forked from lijiext/lammps
378 lines
19 KiB
HTML
378 lines
19 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>pair_style mgpt 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>pair_style mgpt 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-mgpt-command">
|
|
<span id="index-0"></span><h1>pair_style mgpt command</h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">mgpt</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">mgpt</span>
|
|
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">parmin</span> <span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">potin</span> <span class="n">Omega</span>
|
|
<span class="n">cp</span> <span class="o">~/</span><span class="n">lammps</span><span class="o">/</span><span class="n">potentials</span><span class="o">/</span><span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">parmin</span> <span class="n">parmin</span>
|
|
<span class="n">cp</span> <span class="o">~/</span><span class="n">lammps</span><span class="o">/</span><span class="n">potentials</span><span class="o">/</span><span class="n">Ta6</span><span class="o">.</span><span class="mi">8</span><span class="n">x</span><span class="o">.</span><span class="n">mgpt</span><span class="o">.</span><span class="n">potin</span> <span class="n">potin</span>
|
|
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">parmin</span> <span class="n">potin</span> <span class="n">Omega</span> <span class="n">volpress</span> <span class="n">yes</span> <span class="n">nbody</span> <span class="mi">1234</span> <span class="n">precision</span> <span class="n">double</span>
|
|
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="n">parmin</span> <span class="n">potin</span> <span class="n">Omega</span> <span class="n">volpress</span> <span class="n">yes</span> <span class="n">nbody</span> <span class="mi">12</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Within DFT quantum mechanics, generalized pseudopotential theory (GPT)
|
|
(<a class="reference internal" href="#moriarty1"><span class="std std-ref">Moriarty1</span></a>) provides a first-principles approach to
|
|
multi-ion interatomic potentials in d-band transition metals, with a
|
|
volume-dependent, real-space total-energy functional for the N-ion
|
|
elemental bulk material in the form</p>
|
|
<img alt="_images/pair_mgpt.jpg" class="align-center" src="_images/pair_mgpt.jpg" />
|
|
<p>where the prime on each summation sign indicates the exclusion of all
|
|
self-interaction terms from the summation. The leading volume term
|
|
E_vol as well as the two-ion central-force pair potential v_2 and the
|
|
three- and four-ion angular-force potentials, v_3 and v_4, depend
|
|
explicitly on the atomic volume Omega, but are structure independent
|
|
and transferable to all bulk ion configurations, either ordered or
|
|
disordered, and with of without the presence of point and line
|
|
defects. The simplified model GPT or MGPT (<a class="reference internal" href="#moriarty2"><span class="std std-ref">Moriarty2</span></a>,
|
|
<a class="reference internal" href="#moriarty3"><span class="std std-ref">Moriarty3</span></a>), which retains the form of E_tot and permits
|
|
more efficient large-scale atomistic simulations, derives from the GPT
|
|
through a series of systematic approximations applied to E_vol and the
|
|
potentials v_n that are valid for mid-period transition metals with
|
|
nearly half-filled d bands.</p>
|
|
<p>Both analytic (<a class="reference internal" href="#moriarty2"><span class="std std-ref">Moriarty2</span></a>) and matrix
|
|
(<a class="reference internal" href="#moriarty3"><span class="std std-ref">Moriarty3</span></a>) representations of MGPT have been developed.
|
|
In the more general matrix representation, which can also be applied
|
|
to f-band actinide metals and permits both canonical and non-canonical
|
|
d/f bands, the multi-ion potentials are evaluated on the fly during a
|
|
simulation through d- or f-state matrix multiplication, and the forces
|
|
that move the ions are determined analytically. Fast matrix-MGPT
|
|
algorithms have been developed independently by Glosli
|
|
(<a class="reference internal" href="#glosli"><span class="std std-ref">Glosli</span></a>, <a class="reference internal" href="#moriarty3"><span class="std std-ref">Moriarty3</span></a>) and by Oppelstrup
|
|
(<a class="reference internal" href="#oppelstrup"><span class="std std-ref">Oppelstrup</span></a>)</p>
|
|
<p>The <em>mgpt</em> pair style calculates forces, energies, and the total
|
|
energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm.
