git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5952 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/atom_style.html

@@ -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
+per-particle diameter and mass.  If the diameter > 0.0, the particle
-particles are ellipsoids and each stores a per-particle shape vector
+is a finite-size sphere.  If the diameter = 0.0, it is a point
-with the 3 diamters of the ellipsoid.  For the <I>electron</I> style, the
+particle.
-particles representing electrons are 3d Gaussians with a specified
+</P>
-position and bandwidth or uncertainty in position, which is
+<P>For the <I>ellipsoid</I> style, the particles are ellipsoids and each
-represented by the eradius = electron size.  For the <I>peri</I> style, the
+stores a flag which indicates whether it is a finite-size ellipsoid or
-particles are spherical and each stores a per-particle mass and
+a point particle.  If it is an ellipsoid, it also stores a shape
-volume.
+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>
 

doc/create_atoms.html

@@ -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
+<P>Note that the <I>sphere</I> atom style sets the default particle diameter
-diameter/shape and density to 1.0 and thus calculates a mass for the
+to 1.0 as well as the density.  This means the mass for the particle
-particle, which is PI/6 * diameter^3 = 0.5236.  The <I>peri</I> style sets
+is not 1.0, but is PI/6 * diameter^3 = 0.5236.
-the volume and density to 1.0 and thus also set the mass for the
+</P>
-particle to 1.0.
+<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>

doc/dump.html

@@ -51,9 +51,7 @@
 			  vx, vy, vz, fx, fy, fz,
                           q, mux, muy, muz, mu,
                           radius, omegax, omegay, omegaz,
-			  angmomx, angmomy, angmomz,
+			  angmomx, angmomy, angmomz, tqx, tqy, tqz,
-			  shapex,shapey, shapez,
-			  quatw, quati, quatj, quatk, tqx, tqy, tqz,
 			  spin, eradius, ervel, erforce,
 			  c_ID, c_ID[N], f_ID, f_ID[N], v_name 
 </PRE>
@@ -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.

doc/dump_image.html

@@ -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 ... 

doc/dump_image.txt

@@ -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

doc/dump_modify.html

@@ -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

doc/dump_modify.txt

@@ -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

doc/fix_store_state.html

@@ -28,8 +28,7 @@
 		        vx, vy, vz, fx, fy, fz,
                         q, mux, muy, muz,
                         radius, omegax, omegay, omegaz,
-                        angmomx, angmomy, angmomz,
+                        angmomx, angmomy, angmomz, tqx, tqy, tqz
-		        quatw, quati, quatj, quatk, 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

doc/read_data.html

@@ -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
+<P>The ellipseflag determines whether the particle is a finite-size
-finite-size ellipsoidal particle, when it is oriented along the 3
+ellipsoid of finite size, or a point particle.  Additional attributes
-coordinate axes.  They can all be set to 0.0, which means that atom is
+must be defined for each ellipsoid in the <I>Ellipsoids</I> section.
-a point particle.
 </P>
 <P>Some pair styles and fixes and computes that operate on finite-size
 particles allow for a mixture of finite-size and point particles.  See
@@ -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.
+listed in the same order they appear as listed above.  Thus if
-</P>
-<P>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 

doc/read_data.txt

@@ -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
+The ellipseflag determines whether the particle is a finite-size
-finite-size ellipsoidal particle, when it is oriented along the 3
+ellipsoid of finite size, or a point particle.  Additional attributes
-coordinate axes.  They can all be set to 0.0, which means that atom is
+must be defined for each ellipsoid in the {Ellipsoids} section.
-a point particle.
 
 Some pair styles and fixes and computes that operate on finite-size
 particles allow for a mixture of finite-size and point particles.  See
@@ -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.
+listed in the same order they appear as listed above.  Thus if
-
-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

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
+have 3 shape parameters.  The 3 values must be non-zero for each
-an ellipsoidal particle, which is oriented by default with its x-axis
+particle set by this command.  They are used to specify the aspect
-along the simulation box's x-axis, and similarly for y and z.  If this
+ratios of an ellipsoidal particle, which is oriented by default with
-body is rotated (via the right-hand rule) by an angle theta around a
+its x-axis along the simulation box's x-axis, and similarly for y and
-unit rotation vector (a,b,c), then the quaternion that represents its
+z.  If this body is rotated (via the right-hand rule) by an angle
-new orientation is given by (cos(theta/2), a*sin(theta/2),
+theta around a unit rotation vector (a,b,c), then the quaternion that
-b*sin(theta/2), c*sin(theta/2)).  The theta and a,b,c values are the
+represents its new orientation is given by (cos(theta/2),
-arguments to the <I>quat</I> keyword.  LAMMPS normalizes the quaternion in
+a*sin(theta/2), b*sin(theta/2), c*sin(theta/2)).  The theta and a,b,c
-case (a,b,c) was not specified as a unit vector.  For 2d systems, the
+values are the arguments to the <I>quat</I> keyword.  LAMMPS normalizes the
-a,b,c values are ignored, since a rotation vector of (0,0,1) is the
+quaternion in case (a,b,c) was not specified as a unit vector.  For 2d
-only valid choice.
+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
+They can also all be set to 0.0 which means the particle will be
-as a point particle.  Note that this command does not adjust the
+treated as a point particle.  Note that this command does not adjust
-particle mass, even if it was defined with a density, e.g. via the
+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
+<P>Keyword <I>mass</I> sets the mass of all selected particles.  The particles
-particles must have a per-atom mass attribute, as defined by the
+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.