forked from lijiext/lammps
559 lines
32 KiB
HTML
559 lines
32 KiB
HTML
|
|
|
|
<!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>set command — 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 & 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>set 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="set-command">
|
|
<span id="index-0"></span><h1>set command</h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">set</span> <span class="n">style</span> <span class="n">ID</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>style = <em>atom</em> or <em>type</em> or <em>mol</em> or <em>group</em> or <em>region</em></li>
|
|
<li>ID = atom ID range or type range or mol ID range or group ID or region ID</li>
|
|
<li>one or more keyword/value pairs may be appended</li>
|
|
<li>keyword = <em>type</em> or <em>type/fraction</em> or <em>mol</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>charge</em> or <em>dipole</em> or <em>dipole/random</em> or <em>quat</em> or <em>quat/random</em> or <em>diameter</em> or <em>shape</em> or <em>length</em> or <em>tri</em> or <em>theta</em> or <em>theta/random</em> or <em>angmom</em> or <em>omega</em> or <em>mass</em> or <em>density</em> or <em>volume</em> or <em>image</em> or <em>bond</em> or <em>angle</em> or <em>dihedral</em> or <em>improper</em> or <em>meso/e</em> or <em>meso/cv</em> or <em>meso/rho</em> or <em>smd/contact/radius</em> or <em>smd/mass/density</em> or <em>dpd/theta</em> or <em>i_name</em> or <em>d_name</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>type</em> value = atom type
|
|
value can be an atom-style variable (see below)
|
|
<em>type/fraction</em> values = type fraction seed
|
|
type = new atom type
|
|
fraction = fraction of selected atoms to set to new atom type
|
|
seed = random # seed (positive integer)
|
|
<em>mol</em> value = molecule ID
|
|
value can be an atom-style variable (see below)
|
|
<em>x</em>,<em>y</em>,<em>z</em> value = atom coordinate (distance units)
|
|
value can be an atom-style variable (see below)
|
|
<em>charge</em> value = atomic charge (charge units)
|
|
value can be an atom-style variable (see below)
|
|
<em>dipole</em> values = x y z
|
|
x,y,z = orientation of dipole moment vector
|
|
any of x,y,z can be an atom-style variable (see below)
|
|
<em>dipole/random</em> value = seed Dlen
|
|
seed = random # seed (positive integer) for dipole moment orientations
|
|
Dlen = magnitude of dipole moment (dipole units)
|
|
<em>quat</em> values = a b c theta
|
|
a,b,c = unit vector to rotate particle around via right-hand rule
|
|
theta = rotation angle (degrees)
|
|
any of a,b,c,theta can be an atom-style variable (see below)
|
|
<em>quat/random</em> value = seed
|
|
seed = random # seed (positive integer) for quaternion orientations
|
|
<em>diameter</em> value = diameter of spherical particle (distance units)
|
|
value can be an atom-style variable (see below)
|
|
<em>shape</em> value = Sx Sy Sz
|
|
Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
|
|
<em>length</em> value = len
|
|
len = length of line segment (distance units)
|
|
len can be an atom-style variable (see below)
|
|
<em>tri</em> value = side
|
|
side = side length of equilateral triangle (distance units)
|
|
side can be an atom-style variable (see below)
|
|
<em>theta</em> value = angle (degrees)
|
|
angle = orientation of line segment with respect to x-axis
|
|
angle can be an atom-style variable (see below)
|
|
<em>theta/random</em> value = seed
|
|
seed = random # seed (positive integer) for line segment orienations
|
|
<em>angmom</em> values = Lx Ly Lz
|
|
Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
|
|
any of Lx,Ly,Lz can be an atom-style variable (see below)
|
|
<em>omega</em> values = Wx Wy Wz
|
|
Wx,Wy,Wz = components of angular velocity vector (radians/time units)
|
|
any of wx,wy,wz can be an atom-style variable (see below)
|
|
<em>mass</em> value = per-atom mass (mass units)
|
|
value can be an atom-style variable (see below)
|
|
<em>density</em> value = particle density for sphere or ellipsoid (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
|
|
value can be an atom-style variable (see below)
|
|
<em>volume</em> value = particle volume for Peridynamic particle (distance^3 units)
|
|
value can be an atom-style variable (see below)
|
|
<em>image</em> nx ny nz
|
|
nx,ny,nz = which periodic image of the simulation box the atom is in
|
|
<em>bond</em> value = bond type for all bonds between selected atoms
|
|
