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

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5931 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2011-04-13 21:39:34 +00:00
parent 7e9dd09646
commit e45fbd89d1
68 changed files with 871 additions and 1167 deletions
Download Patch File Download Diff File Expand all files Collapse all files

32
doc/Section_commands.html
View File

@ -261,12 +261,11 @@ in the command's documentation.
</P> </P>
<P>Settings: <P>Settings:
</P> </P>
<P><A HREF = "communicate.html">communicate</A>, <A HREF = "dipole.html">dipole</A>, <P><A HREF = "communicate.html">communicate</A>, <A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>,
<A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>, <A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
<A HREF = "min_style.html">min_style</A>, <A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "neighbor.html">neighbor</A>, <A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
<A HREF = "run_style.html">run_style</A>, <A HREF = "set.html">set</A>, <A HREF = "shape.html">shape</A>, <A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
<A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
</P> </P>
<P>Fixes: <P>Fixes:
</P> </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 = "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 = "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 = "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 = "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 = "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 = "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_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 = "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 = "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 = "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 = "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 = "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_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 = "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 = "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 = "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 = "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 = "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 = "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 = "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 = "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 = "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>
<TR ALIGN="center"><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
</TD></TR></TABLE></DIV> </TD></TR></TABLE></DIV>
<HR> <HR>

13
doc/Section_commands.txt
View File

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

110
doc/Section_howto.html
View File

@ -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 <P>To run a simulation of a granular model, you will want to use
the following commands: the following commands:
</P> </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_nve_sphere.html">fix nve/sphere</A>
<LI><A HREF = "fix_gravity.html">fix gravity</A> <LI><A HREF = "fix_gravity.html">fix gravity</A>
</UL> </UL>
@ -913,9 +913,9 @@ profile consistent with the applied shear strain rate.
</H4> </H4>
<P>Typical MD models treat atoms or particles as point masses. <P>Typical MD models treat atoms or particles as point masses.
Sometimes, however, it is desirable to have a model with finite-size Sometimes, however, it is desirable to have a model with finite-size
particles such as spherioids or aspherical ellipsoids. The difference particles such as spheres or aspherical ellipsoids. The difference is
is that such particles have a moment of inertia, rotational energy, that such particles have a moment of inertia, rotational energy, and
and angular momentum. Rotation is induced by torque from interactions angular momentum. Rotation is induced by torque from interactions
with other particles. with other particles.
</P> </P>
<P>LAMMPS has several options for running simulations with these kinds of <P>LAMMPS has several options for running simulations with these kinds of
@ -929,53 +929,61 @@ particles. The following aspects are discussed in turn:
</UL> </UL>
<H5>Atom styles <H5>Atom styles
</H5> </H5>
<P>There are 3 <A HREF = "atom_style.html">atom styles</A> that allow for definition of <P>There are 2 <A HREF = "atom_style.html">atom styles</A> that allow for definition of
finite-size particles: granular, dipole, ellipsoid. 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>
<P>Granular particles are spheriods and each particle can have a unique <P>The sphere style defines particles that are spheriods and each
diameter and mass (or density). These particles store an angular particle can have a unique diameter and mass (or density). These
velocity (omega) and can be acted upon by torque. 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>
<P>Dipolar particles are typically spheriods with a point dipole and each <P>The ellipsoid style defines particles that are ellipsoids and thus can
particle type has a diamater and mass, set by the <A HREF = "shape.html">shape</A> be aspherical. Each particle has a shape, specified by 3 diameters,
and <A HREF = "mass.html">mass</A> commands. These particles store an angular and mass (or density). These particles store an angular momentum and
velocity (omega) and can be acted upon by torque. They also store an their orientation (quaternion), and can be acted upon by torque. They
orientation for the point dipole (mu) which has a length set by the do not store an angular velocity (omega), which can be in a different
<A HREF = "dipole.html">dipole</A> command. The <A HREF = "set.html">set</A> command can be used direction than angular momentum, rather they compute it as needed.
to initialize the orientation of dipole moments. 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>
<P>Ellipsoid particles are aspherical. Each particle type has an <P>The dipole style does not define extended particles, but is often
ellipsoidal shape and mass, defined by the <A HREF = "shape.html">shape</A> and used in conjunction with spherical particles, via a command like
<A HREF = "mass.html">mass</A> commands. These particles store an angular momentum </P>
and their orientation (quaternion), and can be acted upon by torque. <PRE>atom_style hybrid sphere dipole
They do not store an angular velocity (omega), which can be in a </PRE>
different direction than angular momentum, rather they compute it as <P>This is because when dipoles interact with each other, they induce
needed. Ellipsoidal particles can also store a dipole moment if an torques, and a particle must be extended (i.e. have a moment of
<A HREF = "atom_style.html">atom_style hybrid ellipsoid dipole</A> is used. The inertia) in order to respond and rotate. See the <A HREF = "atom_style.html">atom_style
<A HREF = "set.html">set</A> command can be used to initialize the orientation of dipole</A> command for details. The "set" command can be
ellipsoidal particles and has a brief explanation of quaternions. used to modify the orientation and length of the dipole moment of
individual particles, after then are created.
</P> </P>
<P>Note that if one of these atom styles is used (or multiple styles via <P>Note that if one of these atom styles is used (or multiple styles via
the <A HREF = "atom_style.html">atom_style hybrid</A> command), not all particles in the <A HREF = "atom_style.html">atom_style hybrid</A> command), not all particles in
the system are required to be finite-size or aspherical. For example, 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 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 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 particle. If the length of the dipole moment is set to zero, the
have a point dipole associated with it. The pair styles used to particle will not have a point dipole associated with it. The pair
compute pairwise interactions will typically compute the correct styles used to compute pairwise interactions will typically compute
interaction in these simplified (cheaper) cases. <A HREF = "pair_hybrid.html">Pair_style the correct interaction in these simplified (cheaper) cases.
hybrid</A> can be used to insure the correct <A HREF = "pair_hybrid.html">Pair_style hybrid</A> can be used to insure the correct
interactions are computed for the appropriate style of interactions. interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoid versus Likewise, using groups to partition particles (ellipsoids versus
spheroid versus point particles) will allow you to use the appropriate spheres versus point particles) will allow you to use the appropriate
time integrators and temperature computations for each class of time integrators and temperature computations for each class of
particles. See the doc pages for various commands for details. particles. See the doc pages for various commands for details.
</P> </P>
<P>Also note that for <A HREF = "dimension.html">2d simulations</A>, finite-size <P>Also note that for <A HREF = "dimension.html">2d simulations</A>, finite-size
spheroids and ellipsoids are still treated as 3d particles, rather spheres and ellipsoids are still treated as 3d particles, rather than
than as disks or ellipses. This means they have the same moment of as circular disks or ellipses. This means they have the same moment
inertia for a 3d extended object. When their temperature is of inertia for a 3d extended object. When their temperature is
coomputed, the correct degrees of freedom are used for rotation in a coomputed, the correct degrees of freedom are used for rotation in a
2d versus 3d system. 2d versus 3d system.
</P> </P>
@ -994,15 +1002,14 @@ that generate torque:
<LI><A HREF = "pair_resquared.html">pair_style resquared</A> <LI><A HREF = "pair_resquared.html">pair_style resquared</A>
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> <LI><A HREF = "pair_lubricate.html">pair_style lubricate</A>
</UL> </UL>
<P>The <A HREF = "pair_gran.html">granular pair styles</A> are used with <A HREF = "atom_style.html">atom_style <P>The <A HREF = "pair_gran.html">granular pair styles</A> are used with spherical
granular</A>. The <A HREF = "pair_dipole.html">dipole pair style</A> particles. The <A HREF = "pair_dipole.html">dipole pair style</A> is used with
is used with <A HREF = "atom_style.html">atom_style dipole</A>. The <A HREF = "atom_style.html">atom_style dipole</A>, which could be applied to
<A HREF = "pair_gayberne.html">GayBerne</A> and <A HREF = "pair_resquared.html">REsquared</A> spherical or ellipsoidal particles. The <A HREF = "pair_gayberne.html">GayBerne</A>
potentials require particles have a <A HREF = "shape.html">shape</A> and are and <A HREF = "pair_resquared.html">REsquared</A> potentials require ellipsoidal
designed for <A HREF = "atom_style.html">ellipsoidal particles</A>. The particles, though they will also work if the 3 shape parameters are
<A HREF = "pair_lubricate.html">lubrication potential</A> requires that particles the same (a sphere). The <A HREF = "pair_lubricate.html">lubrication potential</A>
have a <A HREF = "shape.html">shape</A>. It can currently only be used with works with spherical particles.
extended spherical particles.
</P> </P>
<H5>Time integration <H5>Time integration
</H5> </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_nvt_sphere.html">fix nvt/sphere</A>
<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A> <LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
</UL> </UL>
<P>Likewise, there are 3 fixes that perform time integration on extended <P>Likewise, there are 3 fixes that perform time integration on
aspherical particles: ellipsoids as extended aspherical particles:
</P> </P>
<UL><LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A> <UL><LI><A HREF = "fix_nve_asphere.html">fix nve/asphere</A>
<LI><A HREF = "fix_nvt_asphere.html">fix nvt/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>Computes, thermodynamics, and dump output
</H5> </H5>
<P>There are 4 computes that calculate the temperature or rotational energy <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> </P>
<UL><LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A> <UL><LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</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 force and torque on the rigid body each timestep due to forces on its
constituent particles, and integrates the motion of the rigid body. constituent particles, and integrates the motion of the rigid body.
</P> </P>
<P>(NOTE: 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 <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 inertia tensor of the body is different than if they were point
particles. This means the rotational dynamics of the rigid body will particles. This means the rotational dynamics of the rigid body will
be different. Thus a model of a dimer is different if the dimer 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 To run a simulation of a granular model, you will want to use
the following commands: the following commands:
"atom_style"_atom_style.html granular "atom_style sphere"_atom_style.html
"fix nve/sphere"_fix_nve_sphere.html "fix nve/sphere"_fix_nve_sphere.html
"fix gravity"_fix_gravity.html :ul "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. Typical MD models treat atoms or particles as point masses.
Sometimes, however, it is desirable to have a model with finite-size Sometimes, however, it is desirable to have a model with finite-size
particles such as spherioids or aspherical ellipsoids. The difference particles such as spheres or aspherical ellipsoids. The difference is
is that such particles have a moment of inertia, rotational energy, that such particles have a moment of inertia, rotational energy, and
and angular momentum. Rotation is induced by torque from interactions angular momentum. Rotation is induced by torque from interactions
with other particles. with other particles.
LAMMPS has several options for running simulations with these kinds of LAMMPS has several options for running simulations with these kinds of
@ -921,53 +921,61 @@ rigid bodies composed of extended particles :ul
Atom styles :h5 Atom styles :h5
There are 3 "atom styles"_atom_style.html that allow for definition of There are 2 "atom styles"_atom_style.html that allow for definition of
finite-size particles: granular, dipole, ellipsoid. 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 The sphere style defines particles that are spheriods and each
diameter and mass (or density). These particles store an angular particle can have a unique diameter and mass (or density). These
velocity (omega) and can be acted upon by torque. 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 The ellipsoid style defines particles that are ellipsoids and thus can
particle type has a diamater and mass, set by the "shape"_shape.html be aspherical. Each particle has a shape, specified by 3 diameters,
and "mass"_mass.html commands. These particles store an angular and mass (or density). These particles store an angular momentum and
velocity (omega) and can be acted upon by torque. They also store an their orientation (quaternion), and can be acted upon by torque. They
orientation for the point dipole (mu) which has a length set by the do not store an angular velocity (omega), which can be in a different
"dipole"_dipole.html command. The "set"_set.html command can be used direction than angular momentum, rather they compute it as needed.
to initialize the orientation of dipole moments. 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 The dipole style does not define extended particles, but is often
ellipsoidal shape and mass, defined by the "shape"_shape.html and used in conjunction with spherical particles, via a command like
"mass"_mass.html commands. These particles store an angular momentum
and their orientation (quaternion), and can be acted upon by torque. atom_style hybrid sphere dipole :pre
They do not store an angular velocity (omega), which can be in a
different direction than angular momentum, rather they compute it as This is because when dipoles interact with each other, they induce
needed. Ellipsoidal particles can also store a dipole moment if an torques, and a particle must be extended (i.e. have a moment of
"atom_style hybrid ellipsoid dipole"_atom_style.html is used. The inertia) in order to respond and rotate. See the "atom_style
"set"_set.html command can be used to initialize the orientation of dipole"_atom_style.html command for details. The "set" command can be
ellipsoidal particles and has a brief explanation of quaternions. 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 Note that if one of these atom styles is used (or multiple styles via
the "atom_style hybrid"_atom_style.html command), not all particles in the "atom_style hybrid"_atom_style.html command), not all particles in
the system are required to be finite-size or aspherical. For example, 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 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 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 particle. If the length of the dipole moment is set to zero, the
have a point dipole associated with it. The pair styles used to particle will not have a point dipole associated with it. The pair
compute pairwise interactions will typically compute the correct styles used to compute pairwise interactions will typically compute
interaction in these simplified (cheaper) cases. "Pair_style the correct interaction in these simplified (cheaper) cases.
hybrid"_pair_hybrid.html can be used to insure the correct "Pair_style hybrid"_pair_hybrid.html can be used to insure the correct
interactions are computed for the appropriate style of interactions. interactions are computed for the appropriate style of interactions.
Likewise, using groups to partition particles (ellipsoid versus Likewise, using groups to partition particles (ellipsoids versus
spheroid versus point particles) will allow you to use the appropriate spheres versus point particles) will allow you to use the appropriate
time integrators and temperature computations for each class of time integrators and temperature computations for each class of
particles. See the doc pages for various commands for details. particles. See the doc pages for various commands for details.
Also note that for "2d simulations"_dimension.html, finite-size Also note that for "2d simulations"_dimension.html, finite-size
spheroids and ellipsoids are still treated as 3d particles, rather spheres and ellipsoids are still treated as 3d particles, rather than
than as disks or ellipses. This means they have the same moment of as circular disks or ellipses. This means they have the same moment
inertia for a 3d extended object. When their temperature is of inertia for a 3d extended object. When their temperature is
coomputed, the correct degrees of freedom are used for rotation in a coomputed, the correct degrees of freedom are used for rotation in a
2d versus 3d system. 2d versus 3d system.
@ -986,15 +994,14 @@ that generate torque:
"pair_style resquared"_pair_resquared.html "pair_style resquared"_pair_resquared.html
"pair_style lubricate"_pair_lubricate.html :ul "pair_style lubricate"_pair_lubricate.html :ul
The "granular pair styles"_pair_gran.html are used with "atom_style The "granular pair styles"_pair_gran.html are used with spherical
granular"_atom_style.html. The "dipole pair style"_pair_dipole.html particles. The "dipole pair style"_pair_dipole.html is used with
is used with "atom_style dipole"_atom_style.html. The "atom_style dipole"_atom_style.html, which could be applied to
"GayBerne"_pair_gayberne.html and "REsquared"_pair_resquared.html spherical or ellipsoidal particles. The "GayBerne"_pair_gayberne.html
potentials require particles have a "shape"_shape.html and are and "REsquared"_pair_resquared.html potentials require ellipsoidal
designed for "ellipsoidal particles"_atom_style.html. The particles, though they will also work if the 3 shape parameters are
"lubrication potential"_pair_lubricate.html requires that particles the same (a sphere). The "lubrication potential"_pair_lubricate.html
have a "shape"_shape.html. It can currently only be used with works with spherical particles.
extended spherical particles.
Time integration :h5 Time integration :h5
@ -1006,8 +1013,8 @@ and angular velocity or angular momentum of the particles:
"fix nvt/sphere"_fix_nvt_sphere.html "fix nvt/sphere"_fix_nvt_sphere.html
"fix npt/sphere"_fix_npt_sphere.html :ul "fix npt/sphere"_fix_npt_sphere.html :ul
Likewise, there are 3 fixes that perform time integration on extended Likewise, there are 3 fixes that perform time integration on
aspherical particles: ellipsoids as extended aspherical particles:
"fix nve/asphere"_fix_nve_asphere.html "fix nve/asphere"_fix_nve_asphere.html
"fix nvt/asphere"_fix_nvt_asphere.html "fix nvt/asphere"_fix_nvt_asphere.html
@ -1027,7 +1034,7 @@ extended particles.
Computes, thermodynamics, and dump output :h5 Computes, thermodynamics, and dump output :h5
There are 4 computes that calculate the temperature or rotational energy 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/sphere"_compute_temp_sphere.html
"compute temp/asphere"_compute_temp_asphere.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 force and torque on the rigid body each timestep due to forces on its
constituent particles, and integrates the motion of the rigid body. constituent particles, and integrates the motion of the rigid body.
(NOTE: 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 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 inertia tensor of the body is different than if they were point
particles. This means the rotational dynamics of the rigid body will particles. This means the rotational dynamics of the rigid body will
be different. Thus a model of a dimer is different if the dimer 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 <P>There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp. to the screen and log file; see the file thermo.cpp.
</P> </P>
<P>There are several styles defined in thermo.cpp: "one", "multi", <P>There are two styles defined in thermo.cpp: "one" and "multi". There
"granular", etc. There is also a flexible "custom" style which allows is also a flexible "custom" style which allows the user to explicitly
the user to explicitly list keywords for quantities to print when list keywords for quantities to print when thermodynamic info is
thermodynamic info is output. See the output. See the <A HREF = "thermo_style.html">thermo_style</A> command for a list
<A HREF = "thermo_style.html">thermo_style</A> command for a list of defined of defined quantities.
quantities.
</P> </P>
<P>The thermo styles (one, multi, etc) are simply lists of keywords. <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. Adding a new style thus only requires defining a new list of keywords.

