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sjplimp 2011-10-20 15:01:56 +00:00
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32
doc/atom_style.html
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@ -15,7 +15,7 @@
</P>
<PRE>atom_style style args
</PRE>
<UL><LI>style = <I>angle</I> or <I>atomic</I> or <I>bond</I> or <I>charge</I> or <I>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</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>dipole</I> or <I>electron</I> or <I>ellipsoid</I> or <I>full</I> or <I>line</I> or <I>meso</I> or <I>molecular</I> or <I>peri</I> or <I>sphere</I> or <I>tri</I> or <I>hybrid</I>
</UL>
<PRE> args = none for any style except <I>hybrid</I>
<I>hybrid</I> args = list of one or more sub-styles
@ -61,10 +61,12 @@ quantities.
<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 > 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>line</I> </TD><TD > end points, angular velocity </TD><TD > rigid bodies </TD></TR>
<TR><TD ><I>meso</I> </TD><TD > rho, e, cv </TD><TD > SPH particles </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 > 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>
<TR><TD ><I>tri</I> </TD><TD > corner points, angular momentum </TD><TD > rigid bodies </TD></TR>
<TR><TD ><I>wavepacket</I> </TD><TD > charge, spin, eradius, etag, cs_re, cs_im </TD><TD > AWPMD
</TD></TR></TABLE></DIV>
@ -73,8 +75,8 @@ the <A HREF = "mass.html">mass</A> command, except for the finite-size particle
styles discussed below. They assign mass on a per-atom basis.
</P>
<P>All of the styles define point particles, except the <I>sphere</I>,
<I>ellipsoid</I>, <I>electron</I>, <I>peri</I>, and <I>wavepacket</I> styles, which define
finite-size particles.
<I>ellipsoid</I>, <I>electron</I>, <I>peri</I>, <I>wavepacket</I>, <I>line</I>, and <I>tri</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. If the diameter > 0.0, the particle
@ -104,6 +106,14 @@ cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical <I>etag</I> values.
</P>
<P>For the <I>line</I> style, the particles are idealized line segments and
each stores a per-particle mass and length and orientation (i.e. the
end points of the line segment).
</P>
<P>For the <I>tri</I> style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
</P>
<HR>
<P>Typically, simulations require only a single (non-hybrid) atom style.
@ -130,14 +140,14 @@ section</A>.
</P>
<P>The <I>angle</I>, <I>bond</I>, <I>full</I>, and <I>molecular</I> styles are part of the
MOLECULAR package. The <I>dipole</I> style is part of the "dipole"
package. The <I>ellipsoid</I> style is part of the "asphere" package. The
<I>peri</I> style is part of the PERI package for Peridynamics. The
<I>electron</I> style is part of the USER-EFF package for <A HREF = "pair_eff.html">electronic force
fields</A>. The <I>meso</I> style is part of the USER-SPH
package for smoothed particle hydrodyanmics (SPH). See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF
guide</A> to using SPH in LAMMPS. The
<I>wavepacket</I> style is part of the USER-AWPMD package for the
<A HREF = "pair_awpmd.html">antisymmetrized wave packet MD method</A>. They are
package. The <I>ellipsoid</I>, <I>line</I>, and <I>tri</I> styles are part of the
"asphere" package. The <I>peri</I> style is part of the PERI package for
Peridynamics. The <I>electron</I> style is part of the USER-EFF package
for <A HREF = "pair_eff.html">electronic force fields</A>. The <I>meso</I> style is part
of the USER-SPH package for smoothed particle hydrodyanmics (SPH).
See <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">this PDF guide</A> to using SPH in
LAMMPS. The <I>wavepacket</I> style is part of the USER-AWPMD package for
the <A HREF = "pair_awpmd.html">antisymmetrized wave packet MD method</A>. They are
only enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>

34
doc/atom_style.txt
View File

@ -13,8 +13,8 @@ atom_style command :h3
atom_style style args :pre
style = {angle} or {atomic} or {bond} or {charge} or {dipole} or \
{electron} or {ellipsoid} or {full} or {meso} or {molecular} or \
{peri} or {sphere} or {hybrid} :ul
{electron} or {ellipsoid} or {full} or {line} or {meso} or \
{molecular} or {peri} or {sphere} or {tri} or {hybrid} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more sub-styles :pre
@ -58,10 +58,12 @@ quantities.
{electron} | charge and spin and eradius | electronic force field |
{ellipsoid} | shape, quaternion for particle orientation, angular momentum | extended aspherical particles |
{full} | molecular + charge | bio-molecules |
{line} | end points, angular velocity | rigid bodies |
{meso} | rho, e, cv | SPH particles |
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
{peri} | mass, volume | mesocopic Peridynamic models |
{sphere} | diameter, mass, angular velocity | granular models |
{tri} | corner points, angular momentum | rigid bodies |
{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
All of the styles assign mass to particles on a per-type basis, using
@ -69,8 +71,8 @@ the "mass"_mass.html command, except for the finite-size particle
styles discussed below. They assign mass on a per-atom basis.
All of the styles define point particles, except the {sphere},
{ellipsoid}, {electron}, {peri}, and {wavepacket} styles, which define
finite-size particles.
{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, and {tri}
styles, which define finite-size particles.
For the {sphere} style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
@ -100,6 +102,14 @@ cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical {etag} values.
For the {line} style, the particles are idealized line segments and
each stores a per-particle mass and length and orientation (i.e. the
end points of the line segment).
For the {tri} style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
:line
Typically, simulations require only a single (non-hybrid) atom style.
@ -126,14 +136,14 @@ This command cannot be used after the simulation box is defined by a
The {angle}, {bond}, {full}, and {molecular} styles are part of the
MOLECULAR package. The {dipole} style is part of the "dipole"
package. The {ellipsoid} style is part of the "asphere" package. The
{peri} style is part of the PERI package for Peridynamics. The
{electron} style is part of the USER-EFF package for "electronic force
fields"_pair_eff.html. The {meso} style is part of the USER-SPH
package for smoothed particle hydrodyanmics (SPH). See "this PDF
guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS. The
{wavepacket} style is part of the USER-AWPMD package for the
"antisymmetrized wave packet MD method"_pair_awpmd.html. They are
package. The {ellipsoid}, {line}, and {tri} styles are part of the
"asphere" package. The {peri} style is part of the PERI package for
Peridynamics. The {electron} style is part of the USER-EFF package
for "electronic force fields"_pair_eff.html. The {meso} style is part
of the USER-SPH package for smoothed particle hydrodyanmics (SPH).
See "this PDF guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in
LAMMPS. The {wavepacket} style is part of the USER-AWPMD package for
the "antisymmetrized wave packet MD method"_pair_awpmd.html. They are
only enabled if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.

