2008-03-12 01:15:19 +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 > fix temp/berendsen command — LAMMPS documentation< / title >
2015-07-30 22:53:28 +08:00
2008-03-12 01:15:19 +08:00
2015-07-30 22:53:28 +08:00
2008-03-12 01:15:19 +08:00
2015-07-30 22:53:28 +08:00
2008-03-12 01:15:19 +08:00
2015-07-30 22:53:28 +08:00
2008-03-12 01:15:19 +08:00
2015-07-30 22:53:28 +08:00
2008-03-12 01:15:19 +08:00
2015-07-30 22:53:28 +08:00
< link rel = "stylesheet" href = "_static/css/theme.css" type = "text/css" / >
2012-05-24 21:31:42 +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" / >
2012-05-24 21:31:42 +08:00
2015-07-30 22:53:28 +08:00
2015-12-21 23:20:41 +08:00
< link rel = "top" title = "LAMMPS documentation" href = "index.html" / >
2012-05-24 21:31:42 +08:00
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 > fix temp/berendsen 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-temp-berendsen-command" >
< span id = "index-0" > < / span > < h1 > fix temp/berendsen command< a class = "headerlink" href = "#fix-temp-berendsen-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< / div >
< div class = "section" id = "fix-temp-berendsen-cuda-command" >
< h1 > fix temp/berendsen/cuda command< a class = "headerlink" href = "#fix-temp-berendsen-cuda-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 temp/berendsen Tstart Tstop Tdamp
< / 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 > temp/berendsen = style name of this fix command< / li >
< li > Tstart,Tstop = desired temperature at start/end of run< / li >
< / ul >
< div class = "highlight-python" > < div class = "highlight" > < pre > Tstart can be a variable (see below)
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > Tdamp = temperature damping parameter (time units)< / 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 1 all temp/berendsen 300.0 300.0 100.0
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Reset the temperature of a group of atoms by using a Berendsen
thermostat < a class = "reference internal" href = "#berendsen" > < span > (Berendsen)< / span > < / a > , which rescales their velocities
every timestep.< / p >
< p > The thermostat is applied to only the translational degrees of freedom
2013-02-01 08:24:05 +08:00
for the particles, which is an important consideration for finite-size
particles which have rotational degrees of freedom are being
thermostatted with this fix. The translational degrees of freedom can
also have a bias velocity removed from them before thermostatting
2015-07-30 22:53:28 +08:00
takes place; see the description below.< / p >
< p > The desired temperature at each timestep is a ramped value during the
run from < em > Tstart< / em > to < em > Tstop< / em > . The < em > Tdamp< / em > parameter is specified in
2008-03-12 01:15:19 +08:00
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
2015-07-30 22:53:28 +08:00
< a class = "reference internal" href = "units.html" > < em > units< / em > < / a > command).< / p >
< p > < em > Tstart< / em > can be specified as an equal-style < a class = "reference internal" href = "variable.html" > < em > variable< / em > < / a > .
In this case, the < em > Tstop< / em > setting is ignored. If the value is a
2012-05-24 21:31:42 +08:00
variable, it should be specified as v_name, where name is the variable
name. In this case, the variable will be evaluated each timestep, and
2015-07-30 22:53:28 +08:00
its value used to determine the target temperature.< / p >
< p > Equal-style variables can specify formulas with various mathematical
functions, and include < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a > command
2012-05-24 21:31:42 +08:00
keywords for the simulation box parameters and timestep and elapsed
2015-07-30 22:53:28 +08:00
time. Thus it is easy to specify a time-dependent temperature.< / p >
2015-12-11 01:23:56 +08:00
< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > Unlike the < a class = "reference internal" href = "fix_nh.html" > < em > fix nvt< / em > < / a > command which performs
Nose/Hoover thermostatting AND time integration, this fix does NOT
perform time integration. It only modifies velocities to effect
thermostatting. Thus you must use a separate time integration fix,
like < a class = "reference internal" href = "fix_nve.html" > < em > fix nve< / em > < / a > to actually update the positions of atoms
using the modified velocities. Likewise, this fix should not normally
be used on atoms that also have their temperature controlled by
another fix - e.g. by < a class = "reference internal" href = "fix_nh.html" > < em > fix nvt< / em > < / a > or < a class = "reference internal" href = "fix_langevin.html" > < em > fix langevin< / em > < / a > commands.< / p >
2015-07-30 22:53:28 +08:00
< / div >
< 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 > This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style “ temp” , as if this command had been
issued:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > compute fix-ID_temp group-ID temp
< / pre > < / div >
< / div >
< p > See the < a class = "reference internal" href = "compute_temp.html" > < em > compute temp< / em > < / a > command for details. Note
that the ID of the new compute is the fix-ID + underscore + “ temp” ,
and the group for the new compute is the same as the fix group.< / p >
< p > Note that this is NOT the compute used by thermodynamic output (see
the < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a > command) with ID = < em > thermo_temp< / em > .
