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<li>fix ave/atom command</li>
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<a href="http://lammps.sandia.gov">Website</a>
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<div itemprop="articleBody">
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<div class="section" id="fix-ave-atom-command">
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<span id="index-0"></span><h1>fix ave/atom command<a class="headerlink" href="#fix-ave-atom-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 ave/atom Nevery Nrepeat Nfreq value1 value2 ...
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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>ave/atom = style name of this fix command</li>
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<li>Nevery = use input values every this many timesteps</li>
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<li>Nrepeat = # of times to use input values for calculating averages</li>
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<li>Nfreq = calculate averages every this many timesteps
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one or more input values can be listed</li>
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<li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name</li>
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</ul>
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<div class="highlight-python"><div class="highlight"><pre>x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
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<HR>
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<H3>fix ave/atom command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID ave/atom Nevery Nrepeat Nfreq value1 value2 ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>ave/atom = style name of this fix command
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<LI>Nevery = use input values every this many timesteps
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<LI>Nrepeat = # of times to use input values for calculating averages
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|
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<LI>Nfreq = calculate averages every this many timesteps
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one or more input values can be listed
|
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|
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<LI>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name
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|
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<PRE> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
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c_ID = per-atom vector calculated by a compute with ID
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c_ID[I] = Ith column of per-atom array calculated by a compute with ID
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f_ID = per-atom vector calculated by a fix with ID
|
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f_ID[I] = Ith column of per-atom array calculated by a fix with ID
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v_name = per-atom vector calculated by an atom-style variable with name
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</pre></div>
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</div>
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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 ave/atom 1 100 100 vx vy vz
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fix 1 all ave/atom 10 20 1000 c_my_stress[1]
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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>Use one or more per-atom vectors as inputs every few timesteps, and
|
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v_name = per-atom vector calculated by an atom-style variable with name
|
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</PRE>
|
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|
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</UL>
|
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<P><B>Examples:</B>
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</P>
|
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<PRE>fix 1 all ave/atom 1 100 100 vx vy vz
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fix 1 all ave/atom 10 20 1000 c_my_stress[1]
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Use one or more per-atom vectors as inputs every few timesteps, and
|
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average them atom by atom over longer timescales. The resulting
|
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per-atom averages can be used by other <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a> such as the <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a> or <a class="reference internal" href="dump.html"><em>dump custom</em></a> commands.</p>
|
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<p>The group specified with the command means only atoms within the group
|
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per-atom averages can be used by other <A HREF = "Section_howto.html#howto_15">output
|
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commands</A> such as the <A HREF = "fix_ave_spatial.html">fix
|
||||
ave/spatial</A> or <A HREF = "dump.html">dump custom</A> commands.
|
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</P>
|
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<P>The group specified with the command means only atoms within the group
|
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have their averages computed. Results are set to 0.0 for atoms not in
|
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the group.</p>
|
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<p>Each input value can be an atom attribute (position, velocity, force
|
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component) or can be the result of a <a class="reference internal" href="compute.html"><em>compute</em></a> or
|
||||
<a class="reference internal" href="fix.html"><em>fix</em></a> or the evaluation of an atom-style
|
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<a class="reference internal" href="variable.html"><em>variable</em></a>. In the latter cases, the compute, fix, or
|
||||
the group.
|
||||
</P>
|
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<P>Each input value can be an atom attribute (position, velocity, force
|
||||
component) or can be the result of a <A HREF = "compute.html">compute</A> or
|
||||
<A HREF = "fix.html">fix</A> or the evaluation of an atom-style
|
||||
<A HREF = "variable.html">variable</A>. In the latter cases, the compute, fix, or
|
||||
variable must produce a per-atom vector, not a global quantity or
|
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local quantity. If you wish to time-average global quantities from a
|
||||
compute, fix, or variable, then see the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a> command.</p>
|
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<p><a class="reference internal" href="compute.html"><em>Computes</em></a> that produce per-atom vectors or arrays are
|
||||
those which have the word <em>atom</em> in their style name. See the doc
|
||||
pages for individual <a class="reference internal" href="fix.html"><em>fixes</em></a> to determine which ones produce
|
||||
per-atom vectors or arrays. <a class="reference internal" href="variable.html"><em>Variables</em></a> of style <em>atom</em>
|
||||
compute, fix, or variable, then see the <A HREF = "fix_ave_time.html">fix
|
||||
ave/time</A> command.
|
||||
</P>
|
||||
<P><A HREF = "compute.html">Computes</A> that produce per-atom vectors or arrays are
|
||||
those which have the word <I>atom</I> in their style name. See the doc
|
||||
pages for individual <A HREF = "fix.html">fixes</A> to determine which ones produce
|
||||
per-atom vectors or arrays. <A HREF = "variable.html">Variables</A> of style <I>atom</I>
|
||||
are the only ones that can be used with this fix since they produce
|
||||
per-atom vectors.</p>
|
||||
<p>Each per-atom value of each input vector is averaged independently.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
|
||||
per-atom vectors.
|
||||
</P>
|
||||
<P>Each per-atom value of each input vector is averaged independently.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
|
||||
timesteps the input values will be used in order to contribute to the
|
||||
average. The final averaged quantities are generated on timesteps
|
||||
that are a multiple of <em>Nfreq</em>. The average is over <em>Nrepeat</em>
|
||||
that are a multiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
|
||||
quantities, computed in the preceding portion of the simulation every
|
||||
<em>Nevery</em> timesteps. <em>Nfreq</em> must be a multiple of <em>Nevery</em> and
|
||||
<em>Nevery</em> must be non-zero even if <em>Nrepeat</em> is 1. Also, the timesteps
|
||||
contributing to the average value cannot overlap, i.e. Nfreq >
|
||||
(Nrepeat-1)*Nevery is required.</p>
|
||||
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
||||
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
|
||||
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
|
||||
contributing to the average value cannot overlap, i.e. Nfreq >
|
||||
(Nrepeat-1)*Nevery is required.