32
doc/compute_erotate_asphere.html
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@ -25,15 +25,19 @@
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the rotational kinetic energy of
a group of aspherical particles.
a group of aspherical particles. The aspherical particles can be
ellipsoids, or line segments, or triangles. See the
<A HREF = "atom_style.html">atom_style</A> and <A HREF = "read_data.html">read_data</A> commands
for descriptions of these options.
</P>
<P>The rotational kinetic energy is computed as 1/2 I w^2, where I is the
inertia tensor for the aspherical particle and w is its angular
velocity, which is computed from its angular momentum.
<P>For all 3 types of particles, the rotational kinetic energy is
computed as 1/2 I w^2, where I is the inertia tensor for the
aspherical particle and w is its angular velocity, which is computed
from its angular momentum if needed.
</P>
<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, particles are treated
as ellipsoids, not ellipses, meaning their moments of inertia will be
the same as in 3d.
<P>IMPORTANT NOTE: For <A HREF = "dimension.html">2d models</A>, ellipsoidal particles
are treated as ellipsoids, not ellipses, meaning their moments of
inertia will be the same as in 3d.
</P>
<P><B>Output info:</B>
</P>
@ -47,9 +51,17 @@ scalar value will be in energy <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute requires that atoms store a shape and quaternion
orientation and angular momentum as defined by the <A HREF = "atom_style.html">atom_style
ellipsoid</A> command.
<P>This compute requires that ellipsoidal particles atoms store a shape
and quaternion orientation and angular momentum as defined by the
<A HREF = "atom_style.html">atom_style ellipsoid</A> command.
</P>
<P>This compute requires that line segment particles atoms store a length
and orientation and angular velocity as defined by the <A HREF = "atom_style.html">atom_style
line</A> command.
</P>
<P>This compute requires that triangular particles atoms store a size and
shape and quaternion orientation and angular momentum as defined by
the <A HREF = "atom_style.html">atom_style tri</A> command.
</P>
<P>All particles in the group must be finite-size. They cannot be point
particles.

32
doc/compute_erotate_asphere.txt
View File

@ -22,15 +22,19 @@ compute 1 all erotate/asphere :pre
[Description:]
Define a computation that calculates the rotational kinetic energy of
a group of aspherical particles.
a group of aspherical particles. The aspherical particles can be
ellipsoids, or line segments, or triangles. See the
"atom_style"_atom_style.html and "read_data"_read_data.html commands
for descriptions of these options.
The rotational kinetic energy is computed as 1/2 I w^2, where I is the
inertia tensor for the aspherical particle and w is its angular
velocity, which is computed from its angular momentum.
For all 3 types of particles, the rotational kinetic energy is
computed as 1/2 I w^2, where I is the inertia tensor for the
aspherical particle and w is its angular velocity, which is computed
from its angular momentum if needed.
IMPORTANT NOTE: For "2d models"_dimension.html, particles are treated
as ellipsoids, not ellipses, meaning their moments of inertia will be
the same as in 3d.
IMPORTANT NOTE: For "2d models"_dimension.html, ellipsoidal particles
are treated as ellipsoids, not ellipses, meaning their moments of
inertia will be the same as in 3d.
[Output info:]
@ -44,9 +48,17 @@ scalar value will be in energy "units"_units.html.
[Restrictions:]
This compute requires that atoms store a shape and quaternion
orientation and angular momentum as defined by the "atom_style
ellipsoid"_atom_style.html command.
This compute requires that ellipsoidal particles atoms store a shape
and quaternion orientation and angular momentum as defined by the
"atom_style ellipsoid"_atom_style.html command.
This compute requires that line segment particles atoms store a length
and orientation and angular velocity as defined by the "atom_style
line"_atom_style.html command.
This compute requires that triangular particles atoms store a size and
shape and quaternion orientation and angular momentum as defined by
the "atom_style tri"_atom_style.html command.
All particles in the group must be finite-size. They cannot be point
particles.

19
doc/compute_property_atom.html
View File

@ -29,7 +29,11 @@
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
spin, eradius, ervel, erforce
spin, eradius, ervel, erforce
end1x, end1y, end1z, end2x, end2y, end2z,
corner1x, corner1y, corner1z,
corner2x, corner2y, corner2z,
corner3x, corner3y, corner3z
</PRE>
<PRE> id = atom ID
mol = molecule ID
@ -47,13 +51,15 @@
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
spin = electron spin
eradius = electron radius
ervel = electron radial velocity
erforce = electron radial force
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
end12x, end12y, end12z = end points of line segment
coner123x, corner123y, corner123z = corner points of triangle
</PRE>
</UL>
@ -94,6 +100,13 @@ and <I>quatk</I> are also defined for ellipsoidal particles and store the
See the <A HREF = "set.html">set</A> command for an explanation of the quaternion
vector.
</P>
<P><I>End1x</I>, <I>end1y</I>, <I>end1z</I>, <I>end2x</I>, <I>end2y</I>, <I>end2z</I>, are defined for
line segment particles and define the end points of each line segment.
</P>
<P><I>Corner1x</I>, <I>corner1y</I>, <I>corner1z</I>, <I>corner2x</I>, <I>corner2y</I>,
<I>corner2z</I>, <I>corner3x</I>, <I>corner3y</I>, <I>corner3z</I>, are defined for
triangular particles and define the corner points of each triangle.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector or per-atom array depending

20
doc/compute_property_atom.txt
View File

@ -23,8 +23,11 @@ input = one or more atom attributes :l
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
spin, eradius, ervel, erforce :pre
spin, eradius, ervel, erforce
end1x, end1y, end1z, end2x, end2y, end2z,
corner1x, corner1y, corner1z,
corner2x, corner2y, corner2z,
corner3x, corner3y, corner3z :pre
id = atom ID
mol = molecule ID
type = atom type
@ -41,13 +44,15 @@ input = one or more atom attributes :l
radius,diameter = radius,diameter of spherical particle
omegax,omegay,omegaz = angular velocity of extended particle
angmomx,angmomy,angmomz = angular momentum of extended particle
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles
tqx,tqy,tqz = torque on extended particles
spin = electron spin
eradius = electron radius
ervel = electron radial velocity
erforce = electron radial force
shapex,shapey,shapez = 3 diameters of aspherical particle
quatw,quati,quatj,quatk = quaternion components for aspherical particles :pre
end12x, end12y, end12z = end points of line segment
coner123x, corner123y, corner123z = corner points of triangle :pre
:ule
[Examples:]
@ -87,6 +92,13 @@ and {quatk} are also defined for ellipsoidal particles and store the
See the "set"_set.html command for an explanation of the quaternion
vector.
{End1x}, {end1y}, {end1z}, {end2x}, {end2y}, {end2z}, are defined for
line segment particles and define the end points of each line segment.
{Corner1x}, {corner1y}, {corner1z}, {corner2x}, {corner2y},
{corner2z}, {corner3x}, {corner3y}, {corner3z}, are defined for
triangular particles and define the corner points of each triangle.
[Output info:]
This compute calculates a per-atom vector or per-atom array depending