|
|
Input potential and control data are entered through the
|
|
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command. Each material treated requires
|
|
input parmin and potin potential files, as shown in the above
|
|
examples, as well as specification by the user of the initial atomic
|
|
volume Omega through pair_coeff. At the beginning of a time step in
|
|
any simulation, the total volume of the simulation cell V should
|
|
always be equal to Omega*N, where N is the number of metal ions
|
|
present, taking into account the presence of any vacancies and/or
|
|
interstitials in the case of a solid. In a constant-volume
|
|
simulation, which is the normal mode of operation for the <em>mgpt</em> pair
|
|
style, Omega, V and N all remain constant throughout the simulation
|
|
and thus are equal to their initial values. In a constant-stress
|
|
simulation, the cell volume V will change (slowly) as the simulation
|
|
proceeds. After each time step, the atomic volume should be updated
|
|
by the code as Omega = V/N. In addition, the volume term E_vol and
|
|
the potentials v_2, v_3 and v_4 have to be removed at the end of the
|
|
time step, and then respecified at the new value of Omega. In all
|
|
smulations, Omega must remain within the defined volume range for
|
|
E_vol and the potentials for the given material.</p>
|
|
<p>The default option volpress yes in the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>
|
|
command includes all volume derivatives of E_tot required to calculate
|
|
the stress tensor and pressure correctly. The option volpress no
|
|
disregards the pressure contribution resulting from the volume term
|
|
E_vol, and can be used for testing and analysis purposes. The
|
|
additional optional variable nbody controls the specific terms in
|
|
E_tot that are calculated. The default option and the normal option
|
|
for mid-period transition and actinide metals is nbody 1234 for which
|
|
all four terms in E_tot are retained. The option nbody 12, for
|
|
example, retains only the volume term and the two-ion pair potential
|
|
term and can be used for GPT series-end transition metals that can be
|
|
well described without v_3 and v_4. The nbody option can also be used
|
|
to test or analyze the contribution of any of the four terms in E_tot
|
|
to a given calculated property.</p>
|
|
<p>The <em>mgpt</em> pair style makes extensive use of matrix algebra and
|
|
includes optimized kernels for the BlueGene/Q architecture and the
|
|
Intel/AMD (x86) architectures. When compiled with the appropriate
|
|
compiler and compiler switches (-msse3 on x86, and using the IBM XL
|
|
compiler on BG/Q), these optimized routines are used automatically.
|
|
For BG/Q machines, building with the default Makefile for that
|
|
architecture (e.g., “make bgq”) should enable the optimized algebra
|
|
routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt
|
|
(build with “make mpi_fastmgpt”) enables the fast algebra routines.
