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32
doc/Section_commands.html
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@ -261,12 +261,11 @@ in the command's documentation.
</P>
<P>Settings:
</P>
<P><A HREF = "communicate.html">communicate</A>, <A HREF = "dipole.html">dipole</A>,
<A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>, <A HREF = "min_modify.html">min_modify</A>,
<A HREF = "min_style.html">min_style</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
<A HREF = "neighbor.html">neighbor</A>, <A HREF = "reset_timestep.html">reset_timestep</A>,
<A HREF = "run_style.html">run_style</A>, <A HREF = "set.html">set</A>, <A HREF = "shape.html">shape</A>,
<A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
<P><A HREF = "communicate.html">communicate</A>, <A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>,
<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
<A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
</P>
<P>Fixes:
</P>
@ -315,17 +314,16 @@ in the command's documentation.
<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD><TD ><A HREF = "bond_style.html">bond_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "communicate.html">communicate</A></TD><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD><TD ><A HREF = "dipole.html">dipole</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "displace_box.html">displace_box</A></TD><TD ><A HREF = "dump.html">dump</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "label.html">label</A></TD><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "neb.html">neb</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "processors.html">processors</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shape.html">shape</A></TD><TD ><A HREF = "shell.html">shell</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "tad.html">tad</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
<TR ALIGN="center"><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "displace_box.html">displace_box</A></TD><TD ><A HREF = "dump.html">dump</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "neb.html">neb</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_modify.html">pair_modify</A></TD><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "tad.html">tad</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
</TD></TR></TABLE></DIV>
<HR>

13
doc/Section_commands.txt
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@ -258,12 +258,11 @@ Force fields:
Settings:
"communicate"_communicate.html, "dipole"_dipole.html,
"group"_group.html, "mass"_mass.html, "min_modify"_min_modify.html,
"min_style"_min_style.html, "neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html, "reset_timestep"_reset_timestep.html,
"run_style"_run_style.html, "set"_set.html, "shape"_shape.html,
"timestep"_timestep.html, "velocity"_velocity.html
"communicate"_communicate.html, "group"_group.html, "mass"_mass.html,
"min_modify"_min_modify.html, "min_style"_min_style.html,
"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html
Fixes:
@ -328,7 +327,6 @@ in the command's documentation.
"dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"dimension"_dimension.html,
"dipole"_dipole.html,
"displace_atoms"_displace_atoms.html,
"displace_box"_displace_box.html,
"dump"_dump.html,
@ -372,7 +370,6 @@ in the command's documentation.
"run"_run.html,
"run_style"_run_style.html,
"set"_set.html,
"shape"_shape.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"tad"_tad.html,

110
doc/Section_howto.html
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@ -390,7 +390,7 @@ velocity and torque can be imparted to them to cause them to rotate.
<P>To run a simulation of a granular model, you will want to use
the following commands:
</P>
<UL><LI><A HREF = "atom_style.html">atom_style</A> granular
<UL><LI><A HREF = "atom_style.html">atom_style sphere</A>
<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
<LI><A HREF = "fix_gravity.html">fix gravity</A>
</UL>
@ -913,9 +913,9 @@ profile consistent with the applied shear strain rate.
</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 spherioids 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
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>
<P>LAMMPS has several options for running simulations with these kinds of
@ -929,53 +929,61 @@ particles. The following aspects are discussed in turn:
</UL>
<H5>Atom styles
</H5>
<P>There are 3 <A HREF = "atom_style.html">atom styles</A> that allow for definition of
finite-size particles: granular, dipole, ellipsoid.
<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>
<P>Granular particles are spheriods and each particle can have a unique
diameter and mass (or density). These particles store an angular
velocity (omega) and can be acted upon by torque.
<P>The sphere style defines particles that are spheriods and each
particle can have a unique diameter and mass (or density). These
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>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>
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
orientation for the point dipole (mu) which has a length set by the
<A HREF = "dipole.html">dipole</A> command. The <A HREF = "set.html">set</A> command can be used
to initialize the orientation of dipole moments.
<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
their orientation (quaternion), and can be acted upon by torque. They
do not store an angular velocity (omega), which can be in a different
direction than angular momentum, rather they compute it as needed.
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>Ellipsoid particles are aspherical. Each particle type has an
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
and their orientation (quaternion), and can be acted upon by torque.
They do not store an angular velocity (omega), which can be in a
different direction than angular momentum, rather they compute it as
needed. Ellipsoidal particles can also store a dipole moment if an
<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>The dipole style does not 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>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 spheroid rather than an ellipsoid. If the 3 shape parameters are
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 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
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 (ellipsoid versus
spheroid versus point particles) will allow you to use the appropriate
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
spheroids and ellipsoids are still treated as 3d particles, rather
than as disks or ellipses. This means they have the same moment of
inertia for a 3d extended object. When their temperature is
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>
@ -994,15 +1002,14 @@ that generate torque:
<LI><A HREF = "pair_resquared.html">pair_style resquared</A>
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A>
</UL>
<P>The <A HREF = "pair_gran.html">granular pair styles</A> are used with <A HREF = "atom_style.html">atom_style
granular</A>. The <A HREF = "pair_dipole.html">dipole pair style</A>
is used with <A HREF = "atom_style.html">atom_style dipole</A>. The
<A HREF = "pair_gayberne.html">GayBerne</A> and <A HREF = "pair_resquared.html">REsquared</A>
potentials require particles have a <A HREF = "shape.html">shape</A> and are
designed for <A HREF = "atom_style.html">ellipsoidal particles</A>. The
<A HREF = "pair_lubricate.html">lubrication potential</A> requires that particles
have a <A HREF = "shape.html">shape</A>. It can currently only be used with
extended spherical particles.
<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>
<H5>Time integration
</H5>
@ -1014,8 +1021,8 @@ and angular velocity or angular momentum of the particles:
<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 extended
aspherical particles:
<P>Likewise, there are 3 fixes that perform time integration on
ellipsoids as extended aspherical 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>
@ -1035,7 +1042,7 @@ extended particles.
<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:
of extended spherical or aspherical particles (ellipsoids):
</P>
<UL><LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
@ -1063,11 +1070,8 @@ 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
constituent particles, and integrates the motion of the rigid body.
</P>
<P>(NOTE: the feature described in the following paragraph has not yet
been released. It will be soon.)
</P>
<P>If any of the constituent particles of a rigid body are extended
particles (spheroids or ellipsoids), then their contribution to the
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

110
doc/Section_howto.txt
View File

@ -386,7 +386,7 @@ velocity and torque can be imparted to them to cause them to rotate.
To run a simulation of a granular model, you will want to use
the following commands:
"atom_style"_atom_style.html granular
"atom_style sphere"_atom_style.html
"fix nve/sphere"_fix_nve_sphere.html
"fix gravity"_fix_gravity.html :ul
@ -905,9 +905,9 @@ An alternative method for calculating viscosities is provided via the
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 spherioids 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
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.
LAMMPS has several options for running simulations with these kinds of
@ -921,53 +921,61 @@ rigid bodies composed of extended particles :ul
Atom styles :h5
There are 3 "atom styles"_atom_style.html that allow for definition of
finite-size particles: granular, dipole, ellipsoid.
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.
Granular particles are spheriods and each particle can have a unique
diameter and mass (or density). These particles store an angular
velocity (omega) and can be acted upon by torque.
The sphere style defines particles that are spheriods and each
particle can have a unique diameter and mass (or density). These
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.
Dipolar particles are typically spheriods with a point dipole and each
particle type has a diamater and mass, set by the "shape"_shape.html
and "mass"_mass.html commands. These particles store an angular
velocity (omega) and can be acted upon by torque. They also store an
orientation for the point dipole (mu) which has a length set by the
"dipole"_dipole.html command. The "set"_set.html command can be used
to initialize the orientation of dipole moments.
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
their orientation (quaternion), and can be acted upon by torque. They
do not store an angular velocity (omega), which can be in a different
direction than angular momentum, rather they compute it as needed.
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.
Ellipsoid particles are aspherical. Each particle type has an
ellipsoidal shape and mass, defined by the "shape"_shape.html and
"mass"_mass.html commands. These particles store an angular momentum
and their orientation (quaternion), and can be acted upon by torque.
They do not store an angular velocity (omega), which can be in a
different direction than angular momentum, rather they compute it as
needed. Ellipsoidal particles can also store a dipole moment if an
"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.
The dipole style does not 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.
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 spheroid rather than an ellipsoid. If the 3 shape parameters are
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 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
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 (ellipsoid versus
spheroid versus point particles) will allow you to use the appropriate
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
spheroids and ellipsoids are still treated as 3d particles, rather
than as disks or ellipses. This means they have the same moment of
inertia for a 3d extended object. When their temperature is
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.
@ -986,15 +994,14 @@ that generate torque:
"pair_style resquared"_pair_resquared.html
"pair_style lubricate"_pair_lubricate.html :ul
The "granular pair styles"_pair_gran.html are used with "atom_style
granular"_atom_style.html. The "dipole pair style"_pair_dipole.html
is used with "atom_style dipole"_atom_style.html. The
"GayBerne"_pair_gayberne.html and "REsquared"_pair_resquared.html
potentials require particles have a "shape"_shape.html and are
designed for "ellipsoidal particles"_atom_style.html. The
"lubrication potential"_pair_lubricate.html requires that particles
have a "shape"_shape.html. It can currently only be used with
extended spherical particles.
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.
Time integration :h5
@ -1006,8 +1013,8 @@ and angular velocity or angular momentum of the particles:
"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 extended
aspherical particles:
Likewise, there are 3 fixes that perform time integration on
ellipsoids as extended aspherical particles:
"fix nve/asphere"_fix_nve_asphere.html
"fix nvt/asphere"_fix_nvt_asphere.html
@ -1027,7 +1034,7 @@ 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:
of extended spherical or aspherical particles (ellipsoids):
"compute temp/sphere"_compute_temp_sphere.html
"compute temp/asphere"_compute_temp_asphere.html
@ -1055,11 +1062,8 @@ 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
constituent particles, and integrates the motion of the rigid body.
(NOTE: the feature described in the following paragraph has not yet
been released. It will be soon.)
If any of the constituent particles of a rigid body are extended
particles (spheroids or ellipsoids), then their contribution to the
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

11
doc/Section_modify.html
View File

@ -468,12 +468,11 @@ class. See region.h for details.
<P>There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
</P>
<P>There are several styles defined in thermo.cpp: "one", "multi",
"granular", etc. There is also a flexible "custom" style which allows
the user to explicitly list keywords for quantities to print when
thermodynamic info is output. See the
<A HREF = "thermo_style.html">thermo_style</A> command for a list of defined
quantities.
<P>There are two styles defined in thermo.cpp: "one" and "multi". There
is also a flexible "custom" style which allows the user to explicitly
list keywords for quantities to print when thermodynamic info is
output. See the <A HREF = "thermo_style.html">thermo_style</A> command for a list
of defined quantities.
</P>
<P>The thermo styles (one, multi, etc) are simply lists of keywords.
Adding a new style thus only requires defining a new list of keywords.

11
doc/Section_modify.txt
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@ -445,12 +445,11 @@ Thermodynamic output options :link(thermo),h4
There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
There are several styles defined in thermo.cpp: "one", "multi",
"granular", etc. There is also a flexible "custom" style which allows
the user to explicitly list keywords for quantities to print when
thermodynamic info is output. See the
"thermo_style"_thermo_style.html command for a list of defined
quantities.
There are two styles defined in thermo.cpp: "one" and "multi". There
is also a flexible "custom" style which allows the user to explicitly
list keywords for quantities to print when thermodynamic info is
output. See the "thermo_style"_thermo_style.html command for a list
of defined quantities.
The thermo styles (one, multi, etc) are simply lists of keywords.
Adding a new style thus only requires defining a new list of keywords.

69
doc/atom_style.html
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@ -15,7 +15,7 @@
</P>
<PRE>atom_style style args
</PRE>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>colloid</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>granular</I> or <I>molecular</I> or <I>peri</I> or <I>hybrid</I>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>colloid</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>hybrid</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more sub-styles
@ -57,36 +57,32 @@ quantities.
<TR><TD ><I>atomic</I> </TD><TD > only the default values </TD><TD > coarse-grain liquids, solids, metals </TD></TR>
<TR><TD ><I>bond</I> </TD><TD > bonds </TD><TD > bead-spring polymers </TD></TR>
<TR><TD ><I>charge</I> </TD><TD > charge </TD><TD > atomic system with charges </TD></TR>
<TR><TD ><I>colloid</I> </TD><TD > angular velocity </TD><TD > extended spherical particles </TD></TR>
<TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > atomic system with dipoles </TD></TR>
<TR><TD ><I>dipole</I> </TD><TD > charge and dipole moment </TD><TD > system with dipolar particles </TD></TR>
<TR><TD ><I>electron</I> </TD><TD > charge and spin and eradius </TD><TD > electronic force field </TD></TR>
<TR><TD ><I>ellipsoid</I> </TD><TD > quaternion for particle orientation, angular momentum </TD><TD > extended aspherical particles </TD></TR>
<TR><TD ><I>ellipsoid</I> </TD><TD > shape, quaternion for particle orientation, angular momentum </TD><TD > extended aspherical particles </TD></TR>
<TR><TD ><I>full</I> </TD><TD > molecular + charge </TD><TD > bio-molecules </TD></TR>
<TR><TD ><I>granular</I> </TD><TD > diameter, density, angular velocity </TD><TD > granular models </TD></TR>
<TR><TD ><I>molecular</I> </TD><TD > bonds, angles, dihedrals, impropers </TD><TD > uncharged molecules </TD></TR>
<TR><TD ><I>peri</I> </TD><TD > density, volume </TD><TD > mesocopic Peridynamic models
<TR><TD ><I>peri</I> </TD><TD > mass, volume </TD><TD > mesocopic Peridynamic models </TD></TR>
<TR><TD ><I>sphere</I> </TD><TD > diameter, mass, angular velocity </TD><TD > granular models
</TD></TR></TABLE></DIV>
<P>All of the styles define point particles, except the <I>colloid</I>,
<I>dipole</I>, <I>electron</I>, <I>ellipsoid</I>, <I>granular</I>, and <I>peri</I> styles,
which define finite-size particles. For <I>colloid</I>, <I>dipole</I>, and
<I>ellipsoid</I> systems, the <A HREF = "shape.html">shape</A> command is used to specify
the size and shape of particles on a per-type basis, which is
spherical for <I>colloid</I> and <I>dipole</I> particles and spherical or
aspherical for <I>ellipsoid</I> particles. For <I>granular</I> systems, the
particles are spherical and each has a per-particle specified
diameter. For <I>peri</I> systems, the particles are spherical and each
has a per-particle specified volume. For <I>electron</I> systems, the
particles representing electrons are three dimensional Gaussians with
a specified position and bandwidth or uncertainty in position, which
is represented by the eradius = electron size.
</P>
<P>All of the styles assign mass to particles on a per-type basis, using
the <A HREF = "mass.html">mass</A> command, except the <I>granular</I> and <I>peri</I> styles
which assign mass on a per-particle basis. For <I>granular</I> systems,
the specified diameter and density are used to calculate each
particle's mass. For <I>peri</I> systems, the speficied volume and density
are used to calculate each particle's mass.
the <A HREF = "mass.html">mass</A> command, except for the finite-size particle
styles discussed below. They assign mass on a per-atom basis.
</P>
<P>All of the styles define point particles, except the <I>sphere</I>,
<I>ellipsoid</I>, <I>electron</I>, and <I>peri</I> styles, which define finite-size
particles.
</P>
<P>For the <I>sphere</I> style, the particles are spheres and each stores a
per-particle diameter and mass. For the <I>ellipsoid</I> style, the
particles are ellipsoids and each stores a per-particle shape vector
with the 3 diamters of the ellipsoid. For the <I>electron</I> style, the
particles representing electrons are 3d Gaussians with a specified
position and bandwidth or uncertainty in position, which is
represented by the eradius = electron size. For the <I>peri</I> style, the
particles are spherical and each stores a per-particle mass and
volume.
</P>
<HR>
@ -99,10 +95,10 @@ If some atoms have bonds, but others do not, use the <I>bond</I> style.
</P>
<P>The only scenario where the <I>hybrid</I> style is needed is if there is no
single style which defines all needed properties of all atoms. For
example, if you want colloidal particles with charge, you would need
to use "atom_style hybrid colloid charge". When a hybrid style is
used, atoms store and communicate the union of all quantities implied
by the individual styles.
example, if you want dipolar particles which will be torqued and
rotate, you would need to use "atom_style hybrid sphere dipole". When
a hybrid style is used, atoms store and communicate the union of all
quantities implied by the individual styles.
</P>
<P>LAMMPS can be extended with new atom styles; see <A HREF = "Section_modify.html">this
section</A>.
@ -113,14 +109,13 @@ section</A>.
<A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
</P>
<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
"molecular" package. The <I>granular</I> style is part of the "granular"
package. The <I>colloid</I> style is part of the "colloid" package. The
<I>dipole</I> style is part of the "dipole" package. The <I>ellipsoid</I> style
is part of the "asphere" package. The <I>peri</I> style is part of the
"peri" package for Peridynamics. The <I>electron</I> style is part of the
"user-eff" package for <A HREF = "pair_eff.html">electronic force fields</A>. They
are only enabled if LAMMPS was built with that package. See the
<A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
"molecular" package. The <I>dipole</I> style is part of the "dipole"
package. The <I>ellipsoid</I> style is part of the "asphere" package. The
<I>peri</I> style is part of the "peri" package for Peridynamics. The
<I>electron</I> style is part of the "user-eff" package for <A HREF = "pair_eff.html">electronic
force fields</A>. They are only enabled if LAMMPS was
built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>

