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<li>compute msd/chunk command</li>
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<div class="section" id="compute-msd-chunk-command">
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<span id="index-0"></span><h1>compute msd/chunk command<a class="headerlink" href="#compute-msd-chunk-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 msd/chunk chunkID
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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>msd/chunk = style name of this compute command</li>
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<li>chunkID = ID of <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> 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 1 all msd/chunk molchunk
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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 mean-squared displacement
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(MSD) for multiple chunks of atoms.</p>
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<p>In LAMMPS, chunks are collections of atoms defined by a <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command, which assigns each atom
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<HR>
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<H3>compute msd/chunk command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>compute ID group-ID msd/chunk chunkID
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
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<LI>msd/chunk = style name of this compute command
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<LI>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
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</UL>
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<P><B>Examples:</B>
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</P>
|
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<PRE>compute 1 all msd/chunk molchunk
|
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</PRE>
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<P><B>Description:</B>
|
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</P>
|
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<P>Define a computation that calculates the mean-squared displacement
|
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(MSD) for multiple chunks of atoms.
|
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</P>
|
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<P>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
|
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chunk/atom</A> command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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as chunkID. For example, a single chunk could be the atoms in a
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molecule or atoms in a spatial bin. See the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> doc page and “<a class="reference internal" href="Section_howto.html#howto-23"><span>Section_howto 23</span></a> for details of how chunks can be
|
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molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
|
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chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
|
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23</A> for details of how chunks can be
|
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defined and examples of how they can be used to measure properties of
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a system.</p>
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<p>Four quantites are calculated by this compute for each chunk. The
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a system.
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</P>
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<P>Four quantites are calculated by this compute for each chunk. The
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first 3 quantities are the squared dx,dy,dz displacements of the
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center-of-mass. The 4th component is the total squared displacement,
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i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These
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calculations include all effects due to atoms passing thru periodic
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boundaries.</p>
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<p>Note that only atoms in the specified group contribute to the
|
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calculation. The <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command
|
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boundaries.
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</P>
|
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<P>Note that only atoms in the specified group contribute to the
|
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calculation. The <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
|
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defines its own group; atoms will have a chunk ID = 0 if they are not
|
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in that group, signifying they are not assigned to a chunk, and will
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thus also not contribute to this calculation. You can specify the
|
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“all” group for this command if you simply want to include atoms with
|
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non-zero chunk IDs.</p>
|
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<p>The slope of the mean-squared displacement (MSD) versus time is
|
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proportional to the diffusion coefficient of the diffusing chunks.</p>
|
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<p>The displacement of the center-of-mass of the chunk is from its
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"all" group for this command if you simply want to include atoms with
|
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non-zero chunk IDs.
|
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</P>
|
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<P>The slope of the mean-squared displacement (MSD) versus time is
|
||||
proportional to the diffusion coefficient of the diffusing chunks.
|
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</P>
|
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<P>The displacement of the center-of-mass of the chunk is from its
|
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original center-of-mass position, calculated on the timestep this
|
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compute command was first invoked.</p>
|
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<div class="admonition warning">
|
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<p class="first admonition-title">Warning</p>
|
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<p class="last">The number of chunks <em>Nchunk</em> calculated by the
|
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<a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command must remain
|
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compute command was first invoked.
|
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</P>
|
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<P>IMPORTANT NOTE: The number of chunks <I>Nchunk</I> calculated by the
|
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<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command must remain
|
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constant each time this compute is invoked, so that the displacement
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for each chunk from its original position can be computed
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consistently. If <em>Nchunk</em> does not remain constant, an error will be
|
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generated. If needed, you can enforce a constant <em>Nchunk</em> by using
|
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the <em>nchunk once</em> or <em>ids once</em> options when specifying the <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command.</p>
|
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</div>
|
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<div class="admonition warning">
|
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<p class="first admonition-title">Warning</p>
|
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<p class="last">This compute stores the original position (of the
|
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consistently. If <I>Nchunk</I> does not remain constant, an error will be
|
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generated. If needed, you can enforce a constant <I>Nchunk</I> by using
|
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the <I>nchunk once</I> or <I>ids once</I> options when specifying the <A HREF = "compute_chunk_atom.html">compute
|
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chunk/atom</A> command.
