git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9357 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Manual.html

@@ -194,8 +194,6 @@ it gives quick access to documentation for all LAMMPS commands.
   6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A> 
 <BR>
   6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A> 
-<BR>
-  6.22 <A HREF = "Section_howto.html#howto_22">Body particles</A> 
 <BR></UL>
 <LI><A HREF = "Section_example.html">Example problems</A> 
 
@@ -414,8 +412,6 @@ it gives quick access to documentation for all LAMMPS commands.
 
 
 
-
-
 
 
 

doc/Manual.txt

@@ -133,8 +133,7 @@ it gives quick access to documentation for all LAMMPS commands.
   6.18 "Elastic constants"_howto_18 :b
   6.19 "Library interface to LAMMPS"_howto_19 :b
   6.20 "Calculating thermal conductivity"_howto_20 :b
-  6.21 "Calculating viscosity"_howto_21 :b
+  6.21 "Calculating viscosity"_howto_21 :ule,b
-  6.22 "Body particles"_howto_22 :ule,b
 "Example problems"_Section_example.html :l
 "Performance & scalability"_Section_perf.html :l
 "Additional tools"_Section_tools.html :l
@@ -225,7 +224,6 @@ it gives quick access to documentation for all LAMMPS commands.
 :link(howto_19,Section_howto.html#howto_19)
 :link(howto_20,Section_howto.html#howto_20)
 :link(howto_21,Section_howto.html#howto_21)
-:link(howto_22,Section_howto.html#howto_22)
 
 :link(mod_1,Section_modify.html#mod_1)
 :link(mod_2,Section_modify.html#mod_2)

doc/Section_howto.html

@@ -1014,12 +1014,12 @@ profile consistent with the applied shear strain rate.
 
