Homec4science
Diffusion lammps (master) Browse

lammps/doc/html/atom_modify.html
df304f8ca196master

Last Change
Raw File

atom_modify.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>atom_modify 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"/>
<link rel="up" title="Commands" href="commands.html"/>
<link rel="next" title="atom_style command" href="atom_style.html"/>
<link rel="prev" title="angle_style command" href="angle_style.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">
<p class="caption"><span class="caption-text">User Documentation</span></p>
<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>
<p class="caption"><span class="caption-text">Index</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="tutorials.html">Tutorials</a></li>
<li class="toctree-l1 current"><a class="reference internal" href="commands.html">Commands</a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="angle_coeff.html">angle_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="angle_style.html">angle_style command</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">atom_modify command</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#syntax">Syntax</a></li>
<li class="toctree-l3"><a class="reference internal" href="#examples">Examples</a></li>
<li class="toctree-l3"><a class="reference internal" href="#description">Description</a></li>
<li class="toctree-l3"><a class="reference internal" href="#restrictions">Restrictions</a></li>
<li class="toctree-l3"><a class="reference internal" href="#default">Default</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="atom_style.html">atom_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="balance.html">balance command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_coeff.html">bond_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_style.html">bond_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="bond_write.html">bond_write command</a></li>
<li class="toctree-l2"><a class="reference internal" href="boundary.html">boundary command</a></li>
<li class="toctree-l2"><a class="reference internal" href="box.html">box command</a></li>
<li class="toctree-l2"><a class="reference internal" href="change_box.html">change_box command</a></li>
<li class="toctree-l2"><a class="reference internal" href="clear.html">clear command</a></li>
<li class="toctree-l2"><a class="reference internal" href="comm_modify.html">comm_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="comm_style.html">comm_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute.html">compute command</a></li>
<li class="toctree-l2"><a class="reference internal" href="compute_modify.html">compute_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="create_atoms.html">create_atoms command</a></li>
<li class="toctree-l2"><a class="reference internal" href="create_bonds.html">create_bonds command</a></li>
<li class="toctree-l2"><a class="reference internal" href="create_box.html">create_box command</a></li>
<li class="toctree-l2"><a class="reference internal" href="delete_atoms.html">delete_atoms command</a></li>
<li class="toctree-l2"><a class="reference internal" href="delete_bonds.html">delete_bonds command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dielectric.html">dielectric command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dihedral_coeff.html">dihedral_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dihedral_style.html">dihedral_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dimension.html">dimension command</a></li>
<li class="toctree-l2"><a class="reference internal" href="displace_atoms.html">displace_atoms command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump.html">dump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-custom-vtk-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">custom/vtk</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-h5md-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">h5md</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-image-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">image</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-movie-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">movie</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump.html#dump-molfile-command"><code class="docutils literal"><span class="pre">dump</span> <span class="pre">molfile</span></code> command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump_custom_vtk.html">dump custom/vtk command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump_h5md.html">dump h5md command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump_image.html">dump image command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump_image.html#dump-movie-command">dump movie command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump_modify.html">dump_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="dump_molfile.html">dump molfile command</a></li>
<li class="toctree-l2"><a class="reference internal" href="echo.html">echo command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix.html">fix command</a></li>
<li class="toctree-l2"><a class="reference internal" href="fix_modify.html">fix_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="group.html">group command</a></li>
<li class="toctree-l2"><a class="reference internal" href="group2ndx.html">group2ndx command</a></li>
<li class="toctree-l2"><a class="reference internal" href="group2ndx.html#ndx2group-command">ndx2group command</a></li>
<li class="toctree-l2"><a class="reference internal" href="if.html">if command</a></li>
<li class="toctree-l2"><a class="reference internal" href="improper_coeff.html">improper_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="improper_style.html">improper_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="include.html">include command</a></li>
<li class="toctree-l2"><a class="reference internal" href="info.html">info command</a></li>
