forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5952 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
e2d5478a6c
commit
d6f7a7383e
|
|
@ -75,14 +75,22 @@ styles discussed below. They assign mass on a per-atom basis.
|
|||
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.
|
||||
per-particle diameter and mass. If the diameter > 0.0, the particle
|
||||
is a finite-size sphere. If the diameter = 0.0, it is a point
|
||||
particle.
|
||||
</P>
|
||||
<P>For the <I>ellipsoid</I> style, the particles are ellipsoids and each
|
||||
stores a flag which indicates whether it is a finite-size ellipsoid or
|
||||
a point particle. If it is an ellipsoid, it also stores a shape
|
||||
vector with the 3 diamters of the ellipsoid and a quaternion 4-vector
|
||||
with its orientation.
|
||||
</P>
|
||||
<P>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.
|
||||
</P>
|
||||
<P>For the <I>peri</I> style, the particles are spherical and each stores a
|
||||
per-particle mass and volume.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
|
|
|||
|
|
@ -148,7 +148,7 @@ to change these values.
|
|||
<UL><LI>charge = 0.0
|
||||
<LI>dipole moment magnitude = 0.0
|
||||
<LI>diameter = 1.0
|
||||
<LI>shape = 1.0 1.0 1.0
|
||||
<LI>shape = 0.0 0.0 0.0
|
||||
<LI>density = 1.0
|
||||
<LI>volume = 1.0
|
||||
<LI>velocity = 0.0 0.0 0.0
|
||||
|
|
@ -157,11 +157,19 @@ to change these values.
|
|||
<LI>quaternion = (1,0,0,0)
|
||||
<LI>bonds, angles, dihedrals, impropers = none
|
||||
</UL>
|
||||
<P>Note that this means the <I>sphere</I> and <I>ellipsoid</I> atom styles set the
|
||||
diameter/shape and density to 1.0 and thus calculates a mass for the
|
||||
particle, which is PI/6 * diameter^3 = 0.5236. The <I>peri</I> style sets
|
||||
the volume and density to 1.0 and thus also set the mass for the
|
||||
particle to 1.0.
|
||||
<P>Note that the <I>sphere</I> atom style sets the default particle diameter
|
||||
to 1.0 as well as the density. This means the mass for the particle
|
||||
is not 1.0, but is PI/6 * diameter^3 = 0.5236.
|
||||
</P>
|
||||
<P>Note that the <I>ellipsoid</I> atom style sets the default particle shape
|
||||
to (0.0 0.0 0.0) and the density to 1.0 which means it is a point
|
||||
particle, not an ellipsoid, and has a mass of 1.0.
|
||||
</P>
|
||||
<P>Note that the <I>peri</I> style sets the default volume and density to 1.0
|
||||
and thus also set the mass for the particle to 1.0.
|
||||
</P>
|
||||
<P>The <A HREF = "set.html">set</A> command can be used to override many of these
|
||||
default settings.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -51,9 +51,7 @@
|
|||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz, mu,
|
||||
radius, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz,
|
||||
shapex,shapey, shapez,
|
||||
quatw, quati, quatj, quatk, tqx, tqy, tqz,
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz,
|
||||
spin, eradius, ervel, erforce,
|
||||
c_ID, c_ID[N], f_ID, f_ID[N], v_name
|
||||
</PRE>
|
||||
|
|
@ -73,8 +71,6 @@
|
|||
radius = radius of spherical particle
|
||||
omegax,omegay,omegaz = angular velocity of extended particle
|
||||
angmomx,angmomy,angmomz = angular momentum of extended particle
|
||||
shapex,shapey,shapez = 3 diameters of ellipsoidal particle
|
||||
quatw,quati,quatj,quatk = quaternion components for aspherical particles
|
||||
tqx,tqy,tqz = torque on extended particles
|
||||
spin = electron spin
|
||||
eradius = electron radius
|
||||
|
|
@ -426,15 +422,6 @@ quantity.
|
|||
extended aspherical particles that have an angular momentum. Only
|
||||
the <I>ellipsoid</I> atom style defines this quantity.
