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<div class="section" id="fix-press-berendsen-command">
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<span id="index-0"></span><h1>fix press/berendsen command<a class="headerlink" href="#fix-press-berendsen-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID press/berendsen keyword value ...
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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"><em>fix</em></a> command</li>
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<li>press/berendsen = style name of this fix command</li>
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</ul>
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<pre class="literal-block">
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one or more keyword value pairs may be appended
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keyword = <em>iso</em> or <em>aniso</em> or <em>x</em> or <em>y</em> or <em>z</em> or <em>couple</em> or <em>dilate</em> or <em>modulus</em>
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<em>iso</em> or <em>aniso</em> values = Pstart Pstop Pdamp
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Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
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Pdamp = pressure damping parameter (time units)
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<em>x</em> or <em>y</em> or <em>z</em> values = Pstart Pstop Pdamp
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Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
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Pdamp = stress damping parameter (time units)
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<em>couple</em> = <em>none</em> or <em>xyz</em> or <em>xy</em> or <em>yz</em> or <em>xz</em>
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<em>modulus</em> value = bulk modulus of system (pressure units)
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<em>dilate</em> value = <em>all</em> or <em>partial</em>
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</pre>
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</div>
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<div class="section" id="examples">
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<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix 1 all press/berendsen iso 0.0 0.0 1000.0
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fix 2 all press/berendsen aniso 0.0 0.0 1000.0 dilate partial
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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<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Reset the pressure of the system by using a Berendsen barostat
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<a class="reference internal" href="fix_temp_berendsen.html#berendsen"><span>(Berendsen)</span></a>, which rescales the system volume and
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(optionally) the atoms coordinates within the simulation box every
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timestep.</p>
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<p>Regardless of what atoms are in the fix group, a global pressure is
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computed for all atoms. Similarly, when the size of the simulation
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box is changed, all atoms are re-scaled to new positions, unless the
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keyword <em>dilate</em> is specified with a value of <em>partial</em>, in which case
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only the atoms in the fix group are re-scaled. The latter can be
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useful for leaving the coordinates of atoms in a solid substrate
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unchanged and controlling the pressure of a surrounding fluid.</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"><em>fix npt</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>
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commands which perform Nose/Hoover barostatting AND time integration,
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this fix does NOT perform time integration. It only modifies the box
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size and atom coordinates to effect barostatting. Thus you must use a
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separate time integration fix, 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 nvt</em></a> to actually update the positions and velocities of
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atoms. This fix can be used in conjunction with thermostatting fixes
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to control the temperature, such as <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> or <a class="reference internal" href="fix_temp_berendsen.html"><em>fix temp/berendsen</em></a>.</p>
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</div>
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<p>See <a class="reference internal" href="Section_howto.html#howto-16"><span>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 and barostatting.</p>
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<hr class="docutils" />
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<p>The barostat is specified using one or more of the <em>iso</em>, <em>aniso</em>,
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<em>x</em>, <em>y</em>, <em>z</em>, and <em>couple</em> keywords. These keywords give you the
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ability to specify the 3 diagonal components of an external stress
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tensor, and to couple various of these components together so that the
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dimensions they represent are varied together during a
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constant-pressure simulation. Unlike the <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a> and
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<a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> commands, this fix cannot be used with triclinic
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(non-orthogonal) simulation boxes to control all 6 components of the
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general pressure tensor.</p>
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<p>The target pressures for each of the 3 diagonal components of the
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stress tensor can be specified independently via the <em>x</em>, <em>y</em>, <em>z</em>,
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keywords, which correspond to the 3 simulation box dimensions. For
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each component, the external pressure or tensor component at each
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timestep is a ramped value during the run from <em>Pstart</em> to <em>Pstop</em>.
