forked from lijiext/lammps
156 lines
6.4 KiB
Plaintext
156 lines
6.4 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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atom_style command :h3
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[Syntax:]
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atom_style style args :pre
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style = {angle} or {atomic} or {bond} or {charge} or {dipole} or \
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{electron} or {ellipsoid} or {full} or {line} or {meso} or \
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{molecular} or {peri} or {sphere} or {tri} or {hybrid} :ul
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args = none for any style except {hybrid}
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{hybrid} args = list of one or more sub-styles :pre
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[Examples:]
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atom_style atomic
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atom_style bond
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atom_style full
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atom_style hybrid charge bond :pre
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[Description:]
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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 "read_data"_read_data.html,
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"read_restart"_read_restart.html, or "create_box"_create_box.html
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command.
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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 {bond}, 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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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 "read_data"_read_data.html command.
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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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"read_data"_read_data.html, "create_atoms"_create_atoms.html, and
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"set"_set.html commands for info on how to set these various
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quantities.
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{angle} | bonds and angles | bead-spring polymers with stiffness |
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{atomic} | only the default values | coarse-grain liquids, solids, metals |
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{bond} | bonds | bead-spring polymers |
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{charge} | charge | atomic system with charges |
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{dipole} | charge and dipole moment | system with dipolar particles |
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{electron} | charge and spin and eradius | electronic force field |
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{ellipsoid} | shape, quaternion for particle orientation, angular momentum | extended aspherical particles |
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{full} | molecular + charge | bio-molecules |
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{line} | end points, angular velocity | rigid bodies |
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{meso} | rho, e, cv | SPH particles |
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{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
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{peri} | mass, volume | mesocopic Peridynamic models |
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{sphere} | diameter, mass, angular velocity | granular models |
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{tri} | corner points, angular momentum | rigid bodies |
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{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
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All of the styles assign mass to particles on a per-type basis, using
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the "mass"_mass.html command, except for the finite-size particle
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styles discussed below. They assign mass on a per-atom basis.
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All of the styles define point particles, except the {sphere},
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{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, and {tri}
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styles, which define finite-size particles.
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For the {sphere} 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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For the {ellipsoid} 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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For the {electron} 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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For the {peri} style, the particles are spherical and each stores a
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per-particle mass and volume.
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The {meso} 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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The {wavepacket} style is similar to {electron}, 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 {etag} values.
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For the {line} 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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For the {tri} 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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:line
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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 {charge} style.
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If some atoms have bonds, but others do not, use the {bond} style.
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The only scenario where the {hybrid} 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 be torqued and
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rotate, 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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LAMMPS can be extended with new atom styles; see "this
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section"_Section_modify.html.
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[Restrictions:]
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This command cannot be used after the simulation box is defined by a
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"read_data"_read_data.html or "create_box"_create_box.html command.
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The {angle}, {bond}, {full}, and {molecular} styles are part of the
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MOLECULAR package. The {dipole} style is part of the "dipole"
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package. The {peri} style is part of the PERI package for
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Peridynamics. The {electron} style is part of the USER-EFF package
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for "electronic force fields"_pair_eff.html. The {meso} style is part
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of the USER-SPH package for smoothed particle hydrodyanmics (SPH).
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See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
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LAMMPS. The {wavepacket} style is part of the USER-AWPMD package for
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the "antisymmetrized wave packet MD method"_pair_awpmd.html. They are
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only enabled if LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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[Related commands:]
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"read_data"_read_data.html, "pair_style"_pair_style.html
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[Default:]
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atom_style atomic
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