<li class="toctree-l2"><a class="reference internal" href="jump.html">jump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="kspace_modify.html">kspace_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="kspace_style.html">kspace_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="label.html">label command</a></li>
<li class="toctree-l2"><a class="reference internal" href="lattice.html">lattice command</a></li>
<li class="toctree-l2"><a class="reference internal" href="log.html">log command</a></li>
<li class="toctree-l2"><a class="reference internal" href="mass.html">mass command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_modify.html">min_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="min_style.html">min_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="minimize.html">minimize command</a></li>
<li class="toctree-l2"><a class="reference internal" href="molecule.html">molecule command</a></li>
<li class="toctree-l2"><a class="reference internal" href="neb.html">neb command</a></li>
<li class="toctree-l2"><a class="reference internal" href="neigh_modify.html">neigh_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="neighbor.html">neighbor command</a></li>
<li class="toctree-l2"><a class="reference internal" href="newton.html">newton command</a></li>
<li class="toctree-l2"><a class="reference internal" href="next.html">next command</a></li>
<li class="toctree-l2"><a class="reference internal" href="package.html">package command</a></li>
<li class="toctree-l2"><a class="reference internal" href="pair_coeff.html">pair_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="pair_modify.html">pair_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="pair_style.html">pair_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="pair_write.html">pair_write command</a></li>
<li class="toctree-l2"><a class="reference internal" href="partition.html">partition command</a></li>
<li class="toctree-l2"><a class="reference internal" href="prd.html">prd command</a></li>
<li class="toctree-l2"><a class="reference internal" href="print.html">print command</a></li>
<li class="toctree-l2"><a class="reference internal" href="processors.html">processors command</a></li>
<li class="toctree-l2"><a class="reference internal" href="python.html">python command</a></li>
<li class="toctree-l2"><a class="reference internal" href="quit.html">quit command</a></li>
<li class="toctree-l2"><a class="reference internal" href="read_data.html">read_data command</a></li>
<li class="toctree-l2"><a class="reference internal" href="read_dump.html">read_dump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="read_restart.html">read_restart command</a></li>
<li class="toctree-l2"><a class="reference internal" href="region.html">region command</a></li>
<li class="toctree-l2"><a class="reference internal" href="replicate.html">replicate command</a></li>
<li class="toctree-l2"><a class="reference internal" href="rerun.html">rerun command</a></li>
<li class="toctree-l2"><a class="reference internal" href="reset_timestep.html">reset_timestep command</a></li>
<li class="toctree-l2"><a class="reference internal" href="restart.html">restart command</a></li>
<li class="toctree-l2"><a class="reference internal" href="run.html">run command</a></li>
<li class="toctree-l2"><a class="reference internal" href="run_style.html">run_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="set.html">set command</a></li>
<li class="toctree-l2"><a class="reference internal" href="shell.html">shell command</a></li>
<li class="toctree-l2"><a class="reference internal" href="special_bonds.html">special_bonds command</a></li>
<li class="toctree-l2"><a class="reference internal" href="suffix.html">suffix command</a></li>
<li class="toctree-l2"><a class="reference internal" href="tad.html">tad command</a></li>
<li class="toctree-l2"><a class="reference internal" href="temper.html">temper command</a></li>
<li class="toctree-l2"><a class="reference internal" href="thermo.html">thermo command</a></li>
<li class="toctree-l2"><a class="reference internal" href="thermo_modify.html">thermo_modify command</a></li>
<li class="toctree-l2"><a class="reference internal" href="thermo_style.html">thermo_style command</a></li>
<li class="toctree-l2"><a class="reference internal" href="timer.html">timer command</a></li>
<li class="toctree-l2"><a class="reference internal" href="timestep.html">timestep command</a></li>
<li class="toctree-l2"><a class="reference internal" href="uncompute.html">uncompute command</a></li>
<li class="toctree-l2"><a class="reference internal" href="undump.html">undump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="unfix.html">unfix command</a></li>
<li class="toctree-l2"><a class="reference internal" href="units.html">units command</a></li>
<li class="toctree-l2"><a class="reference internal" href="variable.html">variable command</a></li>
<li class="toctree-l2"><a class="reference internal" href="velocity.html">velocity command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_coeff.html">write_coeff command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_data.html">write_data command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_dump.html">write_dump command</a></li>
<li class="toctree-l2"><a class="reference internal" href="write_restart.html">write_restart command</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bonds</a></li>
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</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><a href="commands.html">Commands</a> &raquo;</li>
<li>atom_modify 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 class="rst-footer-buttons" style="margin-bottom: 1em" role="navigation" aria-label="footer navigation">
<a href="atom_style.html" class="btn btn-neutral float-right" title="atom_style command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="angle_style.html" class="btn btn-neutral" title="angle_style command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="atom-modify-command">
<span id="index-0"></span><h1>atom_modify command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
atom_modify keyword values ...