 <A NAME = "howto_14"></A><H4>6.14 Extended spherical and aspherical particles 
 </H4>
-<P>Typical MD models treat atoms or particles as point masses.
+<P>Typical MD models treat atoms or particles as point masses.  Sometimes
-Sometimes, however, it is desirable to have a model with finite-size
+it is desirable to have a model with finite-size particles such as
-particles such as spheres or aspherical ellipsoids.  The difference is
+spheroids or ellipsoids or generalized aspherical bodies.  The
-that such particles have a moment of inertia, rotational energy, and
+difference is that such particles have a moment of inertia, rotational
-angular momentum.  Rotation is induced by torque from interactions
+energy, and angular momentum.  Rotation is induced by torque coming
-with other particles.
+from interactions with other particles.
 </P>
 <P>LAMMPS has several options for running simulations with these kinds of
 particles.  The following aspects are discussed in turn:
@@ -1032,11 +1032,9 @@ particles.  The following aspects are discussed in turn:
 </UL>
 <H5>Atom styles 
 </H5>
-<P>There are 2 <A HREF = "atom_style.html">atom styles</A> that allow for definition of
+<P>There are several <A HREF = "atom_style.html">atom styles</A> that allow for
-finite-size particles: sphere and ellipsoid.  The peri atom style also
+definition of finite-size particles: sphere, dipole, ellipsoid, line,
-treats particles as having a volume, but that is internal to the
+tri, peri, and body.
-<A HREF = "pair_peri.html">pair_style peri</A> potentials.  The dipole atom style is
-most often used in conjunction with finite-size particles.
 </P>
 <P>The sphere style defines particles that are spheriods and each
 particle can have a unique diameter and mass (or density).  These
@@ -1044,6 +1042,18 @@ particles store an angular velocity (omega) and can be acted upon by
 torque.  The "set" command can be used to modify the diameter and mass
 of individual particles, after then are created.
 </P>
+<P>The dipole style does not actually define extended particles, but is
+often used in conjunction with spherical particles, via a command like
+</P>
+<PRE>atom_style hybrid sphere dipole 
+</PRE>
+<P>This is because when dipoles interact with each other, they induce
+torques, and a particle must be extended (i.e. have a moment of
+inertia) in order to respond and rotate.  See the <A HREF = "atom_style.html">atom_style
+dipole</A> command for details.  The "set" command can be
+used to modify the orientation and length of the dipole moment of
+individual particles, after then are created.
+</P>
 <P>The ellipsoid style defines particles that are ellipsoids and thus can
 be aspherical.  Each particle has a shape, specified by 3 diameters,
 and mass (or density).  These particles store an angular momentum and
@@ -1054,41 +1064,53 @@ The "set" command can be used to modify the diameter, orientation, and
 mass of individual particles, after then are created.  It also has a
 brief explanation of what quaternions are.
 </P>
-<P>The dipole style does not define extended particles, but is often
+<P>The line style defines line segment particles with two end points and
-used in conjunction with spherical particles, via a command like
+a mass (or density).  They can be used in 2d simulations, and they can
+be joined together to form rigid bodies which represent arbitrary
+polygons.
 </P>
-<PRE>atom_style hybrid sphere dipole 
+<P>The tri style defines triangular particles with three corner points
-</PRE>
+and a mass (or density).  They can be used in 3d simulations, and they
-<P>This is because when dipoles interact with each other, they induce
+can be joined together to form rigid bodies which represent arbitrary
-torques, and a particle must be extended (i.e. have a moment of
+particles with a triangulated surface.
-inertia) in order to respond and rotate.  See the <A HREF = "atom_style.html">atom_style
+</P>
-dipole</A> command for details.  The "set" command can be
+<P>The peri style is used with <A HREF = "pair_peri.html">Peridynamic models</A> and
-used to modify the orientation and length of the dipole moment of
+defines particles as having a volume, that is used internally in the
-individual particles, after then are created.
+<A HREF = "pair_peri.html">pair_style peri</A> potentials.
+</P>
+<P>The body style allows for definition of particles which can represent
+complex entities, such as surface meshes of discrete points,
+collections of sub-particles, deformable objects, etc.  The body style
+is discussed in more detail on the <A HREF = "body.html">body</A> doc page.
 </P>
 <P>Note that if one of these atom styles is used (or multiple styles via
 the <A HREF = "atom_style.html">atom_style hybrid</A> command), not all particles in
-the system are required to be finite-size or aspherical.  For example,
+the system are required to be finite-size or aspherical.
-if the 3 shape parameters are set to the same value, the particle will
-be a sphere rather than an ellipsoid.  If the 3 shape parameters are
-all set to 0.0 or if the diameter is set to 0.0, it will be a point
-particle.  If the length of the dipole moment is set to zero, the
-particle will not have a point dipole associated with it.  The pair
-styles used to compute pairwise interactions will typically compute
-the correct interaction in these simplified (cheaper) cases.
-<A HREF = "pair_hybrid.html">Pair_style hybrid</A> can be used to insure the correct
-interactions are computed for the appropriate style of interactions.
-Likewise, using groups to partition particles (ellipsoids versus
-spheres versus point particles) will allow you to use the appropriate
-time integrators and temperature computations for each class of
-particles.  See the doc pages for various commands for details.
 </P>
-<P>Also note that for <A HREF = "dimension.html">2d simulations</A>, finite-size
+<P>For example, in the ellipsoid style, if the 3 shape parameters are set
-spheres and ellipsoids are still treated as 3d particles, rather than
+to the same value, the particle will be a sphere rather than an
-as circular disks or ellipses.  This means they have the same moment
+ellipsoid.  If the 3 shape parameters are all set to 0.0 or if the
-of inertia for a 3d extended object.  When their temperature is
+diameter is set to 0.0, it will be a point particle.  In the line or
-coomputed, the correct degrees of freedom are used for rotation in a
+tri style, if the lineflag or triflag is specified as 0, then it
-2d versus 3d system.
+will be a point particle.
+</P>
+<P>Many of the pair styles used to compute pairwise interactions between
+extended particles typically compute the correct interaction in these
+simplified (cheaper) cases.  e.g. the interaction between a point
+particle and an extended particle or between two point particles.  If
+necessary, <A HREF = "pair_hybrid.html">pair_style hybrid</A> can be used to insure
+the correct interactions are computed for the appropriate style of
+interactions.  Likewise, using groups to partition particles
+(ellipsoids versus spheres versus point particles) will allow you to
+use the appropriate time integrators and temperature computations for
+each class of particles.  See the doc pages for various commands for
+details.
+</P>
+<P>Also note that for <A HREF = "dimension.html">2d simulations</A>, atom styles sphere
+and ellipsoid still use 3d particles, rather than as circular disks or
+ellipses.  This means they have the same moment of inertia as a 3d
+extended object.  When temperature is computed, the correct degrees of
+freedom are used for rotation in a 2d versus 3d system.
 </P>
 <H5>Pair potentials 
 </H5>
@@ -1103,29 +1125,33 @@ that generate torque:
 <LI><A HREF = "pair_dipole.html">pair_style dipole/cut</A>
 <LI><A HREF = "pair_gayberne.html">pair_style gayberne</A>
 <LI><A HREF = "pair_resquared.html">pair_style resquared</A>
-<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> 