11
doc/Section_modify.txt
View File

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

69
doc/atom_style.html
View File

@ -15,7 +15,7 @@
</P> </P>
<PRE>atom_style style args <PRE>atom_style style args
</PRE> </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> </UL>
<PRE> args = none for any style except <I>hybrid</I> <PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more sub-styles <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>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>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>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 > system with dipolar 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>electron</I> </TD><TD > charge and spin and eradius </TD><TD > electronic force field </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>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>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> </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 <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 the <A HREF = "mass.html">mass</A> command, except for the finite-size particle
which assign mass on a per-particle basis. For <I>granular</I> systems, styles discussed below. They assign mass on a per-atom basis.
the specified diameter and density are used to calculate each </P>
particle's mass. For <I>peri</I> systems, the speficied volume and density <P>All of the styles define point particles, except the <I>sphere</I>,
are used to calculate each particle's mass. <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> </P>
<HR> <HR>
@ -99,10 +95,10 @@ If some atoms have bonds, but others do not, use the <I>bond</I> style.
</P> </P>
<P>The only scenario where the <I>hybrid</I> style is needed is if there is no <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 single style which defines all needed properties of all atoms. For
example, if you want colloidal particles with charge, you would need example, if you want dipolar particles which will be torqued and
to use "atom_style hybrid colloid charge". When a hybrid style is rotate, you would need to use "atom_style hybrid sphere dipole". When
used, atoms store and communicate the union of all quantities implied a hybrid style is used, atoms store and communicate the union of all
by the individual styles. quantities implied by the individual styles.
</P> </P>
<P>LAMMPS can be extended with new atom styles; see <A HREF = "Section_modify.html">this <P>LAMMPS can be extended with new atom styles; see <A HREF = "Section_modify.html">this
section</A>. 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. <A HREF = "read_data.html">read_data</A> or <A HREF = "create_box.html">create_box</A> command.
</P> </P>
<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the <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" "molecular" package. The <I>dipole</I> style is part of the "dipole"
package. The <I>colloid</I> style is part of the "colloid" package. The package. The <I>ellipsoid</I> style is part of the "asphere" package. The
<I>dipole</I> style is part of the "dipole" package. The <I>ellipsoid</I> style <I>peri</I> style is part of the "peri" package for Peridynamics. The
is part of the "asphere" package. The <I>peri</I> style is part of the <I>electron</I> style is part of the "user-eff" package for <A HREF = "pair_eff.html">electronic
"peri" package for Peridynamics. The <I>electron</I> style is part of the force fields</A>. They are only enabled if LAMMPS was
"user-eff" package for <A HREF = "pair_eff.html">electronic force fields</A>. They built with that package. See the <A HREF = "Section_start.html#2_3">Making
are only enabled if LAMMPS was built with that package. See the LAMMPS</A> section for more info.
<A HREF = "Section_start.html#2_3">Making LAMMPS</A> section for more info.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>

