forked from lijiext/lammps
199 lines
9.9 KiB
HTML
199 lines
9.9 KiB
HTML
<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<H3>atom_style command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>atom_style style args
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</PRE>
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<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>body</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>line</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>tri</I> or <I>hybrid</I>
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</UL>
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<PRE> args = none for any style except <I>body</I> and <I>hybrid</I>
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<I>body</I> 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 HREF = "body.html">body</A> doc page for details
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<I>hybrid</I> args = list of one or more sub-styles, each with their args
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>atom_style atomic
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atom_style bond
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atom_style full
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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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</PRE>
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<P><B>Description:</B>
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</P>
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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 HREF = "read_data.html">read_data</A>,
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<A HREF = "read_restart.html">read_restart</A>, or <A HREF = "create_box.html">create_box</A>
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command.
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</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 <I>bond</I>, 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.
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</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 HREF = "read_data.html">read_data</A> command.
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</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 HREF = "read_data.html">read_data</A>, <A HREF = "create_atoms.html">create_atoms</A>, and
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<A HREF = "set.html">set</A> commands for info on how to set these various
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quantities.
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD ><I>angle</I> </TD><TD > bonds and angles </TD><TD > bead-spring polymers with stiffness </TD></TR>
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<TR><TD ><I>atomic</I> </TD><TD > only the default values </TD><TD > coarse-grain liquids, solids, metals </TD></TR>
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<TR><TD ><I>body</I> </TD><TD > mass, inertia moments, quaternion, angular momentum </TD><TD > arbitrary bodies </TD></TR>
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<TR><TD ><I>bond</I> </TD><TD > bonds </TD><TD > bead-spring polymers </TD></TR>
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<TR><TD ><I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges </TD></TR>
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<TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > system with dipolar particles </TD></TR>
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<TR><TD ><I>electron</I> </TD><TD > charge and spin and eradius </TD><TD > electronic force field </TD></TR>
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<TR><TD ><I>ellipsoid</I> </TD><TD > shape, quaternion, angular momentum </TD><TD > aspherical particles </TD></TR>
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<TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
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<TR><TD ><I>line</I> </TD><TD > end points, angular velocity </TD><TD > rigid bodies </TD></TR>
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<TR><TD ><I>meso</I> </TD><TD > rho, e, cv </TD><TD > SPH particles </TD></TR>
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<TR><TD ><I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules </TD></TR>
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<TR><TD ><I>peri</I> </TD><TD > mass, volume </TD><TD > mesocopic Peridynamic models </TD></TR>
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<TR><TD ><I>sphere</I> </TD><TD > diameter, mass, angular velocity </TD><TD > granular models </TD></TR>
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<TR><TD ><I>tri</I> </TD><TD > corner points, angular momentum </TD><TD > rigid bodies </TD></TR>
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<TR><TD ><I>wavepacket</I> </TD><TD > charge, spin, eradius, etag, cs_re, cs_im </TD><TD > AWPMD
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</TD></TR></TABLE></DIV>
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<P>IMPORTANT NOTE: 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 HREF = "fix_property_atom.html">fix
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property/atom</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 HREF = "fix_property_atom.html">fix
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property/atom</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.
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</P>
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<P>All of the above styles define point particles, except the <I>sphere</I>,
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<I>ellipsoid</I>, <I>electron</I>, <I>peri</I>, <I>wavepacket</I>, <I>line</I>, <I>tri</I>, and
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<I>body</I> styles, which define finite-size particles. See <A HREF = "Section_howto.html#howto_14">Section_howto
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14</A> for an overview of using finite-size
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particle models with LAMMPS.
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</P>
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<P>All of the styles assign mass to particles on a per-type basis, using
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the <A HREF = "mass.html">mass</A> command, except for the finite-size particle
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styles. They assign mass to individual particles on a per-particle
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basis.
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</P>
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<P>For the <I>sphere</I> 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.
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</P>
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<P>For the <I>ellipsoid</I> 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.
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</P>
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<P>For the <I>electron</I> 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.
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</P>
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<P>For the <I>peri</I> style, the particles are spherical and each stores a
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per-particle mass and volume.
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</P>
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<P>The <I>meso</I> 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).
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</P>
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<P>The <I>wavepacket</I> style is similar to <I>electron</I>, 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 <I>etag</I> values.
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</P>
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<P>For the <I>line</I> 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).
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</P>
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<P>For the <I>tri</I> 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).
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</P>
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<P>For the <I>body</I> 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 <I>bstyle</I> 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.
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</P>
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<P>The <A HREF = "body.html">body</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.
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</P>
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<P>Note that there may be additional arguments required along with the
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<I>bstyle</I> specification, in the atom_style body command. These
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arguments are described in the <A HREF = "body.html">body</A> doc page.
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</P>
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<HR>
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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 <I>charge</I> style.
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If some atoms have bonds, but others do not, use the <I>bond</I> style.
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</P>
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<P>The only scenario where the <I>hybrid</I> 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.
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</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 HREF = "Section_modify.html">this section</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This command cannot be used after the simulation box is defined by a
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<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
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</P>
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<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
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MOLECULAR package. The <I>line</I> and <I>tri</I> styles are part of the
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ASPHERE pacakge. The <I>body</I> style is part of the BODY package. The
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<I>dipole</I> style is part of the DIPOLE package. The <I>peri</I> style is
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part of the PERI package for Peridynamics. The <I>electron</I> style is
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part of the USER-EFF package for <A HREF = "pair_eff.html">electronic force
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fields</A>. The <I>meso</I> style is part of the USER-SPH
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package for smoothed particle hydrodyanmics (SPH). See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF
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guide</A> to using SPH in LAMMPS. The
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<I>wavepacket</I> style is part of the USER-AWPMD package for the
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<A HREF = "pair_awpmd.html">antisymmetrized wave packet MD method</A>. They are
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only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "read_data.html">read_data</A>, <A HREF = "pair_style.html">pair_style</A>
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</P>
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<P><B>Default:</B>
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</P>
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<P>atom_style atomic
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</P>
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</HTML>
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