71
doc/atom_style.txt
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@ -13,8 +13,8 @@ atom_style command :h3
atom_style style args :pre
style = {angle} or {atomic} or {bond} or {charge} or {colloid} or {dipole} or \
{electron} or {ellipsoid} or {full} or {granular} or {molecular} or \
{peri} or {hybrid} :ul
{electron} or {ellipsoid} or {full} or {molecular} or \
{peri} or {sphere} or {hybrid} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more sub-styles :pre
@ -54,35 +54,31 @@ quantities.
{atomic} | only the default values | coarse-grain liquids, solids, metals |
{bond} | bonds | bead-spring polymers |
{charge} | charge | atomic system with charges |
{colloid} | angular velocity | extended spherical particles |
{dipole} | charge and dipole moment | atomic system with dipoles |
{dipole} | charge and dipole moment | system with dipolar particles |
{electron} | charge and spin and eradius | electronic force field |
{ellipsoid} | quaternion for particle orientation, angular momentum | extended aspherical particles |
{ellipsoid} | shape, quaternion for particle orientation, angular momentum | extended aspherical particles |
{full} | molecular + charge | bio-molecules |
{granular} | diameter, density, angular velocity | granular models |
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
{peri} | density, volume | mesocopic Peridynamic models :tb(c=3,s=|)
All of the styles define point particles, except the {colloid},
{dipole}, {electron}, {ellipsoid}, {granular}, and {peri} styles,
which define finite-size particles. For {colloid}, {dipole}, and
{ellipsoid} systems, the "shape"_shape.html command is used to specify
the size and shape of particles on a per-type basis, which is
spherical for {colloid} and {dipole} particles and spherical or
aspherical for {ellipsoid} particles. For {granular} systems, the
particles are spherical and each has a per-particle specified
diameter. For {peri} systems, the particles are spherical and each
has a per-particle specified volume. For {electron} systems, the
particles representing electrons are three dimensional Gaussians with
a specified position and bandwidth or uncertainty in position, which
is represented by the eradius = electron size.
{peri} | mass, volume | mesocopic Peridynamic models |
{sphere} | diameter, mass, angular velocity | granular models :tb(c=3,s=|)
All of the styles assign mass to particles on a per-type basis, using
the "mass"_mass.html command, except the {granular} and {peri} styles
which assign mass on a per-particle basis. For {granular} systems,
the specified diameter and density are used to calculate each
particle's mass. For {peri} systems, the speficied volume and density
are used to calculate each particle's mass.
the "mass"_mass.html command, except for the finite-size particle
styles discussed below. They assign mass on a per-atom basis.
All of the styles define point particles, except the {sphere},
{ellipsoid}, {electron}, and {peri} styles, which define finite-size
particles.
For the {sphere} style, the particles are spheres and each stores a
per-particle diameter and mass. For the {ellipsoid} style, the
particles are ellipsoids and each stores a per-particle shape vector
with the 3 diamters of the ellipsoid. For the {electron} style, the
particles representing electrons are 3d Gaussians with a specified
position and bandwidth or uncertainty in position, which is
represented by the eradius = electron size. For the {peri} style, the
particles are spherical and each stores a per-particle mass and
volume.
:line
@ -95,10 +91,10 @@ If some atoms have bonds, but others do not, use the {bond} style.
The only scenario where the {hybrid} style is needed is if there is no
single style which defines all needed properties of all atoms. For
example, if you want colloidal particles with charge, you would need
to use "atom_style hybrid colloid charge". When a hybrid style is
used, atoms store and communicate the union of all quantities implied
by the individual styles.
example, if you want dipolar particles which will be torqued and
rotate, you would need to use "atom_style hybrid sphere dipole". When
a hybrid style is used, atoms store and communicate the union of all
quantities implied by the individual styles.
LAMMPS can be extended with new atom styles; see "this
section"_Section_modify.html.
@ -109,14 +105,13 @@ This command cannot be used after the simulation box is defined by a
"read_data"_read_data.html or "create_box"_create_box.html command.
The {angle}, {bond}, {full}, and {molecular} styles are part of the
"molecular" package. The {granular} style is part of the "granular"
package. The {colloid} style is part of the "colloid" package. The
{dipole} style is part of the "dipole" package. The {ellipsoid} style
is part of the "asphere" package. The {peri} style is part of the
"peri" package for Peridynamics. The {electron} style is part of the
"user-eff" package for "electronic force fields"_pair_eff.html. They
are only enabled if LAMMPS was built with that package. See the
"Making LAMMPS"_Section_start.html#2_3 section for more info.
"molecular" package. The {dipole} style is part of the "dipole"
package. The {ellipsoid} style is part of the "asphere" package. The
{peri} style is part of the "peri" package for Peridynamics. The
{electron} style is part of the "user-eff" package for "electronic
force fields"_pair_eff.html. They are only enabled if LAMMPS was
built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:]

15
doc/compute_erotate_asphere.html
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@ -47,19 +47,12 @@ scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute requires that particles be represented as extended
ellipsoids and not point particles. This means they will have an
angular momentum and a shape which is determined by the
<A HREF = "shape.html">shape</A> command.
</P>
<P>This compute requires that atoms store angular momentum and a
quaternion to represent their orientation, as defined by the
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter or per-particle mass.
<P>This compute requires that atoms store a shape and quaternion
orientation and angular momentum as defined by the <A HREF = "atom_style.html">atom_style
ellipsoid</A> command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical.
particles.
</P>
<P><B>Related commands:</B> none
</P>

15
doc/compute_erotate_asphere.txt
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@ -44,19 +44,12 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute requires that particles be represented as extended
ellipsoids and not point particles. This means they will have an
angular momentum and a shape which is determined by the
"shape"_shape.html command.
This compute requires that atoms store angular momentum and a
quaternion to represent their orientation, as defined by the
"atom_style"_atom_style.html. It also require they store a per-type
"shape"_shape.html. The particles cannot store a per-particle
diameter or per-particle mass.
This compute requires that atoms store a shape and quaternion
orientation and angular momentum as defined by the "atom_style
ellipsoid"_atom_style.html command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical.
particles.
[Related commands:] none

5
doc/compute_erotate_sphere.html
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@ -46,9 +46,8 @@ scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute requires that atoms store angular velocity (omega) as
defined by the <A HREF = "atom_style.html">atom_style</A>. It also require they
store either a per-particle diameter or per-type <A HREF = "shape.html">shape</A>.
<P>This compute requires that atoms store a radius and angular velocity
(omega) as defined by the <A HREF = "atom_style.html">atom_style sphere</A> command.
</P>
<P>All particles in the group must be finite-size spheres or point
particles. They cannot be aspherical. Point particles will not

5
doc/compute_erotate_sphere.txt
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@ -43,9 +43,8 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute requires that atoms store angular velocity (omega) as
defined by the "atom_style"_atom_style.html. It also require they
store either a per-particle diameter or per-type "shape"_shape.html.
This compute requires that atoms store a radius and angular velocity
(omega) as defined by the "atom_style sphere"_atom_style.html command.
All particles in the group must be finite-size spheres or point
particles. They cannot be aspherical. Point particles will not

11
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@ -24,9 +24,10 @@
<PRE> possible attributes = id, mol, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
q, mux, muy, muz, mu,
radius, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
spin, eradius, ervel, erforce
</PRE>
@ -41,10 +42,12 @@
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
radius = radius of extended spherical particle
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius = radius of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
shapex,shapey,shapez = 3 diameters of ellipsoidal particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
spin = electron spin

11
doc/compute_property_atom.txt
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@ -18,9 +18,10 @@ input = one or more atom attributes :l
possible attributes = id, mol, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
q, mux, muy, muz, mu,
radius, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
spin, eradius, ervel, erforce :pre
@ -35,10 +36,12 @@ input = one or more atom attributes :l
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
radius = radius of extended spherical particle
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius = radius of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
shapex,shapey,shapez = 3 diameters of ellipsoidal particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
spin = electron spin

28
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@ -47,13 +47,12 @@ this is not the case. Then there are less dof and you should use the
<A HREF = "compute_modify.html">compute_modify extra</A> command to adjust the dof
accordingly.
</P>
<P>For example, an aspherical particle with all three of its
<A HREF = "shape.html">shape</A> parameters the same is a sphere. If it does not
rotate, then it should have 3 dof instead of 6 in 3d (or 2 instead of
3 in 2d). A uniaxial aspherical particle has two of its three shape
parameters the same. If it does not rotate around the axis
perpendicular to its circular cross section, then it should have 5 dof
instead of 6 in 3d.
<P>For example, an aspherical particle with all three of its shape
parameters the same is a sphere. If it does not rotate, then it
should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A
uniaxial aspherical particle has two of its three shape parameters the
same. If it does not rotate around the axis perpendicular to its
circular cross section, then it should have 5 dof instead of 6 in 3d.
</P>
<P>The translational kinetic energy is computed the same as is described
by the <A HREF = "compute_temp.html">compute temp</A> command. The rotational
@ -114,10 +113,17 @@ vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute requires that particles be represented as extended
ellipsoids and not point particles. This means they will have an
angular momentum and a shape which is determined by the
<A HREF = "shape.html">shape</A> command.
<P>This compute is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This compute requires that atoms store angular momementum and a
quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
</P>
<P><B>Related commands:</B>
</P>

28
doc/compute_temp_asphere.txt
View File

@ -44,13 +44,12 @@ this is not the case. Then there are less dof and you should use the
"compute_modify extra"_compute_modify.html command to adjust the dof
accordingly.
For example, an aspherical particle with all three of its
"shape"_shape.html parameters the same is a sphere. If it does not
rotate, then it should have 3 dof instead of 6 in 3d (or 2 instead of
3 in 2d). A uniaxial aspherical particle has two of its three shape
parameters the same. If it does not rotate around the axis
perpendicular to its circular cross section, then it should have 5 dof
instead of 6 in 3d.
For example, an aspherical particle with all three of its shape
parameters the same is a sphere. If it does not rotate, then it
should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A
uniaxial aspherical particle has two of its three shape parameters the
same. If it does not rotate around the axis perpendicular to its
circular cross section, then it should have 5 dof instead of 6 in 3d.
The translational kinetic energy is computed the same as is described
by the "compute temp"_compute_temp.html command. The rotational
@ -111,10 +110,17 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute requires that particles be represented as extended
ellipsoids and not point particles. This means they will have an
angular momentum and a shape which is determined by the
"shape"_shape.html command.
This compute is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This compute requires that atoms store angular momementum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical as defined by their
shape attribute.
[Related commands:]

19
doc/compute_temp_sphere.html
View File

@ -33,10 +33,10 @@ usual <A HREF = "compute_temp.html">compute temp</A> command, which assumes poin
particles with only translational kinetic energy.
</P>
<P>Both point and finite-size particles can be included in the group.
Point particles do not rotate, so they have only translational degrees
of freedom. For 3d spherical particles, each has 6 degrees of freedom
(3 translational, 3 rotational). For 2d spherical particles, each has
3 degrees of freedom (2 translational, 1 rotational).
Point particles do not rotate, so they have only 3 translational
degrees of freedom. For 3d spherical particles, each has 6 degrees of
freedom (3 translational, 3 rotational). For 2d spherical particles,
each has 3 degrees of freedom (2 translational, 1 rotational).
</P>
<P>IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
all finite-size spherical particles in your model will freely rotate,
@ -104,11 +104,12 @@ vector values will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute requires that particles be represented as extended
spheres and not point particles. This means they will have an angular
velocity and a diameter which is determined either by the
<A HREF = "shape.html">shape</A> command or by each particle being assigned an
individual radius, e.g. for <A HREF = "atom_style.html">atom_style granular</A>.
<P>This fix requires that atoms store torque and angular velocity (omega)
and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
command.
</P>
<P>All particles in the group must be finite-size spheres, or point
particles with radius = 0.0.
</P>
<P><B>Related commands:</B>
</P>

