2009-01-20 01:17:01 +08:00
2015-07-30 22:53:28 +08:00
<!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" >
2015-12-20 02:42:24 +08:00
< title > compute cna/atom command — LAMMPS 17 Dec 2015 documentation< / title >
2015-07-30 22:53:28 +08:00
2009-01-20 01:17:01 +08:00
2015-07-30 22:53:28 +08:00
2009-01-20 01:17:01 +08:00
2015-07-30 22:53:28 +08:00
2009-01-20 01:17:01 +08:00
2015-07-30 22:53:28 +08:00
2009-01-20 01:17:01 +08:00
2015-07-30 22:53:28 +08:00
2009-01-20 01:17:01 +08:00
2015-07-30 22:53:28 +08:00
< 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" / >
2015-12-20 02:42:24 +08:00
< link rel = "top" title = "LAMMPS 17 Dec 2015 documentation" href = "index.html" / >
2015-07-30 22:53:28 +08:00
< 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 & 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 & 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 >
< / 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 > » < / li >
< li > compute cna/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-cna-atom-command" >
< span id = "index-0" > < / span > < h1 > compute cna/atom command< a class = "headerlink" href = "#compute-cna-atom-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute ID group-ID cna/atom cutoff
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command< / li >
< li > cna/atom = style name of this compute command< / li >
< li > cutoff = cutoff distance for nearest neighbors (distance units)< / li >
< / ul >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute 1 all cna/atom 3.08
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Define a computation that calculates the CNA (Common Neighbor
2009-01-20 01:17:01 +08:00
Analysis) pattern for each atom in the group. In solid-state systems
the CNA pattern is a useful measure of the local crystal structure
2015-07-30 22:53:28 +08:00
around an atom. The CNA methodology is described in < a class = "reference internal" href = "#faken" > < span > (Faken)< / span > < / a >
and < a class = "reference internal" href = "#tsuzuki" > < span > (Tsuzuki)< / span > < / a > .< / p >
< p > Currently, there are five kinds of CNA patterns LAMMPS recognizes:< / p >
< ul class = "simple" >
< li > fcc = 1< / li >
< li > hcp = 2< / li >
< li > bcc = 3< / li >
< li > icosohedral = 4< / li >
< li > unknown = 5< / li >
< / ul >
< p > The value of the CNA pattern will be 0 for atoms not in the specified
2010-01-24 07:20:05 +08:00
compute group. Note that normally a CNA calculation should only be
2015-07-30 22:53:28 +08:00
performed on mono-component systems.< / p >
< p > The CNA calculation can be sensitive to the specified cutoff value.
2009-01-20 01:17:01 +08:00
You should insure the appropriate nearest neighbors of an atom are
found within the cutoff distance for the presumed crystal strucure.
E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest
neighbors for perfect BCC crystals. These formulas can be used to
2015-07-30 22:53:28 +08:00
obtain a good cutoff distance:< / p >
< img alt = "_images/cna_cutoff1.jpg" class = "align-center" src = "_images/cna_cutoff1.jpg" / >
< p > where a is the lattice constant for the crystal structure concerned
2009-01-20 01:17:01 +08:00
and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a
2015-07-30 22:53:28 +08:00
for HCP crystals.< / p >
< p > Also note that since the CNA calculation in LAMMPS uses the neighbors
2009-01-20 01:17:01 +08:00
of an owned atom to find the nearest neighbors of a ghost atom, the
2015-07-30 22:53:28 +08:00
following relation should also be satisfied:< / p >
< img alt = "_images/cna_cutoff2.jpg" class = "align-center" src = "_images/cna_cutoff2.jpg" / >
< p > where Rc is the cutoff distance of the potential, Rs is the skin
distance as specified by the < a class = "reference internal" href = "neighbor.html" > < em > neighbor< / em > < / a > command, and
2009-01-20 01:17:01 +08:00
cutoff is the argument used with the compute cna/atom command. LAMMPS
2015-07-30 22:53:28 +08:00
will issue a warning if this is not the case.< / p >
< p > The neighbor list needed to compute this quantity is constructed each
2009-01-20 01:17:01 +08:00
time the calculation is performed (e.g. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently or to have multiple compute/dump commands, each with a
2015-07-30 22:53:28 +08:00
< em > cna/atom< / em > style.< / p >
< p > < strong > Output info:< / strong > < / p >
< p > This compute calculates a per-atom vector, which can be accessed by
2009-12-05 05:04:00 +08:00
any command that uses per-atom values from a compute as input. See
2015-07-30 22:53:28 +08:00
< a class = "reference internal" href = "Section_howto.html#howto-15" > < span > Section_howto 15< / span > < / a > for an overview of
LAMMPS output options.< / p >
< p > The per-atom vector values will be a number from 0 to 5, as explained
above.< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< blockquote >
< div > none< / div > < / blockquote >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "compute_centro_atom.html" > < em > compute centro/atom< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
< hr class = "docutils" / >
< p id = "faken" > < strong > (Faken)< / strong > Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).< / p >
< p id = "tsuzuki" > < strong > (Tsuzuki)< / strong > Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).< / p >
< / div >
< / div >
< / div >
< / div >
< footer >
< hr / >
< div role = "contentinfo" >
< p >
2015-12-11 01:23:56 +08:00
© Copyright 2013 Sandia Corporation.
2015-07-30 22:53:28 +08:00
< / 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:'./',
2015-12-20 02:42:24 +08:00
VERSION:'17 Dec 2015',
2015-07-30 22:53:28 +08:00
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 >
