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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<div class="section" id="atom-style-command">
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<span id="index-0"></span><h1>atom_style command<a class="headerlink" href="#atom-style-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>atom_style style args
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</pre></div>
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</div>
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<ul class="simple">
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<li>style = <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dipole</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>meso</em> or <em>molecular</em> or <em>peri</em> or <em>smd</em> or <em>sphere</em> or <em>tri</em> or <em>template</em> or <em>hybrid</em></li>
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</ul>
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<pre class="literal-block">
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args = none for any style except <em>body</em> and <em>hybrid</em>
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<em>body</em> args = bstyle bstyle-args
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bstyle = style of body particles
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bstyle-args = additional arguments specific to the bstyle
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see the <a class="reference internal" href="body.html"><em>body</em></a> doc page for details
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<em>template</em> args = template-ID
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template-ID = ID of molecule template specified in a separate <a class="reference internal" href="molecule.html"><em>molecule</em></a> command
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<em>hybrid</em> args = list of one or more sub-styles, each with their args
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</pre>
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<ul class="simple">
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<li>accelerated styles (with same args) = <em>angle/cuda</em> or <em>angle/kk</em> or <em>atomic/cuda</em> or <em>atomic/kk</em> or <em>bond/kk</em> or <em>charge/cuda</em> or <em>charge/kk</em> or <em>full/cuda</em> or <em>full/kk</em> or <em>molecular/kk</em></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>atom_style atomic
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atom_style bond
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atom_style full
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atom_style full/cuda
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atom_style body nparticle 2 10
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atom_style hybrid charge bond
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atom_style hybrid charge body nparticle 2 5
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atom_style template myMols
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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 what style of atoms to use in a simulation. This determines
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what attributes are associated with the atoms. This command must be
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used before a simulation is setup via a <a class="reference internal" href="read_data.html"><em>read_data</em></a>,
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<a class="reference internal" href="read_restart.html"><em>read_restart</em></a>, or <a class="reference internal" href="create_box.html"><em>create_box</em></a>
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command.</p>
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<p>Once a style is assigned, it cannot be changed, so use a style general
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enough to encompass all attributes. E.g. with style <em>bond</em>, angular
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terms cannot be used or added later to the model. It is OK to use a
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style more general than needed, though it may be slightly inefficient.</p>
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<p>The choice of style affects what quantities are stored by each atom,
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what quantities are communicated between processors to enable forces
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to be computed, and what quantities are listed in the data file read
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by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command.</p>
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<p>These are the additional attributes of each style and the typical
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kinds of physical systems they are used to model. All styles store
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coordinates, velocities, atom IDs and types. See the
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<a class="reference internal" href="read_data.html"><em>read_data</em></a>, <a class="reference internal" href="create_atoms.html"><em>create_atoms</em></a>, and
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<a class="reference internal" href="set.html"><em>set</em></a> commands for info on how to set these various
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quantities.</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="13%" />
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<col width="50%" />
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<col width="36%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td><em>angle</em></td>
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<td>bonds and angles</td>
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<td>bead-spring polymers with stiffness</td>
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</tr>
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<tr class="row-even"><td><em>atomic</em></td>
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<td>only the default values</td>
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<td>coarse-grain liquids, solids, metals</td>
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</tr>
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<tr class="row-odd"><td><em>body</em></td>
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<td>mass, inertia moments, quaternion, angular momentum</td>
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<td>arbitrary bodies</td>
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</tr>
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<tr class="row-even"><td><em>bond</em></td>
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<td>bonds</td>
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<td>bead-spring polymers</td>
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</tr>
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<tr class="row-odd"><td><em>charge</em></td>
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<td>charge</td>
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<td>atomic system with charges</td>
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</tr>
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<tr class="row-even"><td><em>dipole</em></td>
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<td>charge and dipole moment</td>
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<td>system with dipolar particles</td>
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</tr>
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<tr class="row-odd"><td><em>electron</em></td>
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<td>charge and spin and eradius</td>
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<td>electronic force field</td>
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</tr>
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<tr class="row-even"><td><em>ellipsoid</em></td>
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<td>shape, quaternion, angular momentum</td>
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<td>aspherical particles</td>
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</tr>
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<tr class="row-odd"><td><em>full</em></td>
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<td>molecular + charge</td>
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<td>bio-molecules</td>
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</tr>
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<tr class="row-even"><td><em>line</em></td>
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<td>end points, angular velocity</td>
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<td>rigid bodies</td>
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</tr>
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<tr class="row-odd"><td><em>meso</em></td>
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<td>rho, e, cv</td>
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<td>SPH particles</td>
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</tr>