3
doc/fix.html
View File

@ -184,6 +184,7 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_gcmc.html">gcmc</A> - grand canonical insertions/deletions
<LI><A HREF = "fix_heat.html">heat</A> - add/subtract momentum-conserving heat
<LI><A HREF = "fix_indent.html">indent</A> - impose force due to an indenter
<LI><A HREF = "fix_integrateU.html">integrateU</A> - Stokesian Dynamics evolution
<LI><A HREF = "fix_langevin.html">langevin</A> - Langevin temperature control
<LI><A HREF = "fix_lineforce.html">lineforce</A> - constrain atoms to move in a line
<LI><A HREF = "fix_momentum.html">momentum</A> - zero the linear and/or angular momentum of a group of atoms
@ -200,8 +201,10 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_nve.html">nve</A> - constant NVE time integration
<LI><A HREF = "fix_nve_asphere.html">nve/asphere</A> - NVT for aspherical particles
<LI><A HREF = "fix_nve_limit.html">nve/limit</A> - NVE with limited step length
<LI><A HREF = "fix_nve_line.html">nve/line</A> - NVE for line segments
<LI><A HREF = "fix_nve_noforce.html">nve/noforce</A> - NVE without forces (v only)
<LI><A HREF = "fix_nve_sphere.html">nve/sphere</A> - NVT for spherical particles
<LI><A HREF = "fix_nve_tri.html">nve/tri</A> - NVE for triangles
<LI><A HREF = "fix_nh.html">nvt</A> - constant NVT time integration via Nose/Hoover
<LI><A HREF = "fix_nvt_asphere.html">nvt/asphere</A> - NVT for aspherical particles
<LI><A HREF = "fix_nvt_sllod.html">nvt/sllod</A> - NVT for NEMD with SLLOD equations

3
doc/fix.txt
View File

@ -179,6 +179,7 @@ list of fix styles available in LAMMPS:
"gcmc"_fix_gcmc.html - grand canonical insertions/deletions
"heat"_fix_heat.html - add/subtract momentum-conserving heat
"indent"_fix_indent.html - impose force due to an indenter
"integrateU"_fix_integrateU.html - Stokesian Dynamics evolution
"langevin"_fix_langevin.html - Langevin temperature control
"lineforce"_fix_lineforce.html - constrain atoms to move in a line
"momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
@ -195,8 +196,10 @@ list of fix styles available in LAMMPS:
"nve"_fix_nve.html - constant NVE time integration
"nve/asphere"_fix_nve_asphere.html - NVT for aspherical particles
"nve/limit"_fix_nve_limit.html - NVE with limited step length
"nve/line"_fix_nve_line.html - NVE for line segments
"nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
"nve/sphere"_fix_nve_sphere.html - NVT for spherical particles
"nve/tri"_fix_nve_tri.html - NVE for triangles
"nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover
"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
"nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations

29
doc/fix_rigid.html
View File

@ -78,12 +78,13 @@ portions of a large biomolecule such as a protein.
<P>Example of small rigid bodies are patchy nanoparticles, such as those
modeled in <A HREF = "#Zhang">this paper</A> by Sharon Glotzer's group, clumps of
granular particles, lipid molecules consiting of one or more point
dipoles connected to other spheroids or ellipsoids, and coarse-grain
models of nano or colloidal particles consisting of a small number of
constituent particles. Note that the <A HREF = "fix_shake.html">fix shake</A>
command can also be used to rigidify small molecules of 2, 3, or 4
atoms, e.g. water molecules. That fix treats the constituent atoms as
point masses.
dipoles connected to other spheroids or ellipsoids, irregular
particles built from line segments (2d) or triangles (3d), and
coarse-grain models of nano or colloidal particles consisting of a
small number of constituent particles. Note that the <A HREF = "fix_shake.html">fix
shake</A> command can also be used to rigidify small
molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats
the constituent atoms as point masses.
</P>
<P>These fixes also update the positions and velocities of the atoms in
each rigid body via time integration. The <I>rigid</I> and <I>rigid/nve</I>
@ -118,14 +119,14 @@ setforce</A> command), and integrating them as usual
<HR>
<P>The constituent particles within a rigid body can be point particles
(the default in LAMMPS) or finite-size particles, such as spheres and
ellipsoids. See the <A HREF = "atom_style.html">atom_style sphere and ellipsoid</A>
commands for more details on these kinds of particles. Finite-size
particles contribute differently to the moment of inertia of a rigid
body than do point particles. Finite-size particles can also
experience torque (e.g. due to <A HREF = "pair_gran.html">frictional granular
interactions</A>) and have an orientation. These
contributions are accounted for by these fixes.
(the default in LAMMPS) or finite-size particles, such as spheres or
ellipsoids or line segments or triangles. See the <A HREF = "atom_style.html">atom_style sphere
and ellipsoid and line and tri</A> commands for more
details on these kinds of particles. Finite-size particles contribute
differently to the moment of inertia of a rigid body than do point
particles. Finite-size particles can also experience torque (e.g. due
to <A HREF = "pair_gran.html">frictional granular interactions</A>) and have an
orientation. These contributions are accounted for by these fixes.
</P>
<P>Forces between particles within a body do not contribute to the
external force or torque on the body. Thus for computational

29
doc/fix_rigid.txt
View File

@ -67,12 +67,13 @@ portions of a large biomolecule such as a protein.
Example of small rigid bodies are patchy nanoparticles, such as those
modeled in "this paper"_#Zhang by Sharon Glotzer's group, clumps of
granular particles, lipid molecules consiting of one or more point
dipoles connected to other spheroids or ellipsoids, and coarse-grain
models of nano or colloidal particles consisting of a small number of
constituent particles. Note that the "fix shake"_fix_shake.html
command can also be used to rigidify small molecules of 2, 3, or 4
atoms, e.g. water molecules. That fix treats the constituent atoms as
point masses.
dipoles connected to other spheroids or ellipsoids, irregular
particles built from line segments (2d) or triangles (3d), and
coarse-grain models of nano or colloidal particles consisting of a
small number of constituent particles. Note that the "fix
shake"_fix_shake.html command can also be used to rigidify small
molecules of 2, 3, or 4 atoms, e.g. water molecules. That fix treats
the constituent atoms as point masses.
These fixes also update the positions and velocities of the atoms in
each rigid body via time integration. The {rigid} and {rigid/nve}
@ -107,14 +108,14 @@ setforce"_fix_setforce.html command), and integrating them as usual
:line
The constituent particles within a rigid body can be point particles
(the default in LAMMPS) or finite-size particles, such as spheres and
ellipsoids. See the "atom_style sphere and ellipsoid"_atom_style.html
commands for more details on these kinds of particles. Finite-size
particles contribute differently to the moment of inertia of a rigid
body than do point particles. Finite-size particles can also
experience torque (e.g. due to "frictional granular
interactions"_pair_gran.html) and have an orientation. These
contributions are accounted for by these fixes.
(the default in LAMMPS) or finite-size particles, such as spheres or
ellipsoids or line segments or triangles. See the "atom_style sphere
and ellipsoid and line and tri"_atom_style.html commands for more
details on these kinds of particles. Finite-size particles contribute
differently to the moment of inertia of a rigid body than do point
particles. Finite-size particles can also experience torque (e.g. due
to "frictional granular interactions"_pair_gran.html) and have an
orientation. These contributions are accounted for by these fixes.
Forces between particles within a body do not contribute to the
external force or torque on the body. Thus for computational

