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4
doc/Manual.html
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@ -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.

4
doc/Manual.txt
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@ -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
6.22 "Body particles"_howto_22 :ule,b
6.21 "Calculating viscosity"_howto_21 :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)

207
doc/Section_howto.html
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@ -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.
Sometimes, however, it is desirable to have a model with finite-size
particles such as spheres or aspherical ellipsoids. The difference is
that such particles have a moment of inertia, rotational energy, and
angular momentum. Rotation is induced by torque from interactions
with other particles.
<P>Typical MD models treat atoms or particles as point masses. Sometimes
it is desirable to have a model with finite-size particles such as
spheroids or ellipsoids or generalized aspherical bodies. The
difference is that such particles have a moment of inertia, rotational
energy, and angular momentum. Rotation is induced by torque coming
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
finite-size particles: sphere and ellipsoid. The peri atom style also
treats particles as having a volume, but that is internal to the
<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>There are several <A HREF = "atom_style.html">atom styles</A> that allow for
definition of finite-size particles: sphere, dipole, ellipsoid, line,
tri, peri, and body.
</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
used in conjunction with spherical particles, via a command like
<P>The line style defines line segment particles with two end points and
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
</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>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.
</P>
<P>The peri style is used with <A HREF = "pair_peri.html">Peridynamic models</A> and
defines particles as having a volume, that is used internally in the
<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,
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.
the system are required to be finite-size or aspherical.
</P>
<P>Also note that for <A HREF = "dimension.html">2d simulations</A>, finite-size
spheres and ellipsoids are still treated as 3d particles, rather than
as circular disks or ellipses. This means they have the same moment
of inertia for a 3d extended object. When their temperature is
coomputed, the correct degrees of freedom are used for rotation in a
2d versus 3d system.
<P>For example, in the ellipsoid style, 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. In the line or
tri style, if the lineflag or triflag is specified as 0, then it
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_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
particles. The <A HREF = "pair_dipole.html">dipole pair style</A> is used with
<A HREF = "atom_style.html">atom_style dipole</A>, which could be applied to
spherical or ellipsoidal particles. The <A HREF = "pair_gayberne.html">GayBerne</A>
and <A HREF = "pair_resquared.html">REsquared</A> potentials require ellipsoidal
particles, though they will also work if the 3 shape parameters are
the same (a sphere). The <A HREF = "pair_lubricate.html">lubrication potential</A>
works with spherical particles.
<P>The granular pair styles are used with spherical particles. The
dipole pair style is used with the dipole atom style, which could be
applied to spherical or ellipsoidal particles. The GayBerne and
REsquared potentials require ellipsoidal particles, though they will
also work if the 3 shape parameters are the same (a sphere). The
Brownian and lubrication potentials are used with spherical particles.
The line, tri, and body potentials are used with line segment,
triangular, and body particles respectively.
</P>
<H5>Time integration
</H5>
<P>There are 3 fixes that perform time integration on extended spherical
particles, meaning the integrators update the rotational orientation
and angular velocity or angular momentum of the particles:
<P>There are several fixes that perform time integration on extended
spherical particles, meaning the integrators update the rotational
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
fix nve/sphere or fix nve/asphere, such as fix langevin or fix
temp/berendsen, but those thermostats only operate on the
translational kinetic energy of the extended particles.
calculation and thermostatting. The <A HREF = "fix_langevin">fix langevin</A>
command can also be used with its <I>omgea</I> or <I>angmom</I> options to
thermostat the rotational degrees of freedom for spherical or
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
only use these integration fixes on <A HREF = "group.html">groups</A> which contain
extended particles.
<P>These fixes perform constant NVE time integration on line segment,
triangular, and body 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
of extended spherical or aspherical particles (ellipsoids):
<P>There are several computes that calculate the temperature or
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
default thermodynamic quantities will be calculated with a temperature
that only includes translational degrees of freedom. See the
<A HREF = "thermo_modify.html">thermo_modify</A> command used. Note that by default
thermodynamic quantities will be calculated with a temperature that
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
extended particles, including the dipole moment (mu), the angular
velocity (omega), the angular momentum (angmom), the quaternion
(quat), and the torque (tq) on the particle.
<P>These commands can be used to output various attributes
of extended 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 = "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
inertia tensor of the body is different than if they were point
particles. This means the rotational dynamics of the rigid body will
be different. Thus a model of a dimer is different if the dimer
consists of two point masses versus two extended sphereoids, even if
the two particles have the same mass. Extended particles that
experience torque due to their interaction with other particles will
also impart that torque to a rigid body they are part of.
particles (spheres or ellipsoids or line segments or triangles), then
their contribution to the inertia tensor of the body is different than
if they were point particles. This means the rotational dynamics of
the rigid body will be different. Thus a model of a dimer is
different if the dimer consists of two point masses versus two
extended sphereoids, even if the two particles have the same mass.
Extended particles that experience torque due to their interaction
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,