|
||||
</P>
|
||||
<P>The <I>shapex</I>, <I>shapey</I>, and <I>shapez</I> attributes are specific to
|
||||
extended ellipsoidal particles that have a finite size and shape, such
|
||||
those defined with an atom style of <I>ellipsoidal</I>.
|
||||
</P>
|
||||
<P>The <I>quatw</I>, <I>quati</I>, <I>quatj</I>, <I>quatk</I> attributes are for aspherical
|
||||
particles defined with an atom style of <I>ellipsoid</I>. They are the
|
||||
components of the quaternion that defines the orientation of the
|
||||
particle.
|
||||
</P>
|
||||
<P>The <I>tqx</I>, <I>tqy</I>, <I>tqz</I> attributes are for extended spherical or
|
||||
aspherical particles that can sustain a rotational torque due
|
||||
to interactions with other particles.
|
||||
|
|
|
|||
|
|
@ -11,6 +11,9 @@
|
|||
|
||||
<H3>dump image command
|
||||
</H3>
|
||||
<P>NOTE: The dump image command has not yet been released as part of
|
||||
LAMMPS.
|
||||
</P>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>dump ID group-ID image N file keyword value ...
|
||||
|
|
|
|||
|
|
@ -8,6 +8,9 @@
|
|||
|
||||
dump image command :h3
|
||||
|
||||
NOTE: The dump image command has not yet been released as part of
|
||||
LAMMPS.
|
||||
|
||||
[Syntax:]
|
||||
|
||||
dump ID group-ID image N file keyword value ... :pre
|
||||
|
|
|
|||
|
|
@ -11,6 +11,9 @@
|
|||
|
||||
<H3>dump_modify command
|
||||
</H3>
|
||||
<P>NOTE: This options relevant for the dump image command have not yet
|
||||
been released as part of LAMMPS.
|
||||
</P>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>dump_modify dump-ID keyword values ...
|
||||
|
|
@ -99,8 +102,6 @@ dump_modify xtcdump precision 10000
|
|||
dump_modify 1 every 1000
|
||||
dump_modify 1 every v_myVar
|
||||
</PRE>
|
||||
<P>NOTE: add some image examples
|
||||
</P>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Modify the parameters of a previously defined dump command. Not all
|
||||
|
|
|
|||
|
|
@ -8,6 +8,9 @@
|
|||
|
||||
dump_modify command :h3
|
||||
|
||||
NOTE: This options relevant for the dump image command have not yet
|
||||
been released as part of LAMMPS.
|
||||
|
||||
[Syntax:]
|
||||
|
||||
dump_modify dump-ID keyword values ... :pre
|
||||
|
|
@ -92,8 +95,6 @@ dump_modify xtcdump precision 10000
|
|||
dump_modify 1 every 1000
|
||||
dump_modify 1 every v_myVar :pre
|
||||
|
||||
NOTE: add some image examples
|
||||
|
||||
[Description:]
|
||||
|
||||
Modify the parameters of a previously defined dump command. Not all
|
||||
|
|
|
|||
|
|
@ -28,8 +28,7 @@
|
|||
vx, vy, vz, fx, fy, fz,
|
||||
q, mux, muy, muz,
|
||||
radius, omegax, omegay, omegaz,
|
||||
angmomx, angmomy, angmomz,
|
||||
quatw, quati, quatj, quatk, tqx, tqy, tqz
|
||||
angmomx, angmomy, angmomz, tqx, tqy, tqz
|
||||
c_ID, c_ID[N], f_ID, f_ID[N], v_name
|
||||
</PRE>
|
||||
<PRE> id = atom ID
|
||||
|
|
@ -47,7 +46,6 @@
|
|||
radius = radius of extended spherical particle
|
||||
omegax,omegay,omegaz = angular velocity of extended particle
|
||||
angmomx,angmomy,angmomz = angular momentum of extended particle
|
||||
quatw,quati,quatj,quatk = quaternion components for aspherical particles
|
||||
tqx,tqy,tqz = torque on extended particles
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
||||
|
|
|
|||
|
|
@ -79,6 +79,7 @@ is different than the default.
