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" >
< title > fix drude/transform/direct command — LAMMPS 15 May 2015 version 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 15 May 2015 version 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 > fix drude/transform/direct 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 = "fix-drude-transform-direct-command" >
< span id = "index-0" > < / span > < h1 > fix drude/transform/direct command< a class = "headerlink" href = "#fix-drude-transform-direct-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "fix-drude-transform-inverse-command" >
< h1 > fix drude/transform/inverse command< a class = "headerlink" href = "#fix-drude-transform-inverse-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 > fix ID group-ID style keyword value ...
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > command< / li >
< li > style = < em > drude/transform/direct< / em > or < em > drude/transform/inverse< / em > < / li >
< / ul >
< / 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 > fix 3 all drude/transform/direct
fix 1 all drude/transform/inverse
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Transform the coordinates of Drude oscillators from real to reduced
2015-07-25 01:57:41 +08:00
and back for thermalizing the Drude oscillators as described in
2015-07-30 22:53:28 +08:00
< a class = "reference internal" href = "tutorial_drude.html#lamoureux" > < span > (Lamoureux)< / span > < / a > using a Nose-Hoover thermostat. This fix is
designed to be used with the < a class = "reference internal" href = "tutorial_drude.html" > < em > thermalized Drude oscillator model< / em > < / a > . Polarizable models in LAMMPS are
described in < a class = "reference internal" href = "Section_howto.html#howto-25" > < span > this Section< / span > < / a > .< / p >
< p > Drude oscillators are a pair of atoms representing a single
2015-07-25 01:57:41 +08:00
polarizable atom. Ideally, the mass of Drude particles would vanish
and their positions would be determined self-consistently by iterative
2015-07-30 22:53:28 +08:00
minimization of the energy, the cores’ positions being fixed. It is
2015-07-25 01:57:41 +08:00
however more efficient and it yields comparable results, if the Drude
oscillators (the motion of the Drude particle relative to the core)
are thermalized at a low temperature. In that case, the Drude
2015-07-30 22:53:28 +08:00
particles need a small mass.< / p >
< p > The thermostats act on the reduced degrees of freedom, which are
2015-07-25 01:57:41 +08:00
defined by the following equations. Note that in these equations
upper case denotes atomic or center of mass values and lower case
denotes Drude particle or dipole values. Primes denote the transformed
2015-07-30 22:53:28 +08:00
(reduced) values, while bare letters denote the original values.< / p >
< p > Masses: begin{equation} M’ = M + m end{equation}
begin{equation} m’ = frac {M, m } {M’ } end{equation}
Positions: begin{equation} X’ = frac {M, X + m, x} {M’ }
end{equation} begin{equation} x’ = x - X end{equation}
Velocities: begin{equation} V’ = frac {M, V + m, v} {M’ }
end{equation} begin{equation} v’ = v - V end{equation}
Forces: begin{equation} F’ = F + f end{equation}
begin{equation} f’ = frac { M, f - m, F} {M’ }
end{equation}< / p >
< p > This transform conserves the total kinetic energy
begin{equation} frac 1 2 , (M, V^2+ m, v^2)
= frac 1 2 , (M’ , V’ ^2+ m’ , v’ ^2) end{equation}
2015-07-25 01:57:41 +08:00
and the virial defined with absolute positions
2015-07-30 22:53:28 +08:00
begin{equation} X, F + x, f = X’ , F’ + x’ , f’ end{equation}< / p >
< hr class = "docutils" / >
< p > This fix requires each atom know whether it is a Drude particle or
not. You must therefore use the < a class = "reference internal" href = "fix_drude.html" > < em > fix drude< / em > < / a > command to
specify the Drude status of each atom type.< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > only the Drude core atoms need to be in the group
2015-07-25 01:57:41 +08:00
specified for this fix. A Drude electron will be transformed together
with its cores even if it is not itself in the group. It is safe to
include Drude electrons or non-polarizable atoms in the group. The
2015-07-30 22:53:28 +08:00
non-polarizable atoms will simply not be transformed.< / p >
< / div >
< hr class = "docutils" / >
< p > This fix does NOT perform time integration. It only transform masses,
2015-07-25 01:57:41 +08:00
coordinates, velocities and forces. Thus you must use separate time
2015-07-30 22:53:28 +08:00
integration fixes, like < a class = "reference internal" href = "fix_nve.html" > < em > fix nve< / em > < / a > or < a class = "reference internal" href = "fix_nh.html" > < em > fix npt< / em > < / a > to actually update the velocities and positions of