44
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@ -38,10 +38,7 @@
<I>cubic</I> values = style tolerance
style = <I>error</I> or <I>warn</I>
tolerance = fractional difference allowed (0 <= tol <= 1)
<I>shift</I> values = style seed
style = <I>no</I> or <I>yes</I> or <I>possible</I>
seed = random # seed (positive integer)
<I>stream</I> value = <I>yes</I> or <I>no</I> = whether or not streaming velocity is added for shear deformation
<I>tstat</I> value = <I>yes</I> or <I>no</I> = thermostat SRD particles or not
</PRE>
</UL>
@ -58,13 +55,14 @@ particles that serve as a background solvent when interacting with big
in <A HREF = "#Hecht">(Hecht)</A>. The key idea behind using SRD particles as a
cheap coarse-grained solvent is that SRD particles do not interact
with each other, but only with the solute particles, which in LAMMPS
can be spheroids, ellipsoids, or rigid bodies containing multiples
spherioids and ellipsoids. The collision and rotation properties of
the model imbue the SRD particles with fluid-like properties,
including an effective viscosity. Thus simulations with large solute
particles can be run more quickly, to measure solute propoerties like
diffusivity and viscosity in a background fluid. The usual LAMMPS
fixes for such simulations, such as <A HREF = "fix_deform.html">fix deform</A>, <A HREF = "fix_viscosity.html">fix
can be spheroids, ellipsoids, or line segments, or triangles, or rigid
bodies containing multiple spherioids or ellipsoids or line segments
or triangles. The collision and rotation properties of the model
imbue the SRD particles with fluid-like properties, including an
effective viscosity. Thus simulations with large solute particles can
be run more quickly, to measure solute propoerties like diffusivity
and viscosity in a background fluid. The usual LAMMPS fixes for such
simulations, such as <A HREF = "fix_deform.html">fix deform</A>, <A HREF = "fix_viscosity.html">fix
viscosity</A>, and <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>,
can be used in conjunction with the SRD model.
</P>
@ -272,15 +270,19 @@ must still be specified.
<P>Note that shifting of SRD coordinates requires extra communication,
hence it should not normally be enabled unless required.
</P>
<P>The <I>stream</I> keyword should be used when SRD particles are used with
the <A HREF = "fix_deform.html">fix deform</A> command to perform a simulation
undergoing shear, e.g. to measure a viscosity. If the <I>stream</I> style
is set to <I>yes</I>, then the mean velocity of each bin of SRD particles
is set to the streaming velocity of the deforming box, each time SRD
velocities are reset, every N timesteps. If the <I>stream</I> style is set
to <I>no</I>, then the mean velocity is unchanged, which may mean that it
takes a long time for the SRD fluid to come to equilibrium with a
velocity profile that matches the simulation box deformation.
<P>The <I>tstat</I> keyword will thermostat the SRD particles to the specified
<I>Tsrd</I>. This is done every N timesteps, during the velocity rotation
operation, by rescaling the thermal velocity of particles in each SRD
bin to the desired temperature. If there is a streaming velocity
associated with the system, e.g. due to use of the <A HREF = "fix_deform.html">fix
deform</A> command to perform a simulation undergoing
shear, then that is also accounted for. The mean velocity of each bin
of SRD particles is set to the position-dependent streaming velocity,
based on the coordinates of the center of the SRD bin. Note that for
streaming simulations, if no thermostatting is performed (the
default), then it may take a long time for the SRD fluid to come to
equilibrium with a velocity profile that matches the simulation box
deformation.
</P>
<HR>
@ -358,7 +360,7 @@ for more info on packages.
</P>
<P>The option defaults are lamda inferred from Tsrd, collision = noslip,
overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0,
search = hgrid, cubic = error 0.01, shift = no, stream = yes.
search = hgrid, cubic = error 0.01, shift = no, tstat = no.
</P>
<HR>

44
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@ -33,10 +33,7 @@ keyword = {lamda} or {collision} or {overlap} or {inside} or {exact} or {radius}
{cubic} values = style tolerance
style = {error} or {warn}
tolerance = fractional difference allowed (0 <= tol <= 1)
{shift} values = style seed
style = {no} or {yes} or {possible}
seed = random # seed (positive integer)
{stream} value = {yes} or {no} = whether or not streaming velocity is added for shear deformation :pre
{tstat} value = {yes} or {no} = thermostat SRD particles or not :pre
:ule
[Examples:]
@ -52,13 +49,14 @@ particles that serve as a background solvent when interacting with big
in "(Hecht)"_#Hecht. The key idea behind using SRD particles as a
cheap coarse-grained solvent is that SRD particles do not interact
with each other, but only with the solute particles, which in LAMMPS
can be spheroids, ellipsoids, or rigid bodies containing multiples
spherioids and ellipsoids. The collision and rotation properties of
the model imbue the SRD particles with fluid-like properties,
including an effective viscosity. Thus simulations with large solute
particles can be run more quickly, to measure solute propoerties like
diffusivity and viscosity in a background fluid. The usual LAMMPS
fixes for such simulations, such as "fix deform"_fix_deform.html, "fix
can be spheroids, ellipsoids, or line segments, or triangles, or rigid
bodies containing multiple spherioids or ellipsoids or line segments
or triangles. The collision and rotation properties of the model
imbue the SRD particles with fluid-like properties, including an
effective viscosity. Thus simulations with large solute particles can
be run more quickly, to measure solute propoerties like diffusivity
and viscosity in a background fluid. The usual LAMMPS fixes for such
simulations, such as "fix deform"_fix_deform.html, "fix
viscosity"_fix_viscosity.html, and "fix nvt/sllod"_fix_nvt_sllod.html,
can be used in conjunction with the SRD model.
@ -266,15 +264,19 @@ must still be specified.
Note that shifting of SRD coordinates requires extra communication,
hence it should not normally be enabled unless required.
The {stream} keyword should be used when SRD particles are used with
the "fix deform"_fix_deform.html command to perform a simulation
undergoing shear, e.g. to measure a viscosity. If the {stream} style
is set to {yes}, then the mean velocity of each bin of SRD particles
is set to the streaming velocity of the deforming box, each time SRD
velocities are reset, every N timesteps. If the {stream} style is set
to {no}, then the mean velocity is unchanged, which may mean that it
takes a long time for the SRD fluid to come to equilibrium with a
velocity profile that matches the simulation box deformation.
The {tstat} keyword will thermostat the SRD particles to the specified
{Tsrd}. This is done every N timesteps, during the velocity rotation
operation, by rescaling the thermal velocity of particles in each SRD
bin to the desired temperature. If there is a streaming velocity
associated with the system, e.g. due to use of the "fix
deform"_fix_deform.html command to perform a simulation undergoing
shear, then that is also accounted for. The mean velocity of each bin
of SRD particles is set to the position-dependent streaming velocity,
based on the coordinates of the center of the SRD bin. Note that for
streaming simulations, if no thermostatting is performed (the
default), then it may take a long time for the SRD fluid to come to
equilibrium with a velocity profile that matches the simulation box
deformation.
:line
@ -352,7 +354,7 @@ for more info on packages.
The option defaults are lamda inferred from Tsrd, collision = noslip,
overlap = no, inside = error, exact = yes, radius = 1.0, bounce = 0,
search = hgrid, cubic = error 0.01, shift = no, stream = yes.
search = hgrid, cubic = error 0.01, shift = no, tstat = no.
:line