71
doc/atom_style.txt
View File

@ -13,8 +13,8 @@ atom_style command :h3
atom_style style args :pre atom_style style args :pre
style = {angle} or {atomic} or {bond} or {charge} or {colloid} or {dipole} or \ style = {angle} or {atomic} or {bond} or {charge} or {colloid} or {dipole} or \
{electron} or {ellipsoid} or {full} or {granular} or {molecular} or \ {electron} or {ellipsoid} or {full} or {molecular} or \
{peri} or {hybrid} :ul {peri} or {sphere} or {hybrid} :ul
args = none for any style except {hybrid} args = none for any style except {hybrid}
{hybrid} args = list of one or more sub-styles :pre {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 | {atomic} | only the default values | coarse-grain liquids, solids, metals |
{bond} | bonds | bead-spring polymers | {bond} | bonds | bead-spring polymers |
{charge} | charge | atomic system with charges | {charge} | charge | atomic system with charges |
{colloid} | angular velocity | extended spherical particles | {dipole} | charge and dipole moment | system with dipolar particles |
{dipole} | charge and dipole moment | atomic system with dipoles |
{electron} | charge and spin and eradius | electronic force field | {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 | {full} | molecular + charge | bio-molecules |
{granular} | diameter, density, angular velocity | granular models |
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules | {molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
{peri} | density, volume | mesocopic Peridynamic models :tb(c=3,s=|) {peri} | mass, volume | mesocopic Peridynamic models |
{sphere} | diameter, mass, angular velocity | granular 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.
All of the styles assign mass to particles on a per-type basis, using 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 the "mass"_mass.html command, except for the finite-size particle
which assign mass on a per-particle basis. For {granular} systems, styles discussed below. They assign mass on a per-atom basis.
the specified diameter and density are used to calculate each
particle's mass. For {peri} systems, the speficied volume and density All of the styles define point particles, except the {sphere},
are used to calculate each particle's mass. {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 :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 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 single style which defines all needed properties of all atoms. For
example, if you want colloidal particles with charge, you would need example, if you want dipolar particles which will be torqued and
to use "atom_style hybrid colloid charge". When a hybrid style is rotate, you would need to use "atom_style hybrid sphere dipole". When
used, atoms store and communicate the union of all quantities implied a hybrid style is used, atoms store and communicate the union of all
by the individual styles. quantities implied by the individual styles.
LAMMPS can be extended with new atom styles; see "this LAMMPS can be extended with new atom styles; see "this
section"_Section_modify.html. 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. "read_data"_read_data.html or "create_box"_create_box.html command.
The {angle}, {bond}, {full}, and {molecular} styles are part of the The {angle}, {bond}, {full}, and {molecular} styles are part of the
"molecular" package. The {granular} style is part of the "granular" "molecular" package. The {dipole} style is part of the "dipole"
package. The {colloid} style is part of the "colloid" package. The package. The {ellipsoid} style is part of the "asphere" package. The
{dipole} style is part of the "dipole" package. The {ellipsoid} style {peri} style is part of the "peri" package for Peridynamics. The
is part of the "asphere" package. The {peri} style is part of the {electron} style is part of the "user-eff" package for "electronic
"peri" package for Peridynamics. The {electron} style is part of the force fields"_pair_eff.html. They are only enabled if LAMMPS was
"user-eff" package for "electronic force fields"_pair_eff.html. They built with that package. See the "Making
are only enabled if LAMMPS was built with that package. See the LAMMPS"_Section_start.html#2_3 section for more info.
"Making LAMMPS"_Section_start.html#2_3 section for more info.
[Related commands:] [Related commands:]

15
doc/compute_erotate_asphere.html
View File

@ -47,19 +47,12 @@ scalar value will be in energy <A HREF = "units.html">units</A>.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>This compute requires that particles be represented as extended <P>This compute requires that atoms store a shape and quaternion
ellipsoids and not point particles. This means they will have an orientation and angular momentum as defined by the <A HREF = "atom_style.html">atom_style
angular momentum and a shape which is determined by the ellipsoid</A> command.
<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> </P>
<P>All particles in the group must be finite-size. They cannot be point <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>
<P><B>Related commands:</B> none <P><B>Related commands:</B> none
</P> </P>

15
doc/compute_erotate_asphere.txt
View File

@ -44,19 +44,12 @@ scalar value will be in energy "units"_units.html.
[Restrictions:] [Restrictions:]
This compute requires that particles be represented as extended This compute requires that atoms store a shape and quaternion
ellipsoids and not point particles. This means they will have an orientation and angular momentum as defined by the "atom_style
angular momentum and a shape which is determined by the ellipsoid"_atom_style.html command.
"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.
All particles in the group must be finite-size. They cannot be point 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 [Related commands:] none

5
doc/compute_erotate_sphere.html
View File

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

5
doc/compute_erotate_sphere.txt
View File

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

9
doc/compute_property_atom.html
View File

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

9
doc/compute_property_atom.txt
View File

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

28
doc/compute_temp_asphere.html
View File

@ -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 <A HREF = "compute_modify.html">compute_modify extra</A> command to adjust the dof
accordingly. accordingly.
</P> </P>
<P>For example, an aspherical particle with all three of its <P>For example, an aspherical particle with all three of its shape
<A HREF = "shape.html">shape</A> parameters the same is a sphere. If it does not parameters the same is a sphere. If it does not rotate, then it
rotate, then it should have 3 dof instead of 6 in 3d (or 2 instead of should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A
3 in 2d). A uniaxial aspherical particle has two of its three shape uniaxial aspherical particle has two of its three shape parameters the
parameters the same. If it does not rotate around the axis same. If it does not rotate around the axis perpendicular to its
perpendicular to its circular cross section, then it should have 5 dof circular cross section, then it should have 5 dof instead of 6 in 3d.
instead of 6 in 3d.
</P> </P>
<P>The translational kinetic energy is computed the same as is described <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 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>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>This compute requires that particles be represented as extended <P>This compute is part of the "asphere" package. It is only enabled if
ellipsoids and not point particles. This means they will have an LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
angular momentum and a shape which is determined by the LAMMPS</A> section for more info.
<A HREF = "shape.html">shape</A> command. </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>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </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 "compute_modify extra"_compute_modify.html command to adjust the dof
accordingly. accordingly.
For example, an aspherical particle with all three of its For example, an aspherical particle with all three of its shape
"shape"_shape.html parameters the same is a sphere. If it does not parameters the same is a sphere. If it does not rotate, then it
rotate, then it should have 3 dof instead of 6 in 3d (or 2 instead of should have 3 dof instead of 6 in 3d (or 2 instead of 3 in 2d). A
3 in 2d). A uniaxial aspherical particle has two of its three shape uniaxial aspherical particle has two of its three shape parameters the
parameters the same. If it does not rotate around the axis same. If it does not rotate around the axis perpendicular to its
perpendicular to its circular cross section, then it should have 5 dof circular cross section, then it should have 5 dof instead of 6 in 3d.
instead of 6 in 3d.
The translational kinetic energy is computed the same as is described The translational kinetic energy is computed the same as is described
by the "compute temp"_compute_temp.html command. The rotational by the "compute temp"_compute_temp.html command. The rotational
@ -111,10 +110,17 @@ vector values will be in energy "units"_units.html.
[Restrictions:] [Restrictions:]
This compute requires that particles be represented as extended This compute is part of the "asphere" package. It is only enabled if
ellipsoids and not point particles. This means they will have an LAMMPS was built with that package. See the "Making
angular momentum and a shape which is determined by the LAMMPS"_Section_start.html#2_3 section for more info.
"shape"_shape.html command.
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:] [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. particles with only translational kinetic energy.
</P> </P>
<P>Both point and finite-size particles can be included in the group. <P>Both point and finite-size particles can be included in the group.
Point particles do not rotate, so they have only translational degrees Point particles do not rotate, so they have only 3 translational
of freedom. For 3d spherical particles, each has 6 degrees of freedom degrees of freedom. For 3d spherical particles, each has 6 degrees of
(3 translational, 3 rotational). For 2d spherical particles, each has freedom (3 translational, 3 rotational). For 2d spherical particles,
3 degrees of freedom (2 translational, 1 rotational). each has 3 degrees of freedom (2 translational, 1 rotational).
</P> </P>
<P>IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that <P>IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
all finite-size spherical particles in your model will freely rotate, 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>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>This compute requires that particles be represented as extended <P>This fix requires that atoms store torque and angular velocity (omega)
spheres and not point particles. This means they will have an angular and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
velocity and a diameter which is determined either by the command.
<A HREF = "shape.html">shape</A> command or by each particle being assigned an </P>
individual radius, e.g. for <A HREF = "atom_style.html">atom_style granular</A>. <P>All particles in the group must be finite-size spheres, or point
particles with radius = 0.0.
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </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. particles with only translational kinetic energy.
Both point and finite-size particles can be included in the group. Both point and finite-size particles can be included in the group.
Point particles do not rotate, so they have only translational degrees Point particles do not rotate, so they have only 3 translational
of freedom. For 3d spherical particles, each has 6 degrees of freedom degrees of freedom. For 3d spherical particles, each has 6 degrees of
(3 translational, 3 rotational). For 2d spherical particles, each has freedom (3 translational, 3 rotational). For 2d spherical particles,
3 degrees of freedom (2 translational, 1 rotational). each has 3 degrees of freedom (2 translational, 1 rotational).
IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that IMPORTANT NOTE: This choice for degrees of freedom (dof) assumes that
all finite-size spherical particles in your model will freely rotate, 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:] [Restrictions:]
This compute requires that particles be represented as extended This fix requires that atoms store torque and angular velocity (omega)
spheres and not point particles. This means they will have an angular and a radius as defined by the "atom_style sphere"_atom_style.html
velocity and a diameter which is determined either by the command.
"shape"_shape.html command or by each particle being assigned an
individual radius, e.g. for "atom_style granular"_atom_style.html. All particles in the group must be finite-size spheres, or point
particles with radius = 0.0.
[Related commands:] [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. to change these values.
</P> </P>
<UL><LI>charge = 0.0 <UL><LI>charge = 0.0
<LI>dipole moment = 0.0 <LI>dipole moment magnitude = 0.0
<LI>diameter = 1.0 <LI>diameter = 1.0
<LI>volume = 1.0 <LI>shape = 1.0 1.0 1.0
<LI>density = 1.0 <LI>density = 1.0
<LI>velocity = 0.0 <LI>volume = 1.0
<LI>angular velocity = 0.0 <LI>velocity = 0.0 0.0 0.0
<LI>angular momentum = 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>quaternion = (1,0,0,0)
<LI>bonds, angles, dihedrals, impropers = none <LI>bonds, angles, dihedrals, impropers = none
</UL> </UL>
<P>The <I>granular</I> style sets the diameter and density to 1.0 and <P>Note that this means the <I>sphere</I> and <I>ellipsoid</I> atom styles set the
calculates a mass for the particle, which is PI/6 * diameter^3 = diameter/shape and density to 1.0 and thus calculates a mass for the
0.5236. The <I>peri</I> style sets the volume and density to 1.0 and particle, which is PI/6 * diameter^3 = 0.5236. The <I>peri</I> style sets
calculates a mass for the particle, which is also 1.0. the volume and density to 1.0 and thus also set the mass for the
particle to 1.0.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </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. to change these values.
charge = 0.0 charge = 0.0
dipole moment = 0.0 dipole moment magnitude = 0.0
diameter = 1.0 diameter = 1.0
volume = 1.0 shape = 1.0 1.0 1.0
density = 1.0 density = 1.0
velocity = 0.0 volume = 1.0
angular velocity = 0.0 velocity = 0.0 0.0 0.0
angular momentum = 0.0 angular velocity = 0.0 0.0 0.0
angular momentum = 0.0 0.0 0.0
quaternion = (1,0,0,0) quaternion = (1,0,0,0)
bonds, angles, dihedrals, impropers = none :ul bonds, angles, dihedrals, impropers = none :ul
The {granular} style sets the diameter and density to 1.0 and Note that this means the {sphere} and {ellipsoid} atom styles set the
calculates a mass for the particle, which is PI/6 * diameter^3 = diameter/shape and density to 1.0 and thus calculates a mass for the
0.5236. The {peri} style sets the volume and density to 1.0 and particle, which is PI/6 * diameter^3 = 0.5236. The {peri} style sets
calculates a mass for the particle, which is also 1.0. the volume and density to 1.0 and thus also set the mass for the
particle to 1.0.
[Restrictions:] [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