+<LI><A HREF = "pair_brownian.html">pair_style brownian</A>
+<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A>
+<LI><A HREF = "pair_line_lj.html">pair_style line/lj</A>
+<LI><A HREF = "pair_tri_lj.html">pair_style tri/lj</A>
+<LI><A HREF = "pair_body.html">pair_style body</A> 
 </UL>
-<P>The <A HREF = "pair_gran.html">granular pair styles</A> are used with spherical
+<P>The granular pair styles are used with spherical particles.  The
-particles.  The <A HREF = "pair_dipole.html">dipole pair style</A> is used with
+dipole pair style is used with the dipole atom style, which could be
-<A HREF = "atom_style.html">atom_style dipole</A>, which could be applied to
+applied to spherical or ellipsoidal particles.  The GayBerne and
-spherical or ellipsoidal particles.  The <A HREF = "pair_gayberne.html">GayBerne</A>
+REsquared potentials require ellipsoidal particles, though they will
-and <A HREF = "pair_resquared.html">REsquared</A> potentials require ellipsoidal
+also work if the 3 shape parameters are the same (a sphere).  The
-particles, though they will also work if the 3 shape parameters are
+Brownian and lubrication potentials are used with spherical particles.
-the same (a sphere).  The <A HREF = "pair_lubricate.html">lubrication potential</A>
+The line, tri, and body potentials are used with line segment,
-works with spherical particles.
+triangular, and body particles respectively.
 </P>
 <H5>Time integration 
 </H5>
-<P>There are 3 fixes that perform time integration on extended spherical
+<P>There are several fixes that perform time integration on extended
-particles, meaning the integrators update the rotational orientation
+spherical particles, meaning the integrators update the rotational
-and angular velocity or angular momentum of the particles:
+orientation and angular velocity or angular momentum of the particles:
 </P>
 <UL><LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
 <LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
 <LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A> 
 </UL>
 <P>Likewise, there are 3 fixes that perform time integration on
-ellipsoids as extended aspherical particles:
+ellipsoidal particles:
 </P>
 <UL><LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
 <LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
@@ -1133,19 +1159,27 @@ ellipsoids as extended aspherical particles:
 </UL>
 <P>The advantage of these fixes is that those which thermostat the
 particles include the rotational degrees of freedom in the temperature
-calculation and thermostatting.  Other thermostats can be used with
+calculation and thermostatting.  The <A HREF = "fix_langevin">fix langevin</A>
-fix nve/sphere or fix nve/asphere, such as fix langevin or fix
+command can also be used with its <I>omgea</I> or <I>angmom</I> options to
-temp/berendsen, but those thermostats only operate on the
+thermostat the rotational degrees of freedom for spherical or
-translational kinetic energy of the extended particles.
+ellipsoidal particles.  Other thermostatting fixes only operate on the
+translational kinetic energy of extended particles.
 </P>
-<P>Note that for mixtures of point and extended particles, you should
+<P>These fixes perform constant NVE time integration on line segment,
-only use these integration fixes on <A HREF = "group.html">groups</A> which contain
+triangular, and body particles:
-extended particles.
+</P>
+<UL><LI><A HREF = "fix_nve_line.html">fix nve/line</A>
+<LI><A HREF = "fix_nve_tri.html">fix nve/tri</A>
+<LI><A HREF = "fix_nve_body.html">fix nve/body</A> 
+</UL>
+<P>Note that for mixtures of point and extended particles, these
+integration fixes can only be used with <A HREF = "group.html">groups</A> which
+contain extended particles.
 </P>
 <H5>Computes, thermodynamics, and dump output 
 </H5>
-<P>There are 4 computes that calculate the temperature or rotational energy
+<P>There are several computes that calculate the temperature or
-of extended spherical or aspherical particles (ellipsoids):
+rotational energy of spherical or ellipsoidal particles:
 </P>
 <UL><LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
 <LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
@@ -1156,15 +1190,22 @@ of extended spherical or aspherical particles (ellipsoids):
 you wish the thermodynamic output of temperature or pressure to use
 one of these computes (e.g. for a system entirely composed of extended
 particles), then the compute can be defined and the
-<A HREF = "thermo_modify.html">thermo_modify</A> command used.  Note that by
+<A HREF = "thermo_modify.html">thermo_modify</A> command used.  Note that by default
-default thermodynamic quantities will be calculated with a temperature
+thermodynamic quantities will be calculated with a temperature that
-that only includes translational degrees of freedom.  See the
+only includes translational degrees of freedom.  See the
 <A HREF = "thermo_style.html">thermo_style</A> command for details.
 </P>
-<P>The <A HREF = "dump.html">dump custom</A> command can output various attributes of
+<P>These commands can be used to output various attributes
-extended particles, including the dipole moment (mu), the angular
+of extended particles:
-velocity (omega), the angular momentum (angmom), the quaternion
+</P>
-(quat), and the torque (tq) on the particle.
+<UL><LI><A HREF = "dump.html">dump custom</A>
+<LI><A HREF = "compute_property_atom.html">compute property/atom</A>
+<LI><A HREF = "compute_body_local.html">compute body/local</A> 
+</UL>
+<P>Attributes include the dipole moment, the angular velocity, the
+angular momentum, the quaternion, the torque, the end-point and
+corner-point coordinates (for line and tri particles), and
+sub-particle attributes of body particles.
 </P>
 <H5>Rigid bodies composed of extended particles 
 </H5>
@@ -1174,14 +1215,15 @@ force and torque on the rigid body each timestep due to forces on its
 constituent particles, and integrates the motion of the rigid body.
 </P>
 <P>If any of the constituent particles of a rigid body are extended
-particles (spheres or ellipsoids), then their contribution to the
+particles (spheres or ellipsoids or line segments or triangles), then
-inertia tensor of the body is different than if they were point
+their contribution to the inertia tensor of the body is different than
-particles.  This means the rotational dynamics of the rigid body will
+if they were point particles.  This means the rotational dynamics of
-be different.  Thus a model of a dimer is different if the dimer
+the rigid body will be different.  Thus a model of a dimer is
-consists of two point masses versus two extended sphereoids, even if
+different if the dimer consists of two point masses versus two
-the two particles have the same mass.  Extended particles that
+extended sphereoids, even if the two particles have the same mass.
-experience torque due to their interaction with other particles will
+Extended particles that experience torque due to their interaction
-also impart that torque to a rigid body they are part of.
+with other particles will also impart that torque to a rigid body they
+are part of.
 </P>
 <P>See the "fix rigid" command for example of complex rigid-body models
 it is possible to define in LAMMPS.
@@ -1190,6 +1232,15 @@ it is possible to define in LAMMPS.
 treat 2, 3, or 4 particles as a rigid body, but it always assumes the
 particles are point masses.
 </P>
+<P>Also note that body particles cannot be modeled with the <A HREF = "fix_rigid.html">fix
+rigid</A> command.  Body particles are treated by LAMMPS
+as single particles, though they can store internal state, such as a
+list of sub-particles.  Individual body partices are typically treated
+as rigid bodies, and their motion integrated with a command like <A HREF = "fix_nve_body.html">fix
+nve/body</A>.  Interactions between pairs of body
+particles are computed via a command like <A HREF = "pair_body.html">pair_style
+body</A>.
+</P>
 <HR>
 
