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<title>fix property/atom command &mdash; LAMMPS 17 Dec 2015 documentation</title>
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<div class="section" id="fix-property-atom-command">
<span id="index-0"></span><h1>fix property/atom command<a class="headerlink" href="#fix-property-atom-command" title="Permalink to this headline"></a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID property/atom vec1 vec2 ... keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>property/atom = style name of this fix command</li>
<li>vec1,vec2,... = <em>mol</em> or <em>q</em> or <em>i_name</em> or <em>d_name</em></li>
</ul>
<pre class="literal-block">
<em>mol</em> = molecule IDs
<em>q</em> = charge
<em>i_name</em> = new integer vector referenced by name
<em>d_name</em> = new floating-point vector referenced by name
</pre>
<ul class="simple">
<li>zero of more keyword/value pairs may be appended</li>
<li>keyword = <em>ghost</em></li>
</ul>
<pre class="literal-block">
<em>ghost</em> value = <em>no</em> or <em>yes</em> for whether ghost atom info in communicated
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix 1 all property/atom mol
fix 1 all property/atom i_myflag1 i_myflag2
fix 1 all property/atom d_sx d_sy d_sz
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Create one or more additional per-atom vectors to store information
about atoms and to use during a simulation. The specified <em>group-ID</em>
is ignored by this fix.</p>
<p>The atom style used for a simulation defines a set of per-atom
properties, as explained on the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> and
<a class="reference internal" href="read_data.html"><em>read_data</em></a> doc pages. The latter command allows these
properties to be defined for each atom in the system when a data file
is read. This fix will augment the set of properties with new custom
ones.</p>
<p>This can be useful in at least two scenarios.</p>
<p>If the atom style does not define molecule IDs or per-atom charge,
they can be added using the <em>mol</em> or <em>q</em> keywords. This can be
useful, e.g, to define &#8220;molecules&#8221; to use as rigid bodies with the
<a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command, or just to carry around an extra
flag with the atoms (stored as a molecule ID). An alternative is to
use an atom style that does define molecule IDs or charge or to use a
hybrid atom style that combines two styles to allow for molecule IDs
or charge, but that has 2 practical drawbacks. First it typically
necessitates changing the format of the data file. And it may define
additional properties that aren&#8217;t needed such as bond lists, which has
some overhead when there are no bonds.</p>
<p>In the future, we may add additional per-atom properties similar to
<em>mol</em> or <em>q</em>, which &#8220;turn-on&#8221; specific properties defined by some atom
styles, so they can be used by atom styles that don&#8217;t define them.</p>
<p>More generally, the <em>i_name</em> and <em>d_name</em> vectors allow one or more
new custom per-atom properties to be defined. Each name must be
unique and can use alphanumeric or underscore characters. These
vectors can store whatever values you decide are useful in your
simulation. As explained below there are several ways to initialize
and access and output these values, both via input script commands and
in new code that you add to LAMMPS.</p>
<p>This is effectively a simple way to add per-atom properties to a model
without needing to write code for a new <a class="reference internal" href="atom_style.html"><em>atom style</em></a>
that defines the properties. Note however that implementing a new
atom style allows new atom properties to be more tightly and
seamlessly integrated with the rest of the code.</p>
<p>The new atom properties encode values that migrate with atoms to new
processors and are written to restart files. If you want the new
properties to also be defined for ghost atoms, then use the <em>ghost</em>
keyword with a value of <em>yes</em>. This will invoke extra communication
when ghost atoms are created (at every re-neighboring) to insure the
new properties are also defined for the ghost atoms.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you use this command with the <em>mol</em> or <em>charge</em> vectors than
you most likely want to set <em>ghost</em> yes, since these properties are
stored with ghost atoms if you use an <a class="reference internal" href="atom_style.html"><em>atom_style</em></a>
that defines them, and many LAMMPS operations that use molecule IDs or
charge, such as neighbor lists and pair styles, will expect ghost
atoms to have these valuse. LAMMPS will issue a warning it you define
those vectors but do not set <em>ghost</em> yes.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The properties for ghost atoms are not updated every timestep,
but only once every few steps when neighbor lists are re-built. Thus
the <em>ghost</em> keyword is suitable for static properties, like molecule
IDs, but not for dynamic properties that change every step. For the
latter, the code you add to LAMMPS to change the properties will also
need to communicate their new values to/from ghost atoms, an operation
that can be invoked from within a <a class="reference internal" href="pair_style.html"><em>pair style</em></a> or
<a class="reference internal" href="fix.html"><em>fix</em></a> or <a class="reference internal" href="compute.html"><em>compute</em></a> that you write.</p>
</div>
<hr class="docutils" />
<p>This fix is one of a small number that can be defined in an input
script before the simulation box is created or atoms are defined.
