ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2906 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2009-06-26 18:50:39 +00:00
parent 07c15b806a
commit 0f25f3e4e9
2 changed files with 68 additions and 58 deletions
Download Patch File Download Diff File Expand all files Collapse all files

63
doc/Section_howto.html
View File

@ -781,11 +781,11 @@ profile consistent with the applied shear strain rate.
<A NAME = "4_14"></A><H4>4.14 Extended spherical and aspherical particles <A NAME = "4_14"></A><H4>4.14 Extended spherical and aspherical particles
</H4> </H4>
<P>Typical MD models treat atoms or particles as point masses. <P>Typical MD models treat atoms or particles as point masses.
Sometimes, however, it is desirable to have a model where the Sometimes, however, it is desirable to have a model with finite-size
particles are extended spherioids or extended aspherical paticles such particles such as spherioids or aspherical ellipsoids. The difference
as an ellipsoid. The difference is that such particles have a moment is that such particles have a moment of inertia, rotational energy,
of inertia, rotational energy, and angular momentum. Rotation is and angular momentum. Rotation is induced by torque from interactions
induced by torque from interactions with other particles. with other particles.
</P> </P>
<P>LAMMPS has several options for running simulations with these kinds of <P>LAMMPS has several options for running simulations with these kinds of
particles. The following aspects are discussed in turn: particles. The following aspects are discussed in turn:
@ -798,14 +798,14 @@ particles. The following aspects are discussed in turn:
</UL> </UL>
<H5>Atom styles <H5>Atom styles
</H5> </H5>
<P>There are 3 <A HREF = "atom_style.html">atom styles</A> that define extended <P>There are 3 <A HREF = "atom_style.html">atom styles</A> that allow for definition of
particles: granular, dipole, ellipsoid. finite-size particles: granular, dipole, ellipsoid.
</P> </P>
<P>Granular particles are extended spheriods and each particle can have a <P>Granular particles are spheriods and each particle can have a unique
unique diameter and mass (or density). These particles store diameter and mass (or density). These particles store an angular
an angular velocity (omega) and can be acted upon by torque. velocity (omega) and can be acted upon by torque.
</P> </P>
<P>Dipole particles are extended spheriods with a point dipole and each <P>Dipolar particles are typically spheriods with a point dipole and each
particle type has a diamater and mass, set by the <A HREF = "shape.html">shape</A> particle type has a diamater and mass, set by the <A HREF = "shape.html">shape</A>
and <A HREF = "mass.html">mass</A> commands. These particles store an angular and <A HREF = "mass.html">mass</A> commands. These particles store an angular
velocity (omega) and can be acted upon by torque. They also store an velocity (omega) and can be acted upon by torque. They also store an
@ -817,31 +817,36 @@ to initialize the orientation of dipole moments.
ellipsoidal shape and mass, defined by the <A HREF = "shape.html">shape</A> and ellipsoidal shape and mass, defined by the <A HREF = "shape.html">shape</A> and
<A HREF = "mass.html">mass</A> commands. These particles store an angular momentum <A HREF = "mass.html">mass</A> commands. These particles store an angular momentum
and their orientation (quaternion), and can be acted upon by torque. and their orientation (quaternion), and can be acted upon by torque.
They do not store an angular velocity (omega) which can be in a They do not store an angular velocity (omega), which can be in a
different direction than angular momentum. The <A HREF = "set.html">set</A> command different direction than angular momentum, rather they compute it as
can be used to initialize the orientation of ellipsoidal particles and needed. Ellipsoidal particles can also store a dipole moment if an
has a brief explanation of quaternions. <A HREF = "atom_style.html">atom_style hybrid ellipsoid dipole</A> is used. The
<A HREF = "set.html">set</A> command can be used to initialize the orientation of
ellipsoidal particles and has a brief explanation of quaternions.