 <A NAME = "howto_15"></A><H4>6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) 
@@ -2009,6 +2060,8 @@ print        "average viscosity: $v [Pa.s/</B> @ $T K, ${ndens} /A^3"
 
 <HR>
 
+<HR>
+
 <A NAME = "Berendsen"></A>
 
 <P><B>(Berendsen)</B> Berendsen, Grigera, Straatsma, J Phys Chem, 91,

doc/Section_howto.txt

@@ -1005,12 +1005,12 @@ An alternative method for calculating viscosities is provided via the
 
 6.14 Extended spherical and aspherical particles :link(howto_14),h4
 
-Typical MD models treat atoms or particles as point masses.
+Typical MD models treat atoms or particles as point masses.  Sometimes
-Sometimes, however, it is desirable to have a model with finite-size
+it is desirable to have a model with finite-size particles such as
-particles such as spheres or aspherical ellipsoids.  The difference is
+spheroids or ellipsoids or generalized aspherical bodies.  The
-that such particles have a moment of inertia, rotational energy, and
+difference is that such particles have a moment of inertia, rotational
-angular momentum.  Rotation is induced by torque from interactions
+energy, and angular momentum.  Rotation is induced by torque coming
-with other particles.
+from interactions with other particles.
 
 LAMMPS has several options for running simulations with these kinds of
 particles.  The following aspects are discussed in turn:
@@ -1023,11 +1023,9 @@ rigid bodies composed of extended particles :ul
 
 Atom styles :h5
 
-There are 2 "atom styles"_atom_style.html that allow for definition of
+There are several "atom styles"_atom_style.html that allow for
-finite-size particles: sphere and ellipsoid.  The peri atom style also
+definition of finite-size particles: sphere, dipole, ellipsoid, line,
-treats particles as having a volume, but that is internal to the
+tri, peri, and body.
-"pair_style peri"_pair_peri.html potentials.  The dipole atom style is
-most often used in conjunction with finite-size particles.
 
