forked from lijiext/lammps
155 lines
6.5 KiB
Plaintext
155 lines
6.5 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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Body particles :h3
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[Overview:]
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This doc page is not about a LAMMPS input script command, but about
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body particles, which are generalized finite-size particles.
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Individual body particles can represent complex entities, such as
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surface meshes of discrete points, collections of sub-particles,
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deformable objects, etc. Note that other kinds of finite-size
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spherical and aspherical particles are also supported by LAMMPS, such
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as spheres, ellipsoids, line segments, and triangles, but they are
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simpler entities that body particles. See "Section_howto
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14"_Section_howto.html#howto_14 for a general overview of all these
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particle types.
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Body particles are used via the "atom_style body"_atom_style.html
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command. It takes a body style as an argument. The current body
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styles supported by LAMMPS are as follows. The name in the first
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column is used as the {bstyle} argument for the "atom_style
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body"_atom_style.html command.
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{nparticle} | rigid body with N sub-particles :tb(c=2,s=|)
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The body style determines what attributes are stored for each body and
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thus how they can be used to compute pairwise body/body or
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bond/non-body (point particle) interactions. More details of each
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style are described below.
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We hope to add more styles in the future. See "Section_modify
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12"_Section_modify.html#mod_12 for details on how to add a new body
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style to the code.
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:line
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[When to use body particles:]
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You should not use body particles to model a rigid body made of
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simpler particles (e.g. point, sphere, ellipsoid, line segment,
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triangular particles), if the interaction between pairs of rigid
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bodies is just the summation of pairwise interactions between the
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simpler particles. LAMMPS already supports this kind of model via the
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"fix rigid"_fix_rigid.html command. Any of the numerous pair styles
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that compute interactions between simpler particles can be used. The
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"fix rigid"_fix_rigid.html command time integrates the motion of the
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rigid bodies. All of the standard LAMMPS commands for thermostatting,
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adding constraints, performing output, etc will operate as expected on
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the simple particles.
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By contrast, when body particles are used, LAMMPS treats an entire
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body as a single particle for purposes of computing pairwise
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interactions, building neighbor lists, migrating particles between
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processors, outputting particles to a dump file, etc. This means that
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interactions between pairs of bodies or between a body and non-body
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(point) particle need to be encoded in an appropriate pair style. If
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such a pair style were to mimic the "fix rigid"_fix_rigid.html model,
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it would need to loop over the entire collection of interactions
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between pairs of simple particles within the two bodies, each time a
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single body/body interaction was computed.
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Thus it only makes sense to use body particles and develop such a pair
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style, when particle/particle interactions are more complex than what
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the "fix rigid"_fix_rigid.html command can already calculate. For
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example, if particles have one or more of the following attributes:
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represented by a surface mesh
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represented by a collection of geometric entities (e.g. planes + spheres)
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deformable
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internal stress that induces fragmentation :ul
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then the interaction between pairs of particles is likely to be more
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complex than the summation of simple sub-particle interactions. An
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example is contact or frictional forces between particles with planar
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sufaces that inter-penetrate.
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These are additional LAMMPS commands that can be used with body
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particles of different styles
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"fix nve/body"_fix_nve_body.html : integrate motion of a body particle
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"compute body/local"_compute_body_local.html : store sub-particle attributes of a body particle
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"dump local"_dump.html : output sub-particle attributes of a body particle :tb(s=:)
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The pair styles defined for use with specific body styles are listed
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in the sections below.
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:line
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[Specifics of body style nparticle:]
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The {nparticle} body style represents body particles as a rigid body
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with a variable number N of sub-particles. It is provided as a
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vanillia, prototypical example of a body particle, although as
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mentioned above, the "fix rigid"_fix_rigid.html command already
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duplicates its functionality.
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The atom_style body command for this body style takes two additional
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arguments:
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atom_style body nparticle Nmin Nmax
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Nmin = minimum # of sub-particles in any body in the system
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Nmax = maximum # of sub-particles in any body in the system :pre
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The Nmin and Nmax arguments are used to bound the size of data
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structures used internally by each particle.
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When the "read_data"_read_data.html command reads a data file for this
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body style, the following information must be provided for each entry
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in the {Bodies} section of the data file:
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atom-ID 1 M
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N
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ixx iyy izz ixy ixz iyz x1 y1 z1 ...
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...
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... xN yN zN :pre
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N is the number of sub-particles in the body particle. M = 6 + 3*N.
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The integer line has a single value N. The floating point line(s)
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list 6 moments of inertia followed by the coordinates of the N
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sub-particles (x1 to zN) as 3N values on as many lines as required.
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Note that this in not N lines, but 10 values per line; see the
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"read_data"_read_data.html command for details. The 6 moments of
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inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with
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the current orientation of the rigid body around its center of mass.
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The values are with respect to the simulation box XYZ axes, not with
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respect to the prinicpal axes of the rigid body itself. LAMMPS
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performs the latter calculation internally. The coordinates of each
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sub-particle are specified as its x,y,z displacement from the
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center-of-mass of the body particle. The center-of-mass position of
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the particle is specified by the x,y,z values in the {Atoms} section
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of the data file.
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The "pair_style body"_pair_body.html command can be used with this
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body style to compute body/body and body/non-body interactions.
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For output purposes via the "compute
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body/local"_compute_body_local.html and "dump local"_dump.html
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commands, this body style produces one datum for each of the N
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sub-particles in a body particle. The datum has 3 values:
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1 = x position of sub-particle
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2 = y position of sub-particle
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3 = z position of sub-particle :pre
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These values are the current position of the sub-particle within the
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simulation domain, not a displacement from the center-of-mass (COM) of
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the body particle itself. These values are calculated using the
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current COM and orientiation of the body particle.
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