<em>angle</em> value = angle type for all angles between selected atoms
|
|
<em>dihedral</em> value = dihedral type for all dihedrals between selected atoms
|
|
<em>improper</em> value = improper type for all impropers between selected atoms
|
|
<em>meso/e</em> value = energy of SPH particles (need units)
|
|
value can be an atom-style variable (see below)
|
|
<em>meso/cv</em> value = heat capacity of SPH particles (need units)
|
|
value can be an atom-style variable (see below)
|
|
<em>meso/rho</em> value = density of SPH particles (need units)
|
|
value can be an atom-style variable (see below)
|
|
<em>smd/contact/radius</em> = radius for short range interactions, i.e. contact and friction
|
|
value can be an atom-style variable (see below)
|
|
<em>smd/mass/density</em> = set particle mass based on volume by providing a mass density
|
|
value can be an atom-style variable (see below)
|
|
<em>dpd/theta</em> value = internal temperature of DPD particles (temperature units)
|
|
<em>i_name</em> value = value for custom integer vector with name
|
|
<em>d_name</em> value = value for custom floating-point vector with name
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">set</span> <span class="n">group</span> <span class="n">solvent</span> <span class="nb">type</span> <span class="mi">2</span>
|
|
<span class="nb">set</span> <span class="n">group</span> <span class="n">solvent</span> <span class="nb">type</span><span class="o">/</span><span class="n">fraction</span> <span class="mi">2</span> <span class="mf">0.5</span> <span class="mi">12393</span>
|
|
<span class="nb">set</span> <span class="n">group</span> <span class="n">edge</span> <span class="n">bond</span> <span class="mi">4</span>
|
|
<span class="nb">set</span> <span class="n">region</span> <span class="n">half</span> <span class="n">charge</span> <span class="mf">0.5</span>
|
|
<span class="nb">set</span> <span class="nb">type</span> <span class="mi">3</span> <span class="n">charge</span> <span class="mf">0.5</span>
|
|
<span class="nb">set</span> <span class="nb">type</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="n">charge</span> <span class="mf">0.5</span>
|
|
<span class="nb">set</span> <span class="n">atom</span> <span class="o">*</span> <span class="n">charge</span> <span class="n">v_atomfile</span>
|
|
<span class="nb">set</span> <span class="n">atom</span> <span class="mi">100</span><span class="o">*</span><span class="mi">200</span> <span class="n">x</span> <span class="mf">0.5</span> <span class="n">y</span> <span class="mf">1.0</span>
|
|
<span class="nb">set</span> <span class="n">atom</span> <span class="mi">1492</span> <span class="nb">type</span> <span class="mi">3</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Set one or more properties of one or more atoms. Since atom
|
|
properties are initially assigned by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>,
|
|
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> or <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>
|
|
commands, this command changes those assignments. This can be useful
|
|
for overriding the default values assigned by the
|
|
<a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a> command (e.g. charge = 0.0). It can
|
|
be useful for altering pairwise and molecular force interactions,
|
|
since force-field coefficients are defined in terms of types. It can
|
|
be used to change the labeling of atoms by atom type or molecule ID
|
|
when they are output in <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> files. It can also be useful
|
|
for debugging purposes; i.e. positioning an atom at a precise location
|
|
to compute subsequent forces or energy.</p>
|
|
<p>Note that the <em>style</em> and <em>ID</em> arguments determine which atoms have
|
|
their properties reset. The remaining keywords specify which
|
|
properties to reset and what the new values are. Some strings like
|
|
<em>type</em> or <em>mol</em> can be used as a style and/or a keyword.</p>
|
|
<hr class="docutils" />
|
|
<p>This section describes how to select which atoms to change
|
|
the properties of, via the <em>style</em> and <em>ID</em> arguments.</p>
|
|
<p>The style <em>atom</em> selects all the atoms in a range of atom IDs. The
|
|
style <em>type</em> selects all the atoms in a range of types. The style
|
|
<em>mol</em> selects all the atoms in a range of molecule IDs.</p>
|
|
<p>In each of the range cases, the range can be specified as a single
|
|
numeric value, or a wildcard asterisk can be used to specify a range