 The sphere style defines particles that are spheriods and each
 particle can have a unique diameter and mass (or density).  These
@@ -1035,6 +1033,18 @@ particles store an angular velocity (omega) and can be acted upon by
 torque.  The "set" command can be used to modify the diameter and mass
 of individual particles, after then are created.
 
+The dipole style does not actually define extended particles, but is
+often used in conjunction with spherical particles, via a command like
+
+atom_style hybrid sphere dipole :pre
+
+This is because when dipoles interact with each other, they induce
+torques, and a particle must be extended (i.e. have a moment of
+inertia) in order to respond and rotate.  See the "atom_style
+dipole"_atom_style.html command for details.  The "set" command can be
+used to modify the orientation and length of the dipole moment of
+individual particles, after then are created.
+
 The ellipsoid style defines particles that are ellipsoids and thus can
 be aspherical.  Each particle has a shape, specified by 3 diameters,
 and mass (or density).  These particles store an angular momentum and
@@ -1045,41 +1055,53 @@ The "set" command can be used to modify the diameter, orientation, and
 mass of individual particles, after then are created.  It also has a
 brief explanation of what quaternions are.
 
-The dipole style does not define extended particles, but is often
+The line style defines line segment particles with two end points and
-used in conjunction with spherical particles, via a command like
+a mass (or density).  They can be used in 2d simulations, and they can
+be joined together to form rigid bodies which represent arbitrary
+polygons.
 
-atom_style hybrid sphere dipole :pre
+The tri style defines triangular particles with three corner points
+and a mass (or density).  They can be used in 3d simulations, and they
+can be joined together to form rigid bodies which represent arbitrary
+particles with a triangulated surface.
 
-This is because when dipoles interact with each other, they induce
+The peri style is used with "Peridynamic models"_pair_peri.html and
-torques, and a particle must be extended (i.e. have a moment of
+defines particles as having a volume, that is used internally in the
-inertia) in order to respond and rotate.  See the "atom_style
+"pair_style peri"_pair_peri.html potentials.
-dipole"_atom_style.html command for details.  The "set" command can be
+
-used to modify the orientation and length of the dipole moment of
+The body style allows for definition of particles which can represent
-individual particles, after then are created.
+complex entities, such as surface meshes of discrete points,
+collections of sub-particles, deformable objects, etc.  The body style
+is discussed in more detail on the "body"_body.html doc page.
 
 Note that if one of these atom styles is used (or multiple styles via
 the "atom_style hybrid"_atom_style.html command), not all particles in
-the system are required to be finite-size or aspherical.  For example,
+the system are required to be finite-size or aspherical.
-if the 3 shape parameters are set to the same value, the particle will
-be a sphere rather than an ellipsoid.  If the 3 shape parameters are
-all set to 0.0 or if the diameter is set to 0.0, it will be a point
-particle.  If the length of the dipole moment is set to zero, the
-particle will not have a point dipole associated with it.  The pair
-styles used to compute pairwise interactions will typically compute
-the correct interaction in these simplified (cheaper) cases.
-"Pair_style hybrid"_pair_hybrid.html can be used to insure the correct
-interactions are computed for the appropriate style of interactions.
-Likewise, using groups to partition particles (ellipsoids versus
-spheres versus point particles) will allow you to use the appropriate
-time integrators and temperature computations for each class of
-particles.  See the doc pages for various commands for details.
 
-Also note that for "2d simulations"_dimension.html, finite-size
+For example, in the ellipsoid style, if the 3 shape parameters are set
-spheres and ellipsoids are still treated as 3d particles, rather than
+to the same value, the particle will be a sphere rather than an
-as circular disks or ellipses.  This means they have the same moment
+ellipsoid.  If the 3 shape parameters are all set to 0.0 or if the
-of inertia for a 3d extended object.  When their temperature is
+diameter is set to 0.0, it will be a point particle.  In the line or
-coomputed, the correct degrees of freedom are used for rotation in a
+tri style, if the lineflag or triflag is specified as 0, then it
-2d versus 3d system.
+will be a point particle.
+
+Many of the pair styles used to compute pairwise interactions between
+extended particles typically compute the correct interaction in these
+simplified (cheaper) cases.  e.g. the interaction between a point
+particle and an extended particle or between two point particles.  If
+necessary, "pair_style hybrid"_pair_hybrid.html can be used to insure
+the correct interactions are computed for the appropriate style of
+interactions.  Likewise, using groups to partition particles
+(ellipsoids versus spheres versus point particles) will allow you to
+use the appropriate time integrators and temperature computations for
+each class of particles.  See the doc pages for various commands for
+details.
+
+Also note that for "2d simulations"_dimension.html, atom styles sphere
+and ellipsoid still use 3d particles, rather than as circular disks or
+ellipses.  This means they have the same moment of inertia as a 3d
+extended object.  When temperature is computed, the correct degrees of
+freedom are used for rotation in a 2d versus 3d system.
 
