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5
doc/Section_howto.html
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@ -1032,7 +1032,7 @@ particles. The following aspects are discussed in turn:
</UL>
<P>Example input scripts for these kinds of models are in the body,
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
<A HREF = "Section_examples.html">examples directory</A> in the LAMMPS distribution.
<A HREF = "Section_example.html">examples directory</A> in the LAMMPS distribution.
</P>
<H5>Atom styles
</H5>
@ -1204,6 +1204,7 @@ particles:
</P>
<UL><LI><A HREF = "dump.html">dump custom</A>
<LI><A HREF = "compute_property_atom.html">compute property/atom</A>
<LI><A HREF = "dump.html">dump local</A>
<LI><A HREF = "compute_body_local.html">compute body/local</A>
</UL>
<P>Attributes include the dipole moment, the angular velocity, the
@ -1368,7 +1369,7 @@ command.
</P>
<H5><A NAME = "fixoutput"></A>Fixes that write output files
</H5>
<P>Sevarl fixes take various quantities as input and can write output
<P>Several fixes take various quantities as input and can write output
files: <A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>,
<A HREF = "fix_ave_correlate.html">fix ave/correlate</A>, and <A HREF = "fix_print.html">fix

5
doc/Section_howto.txt
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@ -1023,7 +1023,7 @@ rigid bodies composed of finite-size particles :ul
Example input scripts for these kinds of models are in the body,
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
"examples directory"_Section_examples.html in the LAMMPS distribution.
"examples directory"_Section_example.html in the LAMMPS distribution.
Atom styles :h5
@ -1195,6 +1195,7 @@ particles:
"dump custom"_dump.html
"compute property/atom"_compute_property_atom.html
"dump local"_dump.html
"compute body/local"_compute_body_local.html :ul
Attributes include the dipole moment, the angular velocity, the
@ -1357,7 +1358,7 @@ command.
Fixes that write output files :h5,link(fixoutput)
Sevarl fixes take various quantities as input and can write output
Several fixes take various quantities as input and can write output
files: "fix ave/time"_fix_ave_time.html, "fix
ave/spatial"_fix_ave_spatial.html, "fix ave/histo"_fix_ave_histo.html,
"fix ave/correlate"_fix_ave_correlate.html, and "fix

6
doc/atom_style.html
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@ -18,10 +18,10 @@
<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>
</UL>
<PRE> args = none for any style except <I>body</I> and <I>hybrid</I>
<I>body</I> args = bstyle Nmin Nmax
<I>body</I> args = bstyle bstyle-args
bstyle = style of body particles
Nmin = minimum # of sub-particles in any body
Nmax = maximum # of sub-particles in any body
bstyle-args = additional arguments specific to the bstyle
see the <A HREF = "body.html">body</A> doc page for details
<I>hybrid</I> args = list of one or more sub-styles, each with their args
</PRE>
<P><B>Examples:</B>

6
doc/atom_style.txt
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@ -16,10 +16,10 @@ style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
{electron} or {ellipsoid} or {full} or {line} or {meso} or \
{molecular} or {peri} or {sphere} or {tri} or {hybrid} :ul
args = none for any style except {body} and {hybrid}
{body} args = bstyle Nmin Nmax
{body} args = bstyle bstyle-args
bstyle = style of body particles
Nmin = minimum # of sub-particles in any body
Nmax = maximum # of sub-particles in any body
bstyle-args = additional arguments specific to the bstyle
see the "body"_body.html doc page for details
{hybrid} args = list of one or more sub-styles, each with their args :pre
[Examples:]

170
doc/body.html
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@ -9,58 +9,148 @@
<HR>
<H3>body particles
<H3>Body particles
</H3>
<P><B>Description:</B>
<P><B>Overview:</B>
</P>
<P>This doc page is not about a specific LAMMPS input script command, but
about body particles,
<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>which are a specific kind of
<A HREF = "atom_style.html">atom_style</A> supported by LAMMPS
</P>
<P>These are the body styles that LAMMPS currently supports. The name in
the first column is used as the <I>bstyle</I> argument for atom_style body:
<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 > body with N sub-particles
<TR><TD ><I>nparticle</I> </TD><TD > rigid body with N sub-particles
</TD></TR></TABLE></DIV>
<P>Of course, the interactions
between pairs of bodies will need to be encoded in an appropriate pair
style.
<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>Body particles can represent complex entities,
such as surface meshes of discrete points, collections of
sub-particles, deformable objects, etc.
<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>
<P>By contrast, the <A HREF = "fix_rigid.html">fix rigid</A> command constructs rigid
bodies out of multiple particles. The particles can be point
particles or finite-size particles (spheres, ellipsoids, line
segments, triangles). The particles in each rigid body interact with
each other in the usual pairwise fashion via whatever pair style is
defined. The sum of these interactions determine the total force and
torque on each rigid body, which the <A HREF = "fix_rigid.html">fix rigid</A>
command then time integrates.
<HR>
<P><B>When to use body particles:</B>
</P>
<P><B>Syntax:</B>
<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>
<PRE>atom_style style args
</PRE>
<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>
<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>
<PRE> args = none for any style except <I>body</I> and <I>hybrid</I>
<I>body</I> args = bstyle
bstyle = style of body particles
<I>hybrid</I> args = list of one or more sub-styles, each with their args
</PRE>
<P><B>Examples:</B>
<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>
<PRE>atom_style atomic
atom_style bond
atom_style full
atom_style body nparticle 2 10
atom_style hybrid charge bond
atom_style hybrid charge body nparticle 2 5
<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
x1 y1 z1 ...
...
xN yN zN
</PRE>
<P>N is the number of sub-particles in the body particle. M = 3*N. The
integer line has a single value N. The floating point line(s) list
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
coordinates of each sub-particle are specified as its x,y,z
displacement from the center-of-mass of the body particle, which is
specified as its coordinates 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 compute body/local and dump local
commands, this body style produces one datum for each sub-particle in
a body particle. The datum has 3 values:
</P>
<P>1 = x position of sub-particle
2 = y position of sub-particle
3 = z position of sub-particle
</P>
<P>These 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, and the
displacement of the sub-particle from the COM.
</P>
</HTML>