</P> </P>
<P>Note that if one of these atom styles is used (or multiple styles via <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 <A HREF = "atom_style.html">atom_style hybrid</A> command), not all particles in
the system are required to be extended or aspherical. For example, if the system are required to be finite-size or aspherical. For example,
the 3 shape parameters are set to the same value, the particle will be if the 3 shape parameters are set to the same value, the particle will
a spheroid rather than an ellipsoid. If the dipole moment is set to be a spheroid rather than an ellipsoid. If the 3 shape parameters are
zero, the particle will not have a point dipole associated with it. all set to 0.0 or if the diameter is set to 0.0, it will be a point
The pair styles used to compute pairwise interactions will typically particle. If the dipole moment is set to zero, the particle will not
compute the correct interaction in these simplified (cheaper) cases. have a point dipole associated with it. The pair styles used to
<A HREF = "pair_hybrid.html">Pair_style hybrid</A> can be used to insure the correct 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. interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoid versus Likewise, using groups to partition particles (ellipsoid versus
spheroid versus point particles) will allow you to use the appropriate spheroid versus point particles) will allow you to use the appropriate
time integrators and temperature computations for each class of time integrators and temperature computations for each class of
particles. See the doc pages for various commands for details. particles. See the doc pages for various commands for details.
</P> </P>
<P>Also note that for <A HREF = "dimension.html">2d simulations</A>, extended spheroids <P>Also note that for <A HREF = "dimension.html">2d simulations</A>, finite-size
and ellipsoids are still treated as 3d particles, rather than as disks spheroids and ellipsoids are still treated as 3d particles, rather
or ellipses. This means they still have a moment of inertia for a 3d than as disks or ellipses. This means they have the same moment of
extended object. When their temperature is coomputed, the correct inertia for a 3d extended object. When their temperature is
degrees of freedom are used for rotation in a 2d versus 3d system. coomputed, the correct degrees of freedom are used for rotation in a
2d versus 3d system.
</P> </P>
<H5>Pair potentials <H5>Pair potentials
</H5> </H5>
@ -927,8 +932,8 @@ particles as a rigid body, computes its inertia tensor, sums the total
force and torque on the rigid body each timestep due to forces on its force and torque on the rigid body each timestep due to forces on its
constituent particles, and integrates the motion of the rigid body. constituent particles, and integrates the motion of the rigid body.
</P> </P>
<P>(NOTE: 6/08 the feature described in the following paragraph has <P>(NOTE: the feature described in the following paragraph has not yet
not yet been released. It will be soon.) been released. It will be soon.)
</P> </P>
<P>If any of the constituent particles of a rigid body are extended <P>If any of the constituent particles of a rigid body are extended
particles (spheroids or ellipsoids), then their contribution to the particles (spheroids or ellipsoids), then their contribution to the

63
doc/Section_howto.txt
View File

@ -774,11 +774,11 @@ An alternative method for calculating viscosities is provided via the
4.14 Extended spherical and aspherical particles :link(4_14),h4 4.14 Extended spherical and aspherical particles :link(4_14),h4
Typical MD models treat atoms or particles as point masses. Typical MD models treat atoms or particles as point masses.
Sometimes, however, it is desirable to have a model where the Sometimes, however, it is desirable to have a model with finite-size
particles are extended spherioids or extended aspherical paticles such particles such as spherioids or aspherical ellipsoids. The difference
as an ellipsoid. The difference is that such particles have a moment is that such particles have a moment of inertia, rotational energy,
of inertia, rotational energy, and angular momentum. Rotation is and angular momentum. Rotation is induced by torque from interactions
induced by torque from interactions with other particles. with other particles.
LAMMPS has several options for running simulations with these kinds of LAMMPS has several options for running simulations with these kinds of
particles. The following aspects are discussed in turn: particles. The following aspects are discussed in turn:
@ -791,14 +791,14 @@ rigid bodies composed of extended particles :ul
Atom styles :h5 Atom styles :h5
There are 3 "atom styles"_atom_style.html that define extended There are 3 "atom styles"_atom_style.html that allow for definition of
particles: granular, dipole, ellipsoid. finite-size particles: granular, dipole, ellipsoid.
Granular particles are extended spheriods and each particle can have a Granular particles are spheriods and each particle can have a unique
unique diameter and mass (or density). These particles store diameter and mass (or density). These particles store an angular
an angular velocity (omega) and can be acted upon by torque. velocity (omega) and can be acted upon by torque.