This means you can change the attributes of this fix’ s temperature
2008-03-12 01:15:19 +08:00
(e.g. its degrees-of-freedom) via the
2015-07-30 22:53:28 +08:00
< a class = "reference internal" href = "compute_modify.html" > < em > compute_modify< / em > < / a > command or print this temperature
during thermodynamic output via the < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style custom< / em > < / a > command using the appropriate compute-ID.
It also means that changing attributes of < em > thermo_temp< / em > will have no
effect on this fix.< / p >
< p > Like other fixes that perform thermostatting, this fix can be used
with < a class = "reference internal" href = "compute.html" > < em > compute commands< / em > < / a > that calculate a temperature
after removing a “ bias” from the atom velocities. E.g. removing the
2008-03-12 01:15:19 +08:00
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
2015-07-30 22:53:28 +08:00
default, but only if the < a class = "reference internal" href = "fix_modify.html" > < em > fix_modify< / em > < / a > command is used
2008-03-12 01:15:19 +08:00
to assign a temperature compute to this fix that includes such a bias
2015-07-30 22:53:28 +08:00
term. See the doc pages for individual < a class = "reference internal" href = "compute.html" > < em > compute commands< / em > < / a > to determine which ones include a bias. In
2008-03-12 01:15:19 +08:00
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
2015-07-30 22:53:28 +08:00
thermal degrees of freedom, and the bias is added back in.< / p >
< hr class = "docutils" / >
< p > Styles with a < em > cuda< / em > suffix are functionally the same as the
2011-06-09 05:46:03 +08:00
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in
2015-07-30 22:53:28 +08:00
< a class = "reference internal" href = "Section_accelerate.html" > < em > Section_accelerate< / em > < / a > of the manual. The
2011-12-14 04:35:35 +08:00
accelerated styles take the same arguments and should produce the same
2015-07-30 22:53:28 +08:00
results, except for round-off and precision issues.< / p >
< p > These accelerated styles are part of the USER-CUDA package. They are
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 >
< 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 >
< / 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 >
< p > The < a class = "reference internal" href = "fix_modify.html" > < em > fix_modify< / em > < / a > < em > temp< / em > option is supported by this
fix. You can use it to assign a temperature < a class = "reference internal" href = "compute.html" > < em > compute< / em > < / a >
2008-03-12 01:15:19 +08:00
you have defined to this fix which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
2015-07-30 22:53:28 +08:00
this fix and by the compute should be the same.< / p >
< p > The < a class = "reference internal" href = "fix_modify.html" > < em > fix_modify< / em > < / a > < em > energy< / em > option is supported by this
2010-09-11 01:31:34 +08:00
fix to add the energy change implied by a velocity rescaling to the
2015-07-30 22:53:28 +08:00
system’ s potential energy as part of < a class = "reference internal" href = "thermo_style.html" > < em > thermodynamic output< / em > < / a > .< / p >
< p > This fix computes a global scalar which can be accessed by various
< a class = "reference internal" href = "Section_howto.html#howto-15" > < span > output commands< / span > < / a > . The scalar is the
2010-09-11 01:31:34 +08:00
cummulative energy change due to this fix. The scalar value
2015-07-30 22:53:28 +08:00
calculated by this fix is “ extensive” .< / p >
< p > This fix can ramp its target temperature over multiple runs, using the
< em > start< / em > and < em > stop< / em > keywords of the < a class = "reference internal" href = "run.html" > < em > run< / em > < / a > command. See the
< a class = "reference internal" href = "run.html" > < em > run< / em > < / a > command for details of how to do this.< / p >
< p > This fix is not invoked during < a class = "reference internal" href = "minimize.html" > < em > energy minimization< / em > < / a > .< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > This fix can be used with dynamic groups as defined by the
< a class = "reference internal" href = "group.html" > < em > group< / em > < / a > command. Likewise it can be used with groups to
2014-11-18 02:23:26 +08:00
which atoms are added or deleted over time, e.g. a deposition
simulation. However, the conservation properties of the thermostat
and barostat are defined for systems with a static set of atoms. You
may observe odd behavior if the atoms in a group vary dramatically
2015-07-30 22:53:28 +08:00
over time or the atom count becomes very small.< / 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 = "fix_nve.html" > < em > fix nve< / em > < / a > , < a class = "reference internal" href = "fix_nh.html" > < em > fix nvt< / em > < / a > , < a class = "reference internal" href = "fix_temp_rescale.html" > < em > fix temp/rescale< / em > < / a > , < a class = "reference internal" href = "fix_langevin.html" > < em > fix langevin< / em > < / a > ,
< a class = "reference internal" href = "fix_modify.html" > < em > fix_modify< / em > < / a > , < a class = "reference internal" href = "compute_temp.html" > < em > compute temp< / em > < / a > ,
< a class = "reference internal" href = "fix_press_berendsen.html" > < em > fix press/berendsen< / em > < / a > < / p >
< p > < strong > Default:< / strong > none< / p >
< hr class = "docutils" / >
< p id = "berendsen" > < strong > (Berendsen)< / strong > Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
Phys, 81, 3684 (1984).< / 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 >