158
doc/body.txt
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@ -6,62 +6,142 @@
:line
body particles :h3
Body particles :h3
[Description:]
[Overview:]
This doc page is not about a specific LAMMPS input script command, but
about body particles,
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 "Section_howto
14"_Section_howto.html#howto_14 for a general overview of all these
particle types.
Body particles are used via the "atom_style body"_atom_style.html
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 {bstyle} argument for the "atom_style
body"_atom_style.html command.
which are a specific kind of
"atom_style"_atom_style.html supported by LAMMPS
{nparticle} | rigid body with N sub-particles :tb(c=2,s=|)
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.
We hope to add more styles in the future. See "Section_modify
12"_Section_modify.html#mod_12 for details on how to add a new body
style to the code.
These are the body styles that LAMMPS currently supports. The name in
the first column is used as the {bstyle} argument for atom_style body:
:line
{nparticle} | body with N sub-particles :tb(c=2,s=|)
[When to use body particles:]
Of course, the interactions
between pairs of bodies will need to be encoded in an appropriate pair
style.
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
"fix rigid"_fix_rigid.html command. Any of the numerous pair styles
that compute interactions between simpler particles can be used. The
"fix rigid"_fix_rigid.html 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.
Body particles can represent complex entities,
such as surface meshes of discrete points, collections of
sub-particles, deformable objects, etc.
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 "fix rigid"_fix_rigid.html 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.
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 "fix rigid"_fix_rigid.html command can already calculate. For
example, if particles have one or more of the following attributes:
represented by a surface mesh
represented by a collection of geometric entities (e.g. planes + spheres)
deformable
internal stress that induces fragmentation :ul
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.
By contrast, the "fix rigid"_fix_rigid.html command constructs rigid
bodies out of multiple particles. The particles can be point
particles or finite-size particles (spheres, ellipsoids, line
segments, triangles). The particles in each rigid body interact with
each other in the usual pairwise fashion via whatever pair style is
defined. The sum of these interactions determine the total force and
torque on each rigid body, which the "fix rigid"_fix_rigid.html
command then time integrates.
These are additional LAMMPS commands that can be used with body
particles of different styles
[Syntax:]
"fix nve/body"_fix_nve_body.html : integrate motion of a body particle
"compute body/local"_compute_body_local.html : store sub-particle attributes of a body particle
"dump local"_dump.html : output sub-particle attributes of a body particle :tb(s=:)
atom_style style args :pre
The pair styles defined for use with specific body styles are listed
in the sections below.
style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
{electron} or {ellipsoid} or {full} or {line} or {meso} or \
{molecular} or {peri} or {sphere} or {tri} or {hybrid} :ul
args = none for any style except {body} and {hybrid}
{body} args = bstyle
bstyle = style of body particles
{hybrid} args = list of one or more sub-styles, each with their args :pre
:line
[Examples:]
[Specifics of body style nparticle:]
atom_style atomic
atom_style bond
atom_style full
atom_style body nparticle 2 10
atom_style hybrid charge bond
atom_style hybrid charge body nparticle 2 5 :pre
The {nparticle} 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 "fix rigid"_fix_rigid.html command already
duplicates its functionality.
The atom_style body command for this body style takes two additional
arguments:
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
The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.
When the "read_data"_read_data.html command reads a data file for this
body style, the following information must be provided for each entry
in the {Bodies} section of the data file:
atom-ID 1 M
N
x1 y1 z1 ...
...
xN yN zN :pre
N is the number of sub-particles in the body particle. M = 3*N. The
integer line has a single value N. The floating point line(s) list
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 "read_data"_read_data.html command for details. The
coordinates of each sub-particle are specified as its x,y,z
displacement from the center-of-mass of the body particle, which is
specified as its coordinates in the {Atoms} section of the data file.
The "pair_style body"_pair_body.html command can be used with this
body style to compute body/body and body/non-body interactions.
For output purposes via the compute body/local and dump local
commands, this body style produces one datum for each sub-particle in
a body particle. The datum has 3 values:
1 = x position of sub-particle
2 = y position of sub-particle
3 = z position of sub-particle
These 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, and the
displacement of the sub-particle from the COM.