 Pair potentials :h5
 
@@ -1094,29 +1116,33 @@ that generate torque:
 "pair_style dipole/cut"_pair_dipole.html
 "pair_style gayberne"_pair_gayberne.html
 "pair_style resquared"_pair_resquared.html
-"pair_style lubricate"_pair_lubricate.html :ul
+"pair_style brownian"_pair_brownian.html
+"pair_style lubricate"_pair_lubricate.html
+"pair_style line/lj"_pair_line_lj.html
+"pair_style tri/lj"_pair_tri_lj.html
+"pair_style body"_pair_body.html :ul
 
-The "granular pair styles"_pair_gran.html are used with spherical
+The granular pair styles are used with spherical particles.  The
-particles.  The "dipole pair style"_pair_dipole.html is used with
+dipole pair style is used with the dipole atom style, which could be
-"atom_style dipole"_atom_style.html, which could be applied to
+applied to spherical or ellipsoidal particles.  The GayBerne and
-spherical or ellipsoidal particles.  The "GayBerne"_pair_gayberne.html
+REsquared potentials require ellipsoidal particles, though they will
-and "REsquared"_pair_resquared.html potentials require ellipsoidal
+also work if the 3 shape parameters are the same (a sphere).  The
-particles, though they will also work if the 3 shape parameters are
+Brownian and lubrication potentials are used with spherical particles.
-the same (a sphere).  The "lubrication potential"_pair_lubricate.html
+The line, tri, and body potentials are used with line segment,
-works with spherical particles.
+triangular, and body particles respectively.
 
 Time integration :h5
 
-There are 3 fixes that perform time integration on extended spherical
+There are several fixes that perform time integration on extended
-particles, meaning the integrators update the rotational orientation
+spherical particles, meaning the integrators update the rotational
-and angular velocity or angular momentum of the particles:
+orientation and angular velocity or angular momentum of the particles:
 
 "fix nve/sphere"_fix_nve_sphere.html
 "fix nvt/sphere"_fix_nvt_sphere.html
 "fix npt/sphere"_fix_npt_sphere.html :ul
 
 Likewise, there are 3 fixes that perform time integration on
-ellipsoids as extended aspherical particles:
+ellipsoidal particles:
 
 "fix nve/asphere"_fix_nve_asphere.html
 "fix nvt/asphere"_fix_nvt_asphere.html
@@ -1124,19 +1150,27 @@ ellipsoids as extended aspherical particles:
 
 The advantage of these fixes is that those which thermostat the
 particles include the rotational degrees of freedom in the temperature
-calculation and thermostatting.  Other thermostats can be used with
+calculation and thermostatting.  The "fix langevin"_fix_langevin
-fix nve/sphere or fix nve/asphere, such as fix langevin or fix
+command can also be used with its {omgea} or {angmom} options to
-temp/berendsen, but those thermostats only operate on the
+thermostat the rotational degrees of freedom for spherical or
-translational kinetic energy of the extended particles.
+ellipsoidal particles.  Other thermostatting fixes only operate on the
+translational kinetic energy of extended particles.
 
-Note that for mixtures of point and extended particles, you should
+These fixes perform constant NVE time integration on line segment,
-only use these integration fixes on "groups"_group.html which contain
+triangular, and body particles:
-extended particles.
+
+"fix nve/line"_fix_nve_line.html
+"fix nve/tri"_fix_nve_tri.html
+"fix nve/body"_fix_nve_body.html :ul
+
+Note that for mixtures of point and extended particles, these
+integration fixes can only be used with "groups"_group.html which
+contain extended particles.
 
