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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying &amp; extending LAMMPS</a></li>
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<div class="section" id="atom-modify-command">
<span id="index-0"></span><h1>atom_modify command<a class="headerlink" href="#atom-modify-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>atom_modify keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>one or more keyword/value pairs may be appended</li>
<li>keyword = <em>id</em> or <em>map</em> or <em>first</em> or <em>sort</em></li>
</ul>
<pre class="literal-block">
<em>id</em> value = <em>yes</em> or <em>no</em>
<em>map</em> value = <em>array</em> or <em>hash</em>
<em>first</em> value = group-ID = group whose atoms will appear first in internal atom lists
<em>sort</em> values = Nfreq binsize
Nfreq = sort atoms spatially every this many time steps
binsize = bin size for spatial sorting (distance units)
</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>atom_modify map hash
atom_modify map array sort 10000 2.0
atom_modify first colloid
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline"></a></h2>
<p>Modify certain attributes of atoms defined and stored within LAMMPS,
in addition to what is specified by the <a class="reference internal" href="atom_style.html"><em>atom_style</em></a>
command. The <em>id</em> and <em>map</em> keywords must be specified before a
simulation box is defined; other keywords can be specified any time.</p>
<p>The <em>id</em> keyword determines whether non-zero atom IDs can be assigned
to each atom. If the value is <em>yes</em>, which is the default, IDs are
assigned, whether you use the <a class="reference internal" href="create_atoms.html"><em>create atoms</em></a> or
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands to initialize atoms. If the value is <em>no</em> the IDs for all
atoms are assumed to be 0.</p>
<p>If atom IDs are used, they must all be positive integers. They should
also be unique, though LAMMPS does not check for this. Typically they
should also be consecutively numbered (from 1 to Natoms), though this
is not required. Molecular <a class="reference internal" href="atom_style.html"><em>atom styles</em></a> are those
that store bond topology information (styles bond, angle, molecular,
full). These styles require atom IDs since the IDs are used to encode
the topology. Some other LAMMPS commands also require the use of atom
IDs. E.g. some many-body pair styles use them to avoid double
computation of the I-J interaction between two atoms.</p>
<p>The only reason not to use atom IDs is if you are running an atomic
simulation so large that IDs cannot be uniquely assigned. For a
default LAMMPS build this limit is 2^31 or about 2 billion atoms.
However, even in this case, you can use 64-bit atom IDs, allowing 2^63
or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
switch. This is described in <a class="reference internal" href="Section_start.html#start-2"><span>Section 2.2</span></a>
of the manual. If atom IDs are not used, they must be specified as 0
for all atoms, e.g. in a data or restart file.</p>
<p>The <em>map</em> keyword determines how atom ID lookup is done for molecular
atom styles. Lookups are performed by bond (angle, etc) routines in
LAMMPS to find the local atom index associated with a global atom ID.</p>
<p>When the <em>array</em> value is used, each processor stores a lookup table
of length N, where N is the largest atom ID in the system. This is a
fast, simple method for many simulations, but requires too much memory
for large simulations. The <em>hash</em> value uses a hash table to perform
the lookups. This can be slightly slower than the <em>array</em> method, but
its memory cost is proportional to the number of atoms owned by a
processor, i.e. N/P when N is the total number of atoms in the system
and P is the number of processors.</p>
<p>When this setting is not specified in your input script, LAMMPS
creates a map, if one is needed, as an array or hash. See the
discussion of default values below for how LAMMPS chooses which kind
of map to build. Note that atomic systems do not normally need to
create a map. However, even in this case some LAMMPS commands will
create a map to find atoms (and then destroy it), or require a
permanent map. An example of the former is the <a class="reference internal" href="velocity.html"><em>velocity loop all</em></a> command, which uses a map when looping over all
atoms and insuring the same velocity values are assigned to an atom
ID, no matter which processor owns it.</p>
<p>The <em>first</em> keyword allows a <a class="reference internal" href="group.html"><em>group</em></a> to be specified whose
atoms will be maintained as the first atoms in each processor&#8217;s list