|
|||
<LI><I>dihedral types</I> = # of dihedral types in system
|
||||
<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>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
|
||||
|
|
@ -155,11 +156,16 @@ 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 ellipseflag and the <I>Ellipsoids</I> section below.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P>These are the section keywords for the body of the file.
|
||||
</P>
|
||||
<UL><LI><I>Atoms, Velocities, Masses</I> = atom-property sections
|
||||
<UL><LI><I>Atoms, Velocities, Ellipsoids, Masses</I> = atom-property sections
|
||||
<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
|
||||
<LI><I>Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I> = force field sections
|
||||
<LI><I>BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs</I> = class 2 force field sections
|
||||
|
|
@ -282,7 +288,7 @@ of analysis.
|
|||
<TR><TD >charge</TD><TD > atom-ID atom-type q x y z</TD></TR>
|
||||
<TR><TD >dipole</TD><TD > atom-ID atom-type q x y z mux muy muz</TD></TR>
|
||||
<TR><TD >electron</TD><TD > atom-ID atom-type q spin eradius x y z</TD></TR>
|
||||
<TR><TD >ellipsoid</TD><TD > atom-ID atom-type shapex shapey shapez density x y z quatw quati quatj quatk</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 >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>
|
||||
|
|
@ -297,12 +303,11 @@ of analysis.
|
|||
<LI>atom-type = type of atom (1-Ntype)
|
||||
<LI>q = charge on atom (charge units)
|
||||
<LI>diameter = diameter of spherical atom (distance units)
|
||||
<LI>shapex,shapey,shapez = 3 diameters of ellipsoidal atom (distance units)
|
||||
<LI>ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
|
||||
<LI>density = density of atom (mass/distance^3 units)
|
||||
<LI>volume = volume of atom (distance^3 units)
|
||||
<LI>x,y,z = coordinates of atom
|
||||
<LI>mux,muy,muz = components of dipole moment of atom (dipole units)
|
||||
<LI>quatw,quati,quatj,quatk = quaternion components for orientation of atom
|
||||
<LI>spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
|
||||
<LI>eradius = electron radius (or fixed-core radius)
|
||||
</UL>
|
||||
|
|
@ -330,10 +335,9 @@ 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 3 shape values specify the 3 diameters or aspect ratios of a
|
||||
finite-size ellipsoidal particle, when it is oriented along the 3
|
||||
coordinate axes. They can all be set to 0.0, which means that atom is
|
||||
a point particle.
|
||||
<P>The ellipseflag 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>
|
||||
<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
|
||||
|
|
@ -344,18 +348,6 @@ finite-size particles to set the mass of the particle as mass =
|
|||
density * volume. If the volume is 0.0, meaning a point particle,
|
||||
then the density value is used as the mass.
|
||||
</P>
|
||||
<P>The values <I>quatw</I>, <I>quati</I>, <I>quatj</I>, and <I>quatk</I> set the orientation
|
||||
of the atom as a quaternion (4-vector). Note that the shape
|
||||
attributes specify the aspect ratios of an ellipsoidal particle, which
|
||||
is oriented by default with its x-axis along the simulation box's
|
||||
x-axis, and similarly for y and z. If this body is rotated (via the
|
||||
right-hand rule) by an angle theta around a unit vector (a,b,c), then
|
||||
the quaternion that represents its new orientation is given by
|
||||
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
|
||||
4 components are quatw, quati, quatj, and quatk as specified above.
|
||||
LAMMPS normalizes each atom's quaternion in case (a,b,c) was not
|
||||
specified as a unit vector.
|
||||
</P>
|
||||
<P>For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
|
||||
specific values for each sub-style must be listed. The order of the
|
||||
sub-styles is the same as they were listed in the
|
||||
|
|
@ -363,9 +355,7 @@ sub-styles is the same as they were listed in the
|
|||
are those that are not the 5 standard ones (ID,type,x,y,z). For
|
||||
example, for the "charge" sub-style, a "q" value would appear. For
|
||||
the "full" sub-style, a "molecule-ID" and "q" would appear. These are
|
||||
listed in the same order they appear as listed above.
|
||||
</P>
|
||||
<P>Thus if
|
||||
listed in the same order they appear as listed above. Thus if
|
||||
</P>
|
||||
<PRE>atom_style hybrid charge sphere
|
||||
</PRE>
|
||||
|
|
@ -527,6 +517,50 @@ section must be integers (1, not 1.0).