19
doc/compute_temp_sphere.txt
View File

@ -30,10 +30,10 @@ usual "compute temp"_compute_temp.html command, which assumes point
particles with only translational kinetic energy.
Both point and finite-size particles can be included in the group.
Point particles do not rotate, so they have only translational degrees
of freedom. For 3d spherical particles, each has 6 degrees of freedom
(3 translational, 3 rotational). For 2d spherical particles, each has
3 degrees of freedom (2 translational, 1 rotational).
Point particles do not rotate, so they have only 3 translational
degrees of freedom. For 3d spherical particles, each has 6 degrees of
freedom (3 translational, 3 rotational). For 2d spherical particles,
each has 3 degrees of freedom (2 translational, 1 rotational).
IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
all finite-size spherical particles in your model will freely rotate,
@ -101,11 +101,12 @@ vector values will be in energy "units"_units.html.
[Restrictions:]
This compute requires that particles be represented as extended
spheres and not point particles. This means they will have an angular
velocity and a diameter which is determined either by the
"shape"_shape.html command or by each particle being assigned an
individual radius, e.g. for "atom_style granular"_atom_style.html.
This fix requires that atoms store torque and angular velocity (omega)
and a radius as defined by the "atom_style sphere"_atom_style.html
command.
All particles in the group must be finite-size spheres, or point
particles with radius = 0.0.
[Related commands:]

20
doc/create_atoms.html
View File

@ -146,20 +146,22 @@ style</A> command for more details. See the
to change these values.
</P>
<UL><LI>charge = 0.0
<LI>dipole moment = 0.0
<LI>dipole moment magnitude = 0.0
<LI>diameter = 1.0
<LI>volume = 1.0
<LI>shape = 1.0 1.0 1.0
<LI>density = 1.0
<LI>velocity = 0.0
<LI>angular velocity = 0.0
<LI>angular momentum = 0.0
<LI>volume = 1.0
<LI>velocity = 0.0 0.0 0.0
<LI>angular velocity = 0.0 0.0 0.0
<LI>angular momentum = 0.0 0.0 0.0
<LI>quaternion = (1,0,0,0)
<LI>bonds, angles, dihedrals, impropers = none
</UL>
<P>The <I>granular</I> style sets the diameter and density to 1.0 and
calculates a mass for the particle, which is PI/6 * diameter^3 =
0.5236. The <I>peri</I> style sets the volume and density to 1.0 and
calculates a mass for the particle, which is also 1.0.
<P>Note that this means the <I>sphere</I> and <I>ellipsoid</I> atom styles set the
diameter/shape and density to 1.0 and thus calculates a mass for the
particle, which is PI/6 * diameter^3 = 0.5236. The <I>peri</I> style sets
the volume and density to 1.0 and thus also set the mass for the
particle to 1.0.
</P>
<P><B>Restrictions:</B>
</P>

20
doc/create_atoms.txt
View File

@ -137,20 +137,22 @@ style"_atom_style.html command for more details. See the
to change these values.
charge = 0.0
dipole moment = 0.0
dipole moment magnitude = 0.0
diameter = 1.0
volume = 1.0
shape = 1.0 1.0 1.0
density = 1.0
velocity = 0.0
angular velocity = 0.0
angular momentum = 0.0
volume = 1.0
velocity = 0.0 0.0 0.0
angular velocity = 0.0 0.0 0.0
angular momentum = 0.0 0.0 0.0
quaternion = (1,0,0,0)
bonds, angles, dihedrals, impropers = none :ul
The {granular} style sets the diameter and density to 1.0 and
calculates a mass for the particle, which is PI/6 * diameter^3 =
0.5236. The {peri} style sets the volume and density to 1.0 and
calculates a mass for the particle, which is also 1.0.
Note that this means the {sphere} and {ellipsoid} atom styles set the
diameter/shape and density to 1.0 and thus calculates a mass for the
particle, which is PI/6 * diameter^3 = 0.5236. The {peri} style sets
the volume and density to 1.0 and thus also set the mass for the
particle to 1.0.
[Restrictions:]

71
doc/dipole.html
View File

@ -1,71 +0,0 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>dipole command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>dipole I value
</PRE>
<UL><LI>I = atom type (see asterisk form below)
<LI>value = dipole moment (dipole units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>dipole 1 1.0
dipole 3 2.0
dipole 3*5 0.0
</PRE>
<P><B>Description:</B>
</P>
<P>Set the dipole moment for all atoms of one or more atom types. This
command is only used for atom styles that require dipole moments
(<A HREF = "atom_style.html">atom_style</A> dipole). A value of 0.0 should be used
if the atom type has no dipole moment. Dipole values can also be set
in the <A HREF = "read_data.html">read_data</A> data file. See the
<A HREF = "units.html">units</A> command for a discussion of dipole units.
</P>
<P>Currently, only <A HREF = "atom_style.html">atom_style dipole</A> requires dipole
moments be set.
</P>
<P>I can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be
used to set the dipole moment for multiple atom types. This takes the
form "*" or "*n" or "n*" or "m*n". If N = the number of atom types,
then an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
</P>
<P>A line in a data file that specifies a dipole moment uses the same
format as the arguments of the dipole command in an input script,
except that no wild-card asterisk can be used. For example, under the
"Dipoles" section of a data file, the line that corresponds to the 1st
example above would be listed as
</P>
<PRE>1 1.0
</PRE>
<P><B>Restrictions:</B>
</P>
<P>This command must come after the simulation box is defined by a
<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
<A HREF = "create_box.html">create_box</A> command.
</P>
<P>All dipoles moments must be defined before a simulation is run (if the
atom style requires dipoles be set). They must also all be defined
before a <A HREF = "set.html">set dipole</A> or <A HREF = "set.html">set dipole/random</A> command
is used.
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

66
doc/dipole.txt
View File

@ -1,66 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
dipole command :h3
[Syntax:]
dipole I value :pre
I = atom type (see asterisk form below)
value = dipole moment (dipole units) :ul
[Examples:]
dipole 1 1.0
dipole 3 2.0
dipole 3*5 0.0 :pre
[Description:]
Set the dipole moment for all atoms of one or more atom types. This
command is only used for atom styles that require dipole moments
("atom_style"_atom_style.html dipole). A value of 0.0 should be used
if the atom type has no dipole moment. Dipole values can also be set
in the "read_data"_read_data.html data file. See the
"units"_units.html command for a discussion of dipole units.
Currently, only "atom_style dipole"_atom_style.html requires dipole
moments be set.
I can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be
used to set the dipole moment for multiple atom types. This takes the
form "*" or "*n" or "n*" or "m*n". If N = the number of atom types,
then an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
A line in a data file that specifies a dipole moment uses the same
format as the arguments of the dipole command in an input script,
except that no wild-card asterisk can be used. For example, under the
"Dipoles" section of a data file, the line that corresponds to the 1st
example above would be listed as
1 1.0 :pre
[Restrictions:]
This command must come after the simulation box is defined by a
"read_data"_read_data.html, "read_restart"_read_restart.html, or
"create_box"_create_box.html command.
All dipoles moments must be defined before a simulation is run (if the
atom style requires dipoles be set). They must also all be defined
before a "set dipole"_set.html or "set dipole/random"_set.html command
is used.
[Related commands:] none
[Default:] none

28
doc/dump.html
View File

@ -49,9 +49,10 @@
possible attributes = id, mol, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
q, mux, muy, muz, mu,
radius, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
spin, eradius, ervel, erforce,
c_ID, c_ID[N], f_ID, f_ID[N], v_name
@ -67,10 +68,12 @@
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
radius = radius of extended spherical particle
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius = radius of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
shapex,shapey,shapez = 3 diameters of ellipsoidal particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
spin = electron spin
@ -403,21 +406,26 @@ coordinates and the image flags.
</P>
<P>The <I>mux</I>, <I>muy</I>, <I>muz</I> attributes are specific to dipolar systems
defined with an atom style of <I>dipole</I>. They give the orientation of
the atom's point dipole moment.
the atom's point dipole moment. The <I>mu</I> attribute gives the
magnitude of the atom's dipole moment.
</P>
<P>The <I>radius</I> attribute is specific to extended spherical particles
that have a finite size, such as granular particles defined with
an atom style of <I>granular</I>.
that have a finite size, such as those defined with an atom style of
<I>sphere</I>.
</P>
<P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> attributes are specific to extended
spherical or aspherical particles that have an angular velocity. Only
certain atom styles, such as <I>granular</I> or <I>dipole</I> define this
<P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> attributes are specific to
extended spherical or aspherical particles that have an angular
velocity. Only certain atom styles, such as <I>sphere</I> define this
quantity.
</P>
<P>The <I>angmomx</I>, <I>angmomy</I>, and <I>angmomz</I> attributes are specific to
extended aspherical particles that have an angular momentum. Only
the <I>ellipsoid</I> atom style defines this quantity.
</P>
<P>The <I>shapex</I>, <I>shapey</I>, and <I>shapez</I> attributes are specific to
extended ellipsoidal particles that have a finite size and shape, such
those defined with an atom style of <I>ellipsoidal</I>.
</P>
<P>The <I>quatw</I>, <I>quati</I>, <I>quatj</I>, <I>quatk</I> attributes are for aspherical
particles defined with an atom style of <I>ellipsoid</I>. They are the
components of the quaternion that defines the orientation of the

28
doc/dump.txt
View File

@ -39,9 +39,10 @@ args = list of arguments for a particular style :l
possible attributes = id, mol, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz,
q, mux, muy, muz, mu,
radius, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
spin, eradius, ervel, erforce,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
@ -57,10 +58,12 @@ args = list of arguments for a particular style :l
vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms
q = atom charge
mux,muy,muz = orientation of dipolar atom
radius = radius of extended spherical particle
mux,muy,muz = orientation of dipole moment of atom
mu = magnitude of dipole moment of atom
radius = radius of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
shapex,shapey,shapez = 3 diameters of ellipsoidal particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
spin = electron spin
@ -392,21 +395,26 @@ coordinates and the image flags.
The {mux}, {muy}, {muz} attributes are specific to dipolar systems
defined with an atom style of {dipole}. They give the orientation of
the atom's point dipole moment.
the atom's point dipole moment. The {mu} attribute gives the
magnitude of the atom's dipole moment.
The {radius} attribute is specific to extended spherical particles
that have a finite size, such as granular particles defined with
an atom style of {granular}.
that have a finite size, such as those defined with an atom style of
{sphere}.
The {omegax}, {omegay}, and {omegaz} attributes are specific to extended
spherical or aspherical particles that have an angular velocity. Only
certain atom styles, such as {granular} or {dipole} define this
The {omegax}, {omegay}, and {omegaz} attributes are specific to
extended spherical or aspherical particles that have an angular
velocity. Only certain atom styles, such as {sphere} define this
quantity.
The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
extended aspherical particles that have an angular momentum. Only
the {ellipsoid} atom style defines this quantity.
The {shapex}, {shapey}, and {shapez} attributes are specific to
extended ellipsoidal particles that have a finite size and shape, such
those defined with an atom style of {ellipsoidal}.
The {quatw}, {quati}, {quatj}, {quatk} attributes are for aspherical
particles defined with an atom style of {ellipsoid}. They are the
components of the quaternion that defines the orientation of the

2
doc/fix_freeze.html
View File

@ -59,7 +59,7 @@ this fix is applied.
</P>
<P><B>Related commands:</B> none
</P>
<P><A HREF = "atom_style.html">atom_style granular</A>
<P><A HREF = "atom_style.html">atom_style sphere</A>
</P>
<P><B>Default:</B> none
</P>

2
doc/fix_freeze.txt
View File

@ -56,6 +56,6 @@ this fix is applied.
[Related commands:] none
"atom_style granular"_atom_style.html
"atom_style sphere"_atom_style.html
[Default:] none

2
doc/fix_gravity.html
View File

@ -99,7 +99,7 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "atom_style.html">atom_style granular</A>, <A HREF = "fix_addforce.html">fix addforce</A>
<P><A HREF = "atom_style.html">atom_style sphere</A>, <A HREF = "fix_addforce.html">fix addforce</A>
</P>
<P><B>Default:</B> none
</P>

2
doc/fix_gravity.txt
View File

@ -91,6 +91,6 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Related commands:]
"atom_style granular"_atom_style.html, "fix addforce"_fix_addforce.html
"atom_style sphere"_atom_style.html, "fix addforce"_fix_addforce.html
[Default:] none

17
doc/fix_nph_asphere.html
View File

@ -111,18 +111,23 @@ quantities as does the <A HREF = "fix_nh.html">fix nph</A> command.
</P>
<P><B>Restrictions:</B>
</P>
<P>This fix requires that atoms store torque and angular velocity (omega)
as defined by the <A HREF = "atom_style.html">atom_style</A>. It also require they
store either a per-particle diameter or per-type <A HREF = "shape.html">shape</A>.
<P>This fix is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical.
particles, but they can be aspherical or spherical as defined by their
shape attribute.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nh.html">fix nph</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_nvt_asphere.html">fix
nvt_asphere</A>, <A HREF = "fix_npt_asphere.html">fix npt_asphere</A>,
<A HREF = "fix_modify.html">fix_modify</A>
nvt_asphere</A>, <A HREF = "fix_npt_asphere.html">fix
npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
</P>
<P><B>Default:</B> none
</P>

17
doc/fix_nph_asphere.txt
View File

@ -108,17 +108,22 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix requires that atoms store torque and angular velocity (omega)
as defined by the "atom_style"_atom_style.html. It also require they
store either a per-particle diameter or per-type "shape"_shape.html.
This fix is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical.
particles, but they can be aspherical or spherical as defined by their
shape attribute.
[Related commands:]
"fix nph"_fix_nh.html, "fix nve_asphere"_fix_nve_asphere.html, "fix
nvt_asphere"_fix_nvt_asphere.html, "fix npt_asphere"_fix_npt_asphere.html,
"fix_modify"_fix_modify.html
nvt_asphere"_fix_nvt_asphere.html, "fix
npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
[Default:] none

6
doc/fix_nph_sphere.html
View File

@ -112,11 +112,11 @@ quantities as does the <A HREF = "fix_nh.html">fix nph</A> command.
<P><B>Restrictions:</B>
</P>
<P>This fix requires that atoms store torque and angular velocity (omega)
as defined by the <A HREF = "atom_style.html">atom_style</A>. It also require they
store either a per-particle diameter or per-type <A HREF = "shape.html">shape</A>.
and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
command.
</P>
<P>All particles in the group must be finite-size spheres. They cannot
be point particles, nor can they be aspherical.
be point particles.
</P>
<P><B>Related commands:</B>
</P>

6
doc/fix_nph_sphere.txt
View File

@ -109,11 +109,11 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix requires that atoms store torque and angular velocity (omega)
as defined by the "atom_style"_atom_style.html. It also require they
store either a per-particle diameter or per-type "shape"_shape.html.
and a radius as defined by the "atom_style sphere"_atom_style.html
command.
All particles in the group must be finite-size spheres. They cannot
be point particles, nor can they be aspherical.
be point particles.
[Related commands:]

11
doc/fix_npt_asphere.html
View File

@ -140,14 +140,13 @@ this.
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix requires that atoms store torque and angular momentum and a
quaternion to represent their orientation, as defined by the
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter or per-particle mass.
<P>This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical.
particles, but they can be aspherical or spherical as defined by their
shape attribute.
</P>
<P><B>Related commands:</B>
</P>

