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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li>compute temp/deform command</li>
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<div class="section" id="compute-temp-deform-command">
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<span id="index-0"></span><h1>compute temp/deform command<a class="headerlink" href="#compute-temp-deform-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>compute ID group-ID temp/deform
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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="compute.html"><em>compute</em></a> command</li>
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<li>temp/deform = style name of this compute command</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<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>compute myTemp all temp/deform
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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>Define a computation that calculates the temperature of a group of
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atoms, after subtracting out a streaming velocity induced by the
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simulation box changing size and/or shape, for example in a
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non-equilibrium MD (NEMD) simulation. The size/shape change is
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induced by use of the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command. A compute
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of this style is created by the <a class="reference internal" href="fix_nvt_sllod.html"><em>fix nvt/sllod</em></a>
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command to compute the thermal temperature of atoms for thermostatting
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purposes. A compute of this style can also be used by any command
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that computes a temperature, e.g. <a class="reference internal" href="thermo_modify.html"><em>thermo_modify</em></a>,
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<a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix npt</em></a>, etc.</p>
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<p>The deformation fix changes the box size and/or shape over time, so
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each atom in the simulation box can be thought of as having a
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“streaming” velocity. For example, if the box is being sheared in x,
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relative to y, then atoms at the bottom of the box (low y) have a
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small x velocity, while atoms at the top of the box (hi y) have a
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large x velocity. This position-dependent streaming velocity is
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subtracted from each atom’s actual velocity to yield a thermal
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velocity which is used to compute the 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"><a class="reference internal" href="fix_deform.html"><em>Fix deform</em></a> has an option for remapping either
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atom coordinates or velocities to the changing simulation box. When
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using this compute in conjunction with a deforming box, fix deform
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should NOT remap atom positions, but rather should let atoms respond
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to the changing box by adjusting their own velocities (or let <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> remap the atom velocities, see it’s remap
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option). If fix deform does remap atom positions, then they appear to
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move with the box but their velocity is not changed, and thus they do
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NOT have the streaming velocity assumed by this compute. LAMMPS will
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warn you if fix deform is defined and its remap setting is not
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consistent with this compute.</p>
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</div>
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<p>After the streaming velocity has been subtracted from each atom, the
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temperature is calculated by the formula KE = dim/2 N k T, where KE =
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total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2
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or 3 = dimensionality of the simulation, N = number of atoms in the
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group, k = Boltzmann constant, and T = temperature. Note that v in
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the kinetic energy formula is the atom’s thermal velocity.</p>
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<p>A kinetic energy tensor, stored as a 6-element vector, is also
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calculated by this compute for use in the computation of a pressure
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tensor. The formula for the components of the tensor is the same as
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the above formula, except that v^2 is replaced by vx*vy for the xy
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component, etc. The 6 components of the vector are ordered xx, yy,
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zz, xy, xz, yz.</p>
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<p>The number of atoms contributing to the temperature is assumed to be
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constant for the duration of the run; use the <em>dynamic</em> option of the
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<a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command if this is not the case.</p>
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<p>The removal of the box deformation velocity component by this fix is
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essentially computing the temperature after a “bias” has been removed
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from the velocity of the atoms. If this compute is used with a fix
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command that performs thermostatting then this bias will be subtracted
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from each atom, thermostatting of the remaining thermal velocity will
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be performed, and the bias will be added back in. Thermostatting
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fixes that work in this way include <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_temp_berendsen.html"><em>fix temp/berendsen</em></a>, and <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>.</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 temperature calculated by this compute is only accurate if
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the atoms are indeed moving with a stream velocity profile that
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matches the box deformation. If not, then the compute will subtract
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off an incorrect stream velocity, yielding a bogus thermal
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temperature. You should NOT assume that your atoms are streaming at
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the same rate the box is deforming. Rather, you should monitor their
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velocity profile, e.g. via the <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>
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command. And you can compare the results of this compute to <a class="reference internal" href="compute_temp_profile.html"><em>compute temp/profile</em></a>, which actually calculates the
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stream profile before subtracting it. If the two computes do not give
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roughly the same temperature, then your atoms are not streaming
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consistent with the box deformation. See the <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a> command for more details on ways to get atoms
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to stream consistently with the box deformation.</p>
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</div>
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<p>This compute subtracts out degrees-of-freedom due to fixes that
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constrain molecular motion, such as <a class="reference internal" href="fix_shake.html"><em>fix shake</em></a> and
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<a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a>. This means the temperature of groups of
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atoms that include these constraints will be computed correctly. If
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needed, the subtracted degrees-of-freedom can be altered using the
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<em>extra</em> option of the <a class="reference internal" href="compute_modify.html"><em>compute_modify</em></a> command.</p>
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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.</p>
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<p><strong>Output info:</strong></p>
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<p>This compute calculates a global scalar (the temperature) and a global
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vector of length 6 (KE tensor), which can be accessed by indices 1-6.
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These values can be used by any command that uses global scalar or
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vector values from a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>this section</span></a> for an overview of LAMMPS output
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options.</p>
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<p>The scalar value calculated by this compute is “intensive”. The
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vector values are “extensive”.</p>
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<p>The scalar value will be in temperature <a class="reference internal" href="units.html"><em>units</em></a>. The
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vector values will be in energy <a class="reference internal" href="units.html"><em>units</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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<blockquote>
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<div>none</div></blockquote>
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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="compute_temp_ramp.html"><em>compute temp/ramp</em></a>, <a class="reference internal" href="compute_temp_profile.html"><em>compute temp/profile</em></a>, <a class="reference internal" href="fix_deform.html"><em>fix deform</em></a>,
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<a class="reference internal" href="fix_nvt_sllod.html"><em>fix nvt/sllod</em></a></p>
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<p><strong>Default:</strong> none</p>
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