</pre>
<ul>
<li><p class="first">one or more keyword/value pairs may be appended</p>
</li>
<li><p class="first">keyword = <em>id</em> or <em>map</em> or <em>first</em> or <em>sort</em></p>
<pre class="literal-block">
<em>id</em> value = <em>yes</em> or <em>no</em>
<em>map</em> value = <em>array</em> or <em>hash</em>
<em>first</em> value = group-ID = group whose atoms will appear first in internal atom lists
<em>sort</em> values = Nfreq binsize
Nfreq = sort atoms spatially every this many time steps
binsize = bin size for spatial sorting (distance units)
</pre>
</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
atom_modify map hash
atom_modify map array sort 10000 2.0
atom_modify first colloid
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Modify certain attributes of atoms defined and stored within LAMMPS,
in addition to what is specified by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>
command. The <em>id</em> and <em>map</em> keywords must be specified before a
simulation box is defined; other keywords can be specified any time.</p>
<p>The <em>id</em> keyword determines whether non-zero atom IDs can be assigned
to each atom. If the value is <em>yes</em>, which is the default, IDs are
assigned, whether you use the <a class="reference internal" href="create_atoms.html"><span class="doc">create atoms</span></a> or
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> or <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
commands to initialize atoms. If the value is <em>no</em> the IDs for all
atoms are assumed to be 0.</p>
<p>If atom IDs are used, they must all be positive integers. They should
also be unique, though LAMMPS does not check for this. Typically they
should also be consecutively numbered (from 1 to Natoms), though this
is not required. Molecular <a class="reference internal" href="atom_style.html"><span class="doc">atom styles</span></a> are those
that store bond topology information (styles bond, angle, molecular,
full). These styles require atom IDs since the IDs are used to encode
the topology. Some other LAMMPS commands also require the use of atom
IDs. E.g. some many-body pair styles use them to avoid double
computation of the I-J interaction between two atoms.</p>
<p>The only reason not to use atom IDs is if you are running an atomic
simulation so large that IDs cannot be uniquely assigned. For a
default LAMMPS build this limit is 2^31 or about 2 billion atoms.
However, even in this case, you can use 64-bit atom IDs, allowing 2^63
or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
switch. This is described in <a class="reference internal" href="Section_start.html#start-2"><span class="std std-ref">Section 2.2</span></a>
of the manual. If atom IDs are not used, they must be specified as 0
for all atoms, e.g. in a data or restart file.</p>
<p>The <em>map</em> keyword determines how atom ID lookup is done for molecular
atom styles. Lookups are performed by bond (angle, etc) routines in
LAMMPS to find the local atom index associated with a global atom ID.</p>
<p>When the <em>array</em> value is used, each processor stores a lookup table
of length N, where N is the largest atom ID in the system. This is a
fast, simple method for many simulations, but requires too much memory
for large simulations. The <em>hash</em> value uses a hash table to perform
the lookups. This can be slightly slower than the <em>array</em> method, but
its memory cost is proportional to the number of atoms owned by a
processor, i.e. N/P when N is the total number of atoms in the system
and P is the number of processors.</p>
<p>When this setting is not specified in your input script, LAMMPS
creates a map, if one is needed, as an array or hash. See the
discussion of default values below for how LAMMPS chooses which kind
of map to build. Note that atomic systems do not normally need to
create a map. However, even in this case some LAMMPS commands will
create a map to find atoms (and then destroy it), or require a
permanent map. An example of the former is the <a class="reference internal" href="velocity.html"><span class="doc">velocity loop all</span></a> command, which uses a map when looping over all
atoms and insuring the same velocity values are assigned to an atom
ID, no matter which processor owns it.</p>
<p>The <em>first</em> keyword allows a <a class="reference internal" href="group.html"><span class="doc">group</span></a> to be specified whose
atoms will be maintained as the first atoms in each processor&#8217;s list
of owned atoms. This in only useful when the specified group is a
small fraction of all the atoms, and there are other operations LAMMPS
is performing that will be sped-up significantly by being able to loop
over the smaller set of atoms. Otherwise the reordering required by