|
|
The user will be informed in the output files of the matrix kernels in
|
|
use. To further improve speed, on x86 the option precision single can
|
|
be added to the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command line, which
|
|
improves speed (up to a factor of two) at the cost of doing matrix
|
|
calculations with 7 digit precision instead of the default 16. For
|
|
consistency the default option can be specified explicitly by the
|
|
option precision double.</p>
|
|
<p>All remaining potential and control data are contained with the parmin
|
|
and potin files, including cutoffs, atomic mass, and other basic MGPT
|
|
variables. Specific MGPT potential data for the transition metals
|
|
tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials),
|
|
and vanadium (V6.1 potentials) are contained in the LAMMPS potentials
|
|
directory. The stored files are, respectively, Ta4.mgpt.parmin,
|
|
Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin,
|
|
Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and
|
|
V6.1.mgpt.potin . Useful corresponding informational “README” files
|
|
on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the
|
|
potentials directory. These latter files indicate the volume mesh and
|
|
range for each potential and give appropriate references for the
|
|
potentials. It is expected that MGPT potentials for additional
|
|
materials will be added over time.</p>
|
|
<p>Useful example MGPT scripts are given in the examples/USER/mgpt
|
|
directory. These scripts show the necessary steps to perform
|
|
constant-volume calculations and simulations. It is strongly
|
|
recommended that the user work through and understand these examples
|
|
before proceeding to more complex simulations.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">For good performance, LAMMPS should be built with the compiler
|
|
flags “-O3 -msse3 -funroll-loops” when including this pair style. The
|
|
src/MAKE/OPTIONS/Makefile.mpi_fastmgpt is an example machine Makefile
|
|
with these options included as part of a standard MPI build. Note
|
|
that as-is it will build with whatever low-level compiler (g++, icc,
|
|
etc) is the default for your MPI installation.</p>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<p><strong>Mixing, shift, table tail correction, restart</strong>:</p>
|
|
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><span class="doc">pair_modify</span></a>
|
|
mix, shift, table, and tail options.</p>
|
|
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, since it is stored in potential files. Thus, you
|
|
needs to re-specify the pair_style and pair_coeff commands in an input
|
|
script that reads a restart file.</p>
|
|
<p>This pair style can only be used via the <em>pair</em> keyword of the
|
|
<a class="reference internal" href="run_style.html"><span class="doc">run_style respa</span></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</h2>
|
|
<p>This pair style is part of the USER-MGPT package and is only enabled
|
|
if LAMMPS is built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
|
|
<p>The MGPT potentials require the <a class="reference internal" href="newton.html"><span class="doc">newtion</span></a> setting to be
|
|
“on” for pair style interactions.</p>
|
|
<p>The stored parmin and potin potential files provided with LAMMPS in
|
|
the “potentials” directory are written in Rydberg atomic units, with
|
|
energies in Rydbergs and distances in Bohr radii. The <em>mgpt</em> pair
|
|
style converts Rydbergs to Hartrees to make the potential files
|
|
compatible with LAMMPS electron <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
|
|
<p>The form of E_tot used in the <em>mgpt</em> pair style is only appropriate
|
|
for elemental bulk solids and liquids. This includes solids with
|
|
point and extended defects such as vacancies, interstitials, grain
|
|
boundaries and dislocations. Alloys and free surfaces, however,
|
|
require significant modifications, which are not included in the
|
|
<em>mgpt</em> pair style. Likewise, the <em>hybrid</em> pair style is not allowed,
|
|
where MGPT would be used for some atoms but not for others.</p>
|
|
<p>Electron-thermal effects are not included in the standard MGPT
|
|
potentials provided in the “potentials” directory, where the
|
|
potentials have been constructed at zero electron temperature.
|
|
Physically, electron-thermal effects may be important in 3d (e.g., V)
|
|
and 4d (e.g., Mo) transition metals at high temperatures near melt and
|
|
above. It is expected that temperature-dependent MGPT potentials for
|
|
such cases will be added over time.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The options defaults for the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command are
|
|
volpress yes, nbody 1234, and precision double.</p>
|
|
<hr class="docutils" />
|
|
<p id="moriarty1"><strong>(Moriarty1)</strong> Moriarty, Physical Review B, 38, 3199 (1988).</p>
|
|
<p id="moriarty2"><strong>(Moriarty2)</strong> Moriarty, Physical Review B, 42, 1609 (1990).
|
|
Moriarty, Physical Review B 49, 12431 (1994).</p>
|
|
<p id="moriarty3"><strong>(Moriarty3)</strong> Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang,
|
|
Journal of Materials Research, 21, 563 (2006).</p>
|
|
<p id="glosli"><strong>(Glosli)</strong> Glosli, unpublished, 2005.
|
|
Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference
|
|
Series, 46, 254 (2006).</p>
|
|
<p id="oppelstrup"><strong>(Oppelstrup)</strong> Oppelstrup, unpublished, 2015.
|
|
Oppelstrup and Moriarty, to be published.</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> |