Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/html/special_bonds.html
db1e17197fcflammm-master-deprecated

Last Change
Raw File

special_bonds.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>special_bonds 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>special_bonds 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="special-bonds-command">
<span id="index-0"></span><h1>special_bonds command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
special_bonds keyword values ...
</pre>
<ul class="simple">
<li>one or more keyword/value pairs may be appended</li>
<li>keyword = <em>amber</em> or <em>charmm</em> or <em>dreiding</em> or <em>fene</em> or <em>lj/coul</em> or <em>lj</em> or <em>coul</em> or <em>angle</em> or <em>dihedral</em> or <em>extra</em></li>
</ul>
<pre class="literal-block">
<em>amber</em> values = none
<em>charmm</em> values = none
<em>dreiding</em> values = none
<em>fene</em> values = none
<em>lj/coul</em> values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
<em>lj</em> values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
<em>coul</em> values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
<em>angle</em> value = <em>yes</em> or <em>no</em>
<em>dihedral</em> value = <em>yes</em> or <em>no</em>
<em>extra</em> value = N
N = number of extra 1-2,1-3,1-4 interactions to save space for
</pre>
<p>Examples:</p>
<pre class="literal-block">
special_bonds amber
special_bonds charmm
special_bonds fene dihedral no
special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
special_bonds lj/coul 0 1 1 extra 2
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Set weighting coefficients for pairwise energy and force contributions
between pairs of atoms that are also permanently bonded to each other,
either directly or via one or two intermediate bonds. These weighting
factors are used by nearly all <a class="reference internal" href="pair_style.html"><span class="doc">pair styles</span></a> in LAMMPS
that compute simple pairwise interactions. Permanent bonds between
atoms are specified by defining the bond topology in the data file
read by the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command. Typically a
<a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a> command is also used to define a bond
potential. The rationale for using these weighting factors is that
the interaction between a pair of bonded atoms is all (or mostly)
specified by the bond, angle, dihedral potentials, and thus the
non-bonded Lennard-Jones or Coulombic interaction between the pair of
atoms should be excluded (or reduced by a weighting factor).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">These weighting factors are NOT used by <a class="reference internal" href="pair_style.html"><span class="doc">pair styles</span></a> that compute many-body interactions, since the
&#8220;bonds&#8221; that result from such interactions are not permanent, but are
created and broken dynamically as atom conformations change. Examples
of pair styles in this category are EAM, MEAM, Stillinger-Weber,
Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no
sense to define permanent bonds between atoms that interact via these
potentials, though such bonds may exist elsewhere in your system,
e.g. when using the <a class="reference internal" href="pair_hybrid.html"><span class="doc">pair_style hybrid</span></a> command.
Thus LAMMPS ignores special_bonds settings when manybody potentials
are calculated.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Unlike some commands in LAMMPS, you cannot use this command
multiple times in an incremental fashion: e.g. to first set the LJ
settings and then the Coulombic ones. Each time you use this command
it sets all the coefficients to default values and only overrides the
one you specify, so you should set all the options you need each time
you use it. See more details at the bottom of this page.</p>
</div>
<p>The Coulomb factors are applied to any Coulomb (charge interaction)
term that the potential calculates. The LJ factors are applied to the
remaining terms that the potential calculates, whether they represent
LJ interactions or not. The weighting factors are a scaling
pre-factor on the energy and force between the pair of atoms. A value
of 1.0 means include the full interaction; a value of 0.0 means
exclude it completely.</p>
<p>The 1st of the 3 coefficients (LJ or Coulombic) is the weighting
factor on 1-2 atom pairs, which are pairs of atoms directly bonded to
each other. The 2nd coefficient is the weighting factor on 1-3 atom
pairs which are those separated by 2 bonds (e.g. the two H atoms in a
water molecule). The 3rd coefficient is the weighting factor on 1-4
atom pairs which are those separated by 3 bonds (e.g. the 1st and 4th
atoms in a dihedral interaction). Thus if the 1-2 coefficient is set
to 0.0, then the pairwise interaction is effectively turned off for
all pairs of atoms bonded to each other. If it is set to 1.0, then
that interaction will be at full strength.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For purposes of computing weighted pairwise interactions, 1-3
and 1-4 interactions are not defined from the list of angles or
dihedrals used by the simulation. Rather, they are inferred
topologically from the set of bonds specified when the simulation is
defined from a data or restart file (see <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). Thus the set of
1-2,1-3,1-4 interactions that the weights apply to is the same whether
angle and dihedral potentials are computed or not, and remains the
same even if bonds are constrained, or turned off, or removed during a
simulation.</p>
</div>
<p>The two exceptions to this rule are (a) if the <em>angle</em> or <em>dihedral</em>
keywords are set to <em>yes</em> (see below), or (b) if the
<a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command is used with the <em>special</em>
option that recomputes the 1-2,1-3,1-4 topologies after bonds are
deleted; see the <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command for more
details.</p>
<p>The <em>amber</em> keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
is the default for a commonly used version of the AMBER force field,
where the last value is really 5/6. See <a class="reference internal" href="#cornell"><span class="std std-ref">(Cornell)</span></a> for a
description of the AMBER force field.</p>
<p>The <em>charmm</em> keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
LJ and Coulombic interactions, which is the default for a commonly
used version of the CHARMM force field. Note that in pair styles
<em>lj/charmm/coul/charmm</em> and <em>lj/charmm/coul/long</em> the 1-4 coefficients
are defined explicitly, and these pairwise contributions are computed
as part of the charmm dihedral style - see the
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> and <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style</span></a>
commands for more information. See <a class="reference internal" href="#mackerell"><span class="std std-ref">(MacKerell)</span></a> for a
description of the CHARMM force field.</p>
<p>The <em>dreiding</em> keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both
LJ and Coulombic interactions, which is the default for the Dreiding
force field, as discussed in <a class="reference internal" href="#mayo"><span class="std std-ref">(Mayo)</span></a>.</p>
<p>The <em>fene</em> keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
LJ and Coulombic interactions, which is consistent with a
coarse-grained polymer model with <a class="reference internal" href="bond_fene.html"><span class="doc">FENE bonds</span></a>. See
<a class="reference internal" href="#kremer"><span class="std std-ref">(Kremer)</span></a> for a description of FENE bonds.</p>
<p>The <em>lj/coul</em>, <em>lj</em>, and <em>coul</em> keywords allow the 3 coefficients to
be set explicitly. The <em>lj/coul</em> keyword sets both the LJ and
Coulombic coefficients to the same 3 values. The <em>lj</em> and <em>coul</em>
keywords only set either the LJ or Coulombic coefficients. Use both
of them if you wish to set the LJ coefficients to different values
than the Coulombic coefficients.</p>
<p>The <em>angle</em> keyword allows the 1-3 weighting factor to be ignored for
individual atom pairs if they are not listed as the first and last
atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in
any dihedral defined in the simulation. For example, imagine the 1-3
weighting factor is set to 0.5 and you have a linear molecule with 4
atoms and bonds as follows: 1-2-3-4. If your data file defines 1-2-3
as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a
dihedral, then the pairwise interaction between atoms 1 and 3 will
always be weighted by 0.5, but different force fields use different
rules for weighting the pairwise interaction between atoms 2 and 4.