11
doc/fix_npt_asphere.txt
View File

@ -137,14 +137,13 @@ This fix is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion to represent their orientation, as defined by the
"atom_style"_atom_style.html. It also require they store a per-type
"shape"_shape.html. The particles cannot store a per-particle
diameter or per-particle mass.
This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical.
particles, but they can be aspherical or spherical as defined by their
shape attribute.
[Related commands:]

6
doc/fix_npt_sphere.html
View File

@ -136,11 +136,11 @@ this.
<P><B>Restrictions:</B>
</P>
<P>This fix requires that atoms store torque and angular velocity (omega)
as defined by the <A HREF = "atom_style.html">atom_style</A>. It also require they
store either a per-particle diameter or per-type <A HREF = "shape.html">shape</A>.
and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
command.
</P>
<P>All particles in the group must be finite-size spheres. They cannot
be point particles, nor can they be aspherical.
be point particles.
</P>
<P><B>Related commands:</B>
</P>

6
doc/fix_npt_sphere.txt
View File

@ -133,11 +133,11 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix requires that atoms store torque and angular velocity (omega)
as defined by the "atom_style"_atom_style.html. It also require they
store either a per-particle diameter or per-type "shape"_shape.html.
and a radius as defined by the "atom_style sphere"_atom_style.html
command.
All particles in the group must be finite-size spheres. They cannot
be point particles, nor can they be aspherical.
be point particles.
[Related commands:]

11
doc/fix_nve_asphere.html
View File

@ -48,14 +48,13 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix requires that atoms store torque and angular momentum and a
quaternion to represent their orientation, as defined by the
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter or per-particle mass.
<P>This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical.
particles, but they can be aspherical or spherical as defined by their
shape attribute.
</P>
<P><B>Related commands:</B>
</P>

11
doc/fix_nve_asphere.txt
View File

@ -45,14 +45,13 @@ This fix is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion to represent their orientation, as defined by the
"atom_style"_atom_style.html. It also require they store a per-type
"shape"_shape.html. The particles cannot store a per-particle
diameter or per-particle mass.
This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical.
particles, but they can be aspherical or spherical as defined by their
shape attribute.
[Related commands:]

13
doc/fix_nve_sphere.html
View File

@ -46,8 +46,8 @@ assumes point particles and only updates their position and velocity.
<P>If the <I>update</I> keyword is used with the <I>dipole</I> value, then the
orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models
where a dipole moment is assigned to particles via the
<A HREF = "dipole.html">dipole</A> command.
where a dipole moment is assigned to particles via use of the
<A HREF = "atom_style.html">atom_style dipole</A> command.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
@ -62,12 +62,13 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
<P><B>Restrictions:</B>
</P>
<P>This fix requires that atoms store torque and angular velocity (omega)
as defined by the <A HREF = "atom_style.html">atom_style</A>. It also require they
store either a per-particle diameter or per-type <A HREF = "shape.html">shape</A>. If
the <I>dipole</I> keyword is used, then they must store a dipole moment.
and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
command. If the <I>dipole</I> keyword is used, then they must also store a
dipole moment as defined by the <A HREF = "atom_style.html">atom_style dipole</A>
command.
</P>
<P>All particles in the group must be finite-size spheres. They cannot
be point particles, nor can they be aspherical.
be point particles.
</P>
<P><B>Related commands:</B>
</P>

13
doc/fix_nve_sphere.txt
View File

@ -38,8 +38,8 @@ assumes point particles and only updates their position and velocity.
If the {update} keyword is used with the {dipole} value, then the
orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models
where a dipole moment is assigned to particles via the
"dipole"_dipole.html command.
where a dipole moment is assigned to particles via use of the
"atom_style dipole"_atom_style.html command.
[Restart, fix_modify, output, run start/stop, minimize info:]
@ -54,12 +54,13 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix requires that atoms store torque and angular velocity (omega)
as defined by the "atom_style"_atom_style.html. It also require they
store either a per-particle diameter or per-type "shape"_shape.html. If
the {dipole} keyword is used, then they must store a dipole moment.
and a radius as defined by the "atom_style sphere"_atom_style.html
command. If the {dipole} keyword is used, then they must also store a
dipole moment as defined by the "atom_style dipole"_atom_style.html
command.
All particles in the group must be finite-size spheres. They cannot
be point particles, nor can they be aspherical.
be point particles.
[Related commands:]

11
doc/fix_nvt_asphere.html
View File

@ -116,14 +116,13 @@ quantities as does the <A HREF = "fix_nh.html">fix nvt</A> command.
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This fix requires that atoms store torque and angular momentum and a
quaternion to represent their orientation, as defined by the
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter or per-particle mass.
<P>This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical.
particles, but they can be aspherical or spherical as defined by their
shape attribute.
</P>
<P><B>Related commands:</B>
</P>

11
doc/fix_nvt_asphere.txt
View File

@ -113,14 +113,13 @@ This fix is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This fix requires that atoms store torque and angular momentum and a
quaternion to represent their orientation, as defined by the
"atom_style"_atom_style.html. It also require they store a per-type
"shape"_shape.html. The particles cannot store a per-particle
diameter or per-particle mass.
This fix requires that atoms store torque and angular momementum and a
quaternion as defined by the "atom_style ellipsoid"_atom_style.html
command.
All particles in the group must be finite-size. They cannot be point
particles, but they can be aspherical or spherical.
particles, but they can be aspherical or spherical as defined by their
shape attribute.
[Related commands:]

6
doc/fix_nvt_sphere.html
View File

@ -113,11 +113,11 @@ quantities as does the <A HREF = "fix_nh.html">fix nvt</A> command.
<P><B>Restrictions:</B>
</P>
<P>This fix requires that atoms store torque and angular velocity (omega)
as defined by the <A HREF = "atom_style.html">atom_style</A>. It also require they
store either a per-particle radius or per-type <A HREF = "shape.html">shape</A>.
and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
command.
</P>
<P>All particles in the group must be finite-size spheres. They cannot
be point particles, nor can they be aspherical.
be point particles.
</P>
<P><B>Related commands:</B>
</P>

6
doc/fix_nvt_sphere.txt
View File

@ -110,11 +110,11 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
This fix requires that atoms store torque and angular velocity (omega)
as defined by the "atom_style"_atom_style.html. It also require they
store either a per-particle radius or per-type "shape"_shape.html.
and a radius as defined by the "atom_style sphere"_atom_style.html
command.
All particles in the group must be finite-size spheres. They cannot
be point particles, nor can they be aspherical.
be point particles.
[Related commands:]

12
doc/fix_rigid.html
View File

@ -114,12 +114,12 @@ setforce</A> command), and integrating them as usual
<HR>
<P>The constituent particles within a rigid body can be point particles
(the default in LAMMPS) or finite-size particles, such as spheroids
and ellipsoids. See the <A HREF = "shape.html">shape</A> command and <A HREF = "atom_style.html">atom_style
granular</A> for more details on these kinds of
particles. Finite-size particles contribute differently to the moment
of inertia of a rigid body than do point particles. Finite-size
particles can also experience torque (e.g. due to <A HREF = "pair_gran.html">frictional granular
(the default in LAMMPS) or finite-size particles, such as spheres and
ellipsoids. See the <A HREF = "atom_style.html">atom_style sphere and ellipsoid</A>
commands for more details on these kinds of particles. Finite-size
particles contribute differently to the moment of inertia of a rigid
body than do point particles. Finite-size particles can also
experience torque (e.g. due to <A HREF = "pair_gran.html">frictional granular
interactions</A>) and have an orientation. These
contributions are accounted for by these fixes.
</P>

12
doc/fix_rigid.txt
View File

@ -103,12 +103,12 @@ setforce"_fix_setforce.html command), and integrating them as usual
:line
The constituent particles within a rigid body can be point particles
(the default in LAMMPS) or finite-size particles, such as spheroids
and ellipsoids. See the "shape"_shape.html command and "atom_style
granular"_atom_style.html for more details on these kinds of
particles. Finite-size particles contribute differently to the moment
of inertia of a rigid body than do point particles. Finite-size
particles can also experience torque (e.g. due to "frictional granular
(the default in LAMMPS) or finite-size particles, such as spheres and
ellipsoids. See the "atom_style sphere and ellipsoid"_atom_style.html
commands for more details on these kinds of particles. Finite-size
particles contribute differently to the moment of inertia of a rigid
body than do point particles. Finite-size particles can also
experience torque (e.g. due to "frictional granular
interactions"_pair_gran.html) and have an orientation. These
contributions are accounted for by these fixes.

12
doc/mass.html
View File

@ -51,13 +51,13 @@ line that corresponds to the 1st example above would be listed as
</PRE>
<P>Note that the mass command can only be used if the <A HREF = "atom_style.html">atom
style</A> requires per-type atom mass to be set.
Currently, all but the <I>granular</I> and <I>peri</I> styles do. They require
mass to be set for individual particles, not types. Per-atom masses
are defined in the data file read by the <A HREF = "read_data.html">read_data</A>
command, or set to default values by the
Currently, all but the <I>sphere</I> and <I>ellipsoid</I> and <I>peri</I> styles do.
They require mass to be set for individual particles, not types.
Per-atom masses are defined in the data file read by the
<A HREF = "read_data.html">read_data</A> command, or set to default values by the
<A HREF = "create_atoms.html">create_atoms</A> command. Per-atom masses can also be
set to new values by the <A HREF = "set.html">set diameter</A> or <A HREF = "set.html">set
density</A> command.
set to new values by the <A HREF = "set.html">set mass</A> or <A HREF = "set.html">set density</A>
commands.
</P>
<P>Also note that <A HREF = "pair_eam.html">pair_style eam</A> defines the masses of
atom types in the EAM potential file, in which case the mass command

12
doc/mass.txt
View File

@ -48,13 +48,13 @@ line that corresponds to the 1st example above would be listed as
Note that the mass command can only be used if the "atom
style"_atom_style.html requires per-type atom mass to be set.
Currently, all but the {granular} and {peri} styles do. They require
mass to be set for individual particles, not types. Per-atom masses
are defined in the data file read by the "read_data"_read_data.html
command, or set to default values by the
Currently, all but the {sphere} and {ellipsoid} and {peri} styles do.
They require mass to be set for individual particles, not types.
Per-atom masses are defined in the data file read by the
"read_data"_read_data.html command, or set to default values by the
"create_atoms"_create_atoms.html command. Per-atom masses can also be
set to new values by the "set diameter"_set.html or "set
density"_set.html command.
set to new values by the "set mass"_set.html or "set density"_set.html
commands.
Also note that "pair_style eam"_pair_eam.html defines the masses of
atom types in the EAM potential file, in which case the mass command

12
doc/pair_colloid.html
View File

@ -159,6 +159,18 @@ to be specified in an input script that reads a restart file.
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>Normally, this pair style should be used with finite-size particles
which have a diameter, e.g. see the <A HREF = "atom_style.html">atom_style
sphere</A> command. However, this is not a requirement,
since the only definition of particle size is via the pair_coeff
parameters for each type. In other words, the physical radius of the
particle is ignored. Thus you should insure that the d1,d2 parameters
you specify are consistent with the physical size of the particles of
that type.
</P>
<P>Per-particle polydispersity is not yet supported by this pair style;
only per-type polydispersity is enabled via the pair_coeff parameters.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>

12
doc/pair_colloid.txt
View File

@ -156,6 +156,18 @@ This style is part of the "colloid" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
Normally, this pair style should be used with finite-size particles
which have a diameter, e.g. see the "atom_style
sphere"_atom_style.html command. However, this is not a requirement,
since the only definition of particle size is via the pair_coeff
parameters for each type. In other words, the physical radius of the
particle is ignored. Thus you should insure that the d1,d2 parameters
you specify are consistent with the physical size of the particles of
that type.
Per-particle polydispersity is not yet supported by this pair style;
only per-type polydispersity is enabled via the pair_coeff parameters.
[Related commands:]
"pair_coeff"_pair_coeff.html

40
doc/pair_gayberne.html
View File

@ -71,9 +71,7 @@ document</A>.
<I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
ellipsoid</A> should be used since it defines the
rotational state of the ellipsoidal particles. The size and shape of
the ellipsoidal particles are defined by the <A HREF = "shape.html">shape</A>
command.
rotational state and the size and shape of each ellipsoidal particle.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
@ -94,10 +92,11 @@ commands, or by mixing as described below:
<P>The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
</P>
<P>It is typical for the Gay-Berne potential to define <I>sigma</I> as the
minimum of the 3 "shape" diameters for a I,I interaction, though this
is not required. Note that this is a different meaning for <I>sigma</I>
than the <A HREF = "pair_resquared.html">pair_style resquared</A> potential uses.
<P>It is typical with the Gay-Berne potential to define <I>sigma</I> as the
minimum of the 3 shape diameters of the particles involved in an I,I
interaction, though this is not required. Note that this is a
different meaning for <I>sigma</I> than the <A HREF = "pair_resquared.html">pair_style
resquared</A> potential uses.
</P>
<P>The epsilon_i and epsilon_j coefficients are actually defined for atom
types, not for pairs of atom types. Thus, in a series of pair_coeff
@ -122,15 +121,15 @@ still need to insure the epsilon a,b,c coefficients are assigned to
that type in a "pair_coeff I J" command.
</P>
<P>IMPORTANT NOTE: If the epsilon a,b,c for an atom type are all 1.0, and
if the shape of the particle is spherical (see the <A HREF = "shape.html">shape</A>
command), meaning the 3 diameters are all the same, then the particle
is treated as "spherical" by the Gay-Berne potential. This is
significant because if two "spherical" particles interact, then the
simple Lennard-Jones formula is used to compute their interaction
energy/force using epsilon and sigma, which is much cheaper to compute
than the full Gay-Berne formula. Thus you should insure epsilon a,b,c
are set to 1.0 for spherical particle types and use epsilon and sigma
to specify its interaction with other spherical particles.
if the shape of the particle itself is spherical, meaning its 3 shape
parameters are all the same, then the particle is treated as an LJ
sphere by the Gay-Berne potential. This is significant because if two
LJ spheres interact, then the simple Lennard-Jones formula is used to
compute their interaction energy/force using epsilon and sigma. This
is much cheaper to compute than the full Gay-Berne formula. Thus you
should insure epsilon a,b,c are set to 1.0 for spherical particle
types and use epsilon and sigma to specify its interaction with other
spherical particles.
</P>
<HR>
@ -191,14 +190,19 @@ to be specified in an input script that reads a restart file.
enabled if LAMMPS was built with the those packages. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This pair style requires that atoms store torque and a quaternion to
<P>These pair style require that atoms store torque and a quaternion to
represent their orientation, as defined by the
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter.
</P>
<P>This pair style requires that atoms be ellipsoids as defined by the
<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
</P>
<P>Particles acted on by the potential can be extended aspherical or
spherical particles, or point particles.
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.
</P>
<P>The Gay-Berne potential does not become isotropic as r increases
<A HREF = "#Everaers">(Everaers)</A>. The distance-of-closest-approach

