intercepting
reciprocal space (inverse length units)
<em>c</em> values = c1 c2 c3
c1,c2,c3 = parameters to adjust the spacing of the reciprocal
lattice nodes in the h, k, and l directions respectively
<em>manual</em> = flag to use manual spacing of reciprocal lattice points
based on the values of the <em>c</em> parameters
<em>echo</em> = flag to provide extra output for debugging purposes
</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="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>
<p>Define a computation that calculates electron diffraction intensity as
described in <a class="reference internal" href="compute_xrd.html#coleman"><span class="std std-ref">(Coleman)</span></a> on a mesh of reciprocal lattice nodes
defined by the entire simulation domain (or manually) using simulated
radiation of wavelength lambda.</p>
<p>The electron diffraction intensity I at each reciprocal lattice point
is computed from the structure factor F using the equations:</p>
<img alt="_images/compute_saed1.jpg" class="align-center" src="_images/compute_saed1.jpg" />
<img alt="_images/compute_saed2.jpg" class="align-center" src="_images/compute_saed2.jpg" />
<p>Here, K is the location of the reciprocal lattice node, rj is the
position of each atom, fj are atomic scattering factors.</p>
<p>Diffraction intensities are calculated on a three-dimensional mesh of
reciprocal lattice nodes. The mesh spacing is defined either (a) by
the entire simulation domain or (b) manually using selected values as
shown in the 2D diagram below.</p>
<a class=""
data-lightbox="group-default"
href="_images/saed_mesh.jpg"
title=""
data-title=""
><img src="_images/saed_mesh.jpg"
class="align-center"
width="25%"
height="auto"
alt=""/>
</a><p>For a mesh defined by the simulation domain, a rectilinear grid is
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
average of the (inversed) box lengths with periodic boundary conditions.
Meshes defined by the simulation domain must contain at least one periodic
boundary.</p>
<p>If the <em>manual</em> flag is included, the mesh of reciprocal lattice nodes
will defined using the <em>c</em> values for the spacing along each reciprocal
lattice axis. Note that manual mapping of the reciprocal space mesh is
good for comparing diffraction results from multiple simulations; however
it can reduce the likelihood that Bragg reflections will be satisfied
unless small spacing parameters &lt;0.05 Angstrom^(-1) are implemented.
Meshes with manual spacing do not require a periodic boundary.</p>
<p>The limits of the reciprocal lattice mesh are determined by the use of
the <em>Kmax</em>, <em>Zone</em>, and <em>dR_Ewald</em> parameters. The rectilinear mesh
created about the origin of reciprocal space is terminated at the
boundary of a sphere of radius <em>Kmax</em> centered at the origin. If
<em>Zone</em> parameters z1=z2=z3=0 are used, diffraction intensities are
computed throughout the entire spherical volume - note this can
greatly increase the cost of computation. Otherwise, <em>Zone</em>
parameters will denote the z1=h, z2=k, and z3=l (in a global since)
zone axis of an intersecting Ewald sphere. Diffraction intensities
will only be computed at the intersection of the reciprocal lattice
mesh and a <em>dR_Ewald</em> thick surface of the Ewald sphere. See the
example 3D intestiety data and the intersection of a [010] zone axis
in the below image.</p>
<a class=""
data-lightbox="group-default"
href="_images/saed_ewald_intersect.jpg"
title=""
data-title=""
><img src="_images/saed_ewald_intersect.jpg"
class="align-center"
width="25%"
height="auto"
alt=""/>
</a><p>The atomic scattering factors, fj, accounts for the reduction in
diffraction intensity due to Compton scattering. Compute saed uses
analytical approximations of the atomic scattering factors that vary
for each atom type (type1 type2 ... typeN) and angle of diffraction.
The analytic approximation is computed using the formula
<a class="reference internal" href="#brown"><span class="std std-ref">(Brown)</span></a>:</p>
<img alt="_images/compute_saed3.jpg" class="align-center" src="_images/compute_saed3.jpg" />
<p>Coefficients parameterized by <a class="reference internal" href="#fox"><span class="std std-ref">(Fox)</span></a> are assigned for each
atom type designating the chemical symbol and charge of each atom
type. Valid chemical symbols for compute saed are:</p>
<dl class="docutils">
<dt>H: He: Li: Be: B:</dt>
<dd><blockquote class="first">
<div>C: N: O: F: Ne:</div></blockquote>
<dl class="docutils">
<dt>Na: Mg: Al: Si: P:</dt>
<dd>S: Cl: Ar: K: Ca:</dd>
</dl>
<p class="last">Sc: Ti: V: Cr: Mn:
Fe: Co: Ni: Cu: Zn:
Ga: Ge: As: Se: Br:
Kr: Rb: Sr: Y: Zr:
Nb: Mo: Tc: Ru: Rh:
Pd: Ag: Cd: In: Sn:
Sb: Te: I: Xe: Cs:
Ba: La: Ce: Pr: Nd:
Pm: Sm: Eu: Gd: Tb:
Dy: Ho: Er: Tm: Yb:
Lu: Hf: Ta: W: Re:
Os: Ir: Pt: Au: Hg:
Tl: Pb: Bi: Po: At:
Rn: Fr: Ra: Ac: Th:
Pa: U: Np: Pu: Am:
Cm: Bk: Cf:tb(c=5,s=:)</p>
</dd>
</dl>
<p>If the <em>echo</em> keyword is specified, compute saed will provide extra
reporting information to the screen.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector. The length of the vector is
the number of reciprocal lattice nodes that are explored by the mesh.
The entries of the global vector are the computed diffraction
intensities as described above.</p>
<p>The vector can be accessed by any command that uses global values
from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">this section</span></a> for an overview of LAMMPS output
options.</p>
<p>All array values calculated by this compute are &#8220;intensive&#8221;.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This compute is part of the USER-DIFFRACTION package. It is 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>
<p>The compute_saed command does not work for triclinic cells.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="fix_saed_vtk.html"><span class="doc">fix saed_vtk</span></a>, <a class="reference internal" href="compute_xrd.html"><span class="doc">compute xrd</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The option defaults are Kmax = 1.70, Zone 1 0 0, c 1 1 1, dR_Ewald =
0.01.</p>
<hr class="docutils" />
<p id="coleman"><strong>(Coleman)</strong> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
(2013).</p>
<p id="brown"><strong>(Brown)</strong> Brown et al. International Tables for Crystallography
Volume C: Mathematical and Chemical Tables, 554-95 (2004).</p>
<p id="fox"><strong>(Fox)</strong> Fox, O&#8217;Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93
(1989).</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