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<tr class="row-even"><td><em>molecular</em></td>
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<td>bonds, angles, dihedrals, impropers</td>
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<td>uncharged molecules</td>
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</tr>
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<tr class="row-odd"><td><em>peri</em></td>
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<td>mass, volume</td>
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<td>mesocopic Peridynamic models</td>
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</tr>
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<tr class="row-even"><td><em>smd</em></td>
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<td>volume, kernel diameter, contact radius, mass</td>
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<td>solid and fluid SPH particles</td>
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</tr>
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<tr class="row-odd"><td><em>sphere</em></td>
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<td>diameter, mass, angular velocity</td>
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<td>granular models</td>
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</tr>
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<tr class="row-even"><td><em>template</em></td>
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<td>template index, template atom</td>
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<td>small molecules with fixed topology</td>
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</tr>
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<tr class="row-odd"><td><em>tri</em></td>
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<td>corner points, angular momentum</td>
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<td>rigid bodies</td>
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</tr>
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<tr class="row-even"><td><em>wavepacket</em></td>
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<td>charge, spin, eradius, etag, cs_re, cs_im</td>
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<td>AWPMD</td>
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</tr>
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</tbody>
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</table>
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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">It is possible to add some attributes, such as a
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molecule ID, to atom styles that do not have them via the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> command. This command also
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allows new custom attributes consisting of extra integer or
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floating-point values to be added to atoms. See the <a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a> doc page for examples of cases
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where this is useful and details on how to initialize, access, and
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output the custom values.</p>
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</div>
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<p>All of the above styles define point particles, except the <em>sphere</em>,
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<em>ellipsoid</em>, <em>electron</em>, <em>peri</em>, <em>wavepacket</em>, <em>line</em>, <em>tri</em>, and
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<em>body</em> styles, which define finite-size particles. See <a class="reference internal" href="Section_howto.html#howto-14"><span>Section_howto 14</span></a> for an overview of using finite-size
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particle models with LAMMPS.</p>
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<p>All of the point-particle styles assign mass to particles on a
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per-type basis, using the <a class="reference internal" href="mass.html"><em>mass</em></a> command, The finite-size
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particle styles assign mass to individual particles on a per-particle
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basis.</p>
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<p>For the <em>sphere</em> style, the particles are spheres and each stores a
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per-particle diameter and mass. If the diameter > 0.0, the particle
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is a finite-size sphere. If the diameter = 0.0, it is a point
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particle.</p>
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<p>For the <em>ellipsoid</em> style, the particles are ellipsoids and each
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stores a flag which indicates whether it is a finite-size ellipsoid or
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a point particle. If it is an ellipsoid, it also stores a shape
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vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
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with its orientation.</p>
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<p>For the <em>electron</em> style, the particles representing electrons are 3d
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Gaussians with a specified position and bandwidth or uncertainty in
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position, which is represented by the eradius = electron size.</p>
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<p>For the <em>peri</em> style, the particles are spherical and each stores a
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per-particle mass and volume.</p>
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<p>The <em>meso</em> style is for smoothed particle hydrodynamics (SPH)
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particles which store a density (rho), energy (e), and heat capacity
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(cv).</p>
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<p>The <em>smd</em> style is for a general formulation of Smooth Particle
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Hydrodynamics. Both fluids and solids can be modeled. Particles
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store the mass and volume of an integration point, a kernel diameter
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used for calculating the field variables (e.g. stress and deformation)
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and a contact radius for calculating repulsive forces which prevent
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individual physical bodies from penetretating each other.</p>
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<p>The <em>wavepacket</em> style is similar to <em>electron</em>, but the electrons may
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consist of several Gaussian wave packets, summed up with coefficients
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cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
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particle in LAMMPS, wave packets belonging to the same electron must
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have identical <em>etag</em> values.</p>
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<p>For the <em>line</em> style, the particles are idealized line segments and
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each stores a per-particle mass and length and orientation (i.e. the
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end points of the line segment).</p>
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<p>For the <em>tri</em> style, the particles are planar triangles and each
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stores a per-particle mass and size and orientation (i.e. the corner
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points of the triangle).</p>
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<p>The <em>template</em> style allows molecular topolgy (bonds,angles,etc) to be
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defined via a molecule template using the <a class="reference external" href="molecule.txt">molecule</a>
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command. The template stores one or more molecules with a single copy
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of the topology info (bonds,angles,etc) of each. Individual atoms
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only store a template index and template atom to identify which
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molecule and which atom-within-the-molecule they represent. Using the
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<em>template</em> style instead of the <em>bond</em>, <em>angle</em>, <em>molecular</em> styles
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can save memory for systems comprised of a large number of small