|
|
of values. This takes the form “*” or “<em>n” or “n</em>” or “m*n”. For
|
|
example, for the style <em>type</em>, if N = the number of atom types, then
|
|
an asterisk with no numeric values means all types from 1 to N. A
|
|
leading asterisk means all types from 1 to n (inclusive). A trailing
|
|
asterisk means all types from n to N (inclusive). A middle asterisk
|
|
means all types from m to n (inclusive). For all the styles except
|
|
<em>mol</em>, the lowest value for the wildcard is 1; for <em>mol</em> it is 0.</p>
|
|
<p>The style <em>group</em> selects all the atoms in the specified group. The
|
|
style <em>region</em> selects all the atoms in the specified geometric
|
|
region. See the <a class="reference internal" href="group.html"><span class="doc">group</span></a> and <a class="reference internal" href="region.html"><span class="doc">region</span></a> commands
|
|
for details of how to specify a group or region.</p>
|
|
<hr class="docutils" />
|
|
<p>This section describes the keyword options for which properties to
|
|
change, for the selected atoms.</p>
|
|
<p>Note that except where explicitly prohibited below, all of the
|
|
keywords allow an <a class="reference internal" href="variable.html"><span class="doc">atom-style or atomfile-style variable</span></a> to be used as the specified value(s). If the
|
|
value is a variable, it should be specified as v_name, where name is
|
|
the variable name. In this case, the variable will be evaluated, and
|
|
its resulting per-atom value used to determine the value assigned to
|
|
each selected atom. Note that the per-atom value from the variable
|
|
will be ignored for atoms that are not selected via the <em>style</em> and
|
|
<em>ID</em> settings explained above. A simple way to use per-atom values
|
|
from the variable to reset a property for all atoms is to use style
|
|
<em>atom</em> with <em>ID</em> = “*”; this selects all atom IDs.</p>
|
|
<p>Atom-style variables can specify formulas with various mathematical
|
|
functions, and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command
|
|
keywords for the simulation box parameters and timestep and elapsed
|
|
time. They can also include per-atom values, such as atom
|
|
coordinates. Thus it is easy to specify a time-dependent or
|
|
spatially-dependent set of per-atom values. As explained on the
|
|
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a> doc page, atomfile-style variables can be
|
|
used in place of atom-style variables, and thus as arguments to the
|
|
set command. Atomfile-style variables read their per-atoms values
|
|
from a file.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">Atom-style and atomfile-style variables return floating point
|
|
per-atom values. If the values are assigned to an integer variable,
|
|
such as the molecule ID, then the floating point value is truncated to
|
|
its integer portion, e.g. a value of 2.6 would become 2.</p>
|
|
</div>
|
|
<p>Keyword <em>type</em> sets the atom type for all selected atoms. The
|
|
specified value must be from 1 to ntypes, where ntypes was set by the
|
|
<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command or the <em>atom types</em> field in the
|
|
header of the data file read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
|
|
command.</p>
|
|
<p>Keyword <em>type/fraction</em> sets the atom type for a fraction of the
|
|
selected atoms. The actual number of atoms changed is not guaranteed
|
|
to be exactly the requested fraction, but should be statistically
|
|
close. Random numbers are used in such a way that a particular atom
|
|
is changed or not changed, regardless of how many processors are being
|
|
used. This keyword does not allow use of an atom-style variable.</p>
|
|
<p>Keyword <em>mol</em> sets the molecule ID for all selected atoms. The <a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> being used must support the use of molecule
|
|
IDs.</p>
|
|
<p>Keywords <em>x</em>, <em>y</em>, <em>z</em>, and <em>charge</em> set the coordinates or charge of
|
|
all selected atoms. For <em>charge</em>, the <a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a>
|
|
being used must support the use of atomic charge.</p>
|
|
<p>Keyword <em>dipole</em> uses the specified x,y,z values as components of a
|
|
vector to set as the orientation of the dipole moment vectors of the
|
|
selected atoms. The magnitude of the dipole moment is set
|
|
by the length of this orientation vector.</p>
|
|