26
doc/dump.html
View File

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

26
doc/dump.txt
View File

@ -39,9 +39,10 @@ args = list of arguments for a particular style :l
possible attributes = id, mol, type, mass, possible attributes = id, mol, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz, vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, q, mux, muy, muz, mu,
radius, omegax, omegay, omegaz, radius, omegax, omegay, omegaz,
angmomx, angmomy, angmomz, angmomx, angmomy, angmomz,
shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz, quatw, quati, quatj, quatk, tqx, tqy, tqz,
spin, eradius, ervel, erforce, spin, eradius, ervel, erforce,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre 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 vx,vy,vz = atom velocities
fx,fy,fz = forces on atoms fx,fy,fz = forces on atoms
q = atom charge q = atom charge
mux,muy,muz = orientation of dipolar atom mux,muy,muz = orientation of dipole moment of atom
radius = radius of extended spherical particle mu = magnitude of dipole moment of atom
radius = radius of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum 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 quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles tqx,tqy,tqz = torque on extended particles
spin = electron spin spin = electron spin
@ -392,21 +395,26 @@ coordinates and the image flags.
The {mux}, {muy}, {muz} attributes are specific to dipolar systems The {mux}, {muy}, {muz} attributes are specific to dipolar systems
defined with an atom style of {dipole}. They give the orientation of 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 The {radius} attribute is specific to extended spherical particles
that have a finite size, such as granular particles defined with that have a finite size, such as those defined with an atom style of
an atom style of {granular}. {sphere}.
The {omegax}, {omegay}, and {omegaz} attributes are specific to extended The {omegax}, {omegay}, and {omegaz} attributes are specific to
spherical or aspherical particles that have an angular velocity. Only extended spherical or aspherical particles that have an angular
certain atom styles, such as {granular} or {dipole} define this velocity. Only certain atom styles, such as {sphere} define this
quantity. quantity.
The {angmomx}, {angmomy}, and {angmomz} attributes are specific to The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
extended aspherical particles that have an angular momentum. Only extended aspherical particles that have an angular momentum. Only
the {ellipsoid} atom style defines this quantity. 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 The {quatw}, {quati}, {quatj}, {quatk} attributes are for aspherical
particles defined with an atom style of {ellipsoid}. They are the particles defined with an atom style of {ellipsoid}. They are the
components of the quaternion that defines the orientation of 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>
<P><B>Related commands:</B> none <P><B>Related commands:</B> none
</P> </P>
<P><A HREF = "atom_style.html">atom_style granular</A> <P><A HREF = "atom_style.html">atom_style sphere</A>
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B> none
</P> </P>

2
doc/fix_freeze.txt
View File

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

2
doc/fix_gravity.txt
View File

@ -91,6 +91,6 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Related commands:] [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 [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>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>This fix requires that atoms store torque and angular velocity (omega) <P>This fix is part of the "asphere" package. It is only enabled if
as defined by the <A HREF = "atom_style.html">atom_style</A>. It also require they LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
store either a per-particle diameter or per-type <A HREF = "shape.html">shape</A>. 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>
<P>All particles in the group must be finite-size. They cannot be point <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>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </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 <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>, nvt_asphere</A>, <A HREF = "fix_npt_asphere.html">fix
<A HREF = "fix_modify.html">fix_modify</A> npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B> none
</P> </P>

17
doc/fix_nph_asphere.txt
View File

@ -108,17 +108,22 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] [Restrictions:]
This fix requires that atoms store torque and angular velocity (omega) This fix is part of the "asphere" package. It is only enabled if
as defined by the "atom_style"_atom_style.html. It also require they LAMMPS was built with that package. See the "Making
store either a per-particle diameter or per-type "shape"_shape.html. 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 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:] [Related commands:]
"fix nph"_fix_nh.html, "fix nve_asphere"_fix_nve_asphere.html, "fix "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, nvt_asphere"_fix_nvt_asphere.html, "fix
"fix_modify"_fix_modify.html npt_asphere"_fix_npt_asphere.html, "fix_modify"_fix_modify.html
[Default:] none [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><B>Restrictions:</B>
</P> </P>
<P>This fix requires that atoms store torque and angular velocity (omega) <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 and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
store either a per-particle diameter or per-type <A HREF = "shape.html">shape</A>. command.
</P> </P>
<P>All particles in the group must be finite-size spheres. They cannot <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>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>

6
doc/fix_nph_sphere.txt
View File

@ -109,11 +109,11 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] [Restrictions:]
This fix requires that atoms store torque and angular velocity (omega) This fix requires that atoms store torque and angular velocity (omega)
as defined by the "atom_style"_atom_style.html. It also require they and a radius as defined by the "atom_style sphere"_atom_style.html
store either a per-particle diameter or per-type "shape"_shape.html. command.
All particles in the group must be finite-size spheres. They cannot 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:] [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 was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </P>
<P>This fix requires that atoms store torque and angular momentum and a <P>This fix requires that atoms store torque and angular momementum and a
quaternion to represent their orientation, as defined by the quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type command.
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter or per-particle mass.
</P> </P>
<P>All particles in the group must be finite-size. They cannot be point <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>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </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 was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. LAMMPS"_Section_start.html#2_3 section for more info.
This fix requires that atoms store torque and angular momentum and a This fix requires that atoms store torque and angular momementum and a
quaternion to represent their orientation, as defined by the quaternion as defined by the "atom_style ellipsoid"_atom_style.html
"atom_style"_atom_style.html. It also require they store a per-type command.
"shape"_shape.html. The particles cannot store a per-particle
diameter or per-particle mass.
All particles in the group must be finite-size. They cannot be point 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:] [Related commands:]

6
doc/fix_npt_sphere.html
View File

@ -136,11 +136,11 @@ this.
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>This fix requires that atoms store torque and angular velocity (omega) <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 and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
store either a per-particle diameter or per-type <A HREF = "shape.html">shape</A>. command.
</P> </P>
<P>All particles in the group must be finite-size spheres. They cannot <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>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>

6
doc/fix_npt_sphere.txt
View File

@ -133,11 +133,11 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] [Restrictions:]
This fix requires that atoms store torque and angular velocity (omega) This fix requires that atoms store torque and angular velocity (omega)
as defined by the "atom_style"_atom_style.html. It also require they and a radius as defined by the "atom_style sphere"_atom_style.html
store either a per-particle diameter or per-type "shape"_shape.html. command.
All particles in the group must be finite-size spheres. They cannot 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:] [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 was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </P>
<P>This fix requires that atoms store torque and angular momentum and a <P>This fix requires that atoms store torque and angular momementum and a
quaternion to represent their orientation, as defined by the quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type command.
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter or per-particle mass.
</P> </P>
<P>All particles in the group must be finite-size. They cannot be point <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>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </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 was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. LAMMPS"_Section_start.html#2_3 section for more info.
This fix requires that atoms store torque and angular momentum and a This fix requires that atoms store torque and angular momementum and a
quaternion to represent their orientation, as defined by the quaternion as defined by the "atom_style ellipsoid"_atom_style.html
"atom_style"_atom_style.html. It also require they store a per-type command.
"shape"_shape.html. The particles cannot store a per-particle
diameter or per-particle mass.
All particles in the group must be finite-size. They cannot be point 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:] [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 <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 orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models during the time integration. This option should be used for models
where a dipole moment is assigned to particles via the where a dipole moment is assigned to particles via use of the
<A HREF = "dipole.html">dipole</A> command. <A HREF = "atom_style.html">atom_style dipole</A> command.
</P> </P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B> <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P> </P>
@ -62,12 +62,13 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>
<P>This fix requires that atoms store torque and angular velocity (omega) <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 and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
store either a per-particle diameter or per-type <A HREF = "shape.html">shape</A>. If command. If the <I>dipole</I> keyword is used, then they must also store a
the <I>dipole</I> keyword is used, then they must store a dipole moment. dipole moment as defined by the <A HREF = "atom_style.html">atom_style dipole</A>
command.
</P> </P>
<P>All particles in the group must be finite-size spheres. They cannot <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>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </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 If the {update} keyword is used with the {dipole} value, then the
orientation of the dipole moment of each particle is also updated orientation of the dipole moment of each particle is also updated
during the time integration. This option should be used for models during the time integration. This option should be used for models
where a dipole moment is assigned to particles via the where a dipole moment is assigned to particles via use of the
"dipole"_dipole.html command. "atom_style dipole"_atom_style.html command.
[Restart, fix_modify, output, run start/stop, minimize info:] [Restart, fix_modify, output, run start/stop, minimize info:]
@ -54,12 +54,13 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] [Restrictions:]
This fix requires that atoms store torque and angular velocity (omega) This fix requires that atoms store torque and angular velocity (omega)
as defined by the "atom_style"_atom_style.html. It also require they and a radius as defined by the "atom_style sphere"_atom_style.html
store either a per-particle diameter or per-type "shape"_shape.html. If command. If the {dipole} keyword is used, then they must also store a
the {dipole} keyword is used, then they must store a dipole moment. 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 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:] [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 was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </P>
<P>This fix requires that atoms store torque and angular momentum and a <P>This fix requires that atoms store torque and angular momementum and a
quaternion to represent their orientation, as defined by the quaternion as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A>
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type command.
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter or per-particle mass.
</P> </P>
<P>All particles in the group must be finite-size. They cannot be point <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>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </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 was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. LAMMPS"_Section_start.html#2_3 section for more info.
This fix requires that atoms store torque and angular momentum and a This fix requires that atoms store torque and angular momementum and a
quaternion to represent their orientation, as defined by the quaternion as defined by the "atom_style ellipsoid"_atom_style.html
"atom_style"_atom_style.html. It also require they store a per-type command.
"shape"_shape.html. The particles cannot store a per-particle
diameter or per-particle mass.
All particles in the group must be finite-size. They cannot be point 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:] [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><B>Restrictions:</B>
</P> </P>
<P>This fix requires that atoms store torque and angular velocity (omega) <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 and a radius as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
store either a per-particle radius or per-type <A HREF = "shape.html">shape</A>. command.
</P> </P>
<P>All particles in the group must be finite-size spheres. They cannot <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>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>