207
doc/Section_howto.txt
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@ -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.
Sometimes, however, it is desirable to have a model with finite-size
particles such as spheres or aspherical ellipsoids. The difference is
that such particles have a moment of inertia, rotational energy, and
angular momentum. Rotation is induced by torque from interactions
with other particles.
Typical MD models treat atoms or particles as point masses. Sometimes
it is desirable to have a model with finite-size particles such as
spheroids or ellipsoids or generalized aspherical bodies. The
difference is that such particles have a moment of inertia, rotational
energy, and angular momentum. Rotation is induced by torque coming
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
finite-size particles: sphere and ellipsoid. The peri atom style also
treats particles as having a volume, but that is internal to the
"pair_style peri"_pair_peri.html potentials. The dipole atom style is
most often used in conjunction with finite-size particles.
There are several "atom styles"_atom_style.html that allow for
definition of finite-size particles: sphere, dipole, ellipsoid, line,
tri, peri, and body.
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
used in conjunction with spherical particles, via a command like
The line style defines line segment particles with two end points and
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
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 peri style is used with "Peridynamic models"_pair_peri.html and
defines particles as having a volume, that is used internally in the
"pair_style peri"_pair_peri.html potentials.
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 "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,
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.
the system are required to be finite-size or aspherical.
Also note that for "2d simulations"_dimension.html, finite-size
spheres and ellipsoids are still treated as 3d particles, rather than
as circular disks or ellipses. This means they have the same moment
of inertia for a 3d extended object. When their temperature is
coomputed, the correct degrees of freedom are used for rotation in a
2d versus 3d system.
For example, in the ellipsoid style, 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. In the line or
tri style, if the lineflag or triflag is specified as 0, then it
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
particles. The "dipole pair style"_pair_dipole.html is used with
"atom_style dipole"_atom_style.html, which could be applied to
spherical or ellipsoidal particles. The "GayBerne"_pair_gayberne.html
and "REsquared"_pair_resquared.html potentials require ellipsoidal
particles, though they will also work if the 3 shape parameters are
the same (a sphere). The "lubrication potential"_pair_lubricate.html
works with spherical particles.
The granular pair styles are used with spherical particles. The
dipole pair style is used with the dipole atom style, which could be
applied to spherical or ellipsoidal particles. The GayBerne and
REsquared potentials require ellipsoidal particles, though they will
also work if the 3 shape parameters are the same (a sphere). The
Brownian and lubrication potentials are used with spherical particles.
The line, tri, and body potentials are used with line segment,
triangular, and body particles respectively.
Time integration :h5
There are 3 fixes that perform time integration on extended spherical
particles, meaning the integrators update the rotational orientation
and angular velocity or angular momentum of the particles:
There are several fixes that perform time integration on extended
spherical particles, meaning the integrators update the rotational
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
fix nve/sphere or fix nve/asphere, such as fix langevin or fix
temp/berendsen, but those thermostats only operate on the
translational kinetic energy of the extended particles.
calculation and thermostatting. The "fix langevin"_fix_langevin
command can also be used with its {omgea} or {angmom} options to
thermostat the rotational degrees of freedom for spherical or
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
only use these integration fixes on "groups"_group.html which contain
extended particles.
These fixes perform constant NVE time integration on line segment,
triangular, and body 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
of extended spherical or aspherical particles (ellipsoids):
There are several computes that calculate the temperature or
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
default thermodynamic quantities will be calculated with a temperature
that only includes translational degrees of freedom. See the
"thermo_modify"_thermo_modify.html command used. Note that by default
thermodynamic quantities will be calculated with a temperature that
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
extended particles, including the dipole moment (mu), the angular
velocity (omega), the angular momentum (angmom), the quaternion
(quat), and the torque (tq) on the particle.
These commands can be used to output various attributes
of extended particles:
"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
inertia tensor of the body is different than if they were point
particles. This means the rotational dynamics of the rigid body will
be different. Thus a model of a dimer is different if the dimer
consists of two point masses versus two extended sphereoids, even if
the two particles have the same mass. Extended particles that
experience torque due to their interaction with other particles will
also impart that torque to a rigid body they are part of.
particles (spheres or ellipsoids or line segments or triangles), then
their contribution to the inertia tensor of the body is different than
if they were point particles. This means the rotational dynamics of
the rigid body will be different. Thus a model of a dimer is
different if the dimer consists of two point masses versus two
extended sphereoids, even if the two particles have the same mass.
Extended particles that experience torque due to their interaction
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

8
doc/Section_modify.html
View File

@ -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
overview of using body particles and the <A HREF = "body.html">body</A> doc page for
details on the various body styles LAMMPS supports. New styles can be
created to add new kinds of body particles to LAMMPS.
<P>See <A HREF = "Section_howto.html#howto_14">Section_howto 14</A> of the manual for
an overview of using body particles and the <A HREF = "body.html">body</A> doc page
for details on the various body styles LAMMPS supports. New styles
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.

8
doc/Section_modify.txt
View File

@ -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
overview of using body particles and the "body"_body.html doc page for
details on the various body styles LAMMPS supports. New styles can be
created to add new kinds of body particles to LAMMPS.
See "Section_howto 14"_Section_howto.html#howto_14 of the manual for
an overview of using body particles and the "body"_body.html doc page
for details on the various body styles LAMMPS supports. New styles
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.

5
doc/compute_body_local.html
View File

@ -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
manual for an overview of using body particles.
explained below. See <A HREF = "Section_howto.html#howto_14">Section_howto 14</A>
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

5
doc/compute_body_local.txt
View File

@ -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
manual for an overview of using body particles.
explained below. See "Section_howto 14"_Section_howto.html#howto_14
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

6
doc/fix_nve_body.html
View File

@ -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
22</A> of the manual for an overview of using body
particles.
consistent with the microcanonical ensemble. See <A HREF = "Section_howto.html#howto_14">Section_howto
14</A> of the manual and the <A HREF = "body.html">body</A>
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.

4
doc/fix_nve_body.txt
View File

@ -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
particles.
14"_Section_howto.html#howto_14 of the manual and the "body"_body.html
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.

5
doc/pair_body.html
View File

@ -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
manual for an overview of using body particles.
point-particles. See <A HREF = "Section_howto.html#howto_14">Section_howto 14</A>
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.

5
doc/pair_body.txt
View File

@ -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
manual for an overview of using body particles.
point-particles. See "Section_howto 14"_Section_howto.html#howto_14
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.