<p>Keyword <em>dipole/random</em> randomizes the orientation of the dipole
|
|
moment vectors for the selected atoms and sets the magnitude of each
|
|
to the specified <em>Dlen</em> value. For 2d systems, the z component of the
|
|
orientation is set to 0.0. Random numbers are used in such a way that
|
|
the orientation of a particular atom is the same, regardless of how
|
|
many processors are being used. This keyword does not allow use of an
|
|
atom-style variable.</p>
|
|
<p>Keyword <em>quat</em> uses the specified values to create a quaternion
|
|
(4-vector) that represents the orientation of the selected atoms. The
|
|
particles must define a quaternion for their orientation
|
|
(e.g. ellipsoids, triangles, body particles) as defined by the
|
|
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> command. Note that particles defined by
|
|
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style ellipsoid</span></a> have 3 shape parameters. The 3
|
|
values must be non-zero for each particle set by this command. They
|
|
are used to specify the aspect ratios of an ellipsoidal particle,
|
|
which is oriented by default with its x-axis along the simulation
|
|
box’s x-axis, and similarly for y and z. If this body is rotated (via
|
|
the right-hand rule) by an angle theta around a unit rotation vector
|
|
(a,b,c), then the quaternion that represents its new orientation is
|
|
given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2),
|
|
c*sin(theta/2)). The theta and a,b,c values are the arguments to the
|
|
<em>quat</em> keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
|
|
not specified as a unit vector. For 2d systems, the a,b,c values are
|
|
ignored, since a rotation vector of (0,0,1) is the only valid choice.</p>
|
|
<p>Keyword <em>quat/random</em> randomizes the orientation of the quaternion for
|
|
the selected atoms. The particles must define a quaternion for their
|
|
orientation (e.g. ellipsoids, triangles, body particles) as defined by
|
|
the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> command. Random numbers are used in
|
|
such a way that the orientation of a particular atom is the same,
|
|
regardless of how many processors are being used. For 2d systems,
|
|
only orientations in the xy plane are generated. As with keyword
|
|
<em>quat</em>, for ellipsoidal particles, the 3 shape values must be non-zero
|
|
for each particle set by this command. This keyword does not allow
|
|
use of an atom-style variable.</p>
|
|
<p>Keyword <em>diameter</em> sets the size of the selected atoms. The particles
|
|
must be finite-size spheres as defined by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style sphere</span></a> command. The diameter of a particle can be
|
|
set to 0.0, which means they will be treated as point particles. Note
|
|
that this command does not adjust the particle mass, even if it was
|
|
defined with a density, e.g. via the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
|
|
command.</p>
|
|
<p>Keyword <em>shape</em> sets the size and shape of the selected atoms. The
|
|
particles must be ellipsoids as defined by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style ellipsoid</span></a> command. The <em>Sx</em>, <em>Sy</em>, <em>Sz</em> settings are
|
|
the 3 diameters of the ellipsoid in each direction. All 3 can be set
|
|
to the same value, which means the ellipsoid is effectively a sphere.
|
|
They can also all be set to 0.0 which means the particle will be
|
|
treated as a point particle. Note that this command does not adjust
|
|
the particle mass, even if it was defined with a density, e.g. via the
|
|
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command.</p>
|
|
<p>Keyword <em>length</em> sets the length of selected atoms. The particles
|
|
must be line segments as defined by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style line</span></a> command. If the specified value is non-zero the
|
|
line segment is (re)set to a length = the specified value, centered
|
|
around the particle position, with an orientation along the x-axis.
|
|
If the specified value is 0.0, the particle will become a point
|
|
particle. Note that this command does not adjust the particle mass,
|
|
even if it was defined with a density, e.g. via the
|
|
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command.</p>
|
|
<p>Keyword <em>tri</em> sets the size of selected atoms. The particles must be
|
|
triangles as defined by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style tri</span></a> command.