99
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View File

@ -80,6 +80,8 @@ is different than the default.
<LI><I>improper types</I> = # of improper types in system
<LI><I>extra bond per atom</I> = leave space for this many new bonds per atom
<LI><I>ellipsoids</I> = # of ellipsoids in system
<LI><I>lines</I> = # of line segments in system
<LI><I>triangles</I> = # of triangles in system
<LI><I>xlo xhi</I> = simulation box boundaries in x dimension
<LI><I>ylo yhi</I> = simulation box boundaries in y dimension
<LI><I>zlo zhi</I> = simulation box boundaries in z dimension
@ -156,16 +158,19 @@ added to the system when a simulation runs, e.g. by using the <A HREF = "fix_bon
bond/create</A> command. This will pre-allocate
space in LAMMPS data structures for storing the new bonds.
</P>
<P>The "ellipsoids<A HREF = "atom_style.html"> setting is only used with atom_style
ellipsoid</A> and specifies how many of the atoms are
finite-size ellipsoids; the remainder are point particles. See the
discussion of ellipsoidflag and the <I>Ellipsoids</I> section below.
<P>The "ellipsoids" and "lines" and "triangles" settings are only used
with <A HREF = "atom_style.html">atom_style ellipsoid or line or tri</A> and
specifies how many of the atoms are finite-size ellipsoids or lines or
triangles; the remainder are point particles. See the discussion of
ellipsoidflag and the <I>Ellipsoids</I> section below. See the discussion
of lineflag and the <I>Lines</I> section below. See the discussion of
triangleflag and the <I>Triangles</I> section below.
</P>
<HR>
<P>These are the section keywords for the body of the file.
</P>
<UL><LI><I>Atoms, Velocities, Ellipsoids, Masses</I> = atom-property sections
<UL><LI><I>Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles</I> = atom-property sections
<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
<LI><I>Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I> = force field sections
<LI><I>BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs</I> = class 2 force field sections
@ -290,10 +295,12 @@ of analysis.
<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 ellipsoidflag density x y z</TD></TR>
<TR><TD >full</TD><TD > atom-ID molecule-ID atom-type q x y z</TD></TR>
<TR><TD >line</TD><TD > atom-ID molecule-ID atom-type lineflag density x y z</TD></TR>
<TR><TD >meso</TD><TD > atom-ID atom-type rho e cv x y z</TD></TR>
<TR><TD >molecular</TD><TD > atom-ID molecule-ID atom-type x y z</TD></TR>
<TR><TD >peri</TD><TD > atom-ID atom-type volume density x y z</TD></TR>
<TR><TD >sphere</TD><TD > atom-ID atom-type diameter density x y z</TD></TR>
<TR><TD >tri</TD><TD > atom-ID molecule-ID atom-type triangleflag density x y z</TD></TR>
<TR><TD >wavepacket</TD><TD > atom-ID atom-type charge spin eradius etag cs_re cs_im x y z</TD></TR>
<TR><TD >hybrid</TD><TD > atom-ID atom-type x y z sub-style1 sub-style2 ...
</TD></TR></TABLE></DIV>
@ -306,7 +313,9 @@ of analysis.
<LI>q = charge on atom (charge units)
<LI>diameter = diameter of spherical atom (distance units)
<LI>ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
<LI>density = density of atom (mass/distance^3 units)
<LI>lineflag = 1 for line segment particles, 0 for point particles
<LI>triangleflag = 1 for triangular particles, 0 for point particles
<LI>density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
<LI>volume = volume of atom (distance^3 units)
<LI>x,y,z = coordinates of atom
<LI>mux,muy,muz = components of dipole moment of atom (dipole units)
@ -342,9 +351,13 @@ keep track of molecule assignments.
<P>The diameter specifies the size of a finite-size spherical particle.
It can be set to 0.0, which means that atom is a point particle.
</P>
<P>The ellipsoidflag determines whether the particle is a finite-size
ellipsoid of finite size, or a point particle. Additional attributes
must be defined for each ellipsoid in the <I>Ellipsoids</I> section.
<P>The ellipsoidflag, lineflag, and triangleflag determine whether the
particle is a finite-size ellipsoid or line or triangle of finite
size, or a point particle. Additional attributes must be defined for
each ellipsoid in the <I>Ellipsoids</I> section. Additional attributes
must be defined for each line in the <I>Lines</I> section. Additional
attributes must be defined for each triangle in the <I>Triangles</I>
section.
</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
@ -352,8 +365,10 @@ 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.
density * volume. In this context, volume can be a 3d quantity (for
spheres or ellipsoids), a 2d quantity (for triangles), or a 1d
quantity (for line segments). If the volume is 0.0, meaning a point
particle, then the density value is used as the mass.
</P>
<P>For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
specific values for each sub-style must be listed. The order of the
@ -627,6 +642,37 @@ values in this section must be integers (1, not 1.0).
</P>
<HR>
<P><I>Lines</I> section:
</P>
<UL><LI>one line per line segment
<LI>line syntax: atom-ID x1 y1 x2 y2
<LI> atom-ID = ID of atom which is a line segment
x1,y1 = 1st end point
x2,y2 = 2nd end point
example:
<PRE> 12 1.0 0.0 2.0 0.0
</PRE>
</UL>
<P>The <I>Lines</I> section must appear if <A HREF = "atom_style.html">atom_style line</A>
is used and any atoms are listed in the <I>Atoms</I> section with a
lineflag = 1. The number of lines should be specified in the header
section via the "lines" keyword.
</P>
<P>The 2 end points are the end points of the line segment. The ordering
of the 2 points should be such that using a right-hand rule to cross
the line segment with a unit vector in the +z direction, gives an
"outward" normal vector perpendicular to the line segment.
I.e. normal = (c2-c1) x (0,0,1). This orientation may be important
for defining some interactions.
</P>
<P>The <I>Lines</I> section must appear after the <I>Atoms</I> section.
</P>
<HR>
<P><I>Masses</I> section:
</P>
<UL><LI>one line per atom type
@ -685,6 +731,37 @@ script.
</P>
<HR>
<P><I>Triangles</I> section:
</P>
<UL><LI>one line per triangle
<LI>line syntax: atom-ID x1 y1 x2 y2
<LI> atom-ID = ID of atom which is a line segment
x1,y1,z1 = 1st corner point
x2,y2,z2 = 2nd corner point
x3,y3,z3 = 3rd corner point
example:
<PRE> 12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0
</PRE>
</UL>
<P>The <I>Triangles</I> section must appear if <A HREF = "atom_style.html">atom_style
tri</A> is used and any atoms are listed in the <I>Atoms</I>
section with a triangleflag = 1. The number of lines should be
specified in the header section via the "triangles" keyword.
</P>
<P>The 3 corner points are the corner points of the triangle. The
ordering of the 3 points should be such that using a right-hand rule
to go from point1 to point2 to point3 gives an "outward" normal vector
to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). This
orientation may be important for defining some interactions.
</P>
<P>The <I>Triangles</I> section must appear after the <I>Atoms</I> section.
</P>
<HR>
<P><I>Velocities</I> section:
</P>
<UL><LI>one line per atom