Dipole particles are extended spheriods with a point dipole and each Dipolar particles are typically spheriods with a point dipole and each
particle type has a diamater and mass, set by the "shape"_shape.html particle type has a diamater and mass, set by the "shape"_shape.html
and "mass"_mass.html commands. These particles store an angular and "mass"_mass.html commands. These particles store an angular
velocity (omega) and can be acted upon by torque. They also store an velocity (omega) and can be acted upon by torque. They also store an
@ -810,31 +810,36 @@ Ellipsoid particles are aspherical. Each particle type has an
ellipsoidal shape and mass, defined by the "shape"_shape.html and ellipsoidal shape and mass, defined by the "shape"_shape.html and
"mass"_mass.html commands. These particles store an angular momentum "mass"_mass.html commands. These particles store an angular momentum
and their orientation (quaternion), and can be acted upon by torque. and their orientation (quaternion), and can be acted upon by torque.
They do not store an angular velocity (omega) which can be in a They do not store an angular velocity (omega), which can be in a
different direction than angular momentum. The "set"_set.html command different direction than angular momentum, rather they compute it as
can be used to initialize the orientation of ellipsoidal particles and needed. Ellipsoidal particles can also store a dipole moment if an
has a brief explanation of quaternions. "atom_style hybrid ellipsoid dipole"_atom_style.html is used. The
"set"_set.html command can be used to initialize the orientation of
ellipsoidal particles and has a brief explanation of quaternions.
Note that if one of these atom styles is used (or multiple styles via 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 "atom_style hybrid"_atom_style.html command), not all particles in
the system are required to be extended or aspherical. For example, if the system are required to be finite-size or aspherical. For example,
the 3 shape parameters are set to the same value, the particle will be if the 3 shape parameters are set to the same value, the particle will
a spheroid rather than an ellipsoid. If the dipole moment is set to be a spheroid rather than an ellipsoid. If the 3 shape parameters are
zero, the particle will not have a point dipole associated with it. all set to 0.0 or if the diameter is set to 0.0, it will be a point
The pair styles used to compute pairwise interactions will typically particle. If the dipole moment is set to zero, the particle will not
compute the correct interaction in these simplified (cheaper) cases. have a point dipole associated with it. The pair styles used to
"Pair_style hybrid"_pair_hybrid.html can be used to insure the correct 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. interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoid versus Likewise, using groups to partition particles (ellipsoid versus
spheroid versus point particles) will allow you to use the appropriate spheroid versus point particles) will allow you to use the appropriate
time integrators and temperature computations for each class of time integrators and temperature computations for each class of
particles. See the doc pages for various commands for details. particles. See the doc pages for various commands for details.
Also note that for "2d simulations"_dimension.html, extended spheroids Also note that for "2d simulations"_dimension.html, finite-size
and ellipsoids are still treated as 3d particles, rather than as disks spheroids and ellipsoids are still treated as 3d particles, rather
or ellipses. This means they still have a moment of inertia for a 3d than as disks or ellipses. This means they have the same moment of
extended object. When their temperature is coomputed, the correct inertia for a 3d extended object. When their temperature is
degrees of freedom are used for rotation in a 2d versus 3d system. coomputed, the correct degrees of freedom are used for rotation in a
2d versus 3d system.
Pair potentials :h5 Pair potentials :h5
@ -920,8 +925,8 @@ particles as a rigid body, computes its inertia tensor, sums the total
force and torque on the rigid body each timestep due to forces on its force and torque on the rigid body each timestep due to forces on its
constituent particles, and integrates the motion of the rigid body. constituent particles, and integrates the motion of the rigid body.
(NOTE: 6/08 the feature described in the following paragraph has (NOTE: the feature described in the following paragraph has not yet
not yet been released. It will be soon.) been released. It will be soon.)
If any of the constituent particles of a rigid body are extended If any of the constituent particles of a rigid body are extended
particles (spheroids or ellipsoids), then their contribution to the particles (spheroids or ellipsoids), then their contribution to the