|
|
If the specified value is non-zero the triangle is (re)set to be an
|
|
equilateral triangle in the xy plane with side length = the specified
|
|
value, with a centroid at the particle position, with its base
|
|
parallel to the x axis, and the y-axis running from the center of the
|
|
base to the top point of the triangle. If the specified value is 0.0,
|
|
the particle will become a point particle. Note that this command
|
|
does not adjust the particle mass, even if it was defined with a
|
|
density, e.g. via the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command.</p>
|
|
<p>Keyword <em>theta</em> sets the orientation of selected atoms. The particles
|
|
must be line segments as defined by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style line</span></a> command. The specified value is used to set the
|
|
orientation angle of the line segments with respect to the x axis.</p>
|
|
<p>Keyword <em>theta/random</em> randomizes the orientation of theta for the
|
|
selected atoms. The particles must be line segments as defined by the
|
|
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style line</span></a> command. Random numbers are used in
|
|
such a way that the orientation of a particular atom is the same,
|
|
regardless of how many processors are being used. This keyword does
|
|
not allow use of an atom-style variable.</p>
|
|
<p>Keyword <em>angmom</em> sets the angular momentum of selected atoms. The
|
|
particles must be ellipsoids as defined by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style ellipsoid</span></a> command or triangles as defined by the
|
|
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style tri</span></a> command. The angular momentum vector
|
|
of the particles is set to the 3 specified components.</p>
|
|
<p>Keyword <em>omega</em> sets the angular velocity of selected atoms. The
|
|
particles must be spheres as defined by the “atom_style sphere”_
|
|
atom_style.html command. The angular velocity vector of the particles
|
|
is set to the 3 specified components.</p>
|
|
<p>Keyword <em>mass</em> sets the mass of all selected particles. The particles
|
|
must have a per-atom mass attribute, as defined by the
|
|
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> command. See the “mass” command for how
|
|
to set mass values on a per-type basis.</p>
|
|
<p>Keyword <em>density</em> also sets the mass of all selected particles, but in
|
|
a different way. The particles must have a per-atom mass attribute,
|
|
as defined by the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> command. If the atom
|
|
has a radius attribute (see <a class="reference internal" href="atom_style.html"><span class="doc">atom_style sphere</span></a>) and
|
|
its radius is non-zero, its mass is set from the density and particle
|
|
volume. If the atom has a shape attribute (see <a class="reference internal" href="atom_style.html"><span class="doc">atom_style ellipsoid</span></a>) and its 3 shape parameters are non-zero,
|
|
then its mass is set from the density and particle volume. If the
|
|
atom has a length attribute (see <a class="reference internal" href="atom_style.html"><span class="doc">atom_style line</span></a>)
|
|
and its length is non-zero, then its mass is set from the density and
|
|
line segment length (the input density is assumed to be in
|
|
mass/distance units). If the atom has an area attribute (see
|
|
<a class="reference internal" href="atom_style.html"><span class="doc">atom_style tri</span></a>) and its area is non-zero, then its
|
|
mass is set from the density and triangle area (the input density is
|
|
assumed to be in mass/distance^2 units). If none of these cases are
|
|
valid, then the mass is set to the density value directly (the input
|
|
density is assumed to be in mass units).</p>
|
|
<p>Keyword <em>volume</em> sets the volume of all selected particles.
|
|
Currently, only the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style peri</span></a> command defines
|
|
particles with a volume attribute. Note that this command does not
|
|
adjust the particle mass.</p>
|
|
<p>Keyword <em>image</em> sets which image of the simulation box the atom is
|
|
considered to be in. An image of 0 means it is inside the box as
|
|
defined. A value of 2 means add 2 box lengths to get the true value.
|
|
A value of -1 means subtract 1 box length to get the true value.
|
|
LAMMPS updates these flags as atoms cross periodic boundaries during
|
|
the simulation. The flags can be output with atom snapshots via the
|
|
<a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command. If a value of NULL is specified for any of
|
|
nx,ny,nz, then the current image value for that dimension is
|
|
unchanged. For non-periodic dimensions only a value of 0 can be
|
|
specified. This keyword does not allow use of atom-style variables.