40
doc/pair_gayberne.txt
View File

@ -66,9 +66,7 @@ Use of this pair style requires the NVE, NVT, or NPT fixes with the
{asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
order to integrate particle rotation. Additionally, "atom_style
ellipsoid"_atom_style.html should be used since it defines the
rotational state of the ellipsoidal particles. The size and shape of
the ellipsoidal particles are defined by the "shape"_shape.html
command.
rotational state and the size and shape of each ellipsoidal particle.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
@ -89,10 +87,11 @@ cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used.
It is typical for the Gay-Berne potential to define {sigma} as the
minimum of the 3 "shape" diameters for a I,I interaction, though this
is not required. Note that this is a different meaning for {sigma}
than the "pair_style resquared"_pair_resquared.html potential uses.
It is typical with the Gay-Berne potential to define {sigma} as the
minimum of the 3 shape diameters of the particles involved in an I,I
interaction, though this is not required. Note that this is a
different meaning for {sigma} than the "pair_style
resquared"_pair_resquared.html potential uses.
The epsilon_i and epsilon_j coefficients are actually defined for atom
types, not for pairs of atom types. Thus, in a series of pair_coeff
@ -117,15 +116,15 @@ still need to insure the epsilon a,b,c coefficients are assigned to
that type in a "pair_coeff I J" command.
IMPORTANT NOTE: If the epsilon a,b,c for an atom type are all 1.0, and
if the shape of the particle is spherical (see the "shape"_shape.html
command), meaning the 3 diameters are all the same, then the particle
is treated as "spherical" by the Gay-Berne potential. This is
significant because if two "spherical" particles interact, then the
simple Lennard-Jones formula is used to compute their interaction
energy/force using epsilon and sigma, which is much cheaper to compute
than the full Gay-Berne formula. Thus you should insure epsilon a,b,c
are set to 1.0 for spherical particle types and use epsilon and sigma
to specify its interaction with other spherical particles.
if the shape of the particle itself is spherical, meaning its 3 shape
parameters are all the same, then the particle is treated as an LJ
sphere by the Gay-Berne potential. This is significant because if two
LJ spheres interact, then the simple Lennard-Jones formula is used to
compute their interaction energy/force using epsilon and sigma. This
is much cheaper to compute than the full Gay-Berne formula. Thus you
should insure epsilon a,b,c are set to 1.0 for spherical particle
types and use epsilon and sigma to specify its interaction with other
spherical particles.
:line
@ -186,14 +185,19 @@ The {gayberne} style is part of the "asphere" package. The
enabled if LAMMPS was built with the those packages. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This pair style requires that atoms store torque and a quaternion to
These pair style require that atoms store torque and a quaternion to
represent their orientation, as defined by the
"atom_style"_atom_style.html. It also require they store a per-type
"shape"_shape.html. The particles cannot store a per-particle
diameter.
This pair style requires that atoms be ellipsoids as defined by the
"atom_style ellipsoid"_atom_style.html command.
Particles acted on by the potential can be extended aspherical or
spherical particles, or point particles.
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.
The Gay-Berne potential does not become isotropic as r increases
"(Everaers)"_#Everaers. The distance-of-closest-approach

4
doc/pair_gran.html
View File

@ -191,8 +191,8 @@ is only enabled if LAMMPS was built with that package. See the
</P>
<P>These pair styles require that atoms store torque and angular velocity
(omega) as defined by the <A HREF = "atom_style.html">atom_style</A>. They also
require a per-particle radius is stored. The <I>granular</I> atom style
does all of this.
require a per-particle radius is stored. The <I>sphere</I> atom style does
all of this.
</P>
<P>This pair style requires you to use the <A HREF = "communicate.html">communicate vel
yes</A> option so that velocites are stored by ghost

4
doc/pair_gran.txt
View File

@ -181,8 +181,8 @@ is only enabled if LAMMPS was built with that package. See the
These pair styles require that atoms store torque and angular velocity
(omega) as defined by the "atom_style"_atom_style.html. They also
require a per-particle radius is stored. The {granular} atom style
does all of this.
require a per-particle radius is stored. The {sphere} atom style does
all of this.
This pair style requires you to use the "communicate vel
yes"_communicate.html option so that velocites are stored by ghost

14
doc/pair_lubricate.html
View File

@ -128,16 +128,12 @@ to be specified in an input script that reads a restart file.
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This pair style requires that atoms store torque and a quaternion to
represent their orientation, as defined by the
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter or per-particle mass.
<P>This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
command.
</P>
<P>All the shape settings must be for finite-size spheres. They cannot
be point particles, nor can they be aspherical. Additionally all the
shape types must specify particles of the same size, i.e. a
monodisperse system.
<P>Per-particle or per-type polydispersity is not yet supported by this
pair style; all particles must have the same diameter.
</P>
<P>This pair style requires you to use the <A HREF = "communicate.html">communicate vel
yes</A> option so that velocites are stored by ghost

14
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@ -125,16 +125,12 @@ This style is part of the "colloid" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This pair style requires that atoms store torque and a quaternion to
represent their orientation, as defined by the
"atom_style"_atom_style.html. It also require they store a per-type
"shape"_shape.html. The particles cannot store a per-particle
diameter or per-particle mass.
This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the "atom_style sphere"_atom_style.html
command.
All the shape settings must be for finite-size spheres. They cannot
be point particles, nor can they be aspherical. Additionally all the
shape types must specify particles of the same size, i.e. a
monodisperse system.
Per-particle or per-type polydispersity is not yet supported by this
pair style; all particles must have the same diameter.
This pair style requires you to use the "communicate vel
yes"_communicate.html option so that velocites are stored by ghost

47
doc/pair_resquared.html
View File

@ -39,9 +39,7 @@ in <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary document</A>.
<I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
ellipsoid</A> should be used since it defines the
rotational state of the ellipsoidal particles. The size and shape of
the ellipsoidal particles are defined by the <A HREF = "shape.html">shape</A>
command.
rotational state and the size and shape of each ellipsoidal particle.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
@ -68,21 +66,21 @@ different meaning for <I>sigma</I> than the <A HREF = "pair_gayberne.html">pair_
gayberne</A> potential uses.
</P>
<P>The parameters used depend on the type of the interacting particles,
i.e. ellipsoid or LJ sphere. The type of particle is determined by
the diameters specified with the <A HREF = "shape.html">shape</A> command. LJ
spheres have diameters equal to zero and thus represent a single
i.e. ellipsoids or LJ spheres. The type of a particle is determined
by the diameters specified for its 3 shape paramters. LJ spheres have
all 3 diameters equal to zero and thus represent a simple point
particle with size sigma. The epsilon_i_* or epsilon_j_* parameters
are ignored for LJ sphere interactions. The interactions between two
LJ sphere particles are computed using the standard Lennard-Jones
formula.
are ignored for LJ spheres. The interactions between two LJ spheres
are computed using the standard Lennard-Jones formula, which is much
cheaper to compute than the ellipsoidal formulas.
</P>
<P>For ellipsoid-LJ sphere interactions, a correction to the distance-
<P>For ellipsoid/LJ sphere interactions, a correction to the distance-
of-closest approach equation has been implemented to reduce the error
from disparate sizes; see <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary
document</A>.
</P>
<P>A12 specifies the energy prefactor which depends on the type of
particles interacting. For ellipsoid-ellipsoid interactions, A12 is
particles interacting. For ellipsoid/ellipsoid interactions, A12 is
the Hamaker constant as described in <A HREF = "#Everaers">(Everaers)</A>. In LJ
units:
</P>
@ -92,17 +90,17 @@ units:
composing the ellipsoids and epsilon_LJ determines the interaction
strength of the spherical particles.
</P>
<P>For ellipsoid-LJ sphere interactions, A12 gives the energy prefactor
<P>For ellipsoid/LJ sphere interactions, A12 gives the energy prefactor
(see <A HREF = "PDF/pair_resquared_extra.pdf">here</A> for details:
</P>
<CENTER><IMG SRC = "Eqs/pair_resquared2.jpg">
</CENTER>
<P>For LJ sphere-LJ sphere interactions, A12 is the standard epsilon used
in Lennard-Jones pair styles:
<P>For LJ sphere/LJ sphere interactions, A12 is used as the standard
epsilon used in Lennard-Jones pair styles:
</P>
<CENTER><IMG SRC = "Eqs/pair_resquared3.jpg">
</CENTER>
<P>sigma specifies the diameter of the continuous distribution of
<P>Sigma specifies the diameter of the continuous distribution of
constituent particles within each ellipsoid used to model the
RE-squared potential.
</P>
@ -144,13 +142,13 @@ that type in a "pair_coeff I J" command.
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance can be mixed, but only for LJ sphere pairs. The
and cutoff distance can be mixed, but only for sphere pairs. The
default mix value is <I>geometric</I>. See the "pair_modify" command for
details. Other type pairs cannot be mixed, due to the different
meanings of the energy prefactors used to calculate the interactions
and the implicit dependence of the ellipsoid-LJ sphere interaction on
the equation for the Hamaker constant presented here. Mixing of sigma
and epsilon followed by calculation of the energy prefactors using the
and the implicit dependence of the ellipsoid-sphere interaction on the
equation for the Hamaker constant presented here. Mixing of sigma and
epsilon followed by calculation of the energy prefactors using the
equations above is recommended.
</P>
<P>This pair styles supports the <A HREF = "pair_modify.html">pair_modify</A> shift
@ -183,14 +181,13 @@ command</A>.
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>This pair style requires that atoms store torque and a quaternion to
represent their orientation, as defined by the
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter.
<P>This pair style requires that atoms be ellipsoids as defined by the
<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
</P>
<P>Particles acted on by the potential can be extended aspherical or
spherical particles, or point particles.
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.
</P>
<P>The distance-of-closest-approach approximation used by LAMMPS becomes
less accurate when high-aspect ratio ellipsoids are used.

47
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View File

@ -36,9 +36,7 @@ Use of this pair style requires the NVE, NVT, or NPT fixes with the
{asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
order to integrate particle rotation. Additionally, "atom_style
ellipsoid"_atom_style.html should be used since it defines the
rotational state of the ellipsoidal particles. The size and shape of
the ellipsoidal particles are defined by the "shape"_shape.html
command.
rotational state and the size and shape of each ellipsoidal particle.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
@ -65,21 +63,21 @@ different meaning for {sigma} than the "pair_style
gayberne"_pair_gayberne.html potential uses.
The parameters used depend on the type of the interacting particles,
i.e. ellipsoid or LJ sphere. The type of particle is determined by
the diameters specified with the "shape"_shape.html command. LJ
spheres have diameters equal to zero and thus represent a single
i.e. ellipsoids or LJ spheres. The type of a particle is determined
by the diameters specified for its 3 shape paramters. LJ spheres have
all 3 diameters equal to zero and thus represent a simple point
particle with size sigma. The epsilon_i_* or epsilon_j_* parameters
are ignored for LJ sphere interactions. The interactions between two
LJ sphere particles are computed using the standard Lennard-Jones
formula.
are ignored for LJ spheres. The interactions between two LJ spheres
are computed using the standard Lennard-Jones formula, which is much
cheaper to compute than the ellipsoidal formulas.
For ellipsoid-LJ sphere interactions, a correction to the distance-
For ellipsoid/LJ sphere interactions, a correction to the distance-
of-closest approach equation has been implemented to reduce the error
from disparate sizes; see "this supplementary
document"_PDF/pair_resquared_extra.pdf.
A12 specifies the energy prefactor which depends on the type of
particles interacting. For ellipsoid-ellipsoid interactions, A12 is
particles interacting. For ellipsoid/ellipsoid interactions, A12 is
the Hamaker constant as described in "(Everaers)"_#Everaers. In LJ
units:
@ -89,17 +87,17 @@ where rho gives the number density of the spherical particles
composing the ellipsoids and epsilon_LJ determines the interaction
strength of the spherical particles.
For ellipsoid-LJ sphere interactions, A12 gives the energy prefactor
For ellipsoid/LJ sphere interactions, A12 gives the energy prefactor
(see "here"_PDF/pair_resquared_extra.pdf for details:
:c,image(Eqs/pair_resquared2.jpg)
For LJ sphere-LJ sphere interactions, A12 is the standard epsilon used
in Lennard-Jones pair styles:
For LJ sphere/LJ sphere interactions, A12 is used as the standard
epsilon used in Lennard-Jones pair styles:
:c,image(Eqs/pair_resquared3.jpg)
sigma specifies the diameter of the continuous distribution of
Sigma specifies the diameter of the continuous distribution of
constituent particles within each ellipsoid used to model the
RE-squared potential.
@ -141,13 +139,13 @@ that type in a "pair_coeff I J" command.
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance can be mixed, but only for LJ sphere pairs. The
and cutoff distance can be mixed, but only for sphere pairs. The
default mix value is {geometric}. See the "pair_modify" command for
details. Other type pairs cannot be mixed, due to the different
meanings of the energy prefactors used to calculate the interactions
and the implicit dependence of the ellipsoid-LJ sphere interaction on
the equation for the Hamaker constant presented here. Mixing of sigma
and epsilon followed by calculation of the energy prefactors using the
and the implicit dependence of the ellipsoid-sphere interaction on the
equation for the Hamaker constant presented here. Mixing of sigma and
epsilon followed by calculation of the energy prefactors using the
equations above is recommended.
This pair styles supports the "pair_modify"_pair_modify.html shift
@ -180,14 +178,13 @@ This style is part of the "asphere" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
This pair style requires that atoms store torque and a quaternion to
represent their orientation, as defined by the
"atom_style"_atom_style.html. It also require they store a per-type
"shape"_shape.html. The particles cannot store a per-particle
diameter.
This pair style requires that atoms be ellipsoids as defined by the
"atom_style ellipsoid"_atom_style.html command.
Particles acted on by the potential can be extended aspherical or
spherical particles, or point particles.
spherical particles, or point particles. Spherical particles have all
3 of their shape parameters equal to each other. Point particles have
all 3 of their shape parameters equal to 0.0.
The distance-of-closest-approach approximation used by LAMMPS becomes
less accurate when high-aspect ratio ellipsoids are used.