91
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@ -77,6 +77,8 @@ is different than the default.
{improper types} = # of improper types in system
{extra bond per atom} = leave space for this many new bonds per atom
{ellipsoids} = # of ellipsoids in system
{lines} = # of line segments in system
{triangles} = # of triangles in system
{xlo xhi} = simulation box boundaries in x dimension
{ylo yhi} = simulation box boundaries in y dimension
{zlo zhi} = simulation box boundaries in z dimension
@ -153,16 +155,19 @@ added to the system when a simulation runs, e.g. by using the "fix
bond/create"_fix_bond_create.html command. This will pre-allocate
space in LAMMPS data structures for storing the new bonds.
The "ellipsoids" setting is only used with atom_style
ellipsoid"_atom_style.html and specifies how many of the atoms are
finite-size ellipsoids; the remainder are point particles. See the
discussion of ellipsoidflag and the {Ellipsoids} section below.
The "ellipsoids" and "lines" and "triangles" settings are only used
with "atom_style ellipsoid or line or tri"_atom_style.html and
specifies how many of the atoms are finite-size ellipsoids or lines or
triangles; the remainder are point particles. See the discussion of
ellipsoidflag and the {Ellipsoids} section below. See the discussion
of lineflag and the {Lines} section below. See the discussion of
triangleflag and the {Triangles} section below.
:line
These are the section keywords for the body of the file.
{Atoms, Velocities, Ellipsoids, Masses} = atom-property sections
{Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles} = atom-property sections
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
{Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \
Improper Coeffs} = force field sections
@ -270,10 +275,12 @@ dipole: atom-ID atom-type q x y z mux muy muz
electron: atom-ID atom-type q spin eradius x y z
ellipsoid: atom-ID atom-type ellipsoidflag density x y z
full: atom-ID molecule-ID atom-type q x y z
line: atom-ID molecule-ID atom-type lineflag density x y z
meso: atom-ID atom-type rho e cv x y z
molecular: atom-ID molecule-ID atom-type x y z
peri: atom-ID atom-type volume density x y z
sphere: atom-ID atom-type diameter density x y z
tri: atom-ID molecule-ID atom-type triangleflag density x y z
wavepacket: atom-ID atom-type charge spin eradius etag cs_re cs_im x y z
hybrid: atom-ID atom-type x y z sub-style1 sub-style2 ... :tb(s=:)
@ -285,7 +292,9 @@ atom-type = type of atom (1-Ntype)
q = charge on atom (charge units)
diameter = diameter of spherical atom (distance units)
ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
density = density of atom (mass/distance^3 units)
lineflag = 1 for line segment particles, 0 for point particles
triangleflag = 1 for triangular particles, 0 for point particles
density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
volume = volume of atom (distance^3 units)
x,y,z = coordinates of atom
mux,muy,muz = components of dipole moment of atom (dipole units)
@ -321,9 +330,13 @@ keep track of molecule assignments.
The diameter specifies the size of a finite-size spherical particle.
It can be set to 0.0, which means that atom is a point particle.
The ellipsoidflag determines whether the particle is a finite-size
ellipsoid of finite size, or a point particle. Additional attributes
must be defined for each ellipsoid in the {Ellipsoids} section.
The ellipsoidflag, lineflag, and triangleflag determine whether the
particle is a finite-size ellipsoid or line or triangle of finite
size, or a point particle. Additional attributes must be defined for
each ellipsoid in the {Ellipsoids} section. Additional attributes
must be defined for each line in the {Lines} section. Additional
attributes must be defined for each triangle in the {Triangles}
section.
Some pair styles and fixes and computes that operate on finite-size
particles allow for a mixture of finite-size and point particles. See
@ -331,8 +344,10 @@ 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.
density * volume. In this context, volume can be a 3d quantity (for
spheres or ellipsoids), a 2d quantity (for triangles), or a 1d
quantity (for line segments). If the volume is 0.0, meaning a point
particle, then the density value is used as the mass.
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
@ -560,6 +575,33 @@ values in this section must be integers (1, not 1.0).
:line
{Lines} section:
one line per line segment :ulb,l
line syntax: atom-ID x1 y1 x2 y2 :l
atom-ID = ID of atom which is a line segment
x1,y1 = 1st end point
x2,y2 = 2nd end point
example: :l
12 1.0 0.0 2.0 0.0 :pre
:ule
The {Lines} section must appear if "atom_style line"_atom_style.html
is used and any atoms are listed in the {Atoms} section with a
lineflag = 1. The number of lines should be specified in the header
section via the "lines" keyword.
The 2 end points are the end points of the line segment. The ordering
of the 2 points should be such that using a right-hand rule to cross
the line segment with a unit vector in the +z direction, gives an
"outward" normal vector perpendicular to the line segment.
I.e. normal = (c2-c1) x (0,0,1). This orientation may be important
for defining some interactions.
The {Lines} section must appear after the {Atoms} section.
:line
{Masses} section:
one line per atom type :ulb,l
@ -605,6 +647,33 @@ script.
:line
{Triangles} section:
one line per triangle :ulb,l
line syntax: atom-ID x1 y1 x2 y2 :l
atom-ID = ID of atom which is a line segment
x1,y1,z1 = 1st corner point
x2,y2,z2 = 2nd corner point
x3,y3,z3 = 3rd corner point
example: :l
12 0.0 0.0 0.0 2.0 0.0 1.0 0.0 2.0 1.0 :pre
:ule
The {Triangles} section must appear if "atom_style
tri"_atom_style.html is used and any atoms are listed in the {Atoms}
section with a triangleflag = 1. The number of lines should be
specified in the header section via the "triangles" keyword.
The 3 corner points are the corner points of the triangle. The
ordering of the 3 points should be such that using a right-hand rule
to go from point1 to point2 to point3 gives an "outward" normal vector
to the face of the triangle. I.e. normal = (c2-c1) x (c3-c1). This
orientation may be important for defining some interactions.
The {Triangles} section must appear after the {Atoms} section.
:line
{Velocities} section:
one line per atom

