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<div class="section" id="fix-temp-berendsen-command">
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<span id="index-0"></span><h1>fix temp/berendsen command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">berendsen</span> <span class="n">Tstart</span> <span class="n">Tstop</span> <span class="n">Tdamp</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
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<li>temp/berendsen = style name of this fix command</li>
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<li>Tstart,Tstop = desired temperature at start/end of run</li>
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</ul>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Tstart</span> <span class="n">can</span> <span class="n">be</span> <span class="n">a</span> <span class="n">variable</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>Tdamp = temperature damping parameter (time units)</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">berendsen</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span>
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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<p>Reset the temperature of a group of atoms by using a Berendsen
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thermostat <a class="reference internal" href="#berendsen"><span class="std std-ref">(Berendsen)</span></a>, which rescales their velocities
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every timestep.</p>
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<p>The thermostat is applied to only the translational degrees of freedom
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for the particles, which is an important consideration for finite-size
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particles which have rotational degrees of freedom are being
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thermostatted with this fix. The translational degrees of freedom can
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also have a bias velocity removed from them before thermostatting
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takes place; see the description below.</p>
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<p>The desired temperature at each timestep is a ramped value during the
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run from <em>Tstart</em> to <em>Tstop</em>. The <em>Tdamp</em> parameter is specified in
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time units and determines how rapidly the temperature is relaxed. For
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example, a value of 100.0 means to relax the temperature in a timespan
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of (roughly) 100 time units (tau or fmsec or psec - see the
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<a class="reference internal" href="units.html"><span class="doc">units</span></a> command).</p>
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<p><em>Tstart</em> can be specified as an equal-style <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.
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In this case, the <em>Tstop</em> setting is ignored. If the value is a
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variable, it should be specified as v_name, where name is the variable
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name. In this case, the variable will be evaluated each timestep, and
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its value used to determine the target temperature.</p>
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<p>Equal-style variables can specify formulas with various mathematical
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functions, and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent temperature.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Unlike the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> command which performs
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Nose/Hoover thermostatting AND time integration, this fix does NOT
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perform time integration. It only modifies velocities to effect
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thermostatting. Thus you must use a separate time integration fix,
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like <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> to actually update the positions of atoms
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using the modified velocities. Likewise, this fix should not normally
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be used on atoms that also have their temperature controlled by
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another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> commands.</p>
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</div>
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<p>See <a class="reference internal" href="Section_howto.html#howto-16"><span class="std std-ref">this howto section</span></a> of the manual for
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a discussion of different ways to compute temperature and perform
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thermostatting.</p>
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<p>This fix computes a temperature each timestep. To do this, the fix
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creates its own compute of style “temp”, as if this command had been
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issued:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
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</pre></div>
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</div>
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<p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details. Note
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that the ID of the new compute is the fix-ID + underscore + “temp”,
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and the group for the new compute is the same as the fix group.</p>
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<p>Note that this is NOT the compute used by thermodynamic output (see
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the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command) with ID = <em>thermo_temp</em>.
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This means you can change the attributes of this fix’s temperature
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(e.g. its degrees-of-freedom) via the
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<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command or print this temperature
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during thermodynamic output via the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command using the appropriate compute-ID.
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It also means that changing attributes of <em>thermo_temp</em> will have no
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effect on this fix.</p>
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<p>Like other fixes that perform thermostatting, this fix can be used
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with <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> that calculate a temperature
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after removing a “bias” from the atom velocities. E.g. removing the
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center-of-mass velocity from a group of atoms or only calculating
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temperature on the x-component of velocity or only calculating
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temperature for atoms in a geometric region. This is not done by
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default, but only if the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> command is used
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to assign a temperature compute to this fix that includes such a bias
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term. See the doc pages for individual <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> to determine which ones include a bias. In
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this case, the thermostat works in the following manner: the current
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temperature is calculated taking the bias into account, bias is
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removed from each atom, thermostatting is performed on the remaining
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thermal degrees of freedom, and the bias is added back in.</p>
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</div>
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<hr class="docutils" />
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<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
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<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
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fix. You can use it to assign a temperature <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>
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you have defined to this fix which will be used in its thermostatting
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procedure, as described above. For consistency, the group used by
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this fix and by the compute should be the same.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
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fix to add the energy change implied by a velocity rescaling to the
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system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
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<p>This fix computes a global scalar which can be accessed by various
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<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar is the
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cummulative energy change due to this fix. The scalar value
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calculated by this fix is “extensive”.</p>
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<p>This fix can ramp its target temperature over multiple runs, using the
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<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. See the
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<a class="reference internal" href="run.html"><span class="doc">run</span></a> command for details of how to do this.</p>
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<p>This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>This fix can be used with dynamic groups as defined by the
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<a class="reference internal" href="group.html"><span class="doc">group</span></a> command. Likewise it can be used with groups to
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which atoms are added or deleted over time, e.g. a deposition
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simulation. However, the conservation properties of the thermostat
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and barostat are defined for systems with a static set of atoms. You
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may observe odd behavior if the atoms in a group vary dramatically
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over time or the atom count becomes very small.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
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<a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>, <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a>,
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<a class="reference internal" href="fix_press_berendsen.html"><span class="doc">fix press/berendsen</span></a></p>
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<p><strong>Default:</strong> none</p>
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<hr class="docutils" />
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<p id="berendsen"><strong>(Berendsen)</strong> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
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Phys, 81, 3684 (1984).</p>
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