14
doc/pair_yukawa_colloid.html
View File

@ -110,12 +110,14 @@ to be specified in an input script that reads a restart file.
LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info.
</P>
<P>Because this potential uses the radii of the particles, the atom style
must support particles whose size is set via the <A HREF = "shape.html">shape</A>
command. For example <A HREF = "atom_style.html">atom_style</A> colloid or
ellipsoid. Only spherical particles are currently allowed for
pair_style yukawa/colloid, which means that for each particle type,
its 3 shape diameters must be equal to each other.
<P>This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
command.
</P>
<P>Per-particle polydispersity is not yet supported by this pair style;
per-type polydispersity is allowed. This means all particles of the
same type must have the same diameter. Each type can have a different
diameter.
</P>
<P><B>Related commands:</B>
</P>

14
doc/pair_yukawa_colloid.txt
View File

@ -107,12 +107,14 @@ This style is part of the "colloid" package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
Because this potential uses the radii of the particles, the atom style
must support particles whose size is set via the "shape"_shape.html
command. For example "atom_style"_atom_style.html colloid or
ellipsoid. Only spherical particles are currently allowed for
pair_style yukawa/colloid, which means that for each particle type,
its 3 shape diameters must be equal to each other.
This pair style requires that atoms be finite-size spheres with a
diameter, as defined by the "atom_style sphere"_atom_style.html
command.
Per-particle polydispersity is not yet supported by this pair style;
per-type polydispersity is allowed. This means all particles of the
same type must have the same diameter. Each type can have a different
diameter.
[Related commands:]

116
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View File

@ -159,7 +159,7 @@ space in LAMMPS data structures for storing the new bonds.
<P>These are the section keywords for the body of the file.
</P>
<UL><LI><I>Atoms, Velocities, Masses, Shapes, Dipoles</I> = atom-property sections
<UL><LI><I>Atoms, Velocities, Masses</I> = atom-property sections
<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
<LI><I>Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I> = force field sections
<LI><I>BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs</I> = class 2 force field sections
@ -280,14 +280,13 @@ of analysis.
<TR><TD >atomic</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >bond</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
<TR><TD >colloid</TD><TD > atom-ID atom-type x y z</TD></TR>
<TR><TD >dipole</TD><TD > atom-ID atom-type q x y z mux muy muz</TD></TR>
<TR><TD >electron</TD><TD > atom-ID atom-type q spin eradius x y z</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID atom-type x y z quatw quati quatj quatk</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID atom-type shapex shapey shapez density x y z quatw quati quatj quatk</TD></TR>
<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
<TR><TD >granular</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >peri</TD><TD > atom-ID atom-type volume density x y z</TD></TR>
<TR><TD >sphere</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
<TR><TD >hybrid</TD><TD > atom-ID atom-type x y z sub-style1 sub-style2 ...
</TD></TR></TABLE></DIV>
@ -295,13 +294,14 @@ of analysis.
</P>
<UL><LI>atom-ID = integer ID of atom
<LI>molecule-ID = integer ID of molecule the atom belongs to
<LI>type-ID = type of atom (1-Ntype)
<LI>atom-type = type of atom (1-Ntype)
<LI>q = charge on atom (charge units)
<LI>diameter = diameter of atom (distance units)
<LI>diameter = diameter of spherical atom (distance units)
<LI>shapex,shapey,shapez = 3 diameters of ellipsoidal atom (distance units)
<LI>density = density of atom (mass/distance^3 units)
<LI>volume = volume of atom (distance^3 units)
<LI>x,y,z = coordinates of atom
<LI>mux,muy,muz = direction of dipole moment of atom
<LI>mux,muy,muz = components of dipole moment of atom (dipole units)
<LI>quatw,quati,quatj,quatk = quaternion components for orientation of atom
<LI>spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
<LI>eradius = electron radius (or fixed-core radius)
@ -318,40 +318,43 @@ each atom. Unique values larger than Natoms can be used, but they
will cause extra memory to be allocated on each processor, if an atom
map array is used (see the <A HREF = "atom_modify.html">atom_modify</A> command).
If an atom map array is not used (e.g. an atomic system with no
bonds), velocities are not assigned in the data file, and you don't
care if unique atom IDs appear in dump files, then the atom-IDs can all
be set to 0.
bonds), and velocities are not assigned in the data file, and you
don't care if unique atom IDs appear in dump files, then the atom-IDs
can all be set to 0.
</P>
<P>The molecule ID is a 2nd identifier attached to an atom. Normally, it
is a number from 1 to N, identifying which molecule the atom belongs
to. It can be 0 if it is an unbonded atom or if you don't care to
keep track of molecule assignments.
</P>
<P>The diameter specifies the size of a finite size particle, analagous
to the <A HREF = "shape.html">shape</A> command which sets the size on a per-type
basis. A diameter can be set to 0.0, which means that atom is a point
particle and not a finite-size particles. Some pair styles and fixes
and computes that operate on finite-size particles allow for a mixture
of finite-size and point particles. See the doc pages of individual
commands for details.
<P>The diameter specifies the size of a finite-size spherical particle.
It can be set to 0.0, which means that atom is a point particle.
</P>
<P>The density is used in conjunction with the diameter to set the mass
of a particle as mass = density * volume. If the diameter and volume
are 0.0 meaning a point particle, then the mass is not 0.0 but is set
as mass = density.
<P>The 3 shape values specify the 3 diameters or aspect ratios of a
finite-size ellipsoidal particle, when it is oriented along the 3
coordinate axes. They can all be set to 0.0, which means that atom is
a point particle.
</P>
<P>Some pair styles and fixes and computes that operate on finite-size
particles allow for a mixture of finite-size and point particles. See
the doc pages of individual commands for details.
</P>
<P>The density is used in conjunction with the particle volume for
finite-size particles to set the mass of the particle as mass =
density * volume. If the volume is 0.0, meaning a point particle,
then the density value is used as the mass.
</P>
<P>The values <I>quatw</I>, <I>quati</I>, <I>quatj</I>, and <I>quatk</I> set the orientation
of the atom as a quaternion (4-vector). Note that the
<A HREF = "shape.html">shape</A> command or "Shapes" section of the data file
specifies the aspect ratios of an ellipsoidal particle, which is
oriented by default with its x-axis along the simulation box's x-axis,
and similarly for y and z. If this body is rotated (via the
of the atom as a quaternion (4-vector). Note that the shape
attributes specify the aspect ratios of an ellipsoidal particle, which
is oriented by default with its x-axis along the simulation box's
x-axis, and similarly for y and z. If this body is rotated (via the
right-hand rule) by an angle theta around a unit vector (a,b,c), then
the quaternion that represents its new orientation is given by
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
4 components are quatw, quati, quatj, and quatk as specified above.
LAMMPS normalizes each atom's quaternion in case (a,b,c) was not a
unit vector.
LAMMPS normalizes each atom's quaternion in case (a,b,c) was not
specified as a unit vector.
</P>
<P>For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
specific values for each sub-style must be listed. The order of the
@ -364,7 +367,7 @@ listed in the same order they appear as listed above.
</P>
<P>Thus if
</P>
<PRE>atom_style hybrid charge granular
<PRE>atom_style hybrid charge sphere
</PRE>
<P>were used in the input script, each atom line would have these fields:
</P>
@ -524,27 +527,6 @@ section must be integers (1, not 1.0).
</P>
<HR>
<P><I>Dipoles</I> section:
</P>
<UL><LI>one line per atom type
line syntax: ID dipole-moment
<PRE> ID = atom type (1-N)
dipole-moment = value of dipole moment
</PRE>
<LI>example:
<PRE> 2 0.5
</PRE>
</UL>
<P>This defines the dipole moment of each atom type (which can be 0.0 for
some types). This can also be set via the <A HREF = "dipole.html">dipole</A>
command in the input script.
</P>
<HR>
<P><I>EndBondTorsion Coeffs</I> section:
</P>
<UL><LI>one line per dihedral type
@ -623,9 +605,9 @@ values in this section must be integers (1, not 1.0).
</UL>
<P>This defines the mass of each atom type. This can also be set via the
<A HREF = "mass.html">mass</A> command in the input script. This section should not
be used for atom styles that define a mass for individual atoms -
e.g. atom style granular.
<A HREF = "mass.html">mass</A> command in the input script. This section cannot be
used for atom styles that define a mass for individual atoms -
e.g. <A HREF = "atom_style.html">atom_style sphere</A>.
</P>
<HR>
@ -665,30 +647,6 @@ script.
</P>
<HR>
<P><I>Shapes</I> section:
</P>
<UL><LI>one line per atom type
<LI>line syntax: ID x y z
<PRE> ID = atom type (1-N)
x = x diameter
y = y diameter
z = z diameter
</PRE>
<LI>example:
<PRE> 3 2.0 1.0 1.0
</PRE>
</UL>
<P>This defines the shape of each atom type. This can also be set via
the <A HREF = "mass.html">shape</A> command in the input script. This section
should only be used for atom styles that define a shape, e.g. atom
style dipole or ellipsoid.
</P>
<HR>
<P><I>Velocities</I> section:
</P>
<UL><LI>one line per atom
@ -699,14 +657,14 @@ style dipole or ellipsoid.
<TR><TD >dipole</TD><TD > atom-ID vx vy vz wx wy wz</TD></TR>
<TR><TD >electron</TD><TD > atom-ID vx vy vz evel</TD></TR>
<TR><TD >ellipsoid</TD><TD > atom-ID vx vy vz lx ly lz</TD></TR>
<TR><TD >granular</TD><TD > atom-ID vx vy vz wx wy wz
<TR><TD >sphere</TD><TD > atom-ID vx vy vz wx wy wz
</TD></TR></TABLE></DIV>
<P>where the keywords have these meanings:
</P>
<P>vx,vy,vz = translational velocity of atom
lx,ly,lz = angular momentum of aspherical atom
wx,wy,wz = angular velocity of granular atom
wx,wy,wz = angular velocity of spherical atom
evel = electron radial velocity (0 for fixed-core):ul
</P>
<P>The velocity lines can appear in any order. This section can only be

106
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@ -156,7 +156,7 @@ space in LAMMPS data structures for storing the new bonds.
These are the section keywords for the body of the file.
{Atoms, Velocities, Masses, Shapes, Dipoles} = atom-property sections
{Atoms, Velocities, Masses} = atom-property sections
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
{Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \
Improper Coeffs} = force field sections
@ -260,27 +260,27 @@ angle: atom-ID molecule-ID atom-type x y z
atomic: atom-ID atom-type x y z
bond: atom-ID molecule-ID atom-type x y z
charge: atom-ID atom-type q x y z
colloid: atom-ID atom-type x y z
dipole: atom-ID atom-type q x y z mux muy muz
electron: atom-ID atom-type q spin eradius x y z
ellipsoid: atom-ID atom-type x y z quatw quati quatj quatk
ellipsoid: atom-ID atom-type shapex shapey shapez density x y z quatw quati quatj quatk
full: atom-ID molecule-ID atom-type q x y z
granular: atom-ID atom-type diameter density x y z
molecular: atom-ID molecule-ID atom-type x y z
peri: atom-ID atom-type volume density x y z
sphere: atom-ID atom-type diameter density x y z
hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:)
The keywords have these meanings:
atom-ID = integer ID of atom
molecule-ID = integer ID of molecule the atom belongs to
type-ID = type of atom (1-Ntype)
atom-type = type of atom (1-Ntype)
q = charge on atom (charge units)
diameter = diameter of atom (distance units)
diameter = diameter of spherical atom (distance units)
shapex,shapey,shapez = 3 diameters of ellipsoidal atom (distance units)
density = density of atom (mass/distance^3 units)
volume = volume of atom (distance^3 units)
x,y,z = coordinates of atom
mux,muy,muz = direction of dipole moment of atom
mux,muy,muz = components of dipole moment of atom (dipole units)
quatw,quati,quatj,quatk = quaternion components for orientation of atom
spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
eradius = electron radius (or fixed-core radius) :ul
@ -297,40 +297,43 @@ each atom. Unique values larger than Natoms can be used, but they
will cause extra memory to be allocated on each processor, if an atom
map array is used (see the "atom_modify"_atom_modify.html command).
If an atom map array is not used (e.g. an atomic system with no
bonds), velocities are not assigned in the data file, and you don't
care if unique atom IDs appear in dump files, then the atom-IDs can all
be set to 0.
bonds), and velocities are not assigned in the data file, and you
don't care if unique atom IDs appear in dump files, then the atom-IDs
can all be set to 0.
The molecule ID is a 2nd identifier attached to an atom. Normally, it
is a number from 1 to N, identifying which molecule the atom belongs
to. It can be 0 if it is an unbonded atom or if you don't care to
keep track of molecule assignments.
The diameter specifies the size of a finite size particle, analagous
to the "shape"_shape.html command which sets the size on a per-type
basis. A diameter can be set to 0.0, which means that atom is a point
particle and not a finite-size particles. Some pair styles and fixes
and computes that operate on finite-size particles allow for a mixture
of finite-size and point particles. See the doc pages of individual
commands for details.
The diameter specifies the size of a finite-size spherical particle.
It can be set to 0.0, which means that atom is a point particle.
The density is used in conjunction with the diameter to set the mass
of a particle as mass = density * volume. If the diameter and volume
are 0.0 meaning a point particle, then the mass is not 0.0 but is set
as mass = density.
The 3 shape values specify the 3 diameters or aspect ratios of a
finite-size ellipsoidal particle, when it is oriented along the 3
coordinate axes. They can all be set to 0.0, which means that atom is
a point particle.
Some pair styles and fixes and computes that operate on finite-size
particles allow for a mixture of finite-size and point particles. See
the doc pages of individual commands for details.
The density is used in conjunction with the particle volume for
finite-size particles to set the mass of the particle as mass =
density * volume. If the volume is 0.0, meaning a point particle,
then the density value is used as the mass.
The values {quatw}, {quati}, {quatj}, and {quatk} set the orientation
of the atom as a quaternion (4-vector). Note that the
"shape"_shape.html command or "Shapes" section of the data file
specifies the aspect ratios of an ellipsoidal particle, which is
oriented by default with its x-axis along the simulation box's x-axis,
and similarly for y and z. If this body is rotated (via the
of the atom as a quaternion (4-vector). Note that the shape
attributes specify the aspect ratios of an ellipsoidal particle, which
is oriented by default with its x-axis along the simulation box's
x-axis, and similarly for y and z. If this body is rotated (via the
right-hand rule) by an angle theta around a unit vector (a,b,c), then
the quaternion that represents its new orientation is given by
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
4 components are quatw, quati, quatj, and quatk as specified above.
LAMMPS normalizes each atom's quaternion in case (a,b,c) was not a
unit vector.
LAMMPS normalizes each atom's quaternion in case (a,b,c) was not
specified as a unit vector.
For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
specific values for each sub-style must be listed. The order of the
@ -343,7 +346,7 @@ listed in the same order they appear as listed above.
Thus if
atom_style hybrid charge granular :pre
atom_style hybrid charge sphere :pre
were used in the input script, each atom line would have these fields:
@ -474,22 +477,6 @@ section must be integers (1, not 1.0).
:line
{Dipoles} section:
one line per atom type :ulb,l
line syntax: ID dipole-moment :
ID = atom type (1-N)
dipole-moment = value of dipole moment :pre
example: :l
2 0.5 :pre
:ule
This defines the dipole moment of each atom type (which can be 0.0 for
some types). This can also be set via the "dipole"_dipole.html
command in the input script.
:line
{EndBondTorsion Coeffs} section:
one line per dihedral type :ulb,l
@ -550,9 +537,9 @@ example: :l
:ule
This defines the mass of each atom type. This can also be set via the
"mass"_mass.html command in the input script. This section should not
be used for atom styles that define a mass for individual atoms -
e.g. atom style granular.
"mass"_mass.html command in the input script. This section cannot be
used for atom styles that define a mass for individual atoms -
e.g. "atom_style sphere"_atom_style.html.
:line
@ -584,25 +571,6 @@ script.
:line
{Shapes} section:
one line per atom type :ulb,l
line syntax: ID x y z :l
ID = atom type (1-N)
x = x diameter
y = y diameter
z = z diameter :pre
example: :l
3 2.0 1.0 1.0 :pre
:ule
This defines the shape of each atom type. This can also be set via
the "shape"_mass.html command in the input script. This section
should only be used for atom styles that define a shape, e.g. atom
style dipole or ellipsoid.
:line
{Velocities} section:
one line per atom
@ -612,13 +580,13 @@ all styles except those listed: atom-ID vx vy vz
dipole: atom-ID vx vy vz wx wy wz
electron: atom-ID vx vy vz evel
ellipsoid: atom-ID vx vy vz lx ly lz
granular: atom-ID vx vy vz wx wy wz :tb(s=:)
sphere: atom-ID vx vy vz wx wy wz :tb(s=:)
where the keywords have these meanings:
vx,vy,vz = translational velocity of atom
lx,ly,lz = angular momentum of aspherical atom
wx,wy,wz = angular velocity of granular atom
wx,wy,wz = angular velocity of spherical atom
evel = electron radial velocity (0 for fixed-core):ul
The velocity lines can appear in any order. This section can only be

