2010-08-20 07:38:06 +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" >
2015-12-21 23:20:41 +08:00
< title > pair_style comb command — LAMMPS documentation< / title >
2015-07-30 22:53:28 +08:00
2010-08-20 07:38:06 +08:00
2015-07-30 22:53:28 +08:00
2010-08-20 07:38:06 +08:00
2015-07-30 22:53:28 +08:00
2010-08-20 07:38:06 +08:00
2015-07-30 22:53:28 +08:00
2010-08-20 07:38:06 +08:00
2015-07-30 22:53:28 +08:00
2010-08-20 07:38:06 +08:00
2015-07-30 22:53:28 +08:00
< link rel = "stylesheet" href = "_static/css/theme.css" type = "text/css" / >
2013-11-05 01:25:25 +08:00
2015-07-30 22:53:28 +08:00
< link rel = "stylesheet" href = "_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type = "text/css" / >
2015-12-21 23:20:41 +08:00
< link rel = "top" title = "LAMMPS 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 > pair_style comb 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 = "pair-style-comb-command" >
< span id = "index-0" > < / span > < h1 > pair_style comb command< a class = "headerlink" href = "#pair-style-comb-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "pair-style-comb-omp-command" >
< h1 > pair_style comb/omp command< a class = "headerlink" href = "#pair-style-comb-omp-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "pair-style-comb3-command" >
< h1 > pair_style comb3 command< a class = "headerlink" href = "#pair-style-comb3-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 > pair_style comb
pair_style comb3 keyword
< / pre > < / div >
< / div >
< pre class = "literal-block" >
keyword = < em > polar< / em >
< em > polar< / em > value = < em > polar_on< / em > or < em > polar_off< / em > = whether or not to include atomic polarization
< / pre >
< / 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 > pair_style comb
2010-08-20 07:38:06 +08:00
pair_coeff * * ../potentials/ffield.comb Si
2015-07-30 22:53:28 +08:00
pair_coeff * * ../potentials/ffield.comb Hf Si O
< / pre > < / div >
< / div >
< div class = "highlight-python" > < div class = "highlight" > < pre > pair_style comb3 polar_off
pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Style < em > comb< / em > computes the second-generation variable charge COMB
(Charge-Optimized Many-Body) potential. Style < em > comb3< / em > computes the
2013-11-05 01:34:08 +08:00
third-generation COMB potential. These COMB potentials are described
2015-07-30 22:53:28 +08:00
in < a class = "reference internal" href = "#comb" > < span > (COMB)< / span > < / a > and < a class = "reference internal" href = "#comb3" > < span > (COMB3)< / span > < / a > . Briefly, the total energy
< em > E< sub> T< /sub> < / em > of a system of atoms is given by< / p >
< img alt = "_images/pair_comb1.jpg" class = "align-center" src = "_images/pair_comb1.jpg" / >
< p > where < em > E< sub> i< /sub> < sup> self< /sup> < / em > is the self-energy of atom < em > i< / em >
2013-11-05 01:25:25 +08:00
(including atomic ionization energies and electron affinities),
2015-07-30 22:53:28 +08:00
< em > E< sub> ij< /sub> < sup> short< /sup> < / em > is the bond-order potential between
atoms < em > i< / em > and < em > j< / em > ,
< em > E< sub> ij< /sub> < sup> Coul< /sup> < / em > is the Coulomb interactions,
< em > E< sup> polar< /sup> < / em > is the polarization term for organic systems
(style < em > comb3< / em > only),
< em > E< sup> vdW< /sup> < / em > is the van der Waals energy (style < em > comb3< / em > only),
< em > E< sup> barr< /sup> < / em > is a charge barrier function, and
< em > E< sup> corr< /sup> < / em > are angular correction terms.< / p >
< p > The COMB potentials (styles < em > comb< / em > and < em > comb3< / em > ) are variable charge
2013-11-05 01:34:08 +08:00
potentials. The equilibrium charge on each atom is calculated by the
2015-12-11 01:23:56 +08:00
electronegativity equalization (QEq) method. See < a class = "reference internal" href = "pair_smtbq.html#rick" > < span > Rick< / span > < / a > for
2015-07-30 22:53:28 +08:00
further details. This is implemented by the < a class = "reference internal" href = "fix_qeq_comb.html" > < em > fix qeq/comb< / em > < / a > command, which should normally be
2013-11-05 01:34:08 +08:00
specified in the input script when running a model with the COMB