6
doc/fix_nvt_sphere.txt
View File

@ -110,11 +110,11 @@ This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] [Restrictions:]
This fix requires that atoms store torque and angular velocity (omega) This fix requires that atoms store torque and angular velocity (omega)
as defined by the "atom_style"_atom_style.html. It also require they and a radius as defined by the "atom_style sphere"_atom_style.html
store either a per-particle radius or per-type "shape"_shape.html. command.
All particles in the group must be finite-size spheres. They cannot 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:] [Related commands:]

12
doc/fix_rigid.html
View File

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

12
doc/fix_rigid.txt
View File

@ -103,12 +103,12 @@ setforce"_fix_setforce.html command), and integrating them as usual
:line :line
The constituent particles within a rigid body can be point particles The constituent particles within a rigid body can be point particles
(the default in LAMMPS) or finite-size particles, such as spheroids (the default in LAMMPS) or finite-size particles, such as spheres and
and ellipsoids. See the "shape"_shape.html command and "atom_style ellipsoids. See the "atom_style sphere and ellipsoid"_atom_style.html
granular"_atom_style.html for more details on these kinds of commands for more details on these kinds of particles. Finite-size
particles. Finite-size particles contribute differently to the moment particles contribute differently to the moment of inertia of a rigid
of inertia of a rigid body than do point particles. Finite-size body than do point particles. Finite-size particles can also
particles can also experience torque (e.g. due to "frictional granular experience torque (e.g. due to "frictional granular
interactions"_pair_gran.html) and have an orientation. These interactions"_pair_gran.html) and have an orientation. These
contributions are accounted for by these fixes. 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> </PRE>
<P>Note that the mass command can only be used if the <A HREF = "atom_style.html">atom <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. 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 Currently, all but the <I>sphere</I> and <I>ellipsoid</I> and <I>peri</I> styles do.
mass to be set for individual particles, not types. Per-atom masses They require mass to be set for individual particles, not types.
are defined in the data file read by the <A HREF = "read_data.html">read_data</A> Per-atom masses are defined in the data file read by the
command, or set to default values 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 <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 set to new values by the <A HREF = "set.html">set mass</A> or <A HREF = "set.html">set density</A>
density</A> command. commands.
</P> </P>
<P>Also note that <A HREF = "pair_eam.html">pair_style eam</A> defines the masses of <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 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 Note that the mass command can only be used if the "atom
style"_atom_style.html requires per-type atom mass to be set. style"_atom_style.html requires per-type atom mass to be set.
Currently, all but the {granular} and {peri} styles do. They require Currently, all but the {sphere} and {ellipsoid} and {peri} styles do.
mass to be set for individual particles, not types. Per-atom masses They require mass to be set for individual particles, not types.
are defined in the data file read by the "read_data"_read_data.html Per-atom masses are defined in the data file read by the
command, or set to default values 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 "create_atoms"_create_atoms.html command. Per-atom masses can also be
set to new values by the "set diameter"_set.html or "set set to new values by the "set mass"_set.html or "set density"_set.html
density"_set.html command. commands.
Also note that "pair_style eam"_pair_eam.html defines the masses of 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 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 was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </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><B>Related commands:</B>
</P> </P>
<P><A HREF = "pair_coeff.html">pair_coeff</A> <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 was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. 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:] [Related commands:]
"pair_coeff"_pair_coeff.html "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 <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 order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
ellipsoid</A> should be used since it defines the ellipsoid</A> should be used since it defines the
rotational state of the ellipsoidal particles. The size and shape of rotational state and the size and shape of each ellipsoidal particle.
the ellipsoidal particles are defined by the <A HREF = "shape.html">shape</A>
command.
</P> </P>
<P>The following coefficients must be defined for each pair of atoms <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 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 <P>The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used. cutoff specified in the pair_style command is used.
</P> </P>
<P>It is typical for the Gay-Berne potential to define <I>sigma</I> as the <P>It is typical with the Gay-Berne potential to define <I>sigma</I> as the
minimum of the 3 "shape" diameters for a I,I interaction, though this minimum of the 3 shape diameters of the particles involved in an I,I
is not required. Note that this is a different meaning for <I>sigma</I> interaction, though this is not required. Note that this is a
than the <A HREF = "pair_resquared.html">pair_style resquared</A> potential uses. different meaning for <I>sigma</I> than the <A HREF = "pair_resquared.html">pair_style
resquared</A> potential uses.
</P> </P>
<P>The epsilon_i and epsilon_j coefficients are actually defined for atom <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 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. that type in a "pair_coeff I J" command.
</P> </P>
<P>IMPORTANT NOTE: If the epsilon a,b,c for an atom type are all 1.0, and <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> if the shape of the particle itself is spherical, meaning its 3 shape
command), meaning the 3 diameters are all the same, then the particle parameters are all the same, then the particle is treated as an LJ
is treated as "spherical" by the Gay-Berne potential. This is sphere by the Gay-Berne potential. This is significant because if two
significant because if two "spherical" particles interact, then the LJ spheres interact, then the simple Lennard-Jones formula is used to
simple Lennard-Jones formula is used to compute their interaction compute their interaction energy/force using epsilon and sigma. This
energy/force using epsilon and sigma, which is much cheaper to compute is much cheaper to compute than the full Gay-Berne formula. Thus you
than the full Gay-Berne formula. Thus you should insure epsilon a,b,c should insure epsilon a,b,c are set to 1.0 for spherical particle
are set to 1.0 for spherical particle types and use epsilon and sigma types and use epsilon and sigma to specify its interaction with other
to specify its interaction with other spherical particles. spherical particles.
</P> </P>
<HR> <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 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. LAMMPS</A> section for more info.
</P> </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 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 = "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 <A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter. diameter.
</P> </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 <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>
<P>The Gay-Berne potential does not become isotropic as r increases <P>The Gay-Berne potential does not become isotropic as r increases
<A HREF = "#Everaers">(Everaers)</A>. The distance-of-closest-approach <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 {asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
order to integrate particle rotation. Additionally, "atom_style order to integrate particle rotation. Additionally, "atom_style
ellipsoid"_atom_style.html should be used since it defines the ellipsoid"_atom_style.html should be used since it defines the
rotational state of the ellipsoidal particles. The size and shape of rotational state and the size and shape of each ellipsoidal particle.
the ellipsoidal particles are defined by the "shape"_shape.html
command.
The following coefficients must be defined for each pair of atoms The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples 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 The last coefficient is optional. If not specified, the global
cutoff specified in the pair_style command is used. cutoff specified in the pair_style command is used.
It is typical for the Gay-Berne potential to define {sigma} as the It is typical with the Gay-Berne potential to define {sigma} as the
minimum of the 3 "shape" diameters for a I,I interaction, though this minimum of the 3 shape diameters of the particles involved in an I,I
is not required. Note that this is a different meaning for {sigma} interaction, though this is not required. Note that this is a
than the "pair_style resquared"_pair_resquared.html potential uses. 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 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 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. 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 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 if the shape of the particle itself is spherical, meaning its 3 shape
command), meaning the 3 diameters are all the same, then the particle parameters are all the same, then the particle is treated as an LJ
is treated as "spherical" by the Gay-Berne potential. This is sphere by the Gay-Berne potential. This is significant because if two
significant because if two "spherical" particles interact, then the LJ spheres interact, then the simple Lennard-Jones formula is used to
simple Lennard-Jones formula is used to compute their interaction compute their interaction energy/force using epsilon and sigma. This
energy/force using epsilon and sigma, which is much cheaper to compute is much cheaper to compute than the full Gay-Berne formula. Thus you
than the full Gay-Berne formula. Thus you should insure epsilon a,b,c should insure epsilon a,b,c are set to 1.0 for spherical particle
are set to 1.0 for spherical particle types and use epsilon and sigma types and use epsilon and sigma to specify its interaction with other
to specify its interaction with other spherical particles. spherical particles.
:line :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 enabled if LAMMPS was built with the those packages. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. 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 represent their orientation, as defined by the
"atom_style"_atom_style.html. It also require they store a per-type "atom_style"_atom_style.html. It also require they store a per-type
"shape"_shape.html. The particles cannot store a per-particle "shape"_shape.html. The particles cannot store a per-particle
diameter. 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 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 The Gay-Berne potential does not become isotropic as r increases
"(Everaers)"_#Everaers. The distance-of-closest-approach "(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>
<P>These pair styles require that atoms store torque and angular velocity <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 (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 require a per-particle radius is stored. The <I>sphere</I> atom style does
does all of this. all of this.
</P> </P>
<P>This pair style requires you to use the <A HREF = "communicate.html">communicate vel <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 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 These pair styles require that atoms store torque and angular velocity
(omega) as defined by the "atom_style"_atom_style.html. They also (omega) as defined by the "atom_style"_atom_style.html. They also
require a per-particle radius is stored. The {granular} atom style require a per-particle radius is stored. The {sphere} atom style does
does all of this. all of this.
This pair style requires you to use the "communicate vel This pair style requires you to use the "communicate vel
yes"_communicate.html option so that velocites are stored by ghost 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 was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </P>
<P>This pair style requires that atoms store torque and a quaternion to <P>This pair style requires that atoms be finite-size spheres with a
represent their orientation, as defined by the diameter, as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
<A HREF = "atom_style.html">atom_style</A>. It also require they store a per-type command.
<A HREF = "shape.html">shape</A>. The particles cannot store a per-particle
diameter or per-particle mass.
</P> </P>
<P>All the shape settings must be for finite-size spheres. They cannot <P>Per-particle or per-type polydispersity is not yet supported by this
be point particles, nor can they be aspherical. Additionally all the pair style; all particles must have the same diameter.
shape types must specify particles of the same size, i.e. a
monodisperse system.
</P> </P>
<P>This pair style requires you to use the <A HREF = "communicate.html">communicate vel <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 yes</A> option so that velocites are stored by ghost