|
||||
</P>
|
||||
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
||||
timesteps 90,92,94,96,98,100 will be used to compute the final average
|
||||
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
|
||||
timestep 200, etc.</p>
|
||||
<hr class="docutils" />
|
||||
<p>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
|
||||
timestep 200, etc.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
|
||||
self-explanatory. Note that other atom attributes can be used as
|
||||
inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a> command and then specifying
|
||||
an input value from that compute.</p>
|
||||
<div class="admonition warning">
|
||||
<p class="first admonition-title">Warning</p>
|
||||
<p class="last">The x,y,z attributes are values that are re-wrapped
|
||||
inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
|
||||
property/atom</A> command and then specifying
|
||||
an input value from that compute.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: The x,y,z attributes are values that are re-wrapped
|
||||
inside the periodic box whenever an atom crosses a periodic boundary.
|
||||
Thus if you time average an atom that spends half its time on either
|
||||
side of the periodic box, you will get a value in the middle of the
|
||||
box. If this is not what you want, consider averaging unwrapped
|
||||
coordinates, which can be provided by the <a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a> command via its xu,yu,zu
|
||||
attributes.</p>
|
||||
</div>
|
||||
<p>If a value begins with “<a href="#id1"><span class="problematic" id="id2">c_</span></a>”, a compute ID must follow which has been
|
||||
coordinates, which can be provided by the <A HREF = "compute_property_atom.html">compute
|
||||
property/atom</A> command via its xu,yu,zu
|
||||
attributes.
|
||||
</P>
|
||||
<P>If a value begins with "c_", a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the per-atom vector calculated by the compute is used. If a
|
||||
bracketed term containing an index I is appended, the Ith column of
|
||||
the per-atom array calculated by the compute is used. Users can also
|
||||
write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><em>add them to LAMMPS</em></a>.</p>
|
||||
<p>If a value begins with “<a href="#id3"><span class="problematic" id="id4">f_</span></a>”, a fix ID must follow which has been
|
||||
write code for their own compute styles and <A HREF = "Section_modify.html">add them to
|
||||
LAMMPS</A>.
|
||||
</P>
|
||||
<P>If a value begins with "f_", a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the per-atom vector calculated by the fix is used. If a
|
||||
bracketed term containing an index I is appended, the Ith column of
|
||||
the per-atom array calculated by the fix is used. Note that some
|
||||
fixes only produce their values on certain timesteps, which must be
|
||||
compatible with <em>Nevery</em>, else an error will result. Users can also
|
||||
write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><em>add them to LAMMPS</em></a>.</p>
|
||||
<p>If a value begins with “<a href="#id5"><span class="problematic" id="id6">v_</span></a>”, a variable name must follow which has
|
||||
been previously defined in the input script as an <a class="reference internal" href="variable.html"><em>atom-style variable</em></a> Variables of style <em>atom</em> can reference
|
||||
compatible with <I>Nevery</I>, else an error will result. Users can also
|
||||
write code for their own fix styles and <A HREF = "Section_modify.html">add them to
|
||||
LAMMPS</A>.
|
||||
</P>
|
||||
<P>If a value begins with "v_", a variable name must follow which has
|
||||
been previously defined in the input script as an <A HREF = "variable.html">atom-style
|
||||
variable</A> Variables of style <I>atom</I> can reference
|
||||
thermodynamic keywords, or invoke other computes, fixes, or variables
|
||||
when they are evaluated, so this is a very general means of generating
|
||||
per-atom quantities to time average.</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>. None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
|
||||
per-atom quantities to time average.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
||||
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
||||
are relevant to this fix. No global scalar or vector quantities are
|
||||
stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>.</p>
|
||||
<p>This fix produces a per-atom vector or array which can be accessed by
|
||||
various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. A vector is
|
||||
stored by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
|
||||
commands</A>.
|
||||
</P>
|
||||
<P>This fix produces a per-atom vector or array which can be accessed by
|
||||
various <A HREF = "Section_howto.html#howto_15">output commands</A>. A vector is
|
||||
produced if only a single quantity is averaged by this fix. If two or
|
||||
more quantities are averaged, then an array of values is produced.
|
||||
The per-atom values can only be accessed on timesteps that are
|
||||
multiples of <em>Nfreq</em> since that is when averaging is performed.</p>
|
||||
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
|
||||
the <a class="reference internal" href="run.html"><em>run</em></a> command. 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>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</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="compute.html"><em>compute</em></a>, <a class="reference internal" href="fix_ave_histo.html"><em>fix ave/histo</em></a>, <a class="reference internal" href="fix_ave_spatial.html"><em>fix ave/spatial</em></a>, <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>,
|
||||
<a class="reference internal" href="variable.html"><em>variable</em></a>,</p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
© Copyright .
|
||||
</p>
|
||||
</div>
|
||||
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||||
|
||||
</footer>
|
||||
|
||||
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|
||||
</div>
|
||||
|
||||
</section>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<script type="text/javascript">
|
||||
var DOCUMENTATION_OPTIONS = {
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||||
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|
||||
</html>
|
||||
multiples of <I>Nfreq</I> since that is when averaging is performed.
|
||||
</P>
|
||||
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
||||
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
|
||||
minimization</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>, <A HREF = "fix_ave_spatial.html">fix
|
||||
ave/spatial</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
|
||||
<A HREF = "variable.html">variable</A>,
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
||||
Reference in New Issue
Block a user