2015-07-30 22:53:28 +08:00
potential. The < a class = "reference internal" href = "fix_qeq_comb.html" > < em > fix qeq/comb< / em > < / a > command has options
2013-11-05 01:34:08 +08:00
that determine how often charge equilibration is performed, its
convergence criterion, and which atoms are included in the
2015-07-30 22:53:28 +08:00
calculation.< / p >
< p > Only a single pair_coeff command is used with the < em > comb< / em > and < em > comb3< / em >
2013-11-05 01:34:08 +08:00
styles which specifies the COMB potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the potential file in the pair_coeff
2015-07-30 22:53:28 +08:00
command, where N is the number of LAMMPS atom types.< / p >
< p > For example, if your LAMMPS simulation of a Si/SiO< sub> 2< /sub> /
HfO< sub> 2< /sub> interface has 4 atom types, and you want the 1st and
2010-08-20 07:38:06 +08:00
last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
2015-07-30 22:53:28 +08:00
use the following pair_coeff command:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > pair_coeff * * ../potentials/ffield.comb Si Hf O Si
< / pre > < / div >
< / div >
< p > The first two arguments must be * * so as to span all LAMMPS atom
2010-08-20 07:38:06 +08:00
types. The first and last Si arguments map LAMMPS atom types 1 and 4
2015-07-30 22:53:28 +08:00
to the Si element in the < em > ffield.comb< / em > file. The second Hf argument
2010-08-20 07:38:06 +08:00
maps LAMMPS atom type 2 to the Hf element, and the third O argument
maps LAMMPS atom type 3 to the O element in the potential file. If a
mapping value is specified as NULL, the mapping is not performed.
2015-07-30 22:53:28 +08:00
This can be used when a < em > comb< / em > potential is used as part of the
< em > hybrid< / em > pair style. The NULL values are placeholders for atom types
that will be used with other potentials.< / p >
< p > For style < em > comb< / em > , the provided potential file < em > ffield.comb< / em > contains
2013-11-05 01:34:08 +08:00
all currently-available 2nd generation COMB parameterizations: for Si,
Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
2015-07-30 22:53:28 +08:00
< em > comb3< / em > , the potential file < em > ffield.comb3< / em > contains all
2013-11-05 01:34:08 +08:00
currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
2014-02-02 02:04:29 +08:00
H, Ti, Zn and Zr. The status of the optimization of the compounds, for
2015-07-30 22:53:28 +08:00
example Cu< sub> 2< /sub> O, TiN and hydrocarbons, are given in the
following table:< / p >
< img alt = "_images/pair_comb2.jpg" class = "align-center" src = "_images/pair_comb2.jpg" / >
< p > For style < em > comb3< / em > , in addition to ffield.comb3, a special parameter
file, < em > lib.comb3< / em > , that is exclusively used for C/O/H systems, will be
2013-11-05 01:34:08 +08:00
automatically loaded if carbon atom is detected in LAMMPS input
2015-07-23 22:56:58 +08:00
structure. This file must be in your working directory or in the
directory pointed to by the environment variable LAMMPS_POTENTIALS, as
2015-07-30 22:53:28 +08:00
described on the < a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff< / em > < / a > command doc page.< / p >
< p > Keyword < em > polar< / em > indicates whether the force field includes
2015-07-23 22:56:58 +08:00
the atomic polarization. Since the equilibration of the polarization
2015-07-30 22:53:28 +08:00
has not yet been implemented, it can only set polar_off at present.< / p >
2015-12-11 01:23:56 +08:00
< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > You can not use potential file < em > ffield.comb< / em > with style < em > comb3< / em > ,
nor file < em > ffield.comb3< / em > with style < em > comb< / em > .< / p >
2015-07-30 22:53:28 +08:00
< / div >
< hr class = "docutils" / >
< p > Styles with a < em > cuda< / em > , < em > gpu< / em > , < em > intel< / em > , < em > kk< / em > , < em > omp< / em > , or < em > opt< / em > suffix are
2014-08-15 00:30:25 +08:00
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
2015-07-30 22:53:28 +08:00
hardware, as discussed in < a class = "reference internal" href = "Section_accelerate.html" > < em > Section_accelerate< / em > < / a >
2014-08-15 00:30:25 +08:00