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P><I>Ellipsoids</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per ellipsoid
|
||||
|
||||
<LI>line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk
|
||||
|
||||
<PRE> atom-ID = ID of atom which is an ellipsoid
|
||||
shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
|
||||
quatw,quati,quatj,quatk = quaternion components for orientation of atom
|
||||
type = bond type (1-Nbondtype)
|
||||
atom1,atom2 = IDs of 1st,2nd atoms in bond
|
||||
</PRE>
|
||||
<LI>example:
|
||||
|
||||
<PRE> 12 3 17 29
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P>The <I>Ellipsoids</I> section must appear if <A HREF = "atom_style.html">atom_style
|
||||
ellipsoid</A> is used and any atoms are listed in the
|
||||
<I>Atoms</I> section with an ellipsoidflag = 1. The number of ellipsoids
|
||||
should be specified in the header section via the "ellipsoids"
|
||||
keyword.
|
||||
</P>
|
||||
<P>The 3 shape values specify the 3 diameters or aspect ratios of a
|
||||
finite-size ellipsoidal particle, when it is oriented along the 3
|
||||
coordinate axes. They must all be non-zero values.
|
||||
</P>
|
||||
<P>The values <I>quatw</I>, <I>quati</I>, <I>quatj</I>, and <I>quatk</I> set the orientation
|
||||
of the atom as a quaternion (4-vector). Note that the shape
|
||||
attributes specify the aspect ratios of an ellipsoidal particle, which
|
||||
is oriented by default with its x-axis along the simulation box's
|
||||
x-axis, and similarly for y and z. If this body is rotated (via the
|
||||
right-hand rule) by an angle theta around a unit vector (a,b,c), then
|
||||
the quaternion that represents its new orientation is given by
|
||||
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
|
||||
4 components are quatw, quati, quatj, and quatk as specified above.
|
||||
LAMMPS normalizes each atom's quaternion in case (a,b,c) is not
|
||||
specified as a unit vector.
|
||||
</P>
|
||||
<P>The <I>Ellipsoids</I> section must appear after the <I>Atoms</I> section.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><I>EndBondTorsion Coeffs</I> section:
|
||||
</P>
|
||||
<UL><LI>one line per dihedral type
|
||||
|
|
|
|||
|
|
@ -76,6 +76,7 @@ is different than the default.
|
|||
{dihedral types} = # of dihedral types in system
|
||||
{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
|
||||
{xlo xhi} = simulation box boundaries in x dimension
|
||||
{ylo yhi} = simulation box boundaries in y dimension
|
||||
{zlo zhi} = simulation box boundaries in z dimension
|
||||
|
|
@ -152,11 +153,16 @@ 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 ellipseflag and the {Ellipsoids} section below.
|
||||
|
||||
:line
|
||||
|
||||
These are the section keywords for the body of the file.