14
doc/read_restart.html
View File

@ -82,13 +82,13 @@ parallel I/O.
<P>A restart file stores the following information about a simulation:
units and atom style, simulation box size and shape and boundary
settings, group definitions, atom type settings such as mass and
particle shape, individual atoms and their group assignments and
molecular topology attributes, force field styles and coefficients,
and <A HREF = "special_bonds.html">special_bonds</A> settings. This means that
commands for these quantities do not need to be re-specified in the
input script that reads the restart file, though you can redefine
settings after the restart file is read.
settings, group definitions, per-type atom settings such as mass,
per-atom attributes including their group assignments and molecular
topology attributes, force field styles and coefficients, and
<A HREF = "special_bonds.html">special_bonds</A> settings. This means that commands
for these quantities do not need to be re-specified in the input
script that reads the restart file, though you can redefine settings
after the restart file is read.
</P>
<P>One exception is that some pair styles do not store their info in
restart files. The doc pages for individual pair styles note if this

14
doc/read_restart.txt
View File

@ -79,13 +79,13 @@ parallel I/O.
A restart file stores the following information about a simulation:
units and atom style, simulation box size and shape and boundary
settings, group definitions, atom type settings such as mass and
particle shape, individual atoms and their group assignments and
molecular topology attributes, force field styles and coefficients,
and "special_bonds"_special_bonds.html settings. This means that
commands for these quantities do not need to be re-specified in the
input script that reads the restart file, though you can redefine
settings after the restart file is read.
settings, group definitions, per-type atom settings such as mass,
per-atom attributes including their group assignments and molecular
topology attributes, force field styles and coefficients, and
"special_bonds"_special_bonds.html settings. This means that commands
for these quantities do not need to be re-specified in the input
script that reads the restart file, though you can redefine settings
after the restart file is read.
One exception is that some pair styles do not store their info in
restart files. The doc pages for individual pair styles note if this

143
doc/set.html
View File

@ -15,13 +15,13 @@
</P>
<PRE>set style ID keyword values ...
</PRE>
<UL><LI>style = <I>atom</I> or <I>group</I> or <I>region</I>
<UL><LI>style = <I>atom</I> or <I>type</I> or <I>mol</I> or <I>group</I> or <I>region</I>
<LI>ID = atom ID or group ID or region ID
<LI>ID = atom ID range or type range or mol ID range or group ID or region ID
<LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat/random</I> or <I>diameter</I> or <I>density</I> or <I>volume</I> or <I>image</I> or
<LI>keyword = <I>type</I> or <I>type/fraction</I> or <I>mol</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>charge</I> or <I>dipole</I> or <I>dipole/random</I> or <I>quat</I> or <I>quat/random</I> or <I>diameter</I> or <I>shape</I> or <I>mass</I> or <I>density</I> or <I>volume</I> or <I>image</I> or
<I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
<PRE> <I>type</I> value = atom type
@ -34,16 +34,20 @@
<I>charge</I> value = atomic charge (charge units)
<I>dipole</I> values = x y z
x,y,z = orientation of dipole moment vector
<I>dipole/random</I> value = seed
<I>dipole/random</I> value = seed Dlen
seed = random # seed (positive integer) for dipole moment orientations
Dlen = magnitude of dipole moment (dipole units)
<I>quat</I> values = a b c theta
a,b,c = unit vector to rotate particle around via right-hand rule
theta = rotation angle in degrees
<I>quat/random</I> value = seed
seed = random # seed (positive integer) for quaternion orientations
<I>diameter</I> value = particle diameter (distance units)
<I>density</I> value = particle density (mass/distance^3 units)
<I>volume</I> value = particle volume (distance^3 units)
<I>diameter</I> value = diameter of spherical particle (distance units)
<I>shape</I> value = Sx Sy Sz
Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
<I>mass</I> value = per-atom mass (mass units)
<I>density</I> value = particle density for sphere or ellipsoid (mass/distance^3 units)
<I>volume</I> value = particle volume for Peridynamic particle (distance^3 units)
<I>image</I> nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
<I>bond</I> value = bond type for all bonds between selected atoms
@ -59,7 +63,9 @@
set group solvent type/fraction 2 0.5 12393
set group edge bond 4
set region half charge 0.5
set atom 100 x 0.5 y 1.0
set type 3 charge 0.5
set type 1*3 charge 0.5
set atom 100*200 x 0.5 y 1.0
set atom 1492 type 3
</PRE>
<P><B>Description:</B>
@ -72,18 +78,30 @@ for overriding the default values assigned by the
<A HREF = "create_atoms.html">create_atoms</A> command (e.g. charge = 0.0). It can
be useful for altering pairwise and molecular force interactions,
since force-field coefficients are defined in terms of types. It can
be used to change the labeling of atoms by atom type when they are
output in <A HREF = "dump.html">dump</A> files. It can be useful for debugging
purposes; i.e. positioning an atom at a precise location to compute
subsequent forces or energy.
be used to change the labeling of atoms by atom type or molecule ID
when they are output in <A HREF = "dump.html">dump</A> files. It can be useful for
debugging purposes; i.e. positioning an atom at a precise location to
compute subsequent forces or energy.
</P>
<P>The style <I>atom</I> selects a single atom. The style <I>group</I> selects the
entire group of atoms. The style <I>region</I> selects all atoms in the
geometric region. The associated ID for each of these styles is
either the unique atom ID (typically a number from 1 to N = the number
of atoms in the simulation), the group ID, or the region ID. See the
<A HREF = "group.html">group</A> and <A HREF = "region.html">region</A> commands for details of
how to specify a group or region.
<P>The style <I>atom</I> selects one or more atoms in a range of atom IDs.
The style <I>type</I> selects all the atoms in a range of types. The style
<I>mol</I> selects all the atoms in a range of molecule IDs.
</P>
<P>In each of the range cases, a single value can be specified, or a
wildcard asterisk can be used to specify a range of values. This
takes the form "*" or "*n" or "n*" or "m*n". For example, for the
style <I>type</I>, if N = the number of atom types, then an asterisk with
no numeric values means all types from 1 to N. A leading asterisk
means all types from 1 to n (inclusive). A trailing asterisk means
all types from n to N (inclusive). A middle asterisk means all types
from m to n (inclusive). Note that the loweest value for the wildcard
is 1, not 0, so you cannot not use this form to select atoms
with molecule ID = 0, for example.
</P>
<P>The style <I>group</I> selects all the atoms in the specified group. The
style <I>region</I> selects all the atoms in the specified geometric
region. See the <A HREF = "group.html">group</A> and <A HREF = "region.html">region</A> commands
for details of how to specify a group or region.
</P>
<HR>
@ -110,29 +128,30 @@ being used must support the use of atomic charge.
</P>
<P>Keyword <I>dipole</I> uses the specified x,y,z values as components of a
vector to set as the orientation of the dipole moment vectors of the
selected atoms. The magnitude of the dipole moment for each atom is
set by the <A HREF = "dipole.html">dipole</A> command.
selected atoms. The magnitude of the dipole moment is set
by the length of this orientation vector.
</P>
<P>Keyword <I>dipole/random</I> randomizes the orientation of the dipole
moment vectors of the selected atoms. The magnitude of the dipole
moment for each atom is set by the <A HREF = "dipole.html">dipole</A> command. For
2d systems, the z component of the orientation is set to 0.0. Random
numbers are used in such a way that the orientation of a particular
atom is the same, regardless of how many processors are being used.
moment vectors of the selected atoms and sets the magnitude of each to
the specified <I>Dlen</I> value. For 2d systems, the z component of the
orientation is set to 0.0. Random numbers are used in such a way that
the orientation of a particular atom is the same, regardless of how
many processors are being used.
</P>
<P>Keyword <I>quat</I> uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms.
Note that the <A HREF = "shape.html">shape</A> command is used to specify the aspect
ratios of an ellipsoidal particle, which is oriented by default with
its x-axis along the simulation box's x-axis, and similarly for y and
z. If this body is rotated (via the right-hand rule) by an angle
theta around a unit rotation vector (a,b,c), then the quaternion that
represents its new orientation is given by (cos(theta/2),
a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
values are the arguments to the <I>quat</I> keyword. LAMMPS normalizes the
quaternion in case (a,b,c) was not specified as a unit vector. For 2d
systems, the a,b,c values are ignored, since a rotation vector of
(0,0,1) is the only valid choice.
Note that particles defined by <A HREF = "atom_style.html">atom_style ellipsoid</A>
have 3 shape paraeters whicha are used to specify the aspect ratios of
an ellipsoidal particle, which is oriented by default with its x-axis
along the simulation box's x-axis, and similarly for y and z. If this
body is rotated (via the right-hand rule) by an angle theta around a
unit rotation vector (a,b,c), then the quaternion that represents its
new orientation is given by (cos(theta/2), a*sin(theta/2),
b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c values are the
arguments to the <I>quat</I> keyword. LAMMPS normalizes the quaternion in
case (a,b,c) was not specified as a unit vector. For 2d systems, the
a,b,c values are ignored, since a rotation vector of (0,0,1) is the
only valid choice.
</P>
<P>Keyword <I>quat/random</I> randomizes the orientation of the quaternion of
the selected atoms. Random numbers are used in such a way that the
@ -140,20 +159,43 @@ orientation of a particular atom is the same, regardless of how many
processors are being used. For 2d systems, only orientations in the
xy plane are generated.
</P>
<P>For the <I>dipole</I> and <I>quat</I> keywords, the <A HREF = "atom_style.html">atom style</A>
being used must support the use of dipoles or quaternions.
<P>Keyword <I>diameter</I> sets the size of the selected atoms. The particles
must be finite-size spheres as defined by the <A HREF = "atom_style.html">atom_style
sphere</A> command. The diameter of a particle can be
set to 0.0, which means they will be treated as point particles. Note
that this command does not adjust the particle mass, even if it was
defined with a density, e.g. via the <A HREF = "read_data.html">read_data</A>
command.
</P>
<P>Keyword <I>diameter</I> sets the size of all selected particles. If the
particles have a per-atom mass and density, then it also sets their
mass.
<P>Keyword <I>shape</I> sets the size and shape of the selected atoms. The
particles must be aspherical ellipsoids as defined by the <A HREF = "atom_style.html">atom_style
ellipsoid</A> command. The <I>Sx</I>, <I>Sy</I>, <I>Sz</I> settings are
the 3 diameters of the ellipsoid in each direction. All 3 can be set
to the same value, which means the ellipsoid is effectively a sphere.
Or then can all be set to 0.0 which means the particle will be treated
as a point particle. Note that this command does not adjust the
particle mass, even if it was defined with a density, e.g. via the
<A HREF = "read_data.html">read_data</A> command.
</P>
<P>Keyword <I>density</I> sets the density of all selected particles. If the
particles have a per-atom mass and diameter, then it also sets their
mass. If the particles have a per-atom mass and volume (as defined by
PeriDynamics), then it also sets their mass.
<P>Keyword <I>mas</I> sets the mass of all selected particles. The
particles must have a per-atom mass attribute, as defined by the
<A HREF = "atom_style.html">atom_style</A> command. See the "mass" command for how
to set mass values on a per-type basis.
</P>
<P>Keyword <I>volume</I> sets the volume of all selected particles, as defined
by PeriDynamics.
<P>Keyword <I>density</I> sets the mass of all selected particles. The
particles must have a per-atom mass attribute, as defined by the
<A HREF = "atom_style.html">atom_style</A> command. See the "mass" command for how
to set mass values on a per-type basis. If the atom has a radius
attribute (see <A HREF = "atom_style.html">atom_style sphere</A>) and its radius is
non-zero, its mass is set from the density and particle volume. The
same is true if the atom has a shape attribute (see <A HREF = "atom_style.html">atom_style
ellipsoid</A>) and its shape parameters are non-zero.
Otherwise the mass is set to the density value directly.
</P>
<P>Keyword <I>volume</I> sets the volume of all selected particles.
Currently, only the <A HREF = "atom_style.html">atom_style peri</A> command defines
particles with a volume attribute. Note that this command does not
adjust the particle mass.
</P>
<P>Keyword <I>image</I> sets which image of the simulation box the atom is
considered to be in. An image of 0 means it is inside the box as
@ -179,11 +221,6 @@ up analysis of the trajectories if a LAMMPS diagnostic or your own
analysis relies on the image flags to unwrap a molecule which
straddles the periodic box.
</P>
<P>For the <I>diameter</I> and <I>density</I> and <I>volume</I> keywords, the <A HREF = "atom_style.html">atom
style</A> being used must support the use of those
parameters. For example, granular particles store a diameter and
density. Peridynamic particles store a volume and density.
</P>
<P>Keywords <I>bond</I>, <I>angle</I>, <I>dihedral</I>, and <I>improper</I>, set the bond
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value from 1 to nbondtypes (nangletypes, etc). All