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molecules, all of a single type (or small number of types). See the
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paper by Grime and Voth, in <a class="reference internal" href="#grime"><span>(Grime)</span></a>, for examples of how this
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can be advantageous for large-scale coarse-grained systems.</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">When using the <em>template</em> style with a <a class="reference internal" href="molecule.html"><em>molecule template</em></a> that contains multiple molecules, you should
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insure the atom types, bond types, angle_types, etc in all the
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molecules are consistent. E.g. if one molecule represents H2O and
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another CO2, then you probably do not want each molecule file to
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define 2 atom types and a single bond type, because they will conflict
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with each other when a mixture system of H2O and CO2 molecules is
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defined, e.g. by the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command. Rather the
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H2O molecule should define atom types 1 and 2, and bond type 1. And
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the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
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2 if a single oxygen type is desired), and bond type 2.</p>
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</div>
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<p>For the <em>body</em> style, the particles are arbitrary bodies with internal
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attributes defined by the “style” of the bodies, which is specified by
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the <em>bstyle</em> argument. Body particles can represent complex entities,
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such as surface meshes of discrete points, collections of
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sub-particles, deformable objects, etc.</p>
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<p>The <a class="reference internal" href="body.html"><em>body</em></a> doc page descibes the body styles LAMMPS
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currently supports, and provides more details as to the kind of body
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particles they represent. For all styles, each body particle stores
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moments of inertia and a quaternion 4-vector, so that its orientation
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and position can be time integrated due to forces and torques.</p>
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<p>Note that there may be additional arguments required along with the
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<em>bstyle</em> specification, in the atom_style body command. These
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arguments are described in the <a class="reference internal" href="body.html"><em>body</em></a> doc page.</p>
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<hr class="docutils" />
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<p>Typically, simulations require only a single (non-hybrid) atom style.
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If some atoms in the simulation do not have all the properties defined
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by a particular style, use the simplest style that defines all the
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needed properties by any atom. For example, if some atoms in a
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simulation are charged, but others are not, use the <em>charge</em> style.
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If some atoms have bonds, but others do not, use the <em>bond</em> style.</p>
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<p>The only scenario where the <em>hybrid</em> style is needed is if there is no
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single style which defines all needed properties of all atoms. For
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example, if you want dipolar particles which will rotate due to
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torque, you would need to use “atom_style hybrid sphere dipole”. When
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a hybrid style is used, atoms store and communicate the union of all
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quantities implied by the individual styles.</p>
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<p>When using the <em>hybrid</em> style, you cannot combine the <em>template</em> style
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with another molecular style that stores bond,angle,etc info on a
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per-atom basis.</p>
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<p>LAMMPS can be extended with new atom styles as well as new body
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styles; see <a class="reference internal" href="Section_modify.html"><em>this section</em></a>.</p>
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<hr class="docutils" />
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<p>Styles with a <em>cuda</em> or <em>kk</em> suffix are functionally the same as the
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corresponding style without the suffix. They have been optimized to
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run faster, depending on your available hardware, as discussed in
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<a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual. The
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accelerated styles take the same arguments and should produce the same
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results, except for round-off and precision issues.</p>
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<p>Note that other acceleration packages in LAMMPS, specifically the GPU,
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USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
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styles.</p>
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<p>The accelerated styles are part of the USER-CUDA and KOKKOS packages
|
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respectively. They are only enabled if LAMMPS was built with those
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packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section
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for more info.</p>
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<p>You can specify the accelerated styles explicitly in your input script
|
|
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
|
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use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
|
|
more instructions on how to use the accelerated styles effectively.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<p>This command cannot be used after the simulation box is defined by a
|
|
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="create_box.html"><em>create_box</em></a> command.</p>
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<p>The <em>angle</em>, <em>bond</em>, <em>full</em>, <em>molecular</em>, and <em>template</em> styles are
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part of the MOLECULE package. The <em>line</em> and <em>tri</em> styles are part
|
|
of the ASPHERE pacakge. The <em>body</em> style is part of the BODY package.
|
|
The <em>dipole</em> style is part of the DIPOLE package. The <em>peri</em> style is
|
|
part of the PERI package for Peridynamics. The <em>electron</em> style is
|
|
part of the USER-EFF package for <a class="reference internal" href="pair_eff.html"><em>electronic force fields</em></a>. The <em>meso</em> style is part of the USER-SPH
|
|
package for smoothed particle hydrodyanmics (SPH). See <a class="reference external" href="USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</a> to using SPH in LAMMPS. The
|
|
<em>wavepacket</em> style is part of the USER-AWPMD package for the
|
|
<a class="reference internal" href="pair_awpmd.html"><em>antisymmetrized wave packet MD method</em></a>. They are
|
|
only enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
|
|
</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="pair_style.html"><em>pair_style</em></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
|
<p>atom_style atomic</p>
|
|
<hr class="docutils" />
|
|
<p id="grime"><strong>(Grime)</strong> Grime and Voth, to appear in J Chem Theory & Computation
|
|
(2014).</p>
|
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</div>
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