<p>Modify certain attributes of atoms defined and stored within LAMMPS,
in addition to what is specified by the <aclass="reference internal"href="atom_style.html"><spanclass="doc">atom_style</span></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 <aclass="reference internal"href="create_atoms.html"><spanclass="doc">create atoms</span></a> or
<aclass="reference internal"href="read_data.html"><spanclass="doc">read_data</span></a> or <aclass="reference internal"href="read_restart.html"><spanclass="doc">read_restart</span></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 <aclass="reference internal"href="atom_style.html"><spanclass="doc">atom styles</span></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 <aclass="reference internal"href="Section_start.html#start-2"><spanclass="std std-ref">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 <aclass="reference internal"href="velocity.html"><spanclass="doc">velocity loop all</span></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 <aclass="reference internal"href="group.html"><spanclass="doc">group</span></a> to be specified whose
atoms will be maintained as the first atoms in each processor’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 <aclass="reference internal"href="neigh_modify.html"><spanclass="doc">neigh_modify include</span></a> and <aclass="reference internal"href="comm_modify.html"><spanclass="doc">comm_modify group</span></a>
commands are two examples of commands that require this setting to
work efficiently. Several <aclass="reference internal"href="fix.html"><spanclass="doc">fixes</span></a>, most notably time
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