 Computes, thermodynamics, and dump output :h5
 
-There are 4 computes that calculate the temperature or rotational energy
+There are several computes that calculate the temperature or
-of extended spherical or aspherical particles (ellipsoids):
+rotational energy of spherical or ellipsoidal particles:
 
 "compute temp/sphere"_compute_temp_sphere.html
 "compute temp/asphere"_compute_temp_asphere.html
@@ -1147,15 +1181,22 @@ These include rotational degrees of freedom in their computation.  If
 you wish the thermodynamic output of temperature or pressure to use
 one of these computes (e.g. for a system entirely composed of extended
 particles), then the compute can be defined and the
-"thermo_modify"_thermo_modify.html command used.  Note that by
+"thermo_modify"_thermo_modify.html command used.  Note that by default
-default thermodynamic quantities will be calculated with a temperature
+thermodynamic quantities will be calculated with a temperature that
-that only includes translational degrees of freedom.  See the
+only includes translational degrees of freedom.  See the
 "thermo_style"_thermo_style.html command for details.
 
-The "dump custom"_dump.html command can output various attributes of
+These commands can be used to output various attributes
-extended particles, including the dipole moment (mu), the angular
+of extended particles:
-velocity (omega), the angular momentum (angmom), the quaternion
+
-(quat), and the torque (tq) on the particle.
+"dump custom"_dump.html
+"compute property/atom"_compute_property_atom.html
+"compute body/local"_compute_body_local.html :ul
+
+Attributes include the dipole moment, the angular velocity, the
+angular momentum, the quaternion, the torque, the end-point and
+corner-point coordinates (for line and tri particles), and
+sub-particle attributes of body particles.
 
 Rigid bodies composed of extended particles :h5
 
@@ -1165,14 +1206,15 @@ force and torque on the rigid body each timestep due to forces on its
 constituent particles, and integrates the motion of the rigid body.
 
 If any of the constituent particles of a rigid body are extended
-particles (spheres or ellipsoids), then their contribution to the
+particles (spheres or ellipsoids or line segments or triangles), then
-inertia tensor of the body is different than if they were point
+their contribution to the inertia tensor of the body is different than
-particles.  This means the rotational dynamics of the rigid body will
+if they were point particles.  This means the rotational dynamics of
-be different.  Thus a model of a dimer is different if the dimer
+the rigid body will be different.  Thus a model of a dimer is
-consists of two point masses versus two extended sphereoids, even if
+different if the dimer consists of two point masses versus two
-the two particles have the same mass.  Extended particles that
+extended sphereoids, even if the two particles have the same mass.
-experience torque due to their interaction with other particles will
+Extended particles that experience torque due to their interaction
-also impart that torque to a rigid body they are part of.
+with other particles will also impart that torque to a rigid body they
+are part of.
 
 See the "fix rigid" command for example of complex rigid-body models
 it is possible to define in LAMMPS.
@@ -1181,6 +1223,15 @@ Note that the "fix shake"_fix_shake.html command can also be used to
 treat 2, 3, or 4 particles as a rigid body, but it always assumes the
 particles are point masses.
 
+Also note that body particles cannot be modeled with the "fix
+rigid"_fix_rigid.html command.  Body particles are treated by LAMMPS
+as single particles, though they can store internal state, such as a
+list of sub-particles.  Individual body partices are typically treated
+as rigid bodies, and their motion integrated with a command like "fix
+nve/body"_fix_nve_body.html.  Interactions between pairs of body
+particles are computed via a command like "pair_style
+body"_pair_body.html.
+
 :line
 
 6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(howto_15),h4
@@ -1992,6 +2043,8 @@ variable     v equal (v_v11+v_v22+v_v33)/3.0
 variable     ndens equal count(all)/vol
 print        "average viscosity: $v \[Pa.s/] @ $T K, $\{ndens\} /A^3" :pre
 
+:line
+
 :line
 :line
 

doc/Section_modify.html

@@ -507,10 +507,10 @@ Body particles can represent complex entities, such as surface meshes
 of discrete points, collections of sub-particles, deformable objects,
 etc.
 </P>
-<P>See <A HREF = "Section_howto.html">Section_howto 22</A> of the manual for an
+<P>See <A HREF = "Section_howto.html#howto_14">Section_howto 14</A> of the manual for
-overview of using body particles and the <A HREF = "body.html">body</A> doc page for
+an overview of using body particles and the <A HREF = "body.html">body</A> doc page
-details on the various body styles LAMMPS supports.  New styles can be
+for details on the various body styles LAMMPS supports.  New styles
-created to add new kinds of body particles to LAMMPS.
+can be created to add new kinds of body particles to LAMMPS.
 </P>
 <P>Body_nparticle.cpp is an example of a body particle that is treated as
 a rigid body containing N sub-particles.

doc/Section_modify.txt

@@ -484,10 +484,10 @@ Body particles can represent complex entities, such as surface meshes
 of discrete points, collections of sub-particles, deformable objects,
 etc.
 
