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<div class="section" id="compute-temp-profile-command">
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<span id="index-0"></span><h1>compute temp/profile command<a class="headerlink" href="#compute-temp-profile-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/profile xflag yflag zflag binstyle args
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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/profile = style name of this compute command</li>
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<li>xflag,yflag,zflag = 0/1 for whether to exclude/include this dimension</li>
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<li>binstyle = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>yz</em> or <em>xz</em> or <em>xyz</em></li>
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</ul>
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<pre class="literal-block">
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<em>x</em> arg = Nx
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<em>y</em> arg = Ny
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<em>z</em> arg = Nz
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<em>xy</em> args = Nx Ny
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<em>yz</em> args = Ny Nz
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<em>xz</em> args = Nx Nz
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<em>xyz</em> args = Nx Ny Nz
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Nx,Ny,Nz = number of velocity bins in x,y,z dimensions
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</pre>
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<ul class="simple">
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>out</em></li>
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</ul>
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<pre class="literal-block">
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<em>out</em> value = <em>tensor</em> or <em>bin</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>compute myTemp flow temp/profile 1 1 1 x 10
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compute myTemp flow temp/profile 1 1 1 x 10 out bin
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compute myTemp flow temp/profile 0 1 1 xyz 20 20 20
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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 spatially-averaged center-of-mass
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velocity field, before computing the kinetic energy. This can be
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useful for thermostatting a collection of atoms undergoing a complex
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flow, e.g. via a profile-unbiased thermostat (PUT) as described in
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<a class="reference internal" href="fix_nvt_sllod.html#evans"><span>(Evans)</span></a>. A compute of this style can 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 <em>xflag</em>, <em>yflag</em>, <em>zflag</em> settings determine which components of
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average velocity are subtracted out.</p>
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<p>The <em>binstyle</em> setting and its <em>Nx</em>, <em>Ny</em>, <em>Nz</em> arguments determine
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how bins are setup to perform spatial averaging. “Bins” can be 1d
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slabs, 2d pencils, or 3d bricks depending on which <em>binstyle</em> is used.
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The simulation box is partitioned conceptually into <em>Nx</em> by <em>Ny</em> by
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<em>Nz</em> bins. Depending on the <em>binstyle</em>, you may only specify one or
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two of these values; the others are effectively set to 1 (no binning
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in that dimension). For non-orthogonal (triclinic) simulation boxes,
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the bins are “tilted” slabs or pencils or bricks that are parallel to
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the tilted faces of the box. See the <a class="reference internal" href="region.html"><em>region prism</em></a>
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command for a discussion of the geometry of tilted boxes in LAMMPS.</p>
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<p>When a temperature is computed, the center-of-mass velocity for the
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set of atoms that are both in the compute group and in the same
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spatial bin is calculated. This bias velocity is then subtracted from
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the velocities of individual atoms in the bin to yield a thermal
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velocity for each atom. Note that if there is only one atom in the
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bin, its thermal velocity will thus be 0.0.</p>
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<p>After the spatially-averaged velocity field has been subtracted from
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each atom, the temperature is calculated by the formula KE = (dim/2 N
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- dim*Nx*Ny*Nz) k T, where KE = total kinetic energy of the group of
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atoms (sum of 1/2 m v^2), dim = 2 or 3 = dimensionality of the
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simulation, N = number of atoms in the group, k = Boltzmann constant,
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and T = temperature. The dim*Nx*Ny*Nz term are degrees of freedom
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subtracted to adjust for the removal of the center-of-mass velocity in
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each of Nx*Ny*Nz bins, as discussed in the <a class="reference internal" href="fix_nvt_sllod.html#evans"><span>(Evans)</span></a> paper.</p>
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<p>If the <em>out</em> keyword is used with a <em>tensor</em> value, which is the
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default, a kinetic energy tensor, stored as a 6-element vector, is
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also calculated by this compute for use in the computation of a
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pressure tensor. The formula for the components of the tensor is the
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same as the above formula, except that v^2 is replaced by vx*vy for
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the xy component, etc. The 6 components of the vector are ordered xx,
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yy, zz, xy, xz, yz.</p>
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<p>If the <em>out</em> keyword is used with a <em>bin</em> value, the count of atoms
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and computed temperature for each bin are stored for output, as an
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array of values, as described below. The temperature of each bin is
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calculated as described above, where the bias velocity is subtracted
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and only the remaining thermal velocity of atoms in the bin
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contributes to the temperature. See the note below for how the
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temperature is normalized by the degrees-of-freedom of atoms in the
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bin.</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 spatially-averaged velocity field 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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<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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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">When using the <em>out</em> keyword with a value of <em>bin</em>, the
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calculated temperature for each bin does not include the
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degrees-of-freedom adjustment described in the preceeding paragraph,
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for fixes that constrain molecular motion. It does include the
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adjustment due to the <em>extra</em> option, which is applied to each bin.</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. Using this compute in conjunction with a
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thermostatting fix, as explained there, will effectively implement a
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profile-unbiased thermostat (PUT), as described in <a class="reference internal" href="fix_nvt_sllod.html#evans"><span>(Evans)</span></a>.</p>
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<p><strong>Output info:</strong></p>
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<p>This compute calculates a global scalar (the temperature). Depending
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on the setting of the <em>out</em> keyword, it also calculates a global
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vector or array. For <em>out</em> = <em>tensor</em>, it calculates a vector of
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length 6 (KE tensor), which can be accessed by indices 1-6. For <em>out</em>
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= <em>bin</em> it calculates a global array which has 2 columns and N rows,
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where N is the number of bins. The first column contains the number
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of atoms in that bin. The second contains the temperature of that
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bin, calculated as described above. The ordering of rows in the array
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is as follows. Bins in x vary fastest, then y, then z. Thus for a
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10x10x10 3d array of bins, there will be 1000 rows. The bin with
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indices ix,iy,iz = 2,3,4 would map to row M = (iz-1)*10*10 + (iy-1)*10
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+ ix = 322, where the rows are numbered from 1 to 1000 and the bin
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indices are numbered from 1 to 10 in each dimension.</p>
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<p>These values can be used by any command that uses global scalar or
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vector or array 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”. The array values are “intensive”.</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>. The first column
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of array values are counts; the values in the second column will be in
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temperature <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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<p>You should not use too large a velocity-binning grid, especially in
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3d. In the current implementation, the binned velocity averages are
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summed across all processors, so this will be inefficient if the grid
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is too large, and the operation is performed every timestep, as it
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will be for most thermostats.</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="compute_temp.html"><em>compute temp</em></a>, <a class="reference internal" href="compute_temp_ramp.html"><em>compute temp/ramp</em></a>, <a class="reference internal" href="compute_temp_deform.html"><em>compute temp/deform</em></a>, <a class="reference internal" href="compute_pressure.html"><em>compute pressure</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 option default is out = tensor.</p>
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<hr class="docutils" />
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<p id="evans"><strong>(Evans)</strong> Evans and Morriss, Phys Rev Lett, 56, 2172-2175 (1986).</p>
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