|
||||
|
||||
{Atoms, Velocities, Masses} = atom-property sections
|
||||
{Atoms, Velocities, Ellipsoids, Masses} = atom-property sections
|
||||
{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
|
||||
{Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \
|
||||
Improper Coeffs} = force field sections
|
||||
|
|
@ -262,7 +268,7 @@ bond: atom-ID molecule-ID atom-type x y z
|
|||
charge: atom-ID atom-type q x y z
|
||||
dipole: atom-ID atom-type q x y z mux muy muz
|
||||
electron: atom-ID atom-type q spin eradius x y z
|
||||
ellipsoid: atom-ID atom-type shapex shapey shapez density x y z quatw quati quatj quatk
|
||||
ellipsoid: atom-ID atom-type ellipsoidflag density x y z
|
||||
full: atom-ID molecule-ID atom-type q x y z
|
||||
molecular: atom-ID molecule-ID atom-type x y z
|
||||
peri: atom-ID atom-type volume density x y z
|
||||
|
|
@ -276,12 +282,11 @@ molecule-ID = integer ID of molecule the atom belongs to
|
|||
atom-type = type of atom (1-Ntype)
|
||||
q = charge on atom (charge units)
|
||||
diameter = diameter of spherical atom (distance units)
|
||||
shapex,shapey,shapez = 3 diameters of ellipsoidal atom (distance units)
|
||||
ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles
|
||||
density = density of atom (mass/distance^3 units)
|
||||
volume = volume of atom (distance^3 units)
|
||||
x,y,z = coordinates of atom
|
||||
mux,muy,muz = components of dipole moment of atom (dipole units)
|
||||
quatw,quati,quatj,quatk = quaternion components for orientation of atom
|
||||
spin = electron spin (+1/-1), 0 = nuclei, 2 = fixed-core, 3 = pseudo-cores (i.e. ECP)
|
||||
eradius = electron radius (or fixed-core radius) :ul
|
||||
|
||||
|
|
@ -309,10 +314,9 @@ 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 3 shape values specify the 3 diameters or aspect ratios of a
|
||||
finite-size ellipsoidal particle, when it is oriented along the 3
|
||||
coordinate axes. They can all be set to 0.0, which means that atom is
|
||||
a point particle.
|
||||
The ellipseflag 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.
|
||||
|
||||
Some pair styles and fixes and computes that operate on finite-size
|
||||
particles allow for a mixture of finite-size and point particles. See
|
||||
|
|
@ -323,18 +327,6 @@ finite-size particles to set the mass of the particle as mass =
|
|||
density * volume. If the volume is 0.0, meaning a point particle,
|
||||
then the density value is used as the mass.
|
||||
|
||||
The values {quatw}, {quati}, {quatj}, and {quatk} set the orientation
|
||||
of the atom as a quaternion (4-vector). Note that the shape
|
||||
attributes specify the aspect ratios of an ellipsoidal particle, which
|
||||
is oriented by default with its x-axis along the simulation box's
|
||||
x-axis, and similarly for y and z. If this body is rotated (via the
|
||||
right-hand rule) by an angle theta around a unit vector (a,b,c), then
|
||||
the quaternion that represents its new orientation is given by
|
||||
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
|
||||
4 components are quatw, quati, quatj, and quatk as specified above.
|
||||
LAMMPS normalizes each atom's quaternion in case (a,b,c) was not
|
||||
specified as a unit vector.
|
||||
|
||||
For atom_style hybrid, following the 5 initial values (ID,type,x,y,z),
|
||||
specific values for each sub-style must be listed. The order of the
|
||||
sub-styles is the same as they were listed in the
|
||||
|
|
@ -342,9 +334,7 @@ sub-styles is the same as they were listed in the
|
|||
are those that are not the 5 standard ones (ID,type,x,y,z). For
|
||||
example, for the "charge" sub-style, a "q" value would appear. For
|
||||
the "full" sub-style, a "molecule-ID" and "q" would appear. These are
|
||||
listed in the same order they appear as listed above.
|
||||
|
||||
Thus if
|
||||
listed in the same order they appear as listed above. Thus if
|
||||
|
||||
atom_style hybrid charge sphere :pre
|
||||
|
||||
|
|
@ -477,6 +467,45 @@ section must be integers (1, not 1.0).
|
|||
|
||||
:line
|
||||
|
||||
{Ellipsoids} section:
|
||||
|
||||
one line per ellipsoid :ulb,l
|
||||
line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk :l
|
||||
atom-ID = ID of atom which is an ellipsoid
|
||||
shapex,shapey,shapez = 3 diameters of ellipsoid (distance units)
|
||||
quatw,quati,quatj,quatk = quaternion components for orientation of atom
|
||||
type = bond type (1-Nbondtype)
|
||||
atom1,atom2 = IDs of 1st,2nd atoms in bond :pre
|
||||
example: :l
|
||||
12 3 17 29 :pre
|
||||
:ule
|
||||
|
||||
The {Ellipsoids} section must appear if "atom_style
|
||||
ellipsoid"_atom_style.html is used and any atoms are listed in the
|
||||
{Atoms} section with an ellipsoidflag = 1. The number of ellipsoids
|
||||
should be specified in the header section via the "ellipsoids"
|
||||
keyword.