If the <em>angle</em> keyword is specified as <em>yes</em>, then the pairwise
interaction between atoms 2 and 4 will be unaffected (full weighting
of 1.0). If the <em>angle</em> keyword is specified as <em>no</em> which is the
default, then the 2,4 interaction will also be weighted by 0.5.</p>
<p>The <em>dihedral</em> keyword allows the 1-4 weighting factor to be ignored
for individual atom pairs if they are not listed as the first and last
atoms in any dihedral defined in the simulation. For example, imagine
the 1-4 weighting factor is set to 0.5 and you have a linear molecule
with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file
defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
dihedral, then the pairwise interaction between atoms 1 and 4 will
always be weighted by 0.5, but different force fields use different
rules for weighting the pairwise interaction between atoms 2 and 5.
If the <em>dihedral</em> keyword is specified as <em>yes</em>, then the pairwise
interaction between atoms 2 and 5 will be unaffected (full weighting
of 1.0). If the <em>dihedral</em> keyword is specified as <em>no</em> which is the
default, then the 2,5 interaction will also be weighted by 0.5.</p>
<p>The <em>extra</em> keyword can be used when additional bonds will be created
during a simulation run, e.g. by the <a class="reference internal" href="fix_bond_create.html"><span class="doc">fix bond/create</span></a> command. It can also be used if
molecules will be added to the system, e.g. via the <a class="reference internal" href="fix_deposit.html"><span class="doc">fix deposit</span></a>, or <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a> commands, which
will have atoms with more special neighbors than any atom in the
current system has.</p>
<hr class="docutils" />
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">LAMMPS stores and maintains a data structure with a list of the
1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
the system). If new bonds are created (or molecules added containing
atoms with more special neighbors), the size of this list needs to
grow. Note that adding a single bond always adds a new 1st neighbor
but may also induce *many* new 2nd and 3rd neighbors, depending on the
molecular topology of your system. Using the <em>extra</em> keyword leaves
empty space in the list for this N additional 1st, 2nd, or 3rd
neighbors to be added. If you do not do this, you may get an error
when bonds (or molecules) are added.</p>
</div>
<hr class="docutils" />
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you reuse this command in an input script, you should set all
the options you need each time. This command cannot be used a 2nd
time incrementally, e.g. to add some extra storage locations via the
<em>extra</em> keyword. E.g. these two commands:</p>
</div>
<p>special_bonds lj 0.0 1.0 1.0
special_bonds coul 0.0 0.0 1.0</p>
<p>are not the same as</p>
<p>special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0</p>
<p>In the first case you end up with (after the 2nd command):</p>
<p>LJ: 0.0 0.0 0.0
Coul: coul 0.0 0.0 1.0</p>
<p>because the LJ settings are reset to their default values
each time the command is issued.</p>
<p>Likewise</p>
<pre class="literal-block">
special_bonds amber
special_bonds extra 2
</pre>
<p>is not the same as this single command:</p>
<pre class="literal-block">
special_bonds amber extra 2
</pre>
<p>since in the former case, the 2nd command will reset all the LJ and
Coulombic weights to 0.0 (the default).</p>
<p>One exception to this rule is the <em>extra</em> option itself. It is not
reset to its default value of 0 each time the special_bonds command is
invoked. This is because it can also be set by the
<a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> and <a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> commands,
so this command will not override those settings unless you explicitly
use <em>extra</em> as an option.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
<p><a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a>, <a class="reference internal" href="fix_bond_create.html"><span class="doc">fix bond/create</span></a></p>
</div>
<div class="section" id="default">
<h2>Default</h2>
<p>All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0,
angle = no, dihedral = no, and extra = 0.</p>
<hr class="docutils" />
<p id="cornell"><strong>(Cornell)</strong> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).</p>
<p id="kremer"><strong>(Kremer)</strong> Kremer, Grest, J Chem Phys, 92, 5057 (1990).</p>
<p id="mackerell"><strong>(MacKerell)</strong> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).</p>
<p id="mayo"><strong>(Mayo)</strong> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).</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