of owned atoms. This in only useful when the specified group is a
small fraction of all the atoms, and there are other operations LAMMPS
is performing that will be sped-up significantly by being able to loop
over the smaller set of atoms. Otherwise the reordering required by
this option will be a net slow-down. The <a class="reference internal" href="neigh_modify.html"><em>neigh_modify include</em></a> and <a class="reference internal" href="comm_modify.html"><em>comm_modify group</em></a>
commands are two examples of commands that require this setting to
work efficiently. Several <a class="reference internal" href="fix.html"><em>fixes</em></a>, most notably time
integration fixes like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, also take advantage of
this setting if the group they operate on is the group specified by
this command. Note that specifying &#8220;all&#8221; as the group-ID effectively
turns off the <em>first</em> option.</p>
<p>It is OK to use the <em>first</em> keyword with a group that has not yet been
defined, e.g. to use the atom_modify first command at the beginning of
your input script. LAMMPS does not use the group until a simullation
is run.</p>
<p>The <em>sort</em> keyword turns on a spatial sorting or reordering of atoms
within each processor&#8217;s sub-domain every <em>Nfreq</em> timesteps. If
<em>Nfreq</em> is set to 0, then sorting is turned off. Sorting can improve
cache performance and thus speed-up a LAMMPS simulation, as discussed
in a paper by <a class="reference internal" href="#meloni"><span>(Meloni)</span></a>. Its efficacy depends on the problem
size (atoms/processor), how quickly the system becomes disordered, and
various other factors. As a general rule, sorting is typically more
effective at speeding up simulations of liquids as opposed to solids.
In tests we have done, the speed-up can range from zero to 3-4x.</p>
<p>Reordering is peformed every <em>Nfreq</em> timesteps during a dynamics run
or iterations during a minimization. More precisely, reordering
occurs at the first reneighboring that occurs after the target
timestep. The reordering is performed locally by each processor,
using bins of the specified <em>binsize</em>. If <em>binsize</em> is set to 0.0,
then a binsize equal to half the <a class="reference internal" href="neighbor.html"><em>neighbor</em></a> cutoff
distance (force cutoff plus skin distance) is used, which is a
reasonable value. After the atoms have been binned, they are
reordered so that atoms in the same bin are adjacent to each other in
the processor&#8217;s 1d list of atoms.</p>
<p>The goal of this procedure is for atoms to put atoms close to each
other in the processor&#8217;s one-dimensional list of atoms that are also
near to each other spatially. This can improve cache performance when
pairwise intereractions and neighbor lists are computed. Note that if
bins are too small, there will be few atoms/bin. Likewise if bins are
too large, there will be many atoms/bin. In both cases, the goal of
cache locality will be undermined.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Running a simulation with sorting on versus off should
not change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead
to diverging trajectories over time when comparing two simluations.
Various commands, particularly those which use random numbers
(e.g. <a class="reference internal" href="velocity.html"><em>velocity create</em></a>, and <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>), may generate (statistically identical)
results which depend on the order in which atoms are processed. The
order of atoms in a <a class="reference internal" href="dump.html"><em>dump</em></a> file will also typically change
if sorting is enabled.</p>
</div>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline"></a></h2>
<p>The <em>first</em> and <em>sort</em> options cannot be used together. Since sorting
is on by default, it will be turned off if the <em>first</em> keyword is
used with a group-ID that is not &#8220;all&#8221;.</p>
<p><strong>Related commands:</strong> none</p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline"></a></h2>
<p>By default, <em>id</em> is yes. By default, atomic systems (no bond topology
info) do not use a map. For molecular systems (with bond topology
info), a map is used. The default map style is array if no atom ID is
larger than 1 million, otherwise the default is hash. By default, a
&#8220;first&#8221; group is not defined. By default, sorting is enabled with a
frequency of 1000 and a binsize of 0.0, which means the neighbor
cutoff will be used to set the bin size.</p>
<hr class="docutils" />
<p id="meloni"><strong>(Meloni)</strong> Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).</p>
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