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If a target pressure is specified for a component, then the
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corresponding box dimension will change during a simulation. For
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example, if the <em>y</em> keyword is used, the y-box length will change. A
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box dimension will not change if that component is not specified,
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although you have the option to change that dimension via the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command.</p>
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<p>For all barostat keywords, the <em>Pdamp</em> parameter determines the time
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scale on which pressure is relaxed. For example, a value of 1000.0
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means to relax the pressure in a timespan of (roughly) 1000 time units
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(tau or fmsec or psec - see the <a class="reference internal" href="units.html"><em>units</em></a> command).</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">The relaxation time is actually also a function of the bulk
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modulus of the system (inverse of isothermal compressibility). The
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bulk modulus has units of pressure and is the amount of pressure that
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would need to be applied (isotropically) to reduce the volume of the
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system by a factor of 2 (assuming the bulk modulus was a constant,
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independent of density, which it’s not). The bulk modulus can be set
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via the keyword <em>modulus</em>. The <em>Pdamp</em> parameter is effectively
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multiplied by the bulk modulus, so if the pressure is relaxing faster
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than expected or desired, increasing the bulk modulus has the same
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effect as increasing <em>Pdamp</em>. The converse is also true. LAMMPS does
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not attempt to guess a correct value of the bulk modulus; it just uses
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10.0 as a default value which gives reasonable relaxation for a
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Lennard-Jones liquid, but will be way off for other materials and way
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too small for solids. Thus you should experiment to find appropriate
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values of <em>Pdamp</em> and/or the <em>modulus</em> when using this fix.</p>
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</div>
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<hr class="docutils" />
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<p>The <em>couple</em> keyword allows two or three of the diagonal components of
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the pressure tensor to be “coupled” together. The value specified
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with the keyword determines which are coupled. For example, <em>xz</em>
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means the <em>Pxx</em> and <em>Pzz</em> components of the stress tensor are coupled.
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<em>Xyz</em> means all 3 diagonal components are coupled. Coupling means two
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things: the instantaneous stress will be computed as an average of the
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corresponding diagonal components, and the coupled box dimensions will
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be changed together in lockstep, meaning coupled dimensions will be
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dilated or contracted by the same percentage every timestep. The
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<em>Pstart</em>, <em>Pstop</em>, <em>Pdamp</em> parameters for any coupled dimensions must
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be identical. <em>Couple xyz</em> can be used for a 2d simulation; the <em>z</em>
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dimension is simply ignored.</p>
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<hr class="docutils" />
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<p>The <em>iso</em> and <em>aniso</em> keywords are simply shortcuts that are
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equivalent to specifying several other keywords together.</p>
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<p>The keyword <em>iso</em> means couple all 3 diagonal components together when
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pressure is computed (hydrostatic pressure), and dilate/contract the
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dimensions together. Using “iso Pstart Pstop Pdamp” is the same as
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specifying these 4 keywords:</p>
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<div class="highlight-python"><div class="highlight"><pre>x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple xyz
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</pre></div>
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</div>
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<p>The keyword <em>aniso</em> means <em>x</em>, <em>y</em>, and <em>z</em> dimensions are controlled
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independently using the <em>Pxx</em>, <em>Pyy</em>, and <em>Pzz</em> components of the
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stress tensor as the driving forces, and the specified scalar external
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pressure. Using “aniso Pstart Pstop Pdamp” is the same as specifying
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these 4 keywords:</p>
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<div class="highlight-python"><div class="highlight"><pre>x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple none
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</pre></div>
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</div>
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<hr class="docutils" />
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<p>This fix computes a temperature and pressure each timestep. To do
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this, the fix creates its own computes of style “temp” and “pressure”,
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as if these commands had been issued:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute fix-ID_temp group-ID temp
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compute fix-ID_press group-ID pressure fix-ID_temp
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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"><em>compute temp</em></a> and <a class="reference internal" href="compute_pressure.html"><em>compute pressure</em></a> commands for details. Note that the
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IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID
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+ underscore + “press”, and the group for the new computes is the same
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as the fix group.</p>
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<p>Note that these are NOT the computes used by thermodynamic output (see
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the <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command) with ID = <em>thermo_temp</em>
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and <em>thermo_press</em>. This means you can change the attributes of this
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fix’s temperature or pressure via the
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<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command or print this temperature
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or pressure 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.
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It also means that changing attributes of <em>thermo_temp</em> or
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<em>thermo_press</em> will have no effect on this fix.</p>
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</div>
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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<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>temp</em> and <em>press</em> options are
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supported by this fix. You can use them to assign a
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<a class="reference internal" href="compute.html"><em>compute</em></a> you have defined to this fix which will be used
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in its temperature and pressure calculations. If you do this, note
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that the kinetic energy derived from the compute temperature should be
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consistent with the virial term computed using all atoms for the
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pressure. LAMMPS will warn you if you choose to compute temperature
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on a subset of atoms.</p>
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<p>No global or per-atom quantities are stored by this fix for access by
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various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>.</p>
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<p>This fix can ramp its target pressure 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"><em>run</em></a> command. See the
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<a class="reference internal" href="run.html"><em>run</em></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"><em>energy minimization</em></a>.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>Any dimension being adjusted by this fix must be periodic.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>, <a class="reference internal" href="fix_temp_berendsen.html"><em>fix temp/berendsen</em></a>,
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<a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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<p>The keyword defaults are dilate = all, modulus = 10.0 in units of
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pressure for whatever <a class="reference internal" href="units.html"><em>units</em></a> are defined.</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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</div>
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