14
doc/pair_lubricate.txt
View File

@ -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 was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. LAMMPS"_Section_start.html#2_3 section for more info.
This pair style requires that atoms store torque and a quaternion to This pair style requires that atoms be finite-size spheres with a
represent their orientation, as defined by the diameter, as defined by the "atom_style sphere"_atom_style.html
"atom_style"_atom_style.html. It also require they store a per-type command.
"shape"_shape.html. The particles cannot store a per-particle
diameter or per-particle mass.
All the shape settings must be for finite-size spheres. They cannot Per-particle or per-type polydispersity is not yet supported by this
be point particles, nor can they be aspherical. Additionally all the pair style; all particles must have the same diameter.
shape types must specify particles of the same size, i.e. a
monodisperse system.
This pair style requires you to use the "communicate vel This pair style requires you to use the "communicate vel
yes"_communicate.html option so that velocites are stored by ghost 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 <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 order to integrate particle rotation. Additionally, <A HREF = "atom_style.html">atom_style
ellipsoid</A> should be used since it defines the ellipsoid</A> should be used since it defines the
rotational state of the ellipsoidal particles. The size and shape of rotational state and the size and shape of each ellipsoidal particle.
the ellipsoidal particles are defined by the <A HREF = "shape.html">shape</A>
command.
</P> </P>
<P>The following coefficients must be defined for each pair of atoms <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 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. gayberne</A> potential uses.
</P> </P>
<P>The parameters used depend on the type of the interacting particles, <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 i.e. ellipsoids or LJ spheres. The type of a particle is determined
the diameters specified with the <A HREF = "shape.html">shape</A> command. LJ by the diameters specified for its 3 shape paramters. LJ spheres have
spheres have diameters equal to zero and thus represent a single all 3 diameters equal to zero and thus represent a simple point
particle with size sigma. The epsilon_i_* or epsilon_j_* parameters particle with size sigma. The epsilon_i_* or epsilon_j_* parameters
are ignored for LJ sphere interactions. The interactions between two are ignored for LJ spheres. The interactions between two LJ spheres
LJ sphere particles are computed using the standard Lennard-Jones are computed using the standard Lennard-Jones formula, which is much
formula. cheaper to compute than the ellipsoidal formulas.
</P> </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 of-closest approach equation has been implemented to reduce the error
from disparate sizes; see <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary from disparate sizes; see <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary
document</A>. document</A>.
</P> </P>
<P>A12 specifies the energy prefactor which depends on the type of <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 the Hamaker constant as described in <A HREF = "#Everaers">(Everaers)</A>. In LJ
units: units:
</P> </P>
@ -92,17 +90,17 @@ units:
composing the ellipsoids and epsilon_LJ determines the interaction composing the ellipsoids and epsilon_LJ determines the interaction
strength of the spherical particles. strength of the spherical particles.
</P> </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: (see <A HREF = "PDF/pair_resquared_extra.pdf">here</A> for details:
</P> </P>
<CENTER><IMG SRC = "Eqs/pair_resquared2.jpg"> <CENTER><IMG SRC = "Eqs/pair_resquared2.jpg">
</CENTER> </CENTER>
<P>For LJ sphere-LJ sphere interactions, A12 is the standard epsilon used <P>For LJ sphere/LJ sphere interactions, A12 is used as the standard
in Lennard-Jones pair styles: epsilon used in Lennard-Jones pair styles:
</P> </P>
<CENTER><IMG SRC = "Eqs/pair_resquared3.jpg"> <CENTER><IMG SRC = "Eqs/pair_resquared3.jpg">
</CENTER> </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 constituent particles within each ellipsoid used to model the
RE-squared potential. RE-squared potential.
</P> </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><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P> </P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients <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 default mix value is <I>geometric</I>. See the "pair_modify" command for
details. Other type pairs cannot be mixed, due to the different details. Other type pairs cannot be mixed, due to the different
meanings of the energy prefactors used to calculate the interactions meanings of the energy prefactors used to calculate the interactions
and the implicit dependence of the ellipsoid-LJ sphere interaction on and the implicit dependence of the ellipsoid-sphere interaction on the
the equation for the Hamaker constant presented here. Mixing of sigma equation for the Hamaker constant presented here. Mixing of sigma and
and epsilon followed by calculation of the energy prefactors using the epsilon followed by calculation of the energy prefactors using the
equations above is recommended. equations above is recommended.
</P> </P>
<P>This pair styles supports the <A HREF = "pair_modify.html">pair_modify</A> shift <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 was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </P>
<P>This pair style requires that atoms store torque and a quaternion to <P>This pair style requires that atoms be ellipsoids as defined by the
represent their orientation, as defined by the <A HREF = "atom_style.html">atom_style ellipsoid</A> command.
<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>
<P>Particles acted on by the potential can be extended aspherical or <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>
<P>The distance-of-closest-approach approximation used by LAMMPS becomes <P>The distance-of-closest-approach approximation used by LAMMPS becomes
less accurate when high-aspect ratio ellipsoids are used. less accurate when high-aspect ratio ellipsoids are used.

47
doc/pair_resquared.txt
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 {asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
order to integrate particle rotation. Additionally, "atom_style order to integrate particle rotation. Additionally, "atom_style
ellipsoid"_atom_style.html should be used since it defines the ellipsoid"_atom_style.html should be used since it defines the
rotational state of the ellipsoidal particles. The size and shape of rotational state and the size and shape of each ellipsoidal particle.
the ellipsoidal particles are defined by the "shape"_shape.html
command.
The following coefficients must be defined for each pair of atoms The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples 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. gayberne"_pair_gayberne.html potential uses.
The parameters used depend on the type of the interacting particles, The parameters used depend on the type of the interacting particles,
i.e. ellipsoid or LJ sphere. The type of particle is determined by i.e. ellipsoids or LJ spheres. The type of a particle is determined
the diameters specified with the "shape"_shape.html command. LJ by the diameters specified for its 3 shape paramters. LJ spheres have
spheres have diameters equal to zero and thus represent a single all 3 diameters equal to zero and thus represent a simple point
particle with size sigma. The epsilon_i_* or epsilon_j_* parameters particle with size sigma. The epsilon_i_* or epsilon_j_* parameters
are ignored for LJ sphere interactions. The interactions between two are ignored for LJ spheres. The interactions between two LJ spheres
LJ sphere particles are computed using the standard Lennard-Jones are computed using the standard Lennard-Jones formula, which is much
formula. 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 of-closest approach equation has been implemented to reduce the error
from disparate sizes; see "this supplementary from disparate sizes; see "this supplementary
document"_PDF/pair_resquared_extra.pdf. document"_PDF/pair_resquared_extra.pdf.
A12 specifies the energy prefactor which depends on the type of 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 the Hamaker constant as described in "(Everaers)"_#Everaers. In LJ
units: units:
@ -89,17 +87,17 @@ where rho gives the number density of the spherical particles
composing the ellipsoids and epsilon_LJ determines the interaction composing the ellipsoids and epsilon_LJ determines the interaction
strength of the spherical particles. 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: (see "here"_PDF/pair_resquared_extra.pdf for details:
:c,image(Eqs/pair_resquared2.jpg) :c,image(Eqs/pair_resquared2.jpg)
For LJ sphere-LJ sphere interactions, A12 is the standard epsilon used For LJ sphere/LJ sphere interactions, A12 is used as the standard
in Lennard-Jones pair styles: epsilon used in Lennard-Jones pair styles:
:c,image(Eqs/pair_resquared3.jpg) :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 constituent particles within each ellipsoid used to model the
RE-squared potential. RE-squared potential.
@ -141,13 +139,13 @@ that type in a "pair_coeff I J" command.
[Mixing, shift, table, tail correction, restart, rRESPA info]: [Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients 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 default mix value is {geometric}. See the "pair_modify" command for
details. Other type pairs cannot be mixed, due to the different details. Other type pairs cannot be mixed, due to the different
meanings of the energy prefactors used to calculate the interactions meanings of the energy prefactors used to calculate the interactions
and the implicit dependence of the ellipsoid-LJ sphere interaction on and the implicit dependence of the ellipsoid-sphere interaction on the
the equation for the Hamaker constant presented here. Mixing of sigma equation for the Hamaker constant presented here. Mixing of sigma and
and epsilon followed by calculation of the energy prefactors using the epsilon followed by calculation of the energy prefactors using the
equations above is recommended. equations above is recommended.
This pair styles supports the "pair_modify"_pair_modify.html shift 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 was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. LAMMPS"_Section_start.html#2_3 section for more info.
This pair style requires that atoms store torque and a quaternion to This pair style requires that atoms be ellipsoids as defined by the
represent their orientation, as defined by the "atom_style ellipsoid"_atom_style.html command.
"atom_style"_atom_style.html. It also require they store a per-type
"shape"_shape.html. The particles cannot store a per-particle
diameter.
Particles acted on by the potential can be extended aspherical or 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 The distance-of-closest-approach approximation used by LAMMPS becomes
less accurate when high-aspect ratio ellipsoids are used. 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 was built with that package. See the <A HREF = "Section_start.html#2_3">Making
LAMMPS</A> section for more info. LAMMPS</A> section for more info.
</P> </P>
<P>Because this potential uses the radii of the particles, the atom style <P>This pair style requires that atoms be finite-size spheres with a
must support particles whose size is set via the <A HREF = "shape.html">shape</A> diameter, as defined by the <A HREF = "atom_style.html">atom_style sphere</A>
command. For example <A HREF = "atom_style.html">atom_style</A> colloid or command.
ellipsoid. Only spherical particles are currently allowed for </P>
pair_style yukawa/colloid, which means that for each particle type, <P>Per-particle polydispersity is not yet supported by this pair style;
its 3 shape diameters must be equal to each other. 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>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </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 was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info. LAMMPS"_Section_start.html#2_3 section for more info.
Because this potential uses the radii of the particles, the atom style This pair style requires that atoms be finite-size spheres with a
must support particles whose size is set via the "shape"_shape.html diameter, as defined by the "atom_style sphere"_atom_style.html
command. For example "atom_style"_atom_style.html colloid or command.
ellipsoid. Only spherical particles are currently allowed for
pair_style yukawa/colloid, which means that for each particle type, Per-particle polydispersity is not yet supported by this pair style;
its 3 shape diameters must be equal to each other. 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:] [Related commands:]