-See "Section_howto 22"_Section_howto.html of the manual for an
+See "Section_howto 14"_Section_howto.html#howto_14 of the manual for
-overview of using body particles and the "body"_body.html doc page for
+an overview of using body particles and the "body"_body.html doc page
-details on the various body styles LAMMPS supports.  New styles can be
+for details on the various body styles LAMMPS supports.  New styles
-created to add new kinds of body particles to LAMMPS.
+can be created to add new kinds of body particles to LAMMPS.
 
 Body_nparticle.cpp is an example of a body particle that is treated as
 a rigid body containing N sub-particles.

doc/compute_body_local.html

@@ -39,8 +39,9 @@ compute 1 all body/local 3 6
 sub-particles.  The number of datums generated, aggregated across all
 processors, equals the number of body sub-particles plus the number of
 non-body particles in the system, modified by the group parameter as
-explained below.  See <A HREF = "Section_howto.html">Section_howto 22</A> of the
+explained below.  See <A HREF = "Section_howto.html#howto_14">Section_howto 14</A>
-manual for an overview of using body particles.
+of the manual and the <A HREF = "body.html">body</A> doc page for more details on
+using body particles.
 </P>
 <P>The local data stored by this command is generated by looping over all
 the atoms.  An atom will only be included if it is in the group.  If

doc/compute_body_local.txt

@@ -31,8 +31,9 @@ Define a computation that calculates properties of individual body
 sub-particles.  The number of datums generated, aggregated across all
 processors, equals the number of body sub-particles plus the number of
 non-body particles in the system, modified by the group parameter as
-explained below.  See "Section_howto 22"_Section_howto.html of the
+explained below.  See "Section_howto 14"_Section_howto.html#howto_14
-manual for an overview of using body particles.
+of the manual and the "body"_body.html doc page for more details on
+using body particles.
 
 The local data stored by this command is generated by looping over all
 the atoms.  An atom will only be included if it is in the group.  If

doc/fix_nve_body.html

@@ -27,9 +27,9 @@
 <P>Perform constant NVE integration to update position, velocity,
 orientation, and angular velocity for body particles in the group each
 timestep.  V is volume; E is energy.  This creates a system trajectory
-consistent with the microcanonical ensemble.  See <A HREF = "Section_howto.html">Section_howto
+consistent with the microcanonical ensemble.  See <A HREF = "Section_howto.html#howto_14">Section_howto
-22</A> of the manual for an overview of using body
+14</A> of the manual and the <A HREF = "body.html">body</A>
-particles.
+doc page for more details on using body particles.
 </P>
 <P>This fix differs from the <A HREF = "fix_nve.html">fix nve</A> command, which
 assumes point particles and only updates their position and velocity.

doc/fix_nve_body.txt

@@ -25,8 +25,8 @@ Perform constant NVE integration to update position, velocity,
 orientation, and angular velocity for body particles in the group each
 timestep.  V is volume; E is energy.  This creates a system trajectory
 consistent with the microcanonical ensemble.  See "Section_howto
-22"_Section_howto.html of the manual for an overview of using body
+14"_Section_howto.html#howto_14 of the manual and the "body"_body.html
-particles.
+doc page for more details on using body particles.
 
 This fix differs from the "fix nve"_fix_nve.html command, which
 assumes point particles and only updates their position and velocity.

doc/pair_body.html

@@ -27,8 +27,9 @@ pair_coeff 1 1 1.0 1.5 2.5
 </P>
 <P>Style <I>body</I> is for use with body particles and calculates pairwise
 body/body interactions as well as interactions between body and
-point-particles.  See <A HREF = "Section_howto.html">Section_howto 22</A> of the
+point-particles.  See <A HREF = "Section_howto.html#howto_14">Section_howto 14</A>
-manual for an overview of using body particles.
+of the manual and the <A HREF = "body.html">body</A> doc page for more details on
+using body particles.
 </P>
 <P>This pair style is designed for use with the "nparticle" body style,
 which is specified as an argument to the "atom-style body" command.

doc/pair_body.txt

@@ -24,8 +24,9 @@ pair_coeff 1 1 1.0 1.5 2.5 :pre
 
 Style {body} is for use with body particles and calculates pairwise
 body/body interactions as well as interactions between body and
-point-particles.  See "Section_howto 22"_Section_howto.html of the
+point-particles.  See "Section_howto 14"_Section_howto.html#howto_14
-manual for an overview of using body particles.
+of the manual and the "body"_body.html doc page for more details on
+using body particles.
 
 This pair style is designed for use with the "nparticle" body style,
 which is specified as an argument to the "atom-style body" command.