2015-07-25 01:57:41 +08:00
atoms. In order to thermalize the reduced degrees of freedom at
different temperatures, two Nose-Hoover thermostats must be defined,
2015-07-30 22:53:28 +08:00
acting on two distinct groups.< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > The < em > fix drude/transform/direct< / em > command must appear
before any Nose-Hoover thermostating fixes. The < em > fix
drude/transform/inverse< / em > command must appear after any Nose-Hoover
thermostating fixes.< / p >
< / div >
< p > Example:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix fDIRECT all drude/transform/direct
2015-07-25 01:57:41 +08:00
fix fNVT gCORES nvt temp 300.0 300.0 100.0
fix fNVT gDRUDES nvt temp 1.0 1.0 100.0
2015-07-28 02:05:31 +08:00
fix fINVERSE all drude/transform/inverse
compute TDRUDE all temp/drude
2015-07-30 22:53:28 +08:00
thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
< / pre > < / div >
< / div >
< p > In this example, < em > gCORES< / em > is the group of the atom cores and < em > gDRUDES< / em >
2015-07-25 01:57:41 +08:00
is the group of the Drude particles (electrons). The centers of mass
of the Drude oscillators will be thermostated at 300.0 and the
2015-07-28 02:05:31 +08:00
internal degrees of freedom will be thermostated at 1.0. The
temperatures of cores and Drude particles, in center-of-mass and
2015-07-30 22:53:28 +08:00
relatice coordinates, are calculated using < a class = "reference internal" href = "compute_temp_drude.html" > < em > compute temp/drude< / em > < / a > < / p >
< p > In addition, if you want to use a barostat to simulate a system at
constant pressure, only one of the Nose-Hoover fixes must be < em > npt< / em > ,
the other one should be < em > nvt< / em > . You must add a < em > compute temp/com< / em > and a
< em > fix_modify< / em > command so that the temperature of the < em > npt< / em > fix be just
2015-07-25 01:57:41 +08:00
that of its group but the pressure be the overall pressure
2015-07-30 22:53:28 +08:00
< em > thermo_press< / em > .< / p >
< p > Example:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute cTEMP_CORE gCORES temp/com
2015-07-25 01:57:41 +08:00
fix fDIRECT all drude/transform/direct
fix fNPT gCORES npt temp 298.0 298.0 100.0 iso 1.0 1.0 500.0
fix_modify fNPT temp cTEMP_CORE press thermo_press
fix fNVT gDRUDES nvt temp 5.0 5.0 100.0
2015-07-30 22:53:28 +08:00
fix fINVERSE all drude/transform/inverse
< / pre > < / div >
< / div >
< p > In this example, < em > gCORES< / em > is the group of the atom cores and < em > gDRUDES< / em >
2015-07-25 01:57:41 +08:00
is the group of the Drude particles. The centers of mass of the Drude
oscillators will be thermostated at 298.0 and the internal degrees of
freedom will be thermostated at 5.0. The whole system will be
2015-07-30 22:53:28 +08:00
barostated at 1.0.< / p >
< p > In order to avoid the flying ice cube problem (irreversible transfer
2015-07-25 01:57:41 +08:00
of linear momentum to the center of mass of the system), you may need
2015-07-30 22:53:28 +08:00
to add a < em > fix momentum< / em > command like such as< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix fMOMENTUM all momentum 100 linear 1 1 1
< / pre > < / div >
< / div >
< / div >
< hr class = "docutils" / >
< div class = "section" id = "restart-fix-modify-output-run-start-stop-minimize-info" >
< h2 > Restart, fix_modify, output, run start/stop, minimize info< a class = "headerlink" href = "#restart-fix-modify-output-run-start-stop-minimize-info" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > No information about this fix is written to < a class = "reference internal" href = "restart.html" > < em > binary restart files< / em > < / a > .< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< blockquote >
< div > none< / div > < / blockquote >
< / 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 = "fix_drude.html" > < em > fix drude< / em > < / a > ,
< a class = "reference internal" href = "fix_langevin_drude.html" > < em > fix langevin/drude< / em > < / a > ,
< a class = "reference internal" href = "compute_temp_drude.html" > < em > compute temp/drude< / em > < / a > ,
< a class = "reference internal" href = "pair_thole.html" > < em > pair_style thole< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
< hr class = "docutils" / >
< p id = "lamoureux" > < strong > (Lamoureux)< / strong > Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003).< / p >
< / div >
< / div >
< / div >
< / div >
< footer >
< hr / >
< div role = "contentinfo" >
< p >
© Copyright .
< / 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:'15 May 2015 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 >