116
doc/read_data.html
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>These are the section keywords for the body of the file.
</P> </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>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>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 <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 >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 >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 >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 >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 >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 >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 >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 >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 ... <TR><TD >hybrid</TD><TD > atom-ID atom-type x y z sub-style1 sub-style2 ...
</TD></TR></TABLE></DIV> </TD></TR></TABLE></DIV>
@ -295,13 +294,14 @@ of analysis.
</P> </P>
<UL><LI>atom-ID = integer ID of atom <UL><LI>atom-ID = integer ID of atom
<LI>molecule-ID = integer ID of molecule the atom belongs to <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>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>density = density of atom (mass/distance^3 units)
<LI>volume = volume of atom (distance^3 units) <LI>volume = volume of atom (distance^3 units)
<LI>x,y,z = coordinates of atom <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>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>spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
<LI>eradius = electron radius (or fixed-core radius) <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 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). 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 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 bonds), and velocities are not assigned in the data file, and you
care if unique atom IDs appear in dump files, then the atom-IDs can all don't care if unique atom IDs appear in dump files, then the atom-IDs
be set to 0. can all be set to 0.
</P> </P>
<P>The molecule ID is a 2nd identifier attached to an atom. Normally, it <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 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 to. It can be 0 if it is an unbonded atom or if you don't care to
keep track of molecule assignments. keep track of molecule assignments.
</P> </P>
<P>The diameter specifies the size of a finite size particle, analagous <P>The diameter specifies the size of a finite-size spherical particle.
to the <A HREF = "shape.html">shape</A> command which sets the size on a per-type It can be set to 0.0, which means that atom is a point particle.
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> </P>
<P>The density is used in conjunction with the diameter to set the mass <P>The 3 shape values specify the 3 diameters or aspect ratios of a
of a particle as mass = density * volume. If the diameter and volume finite-size ellipsoidal particle, when it is oriented along the 3
are 0.0 meaning a point particle, then the mass is not 0.0 but is set coordinate axes. They can all be set to 0.0, which means that atom is
as mass = density. 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>
<P>The values <I>quatw</I>, <I>quati</I>, <I>quatj</I>, and <I>quatk</I> set the orientation <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 of the atom as a quaternion (4-vector). Note that the shape
<A HREF = "shape.html">shape</A> command or "Shapes" section of the data file attributes specify the aspect ratios of an ellipsoidal particle, which
specifies the aspect ratios of an ellipsoidal particle, which is is oriented by default with its x-axis along the simulation box's
oriented by default with its x-axis along the simulation box's x-axis, x-axis, and similarly for y and z. If this body is rotated (via the
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 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 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 (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. 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 LAMMPS normalizes each atom's quaternion in case (a,b,c) was not
unit vector. specified as a unit vector.
</P> </P>
<P>For atom_style hybrid, following the 5 initial values (ID,type,x,y,z), <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 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>
<P>Thus if <P>Thus if
</P> </P>
<PRE>atom_style hybrid charge granular <PRE>atom_style hybrid charge sphere
</PRE> </PRE>
<P>were used in the input script, each atom line would have these fields: <P>were used in the input script, each atom line would have these fields:
</P> </P>
@ -524,27 +527,6 @@ section must be integers (1, not 1.0).
</P> </P>
<HR> <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><I>EndBondTorsion Coeffs</I> section:
</P> </P>
<UL><LI>one line per dihedral type <UL><LI>one line per dihedral type
@ -623,9 +605,9 @@ values in this section must be integers (1, not 1.0).
</UL> </UL>
<P>This defines the mass of each atom type. This can also be set via the <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 <A HREF = "mass.html">mass</A> command in the input script. This section cannot be
be used for atom styles that define a mass for individual atoms - used for atom styles that define a mass for individual atoms -
e.g. atom style granular. e.g. <A HREF = "atom_style.html">atom_style sphere</A>.
</P> </P>
<HR> <HR>
@ -665,30 +647,6 @@ script.
</P> </P>
<HR> <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><I>Velocities</I> section:
</P> </P>
<UL><LI>one line per atom <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 >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 >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 >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> </TD></TR></TABLE></DIV>
<P>where the keywords have these meanings: <P>where the keywords have these meanings:
</P> </P>
<P>vx,vy,vz = translational velocity of atom <P>vx,vy,vz = translational velocity of atom
lx,ly,lz = angular momentum of aspherical 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 evel = electron radial velocity (0 for fixed-core):ul
</P> </P>
<P>The velocity lines can appear in any order. This section can only be <P>The velocity lines can appear in any order. This section can only be

106
doc/read_data.txt
View File

@ -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. 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 {Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
{Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \ {Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \
Improper Coeffs} = force field sections 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 atomic: atom-ID atom-type x y z
bond: atom-ID molecule-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 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 dipole: atom-ID atom-type q x y z mux muy muz
electron: atom-ID atom-type q spin eradius x y z 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 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 molecular: atom-ID molecule-ID atom-type x y z
peri: atom-ID atom-type volume density 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=:) hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:)
The keywords have these meanings: The keywords have these meanings:
atom-ID = integer ID of atom atom-ID = integer ID of atom
molecule-ID = integer ID of molecule the atom belongs to 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) 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) density = density of atom (mass/distance^3 units)
volume = volume of atom (distance^3 units) volume = volume of atom (distance^3 units)
x,y,z = coordinates of atom 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 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) spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
eradius = electron radius (or fixed-core radius) :ul 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 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). 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 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 bonds), and velocities are not assigned in the data file, and you
care if unique atom IDs appear in dump files, then the atom-IDs can all don't care if unique atom IDs appear in dump files, then the atom-IDs
be set to 0. can all be set to 0.
The molecule ID is a 2nd identifier attached to an atom. Normally, it 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 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 to. It can be 0 if it is an unbonded atom or if you don't care to
keep track of molecule assignments. keep track of molecule assignments.
The diameter specifies the size of a finite size particle, analagous The diameter specifies the size of a finite-size spherical particle.
to the "shape"_shape.html command which sets the size on a per-type It can be set to 0.0, which means that atom is a point particle.
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 density is used in conjunction with the diameter to set the mass The 3 shape values specify the 3 diameters or aspect ratios of a
of a particle as mass = density * volume. If the diameter and volume finite-size ellipsoidal particle, when it is oriented along the 3
are 0.0 meaning a point particle, then the mass is not 0.0 but is set coordinate axes. They can all be set to 0.0, which means that atom is
as mass = density. 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 The values {quatw}, {quati}, {quatj}, and {quatk} set the orientation
of the atom as a quaternion (4-vector). Note that the of the atom as a quaternion (4-vector). Note that the shape
"shape"_shape.html command or "Shapes" section of the data file attributes specify the aspect ratios of an ellipsoidal particle, which
specifies the aspect ratios of an ellipsoidal particle, which is is oriented by default with its x-axis along the simulation box's
oriented by default with its x-axis along the simulation box's x-axis, x-axis, and similarly for y and z. If this body is rotated (via the
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 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 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 (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. 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 LAMMPS normalizes each atom's quaternion in case (a,b,c) was not
unit vector. specified as a unit vector.
For atom_style hybrid, following the 5 initial values (ID,type,x,y,z), 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 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 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: 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 :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: {EndBondTorsion Coeffs} section:
one line per dihedral type :ulb,l one line per dihedral type :ulb,l
@ -550,9 +537,9 @@ example: :l
:ule :ule
This defines the mass of each atom type. This can also be set via the 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 "mass"_mass.html command in the input script. This section cannot be
be used for atom styles that define a mass for individual atoms - used for atom styles that define a mass for individual atoms -
e.g. atom style granular. e.g. "atom_style sphere"_atom_style.html.
:line :line
@ -584,25 +571,6 @@ script.
:line :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: {Velocities} section:
one line per atom 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 dipole: atom-ID vx vy vz wx wy wz
electron: atom-ID vx vy vz evel electron: atom-ID vx vy vz evel
ellipsoid: atom-ID vx vy vz lx ly lz 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: where the keywords have these meanings:
vx,vy,vz = translational velocity of atom vx,vy,vz = translational velocity of atom
lx,ly,lz = angular momentum of aspherical 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 evel = electron radial velocity (0 for fixed-core):ul
The velocity lines can appear in any order. This section can only be 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: <P>A restart file stores the following information about a simulation:
units and atom style, simulation box size and shape and boundary units and atom style, simulation box size and shape and boundary
settings, group definitions, atom type settings such as mass and settings, group definitions, per-type atom settings such as mass,
particle shape, individual atoms and their group assignments and per-atom attributes including their group assignments and molecular
molecular topology attributes, force field styles and coefficients, topology attributes, force field styles and coefficients, and
and <A HREF = "special_bonds.html">special_bonds</A> settings. This means that <A HREF = "special_bonds.html">special_bonds</A> settings. This means that commands
commands for these quantities do not need to be re-specified in the for these quantities do not need to be re-specified in the input
input script that reads the restart file, though you can redefine script that reads the restart file, though you can redefine settings
settings after the restart file is read. after the restart file is read.
</P> </P>
<P>One exception is that some pair styles do not store their info in <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 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: A restart file stores the following information about a simulation:
units and atom style, simulation box size and shape and boundary units and atom style, simulation box size and shape and boundary
settings, group definitions, atom type settings such as mass and settings, group definitions, per-type atom settings such as mass,
particle shape, individual atoms and their group assignments and per-atom attributes including their group assignments and molecular
molecular topology attributes, force field styles and coefficients, topology attributes, force field styles and coefficients, and
and "special_bonds"_special_bonds.html settings. This means that "special_bonds"_special_bonds.html settings. This means that commands
commands for these quantities do not need to be re-specified in the for these quantities do not need to be re-specified in the input
input script that reads the restart file, though you can redefine script that reads the restart file, though you can redefine settings
settings after the restart file is read. after the restart file is read.
One exception is that some pair styles do not store their info in 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 restart files. The doc pages for individual pair styles note if this

