2010-09-02 03:53:20 +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" >
< title > compute temp/eff command — LAMMPS 15 May 2015 version documentation< / title >
2010-09-02 03:53:20 +08:00
2015-07-30 22:53:28 +08:00
2010-09-02 03:53:20 +08:00
2015-07-30 22:53:28 +08:00
2010-09-02 03:53:20 +08:00
2015-07-30 22:53:28 +08:00
2010-09-02 03:53:20 +08:00
2015-07-30 22:53:28 +08:00
2010-09-02 03:53:20 +08:00
2015-07-30 22:53:28 +08:00
< 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 > compute temp/eff 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 = "compute-temp-eff-command" >
< span id = "index-0" > < / span > < h1 > compute temp/eff command< a class = "headerlink" href = "#compute-temp-eff-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 > compute ID group-ID temp/eff
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a > command< / li >
< li > temp/eff = style name of this compute command< / 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 > compute 1 all temp/eff
compute myTemp mobile temp/eff
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Define a computation that calculates the temperature of a group of
nuclei and electrons in the < a class = "reference internal" href = "pair_eff.html" > < em > electron force field< / em > < / a >
2010-09-02 04:48:58 +08:00
model. A compute of this style can be used by commands that compute a
2015-07-30 22:53:28 +08:00
temperature, e.g. < a class = "reference internal" href = "thermo_modify.html" > < em > thermo_modify< / em > < / a > , < code class = "xref doc docutils literal" > < span class = "pre" > fix< / span > < span class = "pre" > npt/eff< / span > < / code > , etc.< / p >
< p > The temperature is calculated by the formula KE = dim/2 N k T, where
2010-09-02 03:53:20 +08:00
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2 for
nuclei and sum of 1/2 (m v^2 + 3/4 m s^2) for electrons, where s
includes the radial electron velocity contributions), dim = 2 or 3 =
dimensionality of the simulation, N = number of atoms (only total
2015-07-30 22:53:28 +08:00
number of nuclei in the eFF (see the < a class = "reference internal" href = "pair_style.html" > < em > pair_eff< / em > < / a >
2010-09-02 03:53:20 +08:00
command) in the group, k = Boltzmann constant, and T = temperature.
This expression is summed over all nuclear and electronic degrees of
freedom, essentially by setting the kinetic contribution to the heat
capacity to 3/2k (where only nuclei contribute). This subtlety is
valid for temperatures well below the Fermi temperature, which for
densities two to five times the density of liquid H2 ranges from
2015-07-30 22:53:28 +08:00
86,000 to 170,000 K.< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > For eFF models, in order to override the default
2010-09-02 03:53:20 +08:00
temperature reported by LAMMPS in the thermodynamic quantities
2015-07-30 22:53:28 +08:00
reported via the < a class = "reference internal" href = "thermo.html" > < em > thermo< / em > < / a > command, the user should apply a
< a class = "reference internal" href = "thermo_modify.html" > < em > thermo_modify< / em > < / a > command, as shown in the following
example:< / p >
< / div >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
< / pre > < / div >
< / div >
< p > A 6-component kinetic energy tensor is also calculated by this compute
2010-09-02 03:53:20 +08:00
for use in the computation of a pressure tensor. The formula for the
components of the tensor is the same as the above formula, except that
v^2 is replaced by vx * vy for the xy component, etc. For the eFF,
2015-07-30 22:53:28 +08:00
again, the radial electronic velocities are also considered.< / p >
< p > The number of atoms contributing to the temperature is assumed to be
constant for the duration of the run; use the < em > dynamic< / em > option of the
< a class = "reference internal" href = "compute_modify.html" > < em > compute_modify< / em > < / a > command if this is not the case.< / p >
< p > This compute subtracts out degrees-of-freedom due to fixes that
constrain molecular motion, such as < a class = "reference internal" href = "fix_shake.html" > < em > fix shake< / em > < / a > and
< a class = "reference internal" href = "fix_rigid.html" > < em > fix rigid< / em > < / a > . This means the temperature of groups of
2010-09-02 03:53:20 +08:00
atoms that include these constraints will be computed correctly. If
needed, the subtracted degrees-of-freedom can be altered using the
2015-07-30 22:53:28 +08:00
< em > extra< / em > option of the < a class = "reference internal" href = "compute_modify.html" > < em > compute_modify< / em > < / a > command.< / p >
< p > See < a class = "reference internal" href = "Section_howto.html#howto-16" > < span > this howto section< / span > < / a > of the manual for
2011-08-26 01:01:01 +08:00
a discussion of different ways to compute temperature and perform
2015-07-30 22:53:28 +08:00
thermostatting.< / p >
< p > < strong > Output info:< / strong > < / p >
< p > The scalar value calculated by this compute is “ intensive” , meaning it
2010-09-02 03:53:20 +08:00
is independent of the number of atoms in the simulation. The vector
2015-07-30 22:53:28 +08:00
values are “ extensive” , meaning they scale with the number of atoms in
the simulation.< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This compute is part of the USER-EFF package. It is only enabled if
LAMMPS was built with that package. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info.< / 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 = "compute_temp_partial.html" > < em > compute temp/partial< / em > < / a > , < a class = "reference internal" href = "compute_temp_region.html" > < em > compute temp/region< / em > < / a > , < a class = "reference internal" href = "compute_pressure.html" > < em > compute pressure< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / 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 >