|
|
This command can be useful after a system has been equilibrated and
|
|
atoms have diffused one or more box lengths in various directions.
|
|
This command can then reset the image values for atoms so that they
|
|
are effectively inside the simulation box, e.g if a diffusion
|
|
coefficient is about to be measured via the <a class="reference internal" href="compute_msd.html"><span class="doc">compute msd</span></a> command. Care should be taken not to reset the
|
|
image flags of two atoms in a bond to the same value if the bond
|
|
straddles a periodic boundary (rather they should be different by +/-
|
|
1). This will not affect the dynamics of a simulation, but may mess
|
|
up analysis of the trajectories if a LAMMPS diagnostic or your own
|
|
analysis relies on the image flags to unwrap a molecule which
|
|
straddles the periodic box.</p>
|
|
<p>Keywords <em>bond</em>, <em>angle</em>, <em>dihedral</em>, and <em>improper</em>, set the bond
|
|
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
|
|
the specified value from 1 to nbondtypes (nangletypes, etc). All
|
|
atoms in a particular bond (angle, etc) must be selected atoms in
|
|
order for the change to be made. The value of nbondtype (nangletypes,
|
|
etc) was set by the <em>bond types</em> (<em>angle types</em>, etc) field in the
|
|
header of the data file read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a>
|
|
command. These keywords do not allow use of an atom-style variable.</p>
|
|
<p>Keywords <em>meso/e</em>, <em>meso/cv</em>, and <em>meso/rho</em> set the energy, heat
|
|
capacity, and density of smmothed particle hydrodynamics (SPH)
|
|
particles. See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to
|
|
using SPH in LAMMPS.</p>
|
|
<p>Keyword <em>smd/mass/density</em> sets the mass of all selected particles,
|
|
but it is only applicable to the Smooth Mach Dynamics package
|
|
USER-SMD. It assumes that the particle volume has already been
|
|
correctly set and calculates particle mass from the provided mass
|
|
density value.</p>
|
|
<p>Keyword <em>smd/contact/radius</em> only applies to simulations with the
|
|
Smooth Mach Dynamics package USER-SMD. Itsets an interaction radius
|
|
for computing short-range interactions, e.g. repulsive forces to
|
|
prevent different individual physical bodies from penetrating each
|
|
other. Note that the SPH smoothing kernel diameter used for computing
|
|
long range, nonlocal interactions, is set using the <em>diameter</em>
|
|
keyword.</p>
|
|
<p>Keyword <em>dpd/theta</em> sets the internal temperature of a DPD particle
|
|
as defined by the USER-DPD package.</p>
|
|
<p>Keywords <em>i_name</em> and <em>d_name</em> refer to custom integer and
|
|
floating-point properties that have been added to each atom via the
|
|
<a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> command. When that command
|
|
is used specific names are given to each attribute which are what is
|
|
specified as the “name” portion of <em>i_name</em> or <em>d_name</em>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<p>You cannot set an atom attribute (e.g. <em>mol</em> or <em>q</em> or <em>volume</em>) if
|
|
the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a> does not have that attribute.</p>
|
|
<p>This command requires inter-processor communication to coordinate the
|
|
setting of bond types (angle types, etc). This means that your system
|
|
must be ready to perform a simulation before using one of these
|
|
keywords (force fields set, atom mass set, etc). This is not
|
|
necessary for other keywords.</p>
|
|
<p>Using the <em>region</em> style with the bond (angle, etc) keywords can give
|
|
unpredictable results if there are bonds (angles, etc) that straddle
|
|
periodic boundaries. This is because the region may only extend up to
|
|
the boundary and partner atoms in the bond (angle, etc) may have
|
|
coordinates outside the simulation box if they are ghost atoms.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a>, <a class="reference internal" href="create_atoms.html"><span class="doc">create_atoms</span></a>,
|
|
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
|
|
<hr/>
|
|
|
|
<div role="contentinfo">
|
|
<p>
|
|
© 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> |