115
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@ -21,7 +21,7 @@
<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</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
<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>length</I> or <I>tri</I> or <I>theta</I> or <I>angmom</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> or
<I>meso_e</I> or <I>meso_cv</I> or <I>meso_rho</I>
@ -40,14 +40,22 @@
Dlen = magnitude of dipole moment (dipole units)
<I>quat</I> values = a b c theta
a,b,c = unit vector to rotate particle around via right-hand rule
theta = rotation angle in degrees
theta = rotation angle (degrees)
<I>quat/random</I> value = seed
seed = random # seed (positive integer) for quaternion orientations
<I>diameter</I> value = diameter of spherical particle (distance units)
<I>shape</I> value = Sx Sy Sz
Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
<I>length</I> value = len
len = length of line segment (distance units)
<I>tri</I> value = side
side = side length of equilateral triangle (distance units)
<I>theta</I> value = angle (degrees)
angle = orientation of line segment with respect to x-axis
<I>angmom</I> values = Lx Ly Lz
Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity 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>density</I> value = particle density for sphere or ellipsoid (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
<I>volume</I> value = particle volume for Peridynamic particle (distance^3 units)
<I>image</I> nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
@ -143,26 +151,31 @@ the orientation of a particular atom is the same, regardless of how
many processors are being used.
</P>
<P>Keyword <I>quat</I> uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms.
Note that particles defined by <A HREF = "atom_style.html">atom_style ellipsoid</A>
have 3 shape parameters. The 3 values must be non-zero for each
particle set by this command. They are used to specify the aspect
ratios of an ellipsoidal particle, which is oriented by default with
its x-axis along the simulation box's x-axis, and similarly for y and
z. If this body is rotated (via the right-hand rule) by an angle
theta around a unit rotation vector (a,b,c), then the quaternion that
represents its new orientation is given by (cos(theta/2),
a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
values are the arguments to the <I>quat</I> keyword. LAMMPS normalizes the
quaternion in case (a,b,c) was not specified as a unit vector. For 2d
systems, the a,b,c values are ignored, since a rotation vector of
(0,0,1) is the only valid choice.
(4-vector) that represents the orientation of the selected atoms. The
particles must be ellipsoids as defined by the <A HREF = "atom_style.html">atom_style
ellipsoid</A> command or triangles as defined by the
<A HREF = "atom_style.html">atom_style tri</A> command. Note that particles defined
by <A HREF = "atom_style.html">atom_style ellipsoid</A> have 3 shape parameters.
The 3 values must be non-zero for each particle set by this command.
They are used to specify the aspect ratios of an ellipsoidal particle,
which is oriented by default with its x-axis along the simulation
box's x-axis, and similarly for y and z. If this body is rotated (via
the right-hand rule) by an angle theta around a unit rotation vector
(a,b,c), then the quaternion that represents its new orientation is
given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2),
c*sin(theta/2)). The theta and a,b,c values are the arguments to the
<I>quat</I> keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
not specified as a unit vector. For 2d systems, the a,b,c values are
ignored, since a rotation vector of (0,0,1) is the only valid choice.
</P>
<P>Keyword <I>quat/random</I> randomizes the orientation of the quaternion of
the selected atoms. Random numbers are used in such a way that the
orientation of a particular atom is the same, regardless of how many
processors are being used. For 2d systems, only orientations in the
xy plane are generated. As with keyword <I>quat</I>, the 3 shape values
the selected atoms. The particles must be ellipsoids as defined by
the <A HREF = "atom_style.html">atom_style ellipsoid</A> command or triangles as
defined by the <A HREF = "atom_style.html">atom_style tri</A> command. Random
numbers are used in such a way that the orientation of a particular
atom is the same, regardless of how many processors are being used.
For 2d systems, only orientations in the xy plane are generated. As
with keyword <I>quat</I>, for ellipsoidal particles, the 3 shape values
must be non-zero for each particle set by this command.
</P>
<P>Keyword <I>diameter</I> sets the size of the selected atoms. The particles
@ -174,7 +187,7 @@ defined with a density, e.g. via the <A HREF = "read_data.html">read_data</A>
command.
</P>
<P>Keyword <I>shape</I> sets the size and shape of the selected atoms. The
particles must be aspherical ellipsoids as defined by the <A HREF = "atom_style.html">atom_style
particles must be ellipsoids as defined by the <A HREF = "atom_style.html">atom_style
ellipsoid</A> command. The <I>Sx</I>, <I>Sy</I>, <I>Sz</I> settings are
the 3 diameters of the ellipsoid in each direction. All 3 can be set
to the same value, which means the ellipsoid is effectively a sphere.
@ -183,20 +196,60 @@ treated as a point particle. Note that this command does not adjust
the particle mass, even if it was defined with a density, e.g. via the
<A HREF = "read_data.html">read_data</A> command.
</P>
<P>Keyword <I>length</I> sets the length of selected atoms. The particles
must be line segments as defined by the <A HREF = "atom_style.html">atom_style
line</A> command. If the specified value is non-zero the
line segment is (re)set to a length = the specified value, centered
around the particle position, with an orientation along the x-axis.
If the specified value is 0.0, the particle will become a point
particle. Note that this command does not adjust the particle mass,
even if it was defined with a density, e.g. via the
<A HREF = "read_data.html">read_data</A> command.
</P>
<P>Keyword <I>tri</I> sets the size of selected atoms. The particles must be
triangles as defined by the <A HREF = "atom_style.html">atom_style tri</A> command.
If the specified value is non-zero the triangle is (re)set to be an
equilateral triangle in the xy plane with side length = the specified
value, with a centroid at the particle position, with its base
parallel to the x axis, and the y-axis running from the center of the
base to the top point of the triangle. If the specified value is 0.0,
the particle will become a point particle. Note that this command
does not adjust the particle mass, even if it was defined with a
density, e.g. via the <A HREF = "read_data.html">read_data</A> command.
</P>
<P>Keyword <I>theta</I> sets the orientation of selected atoms. The particles
must be line segments as defined by the <A HREF = "atom_style.html">atom_style
line</A> command. The specified value is used to set the
orientation angle of the line segments with respect to the x axis.
</P>
<P>Keyword <I>angmom</I> sets the angular momentum of selected atoms. The
particles must be ellipsoids as defined by the <A HREF = "atom_style.html">atom_style
ellipsoid</A> command or triangles as defined by the
<A HREF = "atom_style.html">atom_style tri</A> command. The angular momentum vector
of the particles is set to the 3 specified components.
</P>
<P>Keyword <I>mass</I> sets the mass of all selected particles. The particles
must have a per-atom mass attribute, as defined by the
<A HREF = "atom_style.html">atom_style</A> command. See the "mass" command for how
to set mass values on a per-type basis.
</P>
<P>Keyword <I>density</I> sets the mass of all selected particles. The
particles must have a per-atom mass attribute, as defined by the
<A HREF = "atom_style.html">atom_style</A> command. See the "mass" command for how
to set mass values on a per-type basis. If the atom has a radius
attribute (see <A HREF = "atom_style.html">atom_style sphere</A>) and its radius is
non-zero, its mass is set from the density and particle volume. The
same is true if the atom has a shape attribute (see <A HREF = "atom_style.html">atom_style
ellipsoid</A>) and its 3 shape parameters are non-zero.
Otherwise the mass is set to the density value directly.
<P>Keyword <I>density</I> also sets the mass of all selected particles, but in
a different way. The particles must have a per-atom mass attribute,
as defined by the <A HREF = "atom_style.html">atom_style</A> command. 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. If the atom has a shape attribute (see <A HREF = "atom_style.html">atom_style
ellipsoid</A>) and its 3 shape parameters are non-zero,
then its mass is set from the density and particle volume. If the
atom has a length attribute (see <A HREF = "atom_style.html">atom_style line</A>)
and its length is non-zero, then its mass is set from the density and
line segment length (the input density is assumed to be in
mass/distance units). If the atom has an area attribute (see
<A HREF = "atom_style.html">atom_style tri</A>) and its area is non-zero, then its
mass is set from the density and triangle area (the input density is
assumed to be in mass/distance^2 units). If none of these cases are
valid, then the mass is set to the density value directly (the input
density is assumed to be in mass units).
</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