this option will be a net slow-down. The <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify include</span></a> and <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify group</span></a>
commands are two examples of commands that require this setting to
work efficiently. Several <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a>, most notably time
integration fixes like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, also take advantage of
this setting if the group they operate on is the group specified by
this command. Note that specifying &#8220;all&#8221; as the group-ID effectively
turns off the <em>first</em> option.</p>
<p>It is OK to use the <em>first</em> keyword with a group that has not yet been
defined, e.g. to use the atom_modify first command at the beginning of
your input script. LAMMPS does not use the group until a simullation
is run.</p>
<p>The <em>sort</em> keyword turns on a spatial sorting or reordering of atoms
within each processor&#8217;s sub-domain every <em>Nfreq</em> timesteps. If
<em>Nfreq</em> is set to 0, then sorting is turned off. Sorting can improve
cache performance and thus speed-up a LAMMPS simulation, as discussed
in a paper by <a class="reference internal" href="#meloni"><span class="std std-ref">(Meloni)</span></a>. Its efficacy depends on the problem
size (atoms/processor), how quickly the system becomes disordered, and
various other factors. As a general rule, sorting is typically more
effective at speeding up simulations of liquids as opposed to solids.
In tests we have done, the speed-up can range from zero to 3-4x.</p>
<p>Reordering is peformed every <em>Nfreq</em> timesteps during a dynamics run
or iterations during a minimization. More precisely, reordering
occurs at the first reneighboring that occurs after the target
timestep. The reordering is performed locally by each processor,
using bins of the specified <em>binsize</em>. If <em>binsize</em> is set to 0.0,
then a binsize equal to half the <a class="reference internal" href="neighbor.html"><span class="doc">neighbor</span></a> cutoff
distance (force cutoff plus skin distance) is used, which is a
reasonable value. After the atoms have been binned, they are
reordered so that atoms in the same bin are adjacent to each other in
the processor&#8217;s 1d list of atoms.</p>
<p>The goal of this procedure is for atoms to put atoms close to each
other in the processor&#8217;s one-dimensional list of atoms that are also
near to each other spatially. This can improve cache performance when
pairwise intereractions and neighbor lists are computed. Note that if
bins are too small, there will be few atoms/bin. Likewise if bins are
too large, there will be many atoms/bin. In both cases, the goal of
cache locality will be undermined.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Running a simulation with sorting on versus off should not
change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead
to diverging trajectories over time when comparing two simluations.
Various commands, particularly those which use random numbers
(e.g. <a class="reference internal" href="velocity.html"><span class="doc">velocity create</span></a>, and <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>), may generate (statistically identical)
results which depend on the order in which atoms are processed. The
order of atoms in a <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> file will also typically change
if sorting is enabled.</p>
</div>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>The <em>first</em> and <em>sort</em> options cannot be used together. Since sorting
is on by default, it will be turned off if the <em>first</em> keyword is
used with a group-ID that is not &#8220;all&#8221;.</p>
<p><strong>Related commands:</strong> none</p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>By default, <em>id</em> is yes. By default, atomic systems (no bond topology
info) do not use a map. For molecular systems (with bond topology
info), a map is used. The default map style is array if no atom ID is
larger than 1 million, otherwise the default is hash. By default, a
&#8220;first&#8221; group is not defined. By default, sorting is enabled with a
frequency of 1000 and a binsize of 0.0, which means the neighbor
cutoff will be used to set the bin size.</p>
<hr class="docutils" />
<p id="meloni"><strong>(Meloni)</strong> Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).</p>
</div>
</div>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="atom_style.html" class="btn btn-neutral float-right" title="atom_style command" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="angle_style.html" class="btn btn-neutral" title="angle_style command" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<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