143
doc/set.html
View File

@ -15,13 +15,13 @@
</P> </P>
<PRE>set style ID keyword values ... <PRE>set style ID keyword values ...
</PRE> </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>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> <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I>
<PRE> <I>type</I> value = atom type <PRE> <I>type</I> value = atom type
@ -34,16 +34,20 @@
<I>charge</I> value = atomic charge (charge units) <I>charge</I> value = atomic charge (charge units)
<I>dipole</I> values = x y z <I>dipole</I> values = x y z
x,y,z = orientation of dipole moment vector 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 seed = random # seed (positive integer) for dipole moment orientations
Dlen = magnitude of dipole moment (dipole units)
<I>quat</I> values = a b c theta <I>quat</I> values = a b c theta
a,b,c = unit vector to rotate particle around via right-hand rule a,b,c = unit vector to rotate particle around via right-hand rule
theta = rotation angle in degrees theta = rotation angle in degrees
<I>quat/random</I> value = seed <I>quat/random</I> value = seed
seed = random # seed (positive integer) for quaternion orientations seed = random # seed (positive integer) for quaternion orientations
<I>diameter</I> value = particle diameter (distance units) <I>diameter</I> value = diameter of spherical particle (distance units)
<I>density</I> value = particle density (mass/distance^3 units) <I>shape</I> value = Sx Sy Sz
<I>volume</I> value = particle volume (distance^3 units) 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 <I>image</I> nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in 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 <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 solvent type/fraction 2 0.5 12393
set group edge bond 4 set group edge bond 4
set region half charge 0.5 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 set atom 1492 type 3
</PRE> </PRE>
<P><B>Description:</B> <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 <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, be useful for altering pairwise and molecular force interactions,
since force-field coefficients are defined in terms of types. It can 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 be used to change the labeling of atoms by atom type or molecule ID
output in <A HREF = "dump.html">dump</A> files. It can be useful for debugging when they are output in <A HREF = "dump.html">dump</A> files. It can be useful for
purposes; i.e. positioning an atom at a precise location to compute debugging purposes; i.e. positioning an atom at a precise location to
subsequent forces or energy. compute subsequent forces or energy.
</P> </P>
<P>The style <I>atom</I> selects a single atom. The style <I>group</I> selects the <P>The style <I>atom</I> selects one or more atoms in a range of atom IDs.
entire group of atoms. The style <I>region</I> selects all atoms in the The style <I>type</I> selects all the atoms in a range of types. The style
geometric region. The associated ID for each of these styles is <I>mol</I> selects all the atoms in a range of molecule IDs.
either the unique atom ID (typically a number from 1 to N = the number </P>
of atoms in the simulation), the group ID, or the region ID. See the <P>In each of the range cases, a single value can be specified, or a
<A HREF = "group.html">group</A> and <A HREF = "region.html">region</A> commands for details of wildcard asterisk can be used to specify a range of values. This
how to specify a group or region. 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> </P>
<HR> <HR>
@ -110,29 +128,30 @@ being used must support the use of atomic charge.
</P> </P>
<P>Keyword <I>dipole</I> uses the specified x,y,z values as components of a <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 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 selected atoms. The magnitude of the dipole moment is set
set by the <A HREF = "dipole.html">dipole</A> command. by the length of this orientation vector.
</P> </P>
<P>Keyword <I>dipole/random</I> randomizes the orientation of the dipole <P>Keyword <I>dipole/random</I> randomizes the orientation of the dipole
moment vectors of the selected atoms. The magnitude of the dipole moment vectors of the selected atoms and sets the magnitude of each to
moment for each atom is set by the <A HREF = "dipole.html">dipole</A> command. For the specified <I>Dlen</I> value. For 2d systems, the z component of the
2d systems, the z component of the orientation is set to 0.0. Random orientation is set to 0.0. Random numbers are used in such a way that
numbers are used in such a way that the orientation of a particular the orientation of a particular atom is the same, regardless of how
atom is the same, regardless of how many processors are being used. many processors are being used.
</P> </P>
<P>Keyword <I>quat</I> uses the specified values to create a quaternion <P>Keyword <I>quat</I> uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms. (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 Note that particles defined by <A HREF = "atom_style.html">atom_style ellipsoid</A>
ratios of an ellipsoidal particle, which is oriented by default with have 3 shape paraeters whicha are used to specify the aspect ratios of
its x-axis along the simulation box's x-axis, and similarly for y and an ellipsoidal particle, which is oriented by default with its x-axis
z. If this body is rotated (via the right-hand rule) by an angle along the simulation box's x-axis, and similarly for y and z. If this
theta around a unit rotation vector (a,b,c), then the quaternion that body is rotated (via the right-hand rule) by an angle theta around a
represents its new orientation is given by (cos(theta/2), unit rotation vector (a,b,c), then the quaternion that represents its
a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c new orientation is given by (cos(theta/2), a*sin(theta/2),
values are the arguments to the <I>quat</I> keyword. LAMMPS normalizes the b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c values are the
quaternion in case (a,b,c) was not specified as a unit vector. For 2d arguments to the <I>quat</I> keyword. LAMMPS normalizes the quaternion in
systems, the a,b,c values are ignored, since a rotation vector of case (a,b,c) was not specified as a unit vector. For 2d systems, the
(0,0,1) is the only valid choice. a,b,c values are ignored, since a rotation vector of (0,0,1) is the
only valid choice.
</P> </P>
<P>Keyword <I>quat/random</I> randomizes the orientation of the quaternion of <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 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 processors are being used. For 2d systems, only orientations in the
xy plane are generated. xy plane are generated.
</P> </P>
<P>For the <I>dipole</I> and <I>quat</I> keywords, the <A HREF = "atom_style.html">atom style</A> <P>Keyword <I>diameter</I> sets the size of the selected atoms. The particles
being used must support the use of dipoles or quaternions. 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>
<P>Keyword <I>diameter</I> sets the size of all selected particles. If the <P>Keyword <I>shape</I> sets the size and shape of the selected atoms. The
particles have a per-atom mass and density, then it also sets their particles must be aspherical ellipsoids as defined by the <A HREF = "atom_style.html">atom_style
mass. 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>
<P>Keyword <I>density</I> sets the density of all selected particles. If the <P>Keyword <I>mas</I> sets the mass of all selected particles. The
particles have a per-atom mass and diameter, then it also sets their particles must have a per-atom mass attribute, as defined by the
mass. If the particles have a per-atom mass and volume (as defined by <A HREF = "atom_style.html">atom_style</A> command. See the "mass" command for how
PeriDynamics), then it also sets their mass. to set mass values on a per-type basis.
</P> </P>
<P>Keyword <I>volume</I> sets the volume of all selected particles, as defined <P>Keyword <I>density</I> sets the mass of all selected particles. The
by PeriDynamics. 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>
<P>Keyword <I>image</I> sets which image of the simulation box the atom is <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 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 analysis relies on the image flags to unwrap a molecule which
straddles the periodic box. straddles the periodic box.
</P> </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 <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 type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value from 1 to nbondtypes (nangletypes, etc). All 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 set style ID keyword values ... :pre
style = {atom} or {group} or {region} :ulb,l style = {atom} or {type} or {mol} or {group} or {region} :ulb,l
ID = atom ID or group ID or region ID :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 one or more keyword/value pairs may be appended :l
keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{charge} or {dipole} or {dipole/random} or {quat/random} or \ {charge} or {dipole} or {dipole/random} or {quat} or \
{diameter} or {density} or {volume} or {image} or {quat/random} or {diameter} or {shape} or {mass} or \
{density} or {volume} or {image} or
{bond} or {angle} or {dihedral} or {improper} :l {bond} or {angle} or {dihedral} or {improper} :l
{type} value = atom type {type} value = atom type
{type/fraction} values = type fraction seed {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) {charge} value = atomic charge (charge units)
{dipole} values = x y z {dipole} values = x y z
x,y,z = orientation of dipole moment vector 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 seed = random # seed (positive integer) for dipole moment orientations
Dlen = magnitude of dipole moment (dipole units)
{quat} values = a b c theta {quat} values = a b c theta
a,b,c = unit vector to rotate particle around via right-hand rule a,b,c = unit vector to rotate particle around via right-hand rule
theta = rotation angle in degrees theta = rotation angle in degrees
{quat/random} value = seed {quat/random} value = seed
seed = random # seed (positive integer) for quaternion orientations seed = random # seed (positive integer) for quaternion orientations
{diameter} value = particle diameter (distance units) {diameter} value = diameter of spherical particle (distance units)
{density} value = particle density (mass/distance^3 units) {shape} value = Sx Sy Sz
{volume} value = particle volume (distance^3 units) 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 {image} nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in nx,ny,nz = which periodic image of the simulation box the atom is in
{bond} value = bond type for all bonds between selected atoms {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 solvent type/fraction 2 0.5 12393
set group edge bond 4 set group edge bond 4
set region half charge 0.5 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 set atom 1492 type 3 :pre
[Description:] [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 "create_atoms"_create_atoms.html command (e.g. charge = 0.0). It can
be useful for altering pairwise and molecular force interactions, be useful for altering pairwise and molecular force interactions,
since force-field coefficients are defined in terms of types. It can 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 be used to change the labeling of atoms by atom type or molecule ID
output in "dump"_dump.html files. It can be useful for debugging when they are output in "dump"_dump.html files. It can be useful for
purposes; i.e. positioning an atom at a precise location to compute debugging purposes; i.e. positioning an atom at a precise location to
subsequent forces or energy. compute subsequent forces or energy.
The style {atom} selects a single atom. The style {group} selects the The style {atom} selects one or more atoms in a range of atom IDs.
entire group of atoms. The style {region} selects all atoms in the The style {type} selects all the atoms in a range of types. The style
geometric region. The associated ID for each of these styles is {mol} selects all the atoms in a range of molecule IDs.
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 In each of the range cases, a single value can be specified, or a
"group"_group.html and "region"_region.html commands for details of wildcard asterisk can be used to specify a range of values. This
how to specify a group or region. 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 :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 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 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 selected atoms. The magnitude of the dipole moment is set
set by the "dipole"_dipole.html command. by the length of this orientation vector.
Keyword {dipole/random} randomizes the orientation of the dipole Keyword {dipole/random} randomizes the orientation of the dipole
moment vectors of the selected atoms. The magnitude of the dipole moment vectors of the selected atoms and sets the magnitude of each to
moment for each atom is set by the "dipole"_dipole.html command. For the specified {Dlen} value. For 2d systems, the z component of the
2d systems, the z component of the orientation is set to 0.0. Random orientation is set to 0.0. Random numbers are used in such a way that
numbers are used in such a way that the orientation of a particular the orientation of a particular atom is the same, regardless of how
atom is the same, regardless of how many processors are being used. many processors are being used.
Keyword {quat} uses the specified values to create a quaternion Keyword {quat} uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms. (4-vector) that represents the orientation of the selected atoms.
Note that the "shape"_shape.html command is used to specify the aspect Note that particles defined by "atom_style ellipsoid"_atom_style.html
ratios of an ellipsoidal particle, which is oriented by default with have 3 shape paraeters whicha are used to specify the aspect ratios of
its x-axis along the simulation box's x-axis, and similarly for y and an ellipsoidal particle, which is oriented by default with its x-axis
z. If this body is rotated (via the right-hand rule) by an angle along the simulation box's x-axis, and similarly for y and z. If this
theta around a unit rotation vector (a,b,c), then the quaternion that body is rotated (via the right-hand rule) by an angle theta around a
represents its new orientation is given by (cos(theta/2), unit rotation vector (a,b,c), then the quaternion that represents its
a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c new orientation is given by (cos(theta/2), a*sin(theta/2),
values are the arguments to the {quat} keyword. LAMMPS normalizes the b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c values are the
quaternion in case (a,b,c) was not specified as a unit vector. For 2d arguments to the {quat} keyword. LAMMPS normalizes the quaternion in
systems, the a,b,c values are ignored, since a rotation vector of case (a,b,c) was not specified as a unit vector. For 2d systems, the
(0,0,1) is the only valid choice. 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 Keyword {quat/random} randomizes the orientation of the quaternion of
the selected atoms. Random numbers are used in such a way that the 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 processors are being used. For 2d systems, only orientations in the
xy plane are generated. xy plane are generated.
For the {dipole} and {quat} keywords, the "atom style"_atom_style.html Keyword {diameter} sets the size of the selected atoms. The particles
being used must support the use of dipoles or quaternions. 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 Keyword {shape} sets the size and shape of the selected atoms. The
particles have a per-atom mass and density, then it also sets their particles must be aspherical ellipsoids as defined by the "atom_style
mass. 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 Keyword {mas} sets the mass of all selected particles. The
particles have a per-atom mass and diameter, then it also sets their particles must have a per-atom mass attribute, as defined by the
mass. If the particles have a per-atom mass and volume (as defined by "atom_style"_atom_style.html command. See the "mass" command for how
PeriDynamics), then it also sets their mass. to set mass values on a per-type basis.
Keyword {volume} sets the volume of all selected particles, as defined Keyword {density} sets the mass of all selected particles. The
by PeriDynamics. 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 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 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 analysis relies on the image flags to unwrap a molecule which
straddles the periodic box. 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 Keywords {bond}, {angle}, {dihedral}, and {improper}, set the bond
type (angle type, etc) of all bonds (angles, etc) of selected atoms to type (angle type, etc) of all bonds (angles, etc) of selected atoms to
the specified value from 1 to nbondtypes (nangletypes, etc). All the specified value from 1 to nbondtypes (nangletypes, etc). All

104
doc/shape.html
View File

@ -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
doc/shape.txt
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