Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/doc/html/compute_xrd.html
df5fe6d5de4clammm-devel

Last Change
Raw File

compute_xrd.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 xrd 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 xrd 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-xrd-command">
<span id="index-0"></span><h1>compute xrd 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">xrd</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>xrd = 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>2Theta</em> or <em>c</em> or <em>LP</em> or <em>manual</em> or <em>echo</em></li>
</ul>
<pre class="literal-block">
<em>2Theta</em> values = Min2Theta Max2Theta
Min2Theta,Max2Theta = minimum and maximum 2 theta range to explore
(radians or degrees)
<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>LP</em> value = switch to apply Lorentz-polarization factor
0/1 = off/on
<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">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="mf">0.087</span> <span class="mf">0.87</span> <span class="n">c</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">LP</span> <span class="mi">1</span> <span class="n">echo</span>
<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>
<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>
<p>Define a computation that calculates x-ray diffraction intensity as described
in <a class="reference internal" href="#xrd-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 a simulated radiation
of wavelength lambda.</p>
<p>The x-ray diffraction intensity, I, at each reciprocal lattice point, k,
is computed from the structure factor, F, using the equations:</p>
<img alt="_images/compute_xrd1.jpg" class="align-center" src="_images/compute_xrd1.jpg" />
<img alt="_images/compute_xrd2.jpg" class="align-center" src="_images/compute_xrd2.jpg" />
<img alt="_images/compute_xrd3.jpg" class="align-center" src="_images/compute_xrd3.jpg" />
<img alt="_images/compute_xrd4.jpg" class="align-center" src="_images/compute_xrd4.jpg" />
<p>Here, K is the location of the reciprocal lattice node, rj is the
position of each atom, fj are atomic scattering factors, LP is the
Lorentz-polarization factor, and theta is the scattering angle of
diffraction. The Lorentz-polarization factor can be turned off using
the optional <em>LP</em> keyword.</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/xrd_mesh.jpg"
title=""
data-title=""
><img src="_images/xrd_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 range of
scattering angles explored. The <em>2Theta</em> parameters allows the user
to reduce the scattering angle range to only the region of interest
which reduces the cost of the computation.</p>
<p>The atomic scattering factors, fj, accounts for the reduction in
diffraction intensity due to Compton scattering. Compute xrd 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="#colliex"><span class="std std-ref">(Colliex)</span></a>:</p>
<img alt="_images/compute_xrd5.jpg" class="align-center" src="_images/compute_xrd5.jpg" />
<p>Coefficients parameterized by <a class="reference internal" href="#peng"><span class="std std-ref">(Peng)</span></a> are assigned for each
atom type designating the chemical symbol and charge of each atom
type. Valid chemical symbols for compute xrd are:</p>
<dl class="docutils">
<dt>H: He1-: He: Li: Li1+:</dt>
<dd><blockquote class="first">
<div><blockquote>
<div><dl class="docutils">
<dt>Be: Be2+: B: C: Cval:</dt>
<dd>N: O: O1-: F: F1-:</dd>
</dl>
<p>Ne: Na: Na1+: Mg: Mg2+:
Al: Al3+: Si: Sival: Si4+:</p>
<blockquote>
<div>P: S: Cl: Cl1-: Ar:
K: Ca: Ca2+: Sc: Sc3+:</div></blockquote>
<p>Ti: Ti2+: Ti3+: Ti4+: V:</p>
</div></blockquote>
<p>V2+: V3+: V5+: Cr: Cr2+:</p>
</div></blockquote>
<dl class="docutils">
<dt>Cr3+: Mn: Mn2+: Mn3+: Mn4+:</dt>
<dd>Fe: Fe2+: Fe3+: Co: Co2+:
Co: Ni: Ni2+: Ni3+: Cu:</dd>
</dl>
<p>Cu1+: Cu2+: Zn: Zn2+: Ga:
Ga3+: Ge: Ge4+: As: Se:</p>
<blockquote>
<div>Br: Br1-: Kr: Rb: Rb1+:
Sr: Sr2+: Y: Y3+: Zr:</div></blockquote>
<p>Zr4+: Nb: Nb3+: Nb5+: Mo:
Mo3+: Mo5+: Mo6+: Tc: Ru:
Ru3+: Ru4+: Rh: Rh3+: Rh4+:</p>
<blockquote>
<div>Pd: Pd2+: Pd4+: Ag: Ag1+:</div></blockquote>
<dl class="docutils">
<dt>Ag2+: Cd: Cd2+: In: In3+:</dt>
<dd>Sn: Sn2+: Sn4+: Sb: Sb3+:</dd>
<dt>Sb5+: Te: I: I1-: Xe:</dt>
<dd>Cs: Cs1+: Ba: Ba2+: La:</dd>
</dl>
<p>La3+: Ce: Ce3+: Ce4+: Pr:
Pr3+: Pr4+: Nd: Nd3+: Pm:
Pm3+: Sm: Sm3+: Eu: Eu2+:
Eu3+: Gd: Gd3+: Tb: Tb3+:</p>
<blockquote>
<div>Dy: Dy3+: Ho: Ho3+: Er:</div></blockquote>
<p>Er3+: Tm: Tm3+: Yb: Yb2+:
Yb3+: Lu: Lu3+: Hf: Hf4+:</p>
<blockquote>
<div>Ta: Ta5+: W: W6+: Re:
Os: Os4+: Ir: Ir3+: Ir4+:
Pt: Pt2+: Pt4+: Au: Au1+:</div></blockquote>
<p>Au3+: Hg: Hg1+: Hg2+: Tl:
Tl1+: Tl3+: Pb: Pb2+: Pb4+:</p>
<blockquote>
<div>Bi: Bi3+: Bi5+: Po: At:
Rn: Fr: Ra: Ra2+: Ac:</div></blockquote>
<dl class="docutils">
<dt>Ac3+: Th: Th4+: Pa: U:</dt>
<dd>U3+: U4+: U6+: Np: Np3+:</dd>
</dl>
<p class="last">Np4+: Np6+: Pu: Pu3+: Pu4+:
Pu6+: Am: Cm: Bk: Cf:tb(c=5,s=:)</p>
</dd>
</dl>
<p>If the <em>echo</em> keyword is specified, compute xrd will provide extra
reporting information to the screen.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global array. The number of rows in the
array is the number of reciprocal lattice nodes that are explored
which by the mesh. The global array has 2 columns.</p>
<p>The first column contains the diffraction angle in the units (radians
or degrees) provided with the <em>2Theta</em> values. The second column contains
the computed diffraction intensities as described above.</p>
<p>The array 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_xrd 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_ave_histo.html"><span class="doc">fix ave/histo</span></a>,
<a class="reference internal" href="compute_saed.html"><span class="doc">compute saed</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>The option defaults are 2Theta = 1 179 (degrees), c = 1 1 1, LP = 1,
no manual flag, no echo flag.</p>
<hr class="docutils" />
<p id="xrd-coleman"><strong>(Coleman)</strong> Coleman, Spearot, Capolungo, MSMSE, 21, 055020
(2013).</p>
<p id="colliex"><strong>(Colliex)</strong> Colliex et al. International Tables for Crystallography
Volume C: Mathematical and Chemical Tables, 249-429 (2004).</p>
<p id="peng"><strong>(Peng)</strong> Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76
(1996).</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