146
doc/set.txt
View File

@ -12,12 +12,13 @@ set command :h3
set style ID keyword values ... :pre
style = {atom} or {group} or {region} :ulb,l
ID = atom ID or group ID or region ID :l
style = {atom} or {type} or {mol} or {group} or {region} :ulb,l
ID = atom ID range or type range or mol ID range or group ID or region ID :l
one or more keyword/value pairs may be appended :l
keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{charge} or {dipole} or {dipole/random} or {quat/random} or \
{diameter} or {density} or {volume} or {image} or
{charge} or {dipole} or {dipole/random} or {quat} or \
{quat/random} or {diameter} or {shape} or {mass} or \
{density} or {volume} or {image} or
{bond} or {angle} or {dihedral} or {improper} :l
{type} value = atom type
{type/fraction} values = type fraction seed
@ -29,16 +30,20 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{charge} value = atomic charge (charge units)
{dipole} values = x y z
x,y,z = orientation of dipole moment vector
{dipole/random} value = seed
{dipole/random} value = seed Dlen
seed = random # seed (positive integer) for dipole moment orientations
Dlen = magnitude of dipole moment (dipole units)
{quat} values = a b c theta
a,b,c = unit vector to rotate particle around via right-hand rule
theta = rotation angle in degrees
{quat/random} value = seed
seed = random # seed (positive integer) for quaternion orientations
{diameter} value = particle diameter (distance units)
{density} value = particle density (mass/distance^3 units)
{volume} value = particle volume (distance^3 units)
{diameter} value = diameter of spherical particle (distance units)
{shape} value = Sx Sy Sz
Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
{mass} value = per-atom mass (mass units)
{density} value = particle density for sphere or ellipsoid (mass/distance^3 units)
{volume} value = particle volume for Peridynamic particle (distance^3 units)
{image} nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
{bond} value = bond type for all bonds between selected atoms
@ -53,7 +58,9 @@ set group solvent type 2
set group solvent type/fraction 2 0.5 12393
set group edge bond 4
set region half charge 0.5
set atom 100 x 0.5 y 1.0
set type 3 charge 0.5
set type 1*3 charge 0.5
set atom 100*200 x 0.5 y 1.0
set atom 1492 type 3 :pre
[Description:]
@ -66,18 +73,30 @@ for overriding the default values assigned by the
"create_atoms"_create_atoms.html command (e.g. charge = 0.0). It can
be useful for altering pairwise and molecular force interactions,
since force-field coefficients are defined in terms of types. It can
be used to change the labeling of atoms by atom type when they are
output in "dump"_dump.html files. It can be useful for debugging
purposes; i.e. positioning an atom at a precise location to compute
subsequent forces or energy.
be used to change the labeling of atoms by atom type or molecule ID
when they are output in "dump"_dump.html files. It can be useful for
debugging purposes; i.e. positioning an atom at a precise location to
compute subsequent forces or energy.
The style {atom} selects a single atom. The style {group} selects the
entire group of atoms. The style {region} selects all atoms in the
geometric region. The associated ID for each of these styles is
either the unique atom ID (typically a number from 1 to N = the number
of atoms in the simulation), the group ID, or the region ID. See the
"group"_group.html and "region"_region.html commands for details of
how to specify a group or region.
The style {atom} selects one or more atoms in a range of atom IDs.
The style {type} selects all the atoms in a range of types. The style
{mol} selects all the atoms in a range of molecule IDs.
In each of the range cases, a single value can be specified, or a
wildcard asterisk can be used to specify a range of values. This
takes the form "*" or "*n" or "n*" or "m*n". For example, for the
style {type}, if N = the number of atom types, then an asterisk with
no numeric values means all types from 1 to N. A leading asterisk
means all types from 1 to n (inclusive). A trailing asterisk means
all types from n to N (inclusive). A middle asterisk means all types
from m to n (inclusive). Note that the loweest value for the wildcard
is 1, not 0, so you cannot not use this form to select atoms
with molecule ID = 0, for example.
The style {group} selects all the atoms in the specified group. The
style {region} selects all the atoms in the specified geometric
region. See the "group"_group.html and "region"_region.html commands
for details of how to specify a group or region.
:line
@ -104,29 +123,30 @@ being used must support the use of atomic charge.
Keyword {dipole} uses the specified x,y,z values as components of a
vector to set as the orientation of the dipole moment vectors of the
selected atoms. The magnitude of the dipole moment for each atom is
set by the "dipole"_dipole.html command.
selected atoms. The magnitude of the dipole moment is set
by the length of this orientation vector.
Keyword {dipole/random} randomizes the orientation of the dipole
moment vectors of the selected atoms. The magnitude of the dipole
moment for each atom is set by the "dipole"_dipole.html command. For
2d systems, the z component of the orientation is set to 0.0. Random
numbers are used in such a way that the orientation of a particular
atom is the same, regardless of how many processors are being used.
moment vectors of the selected atoms and sets the magnitude of each to
the specified {Dlen} value. For 2d systems, the z component of the
orientation is set to 0.0. Random numbers are used in such a way that
the orientation of a particular atom is the same, regardless of how
many processors are being used.
Keyword {quat} uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms.
Note that the "shape"_shape.html command is used to specify the aspect
ratios of an ellipsoidal particle, which is oriented by default with
its x-axis along the simulation box's x-axis, and similarly for y and
z. If this body is rotated (via the right-hand rule) by an angle
theta around a unit rotation vector (a,b,c), then the quaternion that
represents its new orientation is given by (cos(theta/2),
a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
values are the arguments to the {quat} keyword. LAMMPS normalizes the
quaternion in case (a,b,c) was not specified as a unit vector. For 2d
systems, the a,b,c values are ignored, since a rotation vector of
(0,0,1) is the only valid choice.
Note that particles defined by "atom_style ellipsoid"_atom_style.html
have 3 shape paraeters whicha are used to specify the aspect ratios of
an ellipsoidal particle, which is oriented by default with its x-axis
along the simulation box's x-axis, and similarly for y and z. If this
body is rotated (via the right-hand rule) by an angle theta around a
unit rotation vector (a,b,c), then the quaternion that represents its
new orientation is given by (cos(theta/2), a*sin(theta/2),
b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c values are the
arguments to the {quat} keyword. LAMMPS normalizes the quaternion in
case (a,b,c) was not specified as a unit vector. For 2d systems, the
a,b,c values are ignored, since a rotation vector of (0,0,1) is the
only valid choice.
Keyword {quat/random} randomizes the orientation of the quaternion of
the selected atoms. Random numbers are used in such a way that the
@ -134,20 +154,43 @@ orientation of a particular atom is the same, regardless of how many
processors are being used. For 2d systems, only orientations in the
xy plane are generated.
For the {dipole} and {quat} keywords, the "atom style"_atom_style.html
being used must support the use of dipoles or quaternions.
Keyword {diameter} sets the size of the selected atoms. The particles
must be finite-size spheres as defined by the "atom_style
sphere"_atom_style.html command. The diameter of a particle can be
set to 0.0, which means they will be treated as point particles. Note
that this command does not adjust the particle mass, even if it was
defined with a density, e.g. via the "read_data"_read_data.html
command.
Keyword {diameter} sets the size of all selected particles. If the
particles have a per-atom mass and density, then it also sets their
mass.
Keyword {shape} sets the size and shape of the selected atoms. The
particles must be aspherical ellipsoids as defined by the "atom_style
ellipsoid"_atom_style.html command. The {Sx}, {Sy}, {Sz} settings are
the 3 diameters of the ellipsoid in each direction. All 3 can be set
to the same value, which means the ellipsoid is effectively a sphere.
Or then can all be set to 0.0 which means the particle will be treated
as a point particle. Note that this command does not adjust the
particle mass, even if it was defined with a density, e.g. via the
"read_data"_read_data.html command.
Keyword {density} sets the density of all selected particles. If the
particles have a per-atom mass and diameter, then it also sets their
mass. If the particles have a per-atom mass and volume (as defined by
PeriDynamics), then it also sets their mass.
Keyword {mas} sets the mass of all selected particles. The
particles must have a per-atom mass attribute, as defined by the
"atom_style"_atom_style.html command. See the "mass" command for how
to set mass values on a per-type basis.
Keyword {volume} sets the volume of all selected particles, as defined
by PeriDynamics.
Keyword {density} sets the mass of all selected particles. The
particles must have a per-atom mass attribute, as defined by the
"atom_style"_atom_style.html command. See the "mass" command for how
to set mass values on a per-type basis. If the atom has a radius
attribute (see "atom_style sphere"_atom_style.html) and its radius is
non-zero, its mass is set from the density and particle volume. The
same is true if the atom has a shape attribute (see "atom_style
ellipsoid"_atom_style.html) and its shape parameters are non-zero.
Otherwise the mass is set to the density value directly.
Keyword {volume} sets the volume of all selected particles.
Currently, only the "atom_style peri"_atom_style.html command defines
particles with a volume attribute. Note that this command does not
adjust the particle mass.
Keyword {image} sets which image of the simulation box the atom is
considered to be in. An image of 0 means it is inside the box as
@ -173,11 +216,6 @@ up analysis of the trajectories if a LAMMPS diagnostic or your own
analysis relies on the image flags to unwrap a molecule which
straddles the periodic box.
For the {diameter} and {density} and {volume} keywords, the "atom
style"_atom_style.html being used must support the use of those
parameters. For example, granular particles store a diameter and
density. Peridynamic particles store a volume and density.
Keywords {bond}, {angle}, {dihedral}, and {improper}, set the bond
type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value from 1 to nbondtypes (nangletypes, etc). All

104
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@ -1,104 +0,0 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>shape command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>shape I x y z
</PRE>
<UL><LI>I = atom type (see asterisk form below)
<LI>x = x diameter (distance units)
<LI>y = y diameter (distance units)
<LI>z = z diameter (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>shape 1 1.0 1.0 1.0
shape * 3.0 1.0 1.0
shape 2* 3.0 1.0 1.0
</PRE>
<P><B>Description:</B>
</P>
<P>Set the shape for all atoms of one or more atom types. In LAMMPS,
particles that have a finite size are said to have a "shape", as
opposed to being a point mass. The shape can be spherical or
aspherical, depending on whether the 3 shape values are the same or
different. Shape values can also be set in the
<A HREF = "read_data.html">read_data</A> data file using the "Shapes" keyword. See
the <A HREF = "units.html">units</A> command for what distance units to use.
</P>
<P>The I index can be specified in one of two ways. An explicit numeric
value can be used, as in the 1st example above. Or a wild-card
asterisk can be used to set the shape for multiple atom types. This
takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
atom types, then an asterisk with no numeric values means all types
from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
</P>
<P>A line in a <A HREF = "read_data.html">data file</A> that follows the "Shapes"
keyword specifies shape using the same format as the arguments of the
shape command in an input script, except that no wild-card asterisk
can be used. For example, under the "Shapes" section of a data file,
the line that corresponds to the 1st example above would be listed as
</P>
<PRE>1 1.0 1.0 1.0
</PRE>
<P>The shape values can be set to all 0.0, which means that atoms of that
type are point particles and not finite-size particles. Some pair
styles and fixes and computes that operate on finite-size particles
allow for a mixture of finite-size and point particles. See the doc
pages of individual commands for details.
</P>
<P>Note that the shape command can only be used if the <A HREF = "atom_style.html">atom
style</A> requires per-type atom shape to be set.
Currently, only the <I>colloid</I>, <I>dipole</I>, and <I>ellipsoid</I> styles do.
The <I>granular</I> and <I>peri</I> styles also define finite-size spherical
particles, but their size is set on a per-particle basis. These are
are defined in the data file read by the <A HREF = "read_data.html">read_data</A>
command, or set to default values by the
<A HREF = "create_atoms.html">create_atoms</A> command, or set to new values by the
<A HREF = "set.html">set diameter</A> command.
</P>
<P>Dipoles use the atom shape to compute a moment of inertia for
rotational energy. See the <A HREF = "pair_dipole.html">pair_style dipole</A>
command. Only the 1st component of the shape is used since the
particles are assumed to be spherical.
</P>
<P>Ellipsoids use the atom shape to compute a generalized inertia tensor.
For example, a shape setting of 3.0 1.0 1.0 defines a particle 3x
longer in x than in y or z and with a circular cross-section in yz.
Ellipsoids which are in fact spherical can be defined by setting all 3
shape components the same.
</P>
<P>If you define a <A HREF = "atom_style.html">hybrid atom style</A> which includes one
(or more) sub-styles which require per-type shape and one (or more)
sub-styles which require per-atom diameter, then you must define both.
However, in this case the per-type shape will be ignored; only the
per-atom diameter will be used by LAMMPS. This means you cannot
currently mix aspherical particles with per-atom diameter particles.
</P>
<P><B>Restrictions:</B>
</P>
<P>This command must come after the simulation box is defined by a
<A HREF = "read_data.html">read_data</A>, <A HREF = "read_restart.html">read_restart</A>, or
<A HREF = "create_box.html">create_box</A> command.
</P>
<P>All shapes must be defined before a simulation is run (if the atom
style requires shapes be set).
</P>
<P><B>Related commands:</B> none
</P>
<P><B>Default:</B> none
</P>
</HTML>

99
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View File

@ -1,99 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
shape command :h3
[Syntax:]
shape I x y z :pre
I = atom type (see asterisk form below)
x = x diameter (distance units)
y = y diameter (distance units)
z = z diameter (distance units) :ul
[Examples:]
shape 1 1.0 1.0 1.0
shape * 3.0 1.0 1.0
shape 2* 3.0 1.0 1.0 :pre
[Description:]
Set the shape for all atoms of one or more atom types. In LAMMPS,
particles that have a finite size are said to have a "shape", as
opposed to being a point mass. The shape can be spherical or
aspherical, depending on whether the 3 shape values are the same or
different. Shape values can also be set in the
"read_data"_read_data.html data file using the "Shapes" keyword. See
the "units"_units.html command for what distance units to use.
The I index can be specified in one of two ways. An explicit numeric
value can be used, as in the 1st example above. Or a wild-card
asterisk can be used to set the shape for multiple atom types. This
takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
atom types, then an asterisk with no numeric values means all types
from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n
(inclusive).
A line in a "data file"_read_data.html that follows the "Shapes"
keyword specifies shape using the same format as the arguments of the
shape command in an input script, except that no wild-card asterisk
can be used. For example, under the "Shapes" section of a data file,
the line that corresponds to the 1st example above would be listed as
1 1.0 1.0 1.0 :pre
The shape values can be set to all 0.0, which means that atoms of that
type are point particles and not finite-size particles. Some pair
styles and fixes and computes that operate on finite-size particles
allow for a mixture of finite-size and point particles. See the doc
pages of individual commands for details.
Note that the shape command can only be used if the "atom
style"_atom_style.html requires per-type atom shape to be set.
Currently, only the {colloid}, {dipole}, and {ellipsoid} styles do.
The {granular} and {peri} styles also define finite-size spherical
particles, but their size is set on a per-particle basis. These are
are defined in the data file read by the "read_data"_read_data.html
command, or set to default values by the
"create_atoms"_create_atoms.html command, or set to new values by the
"set diameter"_set.html command.
Dipoles use the atom shape to compute a moment of inertia for
rotational energy. See the "pair_style dipole"_pair_dipole.html
command. Only the 1st component of the shape is used since the
particles are assumed to be spherical.
Ellipsoids use the atom shape to compute a generalized inertia tensor.
For example, a shape setting of 3.0 1.0 1.0 defines a particle 3x
longer in x than in y or z and with a circular cross-section in yz.
Ellipsoids which are in fact spherical can be defined by setting all 3
shape components the same.
If you define a "hybrid atom style"_atom_style.html which includes one
(or more) sub-styles which require per-type shape and one (or more)
sub-styles which require per-atom diameter, then you must define both.
However, in this case the per-type shape will be ignored; only the
per-atom diameter will be used by LAMMPS. This means you cannot
currently mix aspherical particles with per-atom diameter particles.
[Restrictions:]
This command must come after the simulation box is defined by a
"read_data"_read_data.html, "read_restart"_read_restart.html, or
"create_box"_create_box.html command.
All shapes must be defined before a simulation is run (if the atom
style requires shapes be set).
[Related commands:] none
[Default:] none