|
||||
|
||||
The 3 shape values specify the 3 diameters or aspect ratios of a
|
||||
finite-size ellipsoidal particle, when it is oriented along the 3
|
||||
coordinate axes. They must all be non-zero values.
|
||||
|
||||
The values {quatw}, {quati}, {quatj}, and {quatk} set the orientation
|
||||
of the atom as a quaternion (4-vector). Note that the shape
|
||||
attributes specify the aspect ratios of an ellipsoidal particle, which
|
||||
is oriented by default with its x-axis along the simulation box's
|
||||
x-axis, and similarly for y and z. If this body is rotated (via the
|
||||
right-hand rule) by an angle theta around a unit vector (a,b,c), then
|
||||
the quaternion that represents its new orientation is given by
|
||||
(cos(theta/2), a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)). These
|
||||
4 components are quatw, quati, quatj, and quatk as specified above.
|
||||
LAMMPS normalizes each atom's quaternion in case (a,b,c) is not
|
||||
specified as a unit vector.
|
||||
|
||||
The {Ellipsoids} section must appear after the {Atoms} section.
|
||||
|
||||
:line
|
||||
|
||||
{EndBondTorsion Coeffs} section:
|
||||
|
||||
one line per dihedral type :ulb,l
|
||||
|
|
|
|||
38
doc/set.html
38
doc/set.html
|
|
@ -141,23 +141,25 @@ many processors are being used.
|
|||
<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 paraeters whicha are used to specify the aspect ratios of
|
||||
an ellipsoidal particle, which is oriented by default with its x-axis
|
||||
along the simulation box's x-axis, and similarly for y and z. If this
|
||||
body is rotated (via the right-hand rule) by an angle theta around a
|
||||
unit rotation vector (a,b,c), then the quaternion that represents its
|
||||
new orientation is given by (cos(theta/2), a*sin(theta/2),
|
||||
b*sin(theta/2), c*sin(theta/2)). The theta and a,b,c values are the
|
||||
arguments to the <I>quat</I> keyword. LAMMPS normalizes the quaternion in
|
||||
case (a,b,c) was not specified as a unit vector. For 2d systems, the
|
||||
a,b,c values are ignored, since a rotation vector of (0,0,1) is the
|
||||
only valid choice.
|
||||
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.
|
||||
xy plane are generated. As with keyword <I>quat</I>, 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
|
||||
must be finite-size spheres as defined by the <A HREF = "atom_style.html">atom_style
|
||||
|
|
@ -172,13 +174,13 @@ particles must be aspherical ellipsoids as defined by the <A HREF = "atom_style.
|
|||
ellipsoid</A> command. The <I>Sx</I>, <I>Sy</I>, <I>Sz</I> settings are
|
||||
the 3 diameters of the ellipsoid in each direction. All 3 can be set
|
||||
to the same value, which means the ellipsoid is effectively a sphere.
|
||||
Or then can all be set to 0.0 which means the particle will be treated
|
||||
as a point particle. Note that this command does not adjust the
|
||||
particle mass, even if it was defined with a density, e.g. via the
|
||||
They can also all be set to 0.0 which means the particle will be
|
||||
treated as a point particle. Note that this command does not adjust
|
||||
the particle mass, even if it was defined with a density, e.g. via the
|
||||
<A HREF = "read_data.html">read_data</A> command.
|
||||
</P>
|
||||
<P>Keyword <I>mas</I> sets the mass of all selected particles. The
|
||||
particles must have a per-atom mass attribute, as defined by the
|
||||
<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>
|
||||
|
|
@ -189,7 +191,7 @@ 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.
|
||||
ellipsoid</A>) and its 3 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.
|
||||
|
|
|
|||
Loading…
Reference in New Issue