Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/doc/doc2/body.html
fbfd916c6998lammm-devel

Last Change
Raw File

body.html
View Options

<HTML>
<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>
</CENTER>
<HR>
<H3>Body particles
</H3>
<P><B>Overview:</B>
</P>
<P>This doc page is not about a LAMMPS input script command, but about
body particles, which are generalized finite-size particles.
Individual body particles can represent complex entities, such as
surface meshes of discrete points, collections of sub-particles,
deformable objects, etc. Note that other kinds of finite-size
spherical and aspherical particles are also supported by LAMMPS, such
as spheres, ellipsoids, line segments, and triangles, but they are
simpler entities that body particles. See <A HREF = "Section_howto.html#howto_14">Section_howto
14</A> for a general overview of all these
particle types.
</P>
<P>Body particles are used via the <A HREF = "atom_style.html">atom_style body</A>
command. It takes a body style as an argument. The current body
styles supported by LAMMPS are as follows. The name in the first
column is used as the <I>bstyle</I> argument for the <A HREF = "atom_style.html">atom_style
body</A> command.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD ><I>nparticle</I> </TD><TD > rigid body with N sub-particles
</TD></TR></TABLE></DIV>
<P>The body style determines what attributes are stored for each body and
thus how they can be used to compute pairwise body/body or
bond/non-body (point particle) interactions. More details of each
style are described below.
</P>
<P>We hope to add more styles in the future. See <A HREF = "Section_modify.html#mod_12">Section_modify
12</A> for details on how to add a new body
style to the code.
</P>
<HR>
<P><B>When to use body particles:</B>
</P>
<P>You should not use body particles to model a rigid body made of
simpler particles (e.g. point, sphere, ellipsoid, line segment,
triangular particles), if the interaction between pairs of rigid
bodies is just the summation of pairwise interactions between the
simpler particles. LAMMPS already supports this kind of model via the
<A HREF = "fix_rigid.html">fix rigid</A> command. Any of the numerous pair styles
that compute interactions between simpler particles can be used. The
<A HREF = "fix_rigid.html">fix rigid</A> command time integrates the motion of the
rigid bodies. All of the standard LAMMPS commands for thermostatting,
adding constraints, performing output, etc will operate as expected on
the simple particles.
</P>
<P>By contrast, when body particles are used, LAMMPS treats an entire
body as a single particle for purposes of computing pairwise
interactions, building neighbor lists, migrating particles between
processors, outputting particles to a dump file, etc. This means that
interactions between pairs of bodies or between a body and non-body
(point) particle need to be encoded in an appropriate pair style. If
such a pair style were to mimic the <A HREF = "fix_rigid.html">fix rigid</A> model,
it would need to loop over the entire collection of interactions
between pairs of simple particles within the two bodies, each time a
single body/body interaction was computed.
</P>
<P>Thus it only makes sense to use body particles and develop such a pair
style, when particle/particle interactions are more complex than what
the <A HREF = "fix_rigid.html">fix rigid</A> command can already calculate. For
example, if particles have one or more of the following attributes:
</P>
<UL><LI>represented by a surface mesh
<LI>represented by a collection of geometric entities (e.g. planes + spheres)
<LI>deformable
<LI>internal stress that induces fragmentation
</UL>
<P>then the interaction between pairs of particles is likely to be more
complex than the summation of simple sub-particle interactions. An
example is contact or frictional forces between particles with planar
sufaces that inter-penetrate.
</P>
<P>These are additional LAMMPS commands that can be used with body
particles of different styles
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR><TD ><A HREF = "fix_nve_body.html">fix nve/body</A> </TD><TD > integrate motion of a body particle</TD></TR>
<TR><TD ><A HREF = "compute_body_local.html">compute body/local</A> </TD><TD > store sub-particle attributes of a body particle</TD></TR>
<TR><TD ><A HREF = "dump.html">dump local</A> </TD><TD > output sub-particle attributes of a body particle
</TD></TR></TABLE></DIV>
<P>The pair styles defined for use with specific body styles are listed
in the sections below.
</P>
<HR>
<P><B>Specifics of body style nparticle:</B>
</P>
<P>The <I>nparticle</I> body style represents body particles as a rigid body
with a variable number N of sub-particles. It is provided as a
vanillia, prototypical example of a body particle, although as
mentioned above, the <A HREF = "fix_rigid.html">fix rigid</A> command already
duplicates its functionality.
</P>
<P>The atom_style body command for this body style takes two additional
arguments:
</P>
<PRE>atom_style body nparticle Nmin Nmax
Nmin = minimum # of sub-particles in any body in the system
Nmax = maximum # of sub-particles in any body in the system
</PRE>
<P>The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.
</P>
<P>When the <A HREF = "read_data.html">read_data</A> command reads a data file for this
body style, the following information must be provided for each entry
in the <I>Bodies</I> section of the data file:
</P>
<PRE>atom-ID 1 M
N
ixx iyy izz ixy ixz iyz x1 y1 z1 ...
...
... xN yN zN
</PRE>
<P>N is the number of sub-particles in the body particle. M = 6 + 3*N.
The integer line has a single value N. The floating point line(s)
list 6 moments of inertia followed by the coordinates of the N
sub-particles (x1 to zN) as 3N values on as many lines as required.
Note that this in not N lines, but 10 values per line; see the
<A HREF = "read_data.html">read_data</A> command for details. The 6 moments of
inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with
the current orientation of the rigid body around its center of mass.
The values are with respect to the simulation box XYZ axes, not with
respect to the prinicpal axes of the rigid body itself. LAMMPS
performs the latter calculation internally. The coordinates of each
sub-particle are specified as its x,y,z displacement from the
center-of-mass of the body particle. The center-of-mass position of
the particle is specified by the x,y,z values in the <I>Atoms</I> section
of the data file.
</P>
<P>The <A HREF = "pair_body.html">pair_style body</A> command can be used with this
body style to compute body/body and body/non-body interactions.
</P>
<P>For output purposes via the <A HREF = "compute_body_local.html">compute
body/local</A> and <A HREF = "dump.html">dump local</A>
commands, this body style produces one datum for each of the N
sub-particles in a body particle. The datum has 3 values:
</P>
<PRE>1 = x position of sub-particle
2 = y position of sub-particle
3 = z position of sub-particle
</PRE>
<P>These values are the current position of the sub-particle within the
simulation domain, not a displacement from the center-of-mass (COM) of
the body particle itself. These values are calculated using the
current COM and orientiation of the body particle.
</P>
</HTML>
c4science · Help