This is so it can be used with the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command
as described below.</p>
<p>Per-atom properties that are defined by the <a class="reference internal" href="atom_style.html"><em>atom style</em></a> are initialized when atoms are created, e.g. by
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>
commands. The per-atom properaties defined by this fix are not. So
you need to initialize them explicitly. This can be done by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command, using its <em>fix</em> keyword and
passing it the fix-ID of this fix.</p>
<p>Thus these commands:</p>
<div class="highlight-python"><div class="highlight"><pre>fix prop all property/atom mol d_flag
read_data data.txt fix prop NULL Molecules
</pre></div>
</div>
<p>would allow a data file to have a section like this:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">Molecules</span>
</pre></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>1 4 1.5
2 4 3.0
3 10 1.0
4 10 1.0
5 10 1.0
...
N 763 4.5
</pre></div>
</div>
<p>where N is the number of atoms, and the first field on each line is
the atom-ID, followed by a molecule-ID and a floating point value that
will be stored in a new property called &#8220;flag&#8221;. Note that the list of
per-atom properties can be in any order.</p>
<p>Another way of initializing the new properties is via the
<a class="reference internal" href="set.html"><em>set</em></a> command. For example, if you wanted molecules
defined for every set of 10 atoms, based on their atom-IDs,
these commands could be used:</p>
<div class="highlight-python"><div class="highlight"><pre>fix prop all property/atom mol
variable cluster atom ((id-1)/10)+1
set id * mol v_cluster
</pre></div>
</div>
<p>The <a class="reference internal" href="variable.html"><em>atom-style variable</em></a> will create values for atoms
with IDs 31,32,33,...40 that are 4.0,4.1,4.2,...,4.9. When the
<a class="reference internal" href="set.html"><em>set</em></a> commands assigns them to the molecule ID for each atom,
they will be truncated to an integer value, so atoms 31-40 will all be
assigned a molecule ID of 4.</p>
<p>Note that <a class="reference internal" href="variable.html"><em>atomfile-style variables</em></a> can also be used in
place of atom-style variables, which means in this case that the
molecule IDs could be read-in from a separate file and assinged by the
<a class="reference internal" href="set.html"><em>set</em></a> command. This allows you to initialize new per-atom
properties in a completely general fashion.</p>
<hr class="docutils" />
<p>For new atom properties specified as <em>i_name</em> or <em>d_name</em>, the
<a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a> command can access
their values. This means that the values can be output via the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command, accessed by fixes like <a class="reference internal" href="fix_ave_atom.html"><em>fix ave/atom</em></a>, accessed by other computes like <a class="reference internal" href="compute_reduce.html"><em>compute reduce</em></a>, or used in <a class="reference external" href="variables">atom-style variables</a>.</p>
<p>For example, these commands will output two new properties to a custom
dump file:</p>
<div class="highlight-python"><div class="highlight"><pre>fix prop all property/atom i_flag1 d_flag2
compute 1 all property/atom i_flag1 d_flag2
dump 1 all custom 100 tmp.dump id x y z c_1[1] c_1[2]
</pre></div>
</div>
<hr class="docutils" />
<p>If you wish to add new <a class="reference internal" href="pair_style.html"><em>pair styles</em></a>,
<a class="reference internal" href="fix.html"><em>fixes</em></a>, or <a class="reference internal" href="compute.html"><em>computes</em></a> that use the per-atom
properties defined by this fix, see <a class="reference internal" href="Section_modify.html#mod-1"><span>Section modify</span></a> of the manual which has some details
on how the properties can be accessed from added classes.</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>This fix writes the per-atom values it stores to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so that the values can be restored when a
simulation is restarted. See the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.</p>
<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options
are relevant to this fix. No global or per-atom 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>. 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="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="set.html"><em>set</em></a>, <a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>The default keyword values are ghost = no.</p>
</div>
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