<p>In each case, the single, double, or triple quotes are removed when
the single argument they enclose is stored internally.</p>
<p>See the <aclass="reference internal"href="dump_modify.html"><spanclass="doc">dump modify format</span></a>, <aclass="reference internal"href="print.html"><spanclass="doc">print</span></a>,
<aclass="reference internal"href="if.html"><spanclass="doc">if</span></a>, and <aclass="reference internal"href="python.html"><spanclass="doc">python</span></a> commands for examples.</p>
<p>A “#” or “$” character that is between quotes will not be treated as a
comment indicator in (2) or substituted for as a variable in (3).</p>
<divclass="admonition note">
<pclass="first admonition-title">Note</p>
<pclass="last">If the argument is itself a command that requires a quoted
argument (e.g. using a <aclass="reference internal"href="print.html"><spanclass="doc">print</span></a> command as part of an
<aclass="reference internal"href="if.html"><spanclass="doc">if</span></a> or <aclass="reference internal"href="run.html"><spanclass="doc">run every</span></a> command), then single, double, or
triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.</p>
<p>This section describes the structure of a typical LAMMPS input script.
The “examples” directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
<aclass="reference internal"href="Section_example.html"><spanclass="doc">Section 7</span></a>, and animated on the <aclass="reference external"href="http://lammps.sandia.gov">LAMMPS WWW Site</a>.</p>
<p>A LAMMPS input script typically has 4 parts:</p>
<olclass="arabic simple">
<li>Initialization</li>
<li>Atom definition</li>
<li>Settings</li>
<li>Run a simulation</li>
</ol>
<p>The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all the
commands need only be used if a non-default value is desired.</p>
<olclass="arabic simple">
<li>Initialization</li>
</ol>
<p>Set parameters that need to be defined before atoms are created or
read-in from a file.</p>
<p>The relevant commands are <aclass="reference internal"href="units.html"><spanclass="doc">units</span></a>,
<p>Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The <aclass="reference internal"href="fix.html"><spanclass="doc">fix</span></a> command comes in many flavors.</p>
<p>Various computations can be specified for execution during a
simulation using the <aclass="reference internal"href="compute.html"><spanclass="doc">compute</span></a>,
<aclass="reference internal"href="compute_modify.html"><spanclass="doc">compute_modify</span></a>, and <aclass="reference internal"href="variable.html"><spanclass="doc">variable</span></a>
commands.</p>
<p>Output options are set by the <aclass="reference internal"href="thermo.html"><spanclass="doc">thermo</span></a>, <aclass="reference internal"href="dump.html"><spanclass="doc">dump</span></a>,
and <aclass="reference internal"href="restart.html"><spanclass="doc">restart</span></a> commands.</p>
<olclass="arabic simple"start="4">
<li>Run a simulation</li>
</ol>
<p>A molecular dynamics simulation is run using the <aclass="reference internal"href="run.html"><spanclass="doc">run</span></a>
command. Energy minimization (molecular statics) is performed using
the <aclass="reference internal"href="minimize.html"><spanclass="doc">minimize</span></a> command. A parallel tempering
(replica-exchange) simulation can be run using the
<p>This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The <aclass="reference internal"href="#cmd-4"><spanclass="std std-ref">previous section</span></a> lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
<p>See the <aclass="reference internal"href="compute.html"><spanclass="doc">compute</span></a> command for one-line descriptions of
each style or click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">appropriate accelerated package</span></a>. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k =
<p>These are additional compute styles in USER packages, which can be
used if <aclass="reference internal"href="Section_start.html#start-3"><spanclass="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<p>See the <aclass="reference internal"href="pair_style.html"><spanclass="doc">pair_style</span></a> command for an overview of pair
potentials. Click on the style itself for a full description. Many
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">appropriate accelerated package</span></a>. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k =
<p>See the <aclass="reference internal"href="bond_style.html"><spanclass="doc">bond_style</span></a> command for an overview of bond
potentials. Click on the style itself for a full description. Some
of the styles have accelerated versions, which can be used if LAMMPS
is built with the <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">appropriate accelerated package</span></a>. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k =
<p>See the <aclass="reference internal"href="angle_style.html"><spanclass="doc">angle_style</span></a> command for an overview of
angle potentials. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">appropriate accelerated package</span></a>. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
<p>See the <aclass="reference internal"href="dihedral_style.html"><spanclass="doc">dihedral_style</span></a> command for an overview
of dihedral potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">appropriate accelerated package</span></a>. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
<p>These are additional dihedral styles in USER packages, which can be
used if <aclass="reference internal"href="Section_start.html#start-3"><spanclass="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<p>See the <aclass="reference internal"href="improper_style.html"><spanclass="doc">improper_style</span></a> command for an overview
of improper potentials. Click on the style itself for a full
description. Some of the styles have accelerated versions, which can
be used if LAMMPS is built with the <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">appropriate accelerated package</span></a>. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
<p>These are additional improper styles in USER packages, which can be
used if <aclass="reference internal"href="Section_start.html#start-3"><spanclass="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>
<p>See the <aclass="reference internal"href="kspace_style.html"><spanclass="doc">kspace_style</span></a> command for an overview of
Kspace solvers. Click on the style itself for a full description.
Some of the styles have accelerated versions, which can be used if
LAMMPS is built with the <aclass="reference internal"href="Section_accelerate.html"><spanclass="doc">appropriate accelerated package</span></a>. This is indicated by additional
letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o =
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