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
2015-07-30 22:53:28 +08:00
issues.< / p >
< p > These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
2014-08-15 00:30:25 +08:00
KOKKOS, USER-OMP and OPT packages, respectively. They are only
2015-07-30 22:53:28 +08:00
enabled if LAMMPS was built with those packages. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info.< / p >
< p > You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the < a class = "reference internal" href = "Section_start.html#start-7" > < span > -suffix command-line switch< / span > < / a > when you invoke LAMMPS, or you can
use the < a class = "reference internal" href = "suffix.html" > < em > suffix< / em > < / a > command in your input script.< / p >
< p > See < a class = "reference internal" href = "Section_accelerate.html" > < em > Section_accelerate< / em > < / a > of the manual for
more instructions on how to use the accelerated styles effectively.< / p >
< hr class = "docutils" / >
< p > < strong > Mixing, shift, table, tail correction, restart, rRESPA info< / strong > :< / p >
< p > For atom type pairs I,J and I != J, where types I and J correspond to
2010-08-20 07:38:06 +08:00
two different element types, mixing is performed by LAMMPS as
2015-07-30 22:53:28 +08:00
described above from values in the potential file.< / p >
< p > These pair styles does not support the < a class = "reference internal" href = "pair_modify.html" > < em > pair_modify< / em > < / a >
shift, table, and tail options.< / p >
< p > These pair styles do not write its information to < a class = "reference internal" href = "restart.html" > < em > binary restart files< / em > < / a > , since it is stored in potential files. Thus, you
need to re-specify the pair_style, pair_coeff, and < a class = "reference internal" href = "fix_qeq_comb.html" > < em > fix qeq/comb< / em > < / a > commands in an input script that reads a
restart file.< / p >
< p > These pair styles can only be used via the < em > pair< / em > keyword of the
< a class = "reference internal" href = "run_style.html" > < em > run_style respa< / em > < / a > command. It does not support the
< em > inner< / em > , < em > middle< / em > , < em > outer< / em > keywords.< / p >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > These pair styles are part of the MANYBODY package. It is only enabled
2010-08-20 07:38:06 +08:00
if LAMMPS was built with that package (which it is by default). See
2015-07-30 22:53:28 +08:00
the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info.< / p >
< p > These pair styles requires the < a class = "reference internal" href = "newton.html" > < em > newton< / em > < / a > setting to be “ on”
for pair interactions.< / p >
< p > The COMB potentials in the < em > ffield.comb< / em > and < em > ffield.comb3< / em > files provided
2013-11-05 01:25:25 +08:00
with LAMMPS (see the potentials directory) are parameterized for metal
2015-07-30 22:53:28 +08:00
< a class = "reference internal" href = "units.html" > < em > units< / em > < / a > . You can use the COMB potential with any LAMMPS
2010-08-20 07:38:06 +08:00
units, but you would need to create your own COMB potential file with
coefficients listed in the appropriate units if your simulation
2015-07-30 22:53:28 +08:00
doesn’ t use “ metal” units.< / p >
< / 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 = "pair_style.html" > < em > pair_style< / em > < / a > , < a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff< / em > < / a > ,
< a class = "reference internal" href = "fix_qeq_comb.html" > < em > fix_qeq/comb< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
< hr class = "docutils" / >
< p id = "comb" > < strong > (COMB)< / strong > T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and
S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)< / p >
< p id = "comb3" > < strong > (COMB3)< / strong > T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74,
255-279 (2013).< / p >
< p id = "rick" > < strong > (Rick)< / strong > S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
(1994).< / 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:'./',
2015-12-21 23:20:41 +08:00
VERSION:'',
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 >