118
doc/set.txt
View File

@ -17,8 +17,9 @@ ID = atom ID range or type range or mol ID range or group ID or region ID :l
one or more keyword/value pairs may be appended :l
keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
{charge} or {dipole} or {dipole/random} or {quat} or \
{quat/random} or {diameter} or {shape} or {mass} or \
{density} or {volume} or {image} or
{quat/random} or {diameter} or {shape} or \
{length} or {tri} or {theta} or {angmom} or \
{mass} or {density} or {volume} or {image} or
{bond} or {angle} or {dihedral} or {improper} or
{meso_e} or {meso_cv} or {meso_rho} :l
{type} value = atom type
@ -36,14 +37,22 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
Dlen = magnitude of dipole moment (dipole units)
{quat} values = a b c theta
a,b,c = unit vector to rotate particle around via right-hand rule
theta = rotation angle in degrees
theta = rotation angle (degrees)
{quat/random} value = seed
seed = random # seed (positive integer) for quaternion orientations
{diameter} value = diameter of spherical particle (distance units)
{shape} value = Sx Sy Sz
Sx,Sy,Sz = 3 diameters of ellipsoid (distance units)
{length} value = len
len = length of line segment (distance units)
{tri} value = side
side = side length of equilateral triangle (distance units)
{theta} value = angle (degrees)
angle = orientation of line segment with respect to x-axis
{angmom} values = Lx Ly Lz
Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
{mass} value = per-atom mass (mass units)
{density} value = particle density for sphere or ellipsoid (mass/distance^3 units)
{density} value = particle density for sphere or ellipsoid (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle)
{volume} value = particle volume for Peridynamic particle (distance^3 units)
{image} nx ny nz
nx,ny,nz = which periodic image of the simulation box the atom is in
@ -138,26 +147,31 @@ the orientation of a particular atom is the same, regardless of how
many processors are being used.
Keyword {quat} uses the specified values to create a quaternion
(4-vector) that represents the orientation of the selected atoms.
Note that particles defined by "atom_style ellipsoid"_atom_style.html
have 3 shape parameters. The 3 values must be non-zero for each
particle set by this command. They are used to specify the aspect
ratios of an ellipsoidal particle, which is oriented by default with
its x-axis along the simulation box's x-axis, and similarly for y and
z. If this body is rotated (via the right-hand rule) by an angle
theta around a unit rotation vector (a,b,c), then the quaternion that
represents its new orientation is given by (cos(theta/2),
a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c
values are the arguments to the {quat} keyword. LAMMPS normalizes the
quaternion in case (a,b,c) was not specified as a unit vector. For 2d
systems, the a,b,c values are ignored, since a rotation vector of
(0,0,1) is the only valid choice.
(4-vector) that represents the orientation of the selected atoms. The
particles must be ellipsoids as defined by the "atom_style
ellipsoid"_atom_style.html command or triangles as defined by the
"atom_style tri"_atom_style.html command. Note that particles defined
by "atom_style ellipsoid"_atom_style.html have 3 shape parameters.
The 3 values must be non-zero for each particle set by this command.
They are used to specify the aspect ratios of an ellipsoidal particle,
which is oriented by default with its x-axis along the simulation
box's x-axis, and similarly for y and z. If this body is rotated (via
the right-hand rule) by an angle theta around a unit rotation vector
(a,b,c), then the quaternion that represents its new orientation is
given by (cos(theta/2), a*sin(theta/2), b*sin(theta/2),
c*sin(theta/2)). The theta and a,b,c values are the arguments to the
{quat} keyword. LAMMPS normalizes the quaternion in case (a,b,c) was
not specified as a unit vector. For 2d systems, the a,b,c values are
ignored, since a rotation vector of (0,0,1) is the only valid choice.
Keyword {quat/random} randomizes the orientation of the quaternion of
the selected atoms. Random numbers are used in such a way that the
orientation of a particular atom is the same, regardless of how many
processors are being used. For 2d systems, only orientations in the
xy plane are generated. As with keyword {quat}, the 3 shape values
the selected atoms. The particles must be ellipsoids as defined by
the "atom_style ellipsoid"_atom_style.html command or triangles as
defined by the "atom_style tri"_atom_style.html command. Random
numbers are used in such a way that the orientation of a particular
atom is the same, regardless of how many processors are being used.
For 2d systems, only orientations in the xy plane are generated. As
with keyword {quat}, for ellipsoidal particles, the 3 shape values
must be non-zero for each particle set by this command.
Keyword {diameter} sets the size of the selected atoms. The particles
@ -169,7 +183,7 @@ defined with a density, e.g. via the "read_data"_read_data.html
command.
Keyword {shape} sets the size and shape of the selected atoms. The
particles must be aspherical ellipsoids as defined by the "atom_style
particles must be ellipsoids as defined by the "atom_style
ellipsoid"_atom_style.html command. The {Sx}, {Sy}, {Sz} settings are
the 3 diameters of the ellipsoid in each direction. All 3 can be set
to the same value, which means the ellipsoid is effectively a sphere.
@ -178,20 +192,60 @@ 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 {length} sets the length of selected atoms. The particles
must be line segments as defined by the "atom_style
line"_atom_style.html command. If the specified value is non-zero the
line segment is (re)set to a length = the specified value, centered
around the particle position, with an orientation along the x-axis.
If the specified value is 0.0, the particle will become 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 {tri} sets the size of selected atoms. The particles must be
triangles as defined by the "atom_style tri"_atom_style.html command.
If the specified value is non-zero the triangle is (re)set to be an
equilateral triangle in the xy plane with side length = the specified
value, with a centroid at the particle position, with its base
parallel to the x axis, and the y-axis running from the center of the
base to the top point of the triangle. If the specified value is 0.0,
the particle will become 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 {theta} sets the orientation of selected atoms. The particles
must be line segments as defined by the "atom_style
line"_atom_style.html command. The specified value is used to set the
orientation angle of the line segments with respect to the x axis.
Keyword {angmom} sets the angular momentum of selected atoms. The
particles must be ellipsoids as defined by the "atom_style
ellipsoid"_atom_style.html command or triangles as defined by the
"atom_style tri"_atom_style.html command. The angular momentum vector
of the particles is set to the 3 specified components.
Keyword {mass} sets the mass of all selected particles. The particles
must have a per-atom mass attribute, as defined by the
"atom_style"_atom_style.html command. See the "mass" command for how
to set mass values on a per-type basis.
Keyword {density} sets the mass of all selected particles. The
particles must have a per-atom mass attribute, as defined by the
"atom_style"_atom_style.html command. See the "mass" command for how
to set mass values on a per-type basis. If the atom has a radius
attribute (see "atom_style sphere"_atom_style.html) and its radius is
non-zero, its mass is set from the density and particle volume. The
same is true if the atom has a shape attribute (see "atom_style
ellipsoid"_atom_style.html) and its 3 shape parameters are non-zero.
Otherwise the mass is set to the density value directly.
Keyword {density} also sets the mass of all selected particles, but in
a different way. The particles must have a per-atom mass attribute,
as defined by the "atom_style"_atom_style.html command. 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. If the atom has a shape attribute (see "atom_style
ellipsoid"_atom_style.html) and its 3 shape parameters are non-zero,
then its mass is set from the density and particle volume. If the
atom has a length attribute (see "atom_style line"_atom_style.html)
and its length is non-zero, then its mass is set from the density and
line segment length (the input density is assumed to be in
mass/distance units). If the atom has an area attribute (see
"atom_style tri"_atom_style.html) and its area is non-zero, then its
mass is set from the density and triangle area (the input density is
assumed to be in mass/distance^2 units). If none of these cases are
valid, then the mass is set to the density value directly (the input
density is assumed to be in mass units).
Keyword {volume} sets the volume of all selected particles.
Currently, only the "atom_style peri"_atom_style.html command defines