|
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</P>
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<P>IMPORTANT NOTE: This compute stores the original position (of the
|
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center-of-mass) of each chunk. When a displacement is calculated on a
|
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later timestep, it is assumed that the same atoms are assigned to the
|
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same chunk ID. However LAMMPS has no simple way to insure this is the
|
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case, though you can use the <em>ids once</em> option when specifying the
|
||||
<a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command. Note that if
|
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case, though you can use the <I>ids once</I> option when specifying the
|
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<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command. Note that if
|
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this is not the case, the MSD calculation does not have a sensible
|
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meaning.</p>
|
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</div>
|
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<div class="admonition warning">
|
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<p class="first admonition-title">Warning</p>
|
||||
<p class="last">The initial coordinates of the atoms in each chunk are
|
||||
stored in “unwrapped” form, by using the image flags associated with
|
||||
each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command for a discussion
|
||||
of “unwrapped” coordinates. See the Atoms section of the
|
||||
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags and
|
||||
meaning.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: The initial coordinates of the atoms in each chunk are
|
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stored in "unwrapped" form, by using the image flags associated with
|
||||
each atom. See the <A HREF = "dump.html">dump custom</A> command for a discussion
|
||||
of "unwrapped" coordinates. See the Atoms section of the
|
||||
<A HREF = "read_data.html">read_data</A> command for a discussion of image flags and
|
||||
how they are set for each atom. You can reset the image flags
|
||||
(e.g. to 0) before invoking this compute by using the <a class="reference internal" href="set.html"><em>set image</em></a> command.</p>
|
||||
</div>
|
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<div class="admonition warning">
|
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<p class="first admonition-title">Warning</p>
|
||||
<p class="last">Unlike the <a class="reference internal" href="compute_msd.html"><em>compute msd</em></a> command,
|
||||
(e.g. to 0) before invoking this compute by using the <A HREF = "set.html">set
|
||||
image</A> command.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: Unlike the <A HREF = "compute_msd.html">compute msd</A> command,
|
||||
this compute does not store the initial center-of-mass coorindates of
|
||||
its molecules in a restart file. Thus you cannot continue the MSD per
|
||||
chunk calculation of this compute when running from a <a class="reference internal" href="read_restart.html"><em>restart file</em></a>.</p>
|
||||
</div>
|
||||
<p>The simplest way to output the results of the compute com/msd
|
||||
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><em>fix ave/time</em></a>
|
||||
command, for example:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre>compute cc1 all chunk/atom molecule
|
||||
chunk calculation of this compute when running from a <A HREF = "read_restart.html">restart
|
||||
file</A>.
|
||||
</P>
|
||||
<P>The simplest way to output the results of the compute com/msd
|
||||
calculation to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A>
|
||||
command, for example:
|
||||
</P>
|
||||
<PRE>compute cc1 all chunk/atom molecule
|
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compute myChunk all com/msd cc1
|
||||
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
|
||||
</pre></div>
|
||||
</div>
|
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<p><strong>Output info:</strong></p>
|
||||
<p>This compute calculates a global array where the number of rows = the
|
||||
number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><em>compute chunk/atom</em></a> command. The number of columns =
|
||||
fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
|
||||
</PRE>
|
||||
<P><B>Output info:</B>
|
||||
</P>
|
||||
<P>This compute calculates a global array where the number of rows = the
|
||||
number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
|
||||
chunk/atom</A> command. The number of columns =
|
||||
4 for dx,dy,dz and the total displacement. These values can be
|
||||
accessed by any command that uses global 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 options.</p>
|
||||
<p>The array values are “intensive”. The array values will be in
|
||||
distance^2 <a class="reference internal" href="units.html"><em>units</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_msd.html"><em>compute msd</em></a></p>
|
||||
<p><strong>Default:</strong> none</p>
|
||||
</div>
|
||||
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|
||||
|
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|
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|
||||
<P>The array values are "intensive". The array values will be in
|
||||
distance^2 <A HREF = "units.html">units</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_msd.html">compute msd</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
</HTML>
|
||||
|
||||
Reference in New Issue
Block a user