From d6f7a7383ef84dadce35330be5f04a851517efdd Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 15 Apr 2011 23:14:41 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5952 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/atom_style.html | 24 ++++++++---- doc/create_atoms.html | 20 +++++++--- doc/dump.html | 15 +------- doc/dump_image.html | 3 ++ doc/dump_image.txt | 3 ++ doc/dump_modify.html | 5 ++- doc/dump_modify.txt | 5 ++- doc/fix_store_state.html | 4 +- doc/read_data.html | 80 ++++++++++++++++++++++++++++------------ doc/read_data.txt | 75 +++++++++++++++++++++++++------------ doc/set.html | 38 ++++++++++--------- 11 files changed, 173 insertions(+), 99 deletions(-) diff --git a/doc/atom_style.html b/doc/atom_style.html index 355f42c6a1..85690fb039 100644 --- a/doc/atom_style.html +++ b/doc/atom_style.html @@ -75,14 +75,22 @@ styles discussed below. They assign mass on a per-atom basis. particles.

For the sphere style, the particles are spheres and each stores a -per-particle diameter and mass. For the ellipsoid style, the -particles are ellipsoids and each stores a per-particle shape vector -with the 3 diamters of the ellipsoid. For the electron style, the -particles representing electrons are 3d Gaussians with a specified -position and bandwidth or uncertainty in position, which is -represented by the eradius = electron size. For the peri style, the -particles are spherical and each stores a per-particle mass and -volume. +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. +

+

For the ellipsoid 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. +

+

For the electron style, the particles representing electrons are 3d +Gaussians with a specified position and bandwidth or uncertainty in +position, which is represented by the eradius = electron size. +

+

For the peri style, the particles are spherical and each stores a +per-particle mass and volume.

diff --git a/doc/create_atoms.html b/doc/create_atoms.html index e8a7df4ba6..30ae86cb05 100644 --- a/doc/create_atoms.html +++ b/doc/create_atoms.html @@ -148,7 +148,7 @@ to change these values. -

Note that this means the sphere and ellipsoid atom styles set the -diameter/shape and density to 1.0 and thus calculates a mass for the -particle, which is PI/6 * diameter^3 = 0.5236. The peri style sets -the volume and density to 1.0 and thus also set the mass for the -particle to 1.0. +

Note that the sphere 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. +

+

Note that the ellipsoid 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. +

+

Note that the peri style sets the default volume and density to 1.0 +and thus also set the mass for the particle to 1.0. +

+

The set command can be used to override many of these +default settings.

Restrictions:

diff --git a/doc/dump.html b/doc/dump.html index 0b155e3514..418f4996b5 100644 --- a/doc/dump.html +++ b/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, - 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 @@ -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 ellipsoid atom style defines this quantity.

-

The shapex, shapey, and shapez attributes are specific to -extended ellipsoidal particles that have a finite size and shape, such -those defined with an atom style of ellipsoidal. -

-

The quatw, quati, quatj, quatk attributes are for aspherical -particles defined with an atom style of ellipsoid. They are the -components of the quaternion that defines the orientation of the -particle. -

The tqx, tqy, tqz attributes are for extended spherical or aspherical particles that can sustain a rotational torque due to interactions with other particles. diff --git a/doc/dump_image.html b/doc/dump_image.html index 82826a4fd6..a700b3e8e0 100644 --- a/doc/dump_image.html +++ b/doc/dump_image.html @@ -11,6 +11,9 @@

dump image command

+

NOTE: The dump image command has not yet been released as part of +LAMMPS. +

Syntax: 

dump ID group-ID image N file keyword value ... 
diff --git a/doc/dump_image.txt b/doc/dump_image.txt
index 324ba2d7a7..80153f265b 100644
--- a/doc/dump_image.txt
+++ b/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
diff --git a/doc/dump_modify.html b/doc/dump_modify.html
index aad55efb16..c4a2f9c46b 100644
--- a/doc/dump_modify.html
+++ b/doc/dump_modify.html
@@ -11,6 +11,9 @@
 
 
dump_modify command 
 

+
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 ... 
@@ -99,8 +102,6 @@ dump_modify xtcdump precision 10000
 dump_modify 1 every 1000
 dump_modify 1 every v_myVar 
 

-
NOTE: add some image examples
-

 
Description:
 

 
Modify the parameters of a previously defined dump command.  Not all
diff --git a/doc/dump_modify.txt b/doc/dump_modify.txt
index 081a252ec6..715775d416 100644
--- a/doc/dump_modify.txt
+++ b/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
diff --git a/doc/fix_store_state.html b/doc/fix_store_state.html
index 0d1ad87faf..210a552d28 100644
--- a/doc/fix_store_state.html
+++ b/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,
-		        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 
 
      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
diff --git a/doc/read_data.html b/doc/read_data.html
index 136b3b0398..af3d2c5700 100644
--- a/doc/read_data.html
+++ b/doc/read_data.html
@@ -79,6 +79,7 @@ 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
@@ -155,11 +156,16 @@ added to the system when a simulation runs, e.g. by using the  setting is only used with atom_style
+ellipsoid 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.
+
    
 
    
 
 
    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
 
      • BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs,    EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs,    BondBond13 Coeffs, AngleAngle Coeffs = class 2 force field sections 
@@ -282,7 +288,7 @@ of analysis.
 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
@@ -297,12 +303,11 @@ of analysis.
 
      • 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) 
 
      
@@ -330,10 +335,9 @@ 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
@@ -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.
 
      
-
      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
@@ -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.
-
      
-
      Thus if
+listed in the same order they appear as listed above.  Thus if
 
      
 
      atom_style hybrid charge sphere 
 
      
@@ -527,6 +517,50 @@ section must be integers (1, not 1.0).
 
      
 
      
 
+
      Ellipsoids section:
+
      
+
      • one line per ellipsoid 
+
+
      • line syntax: atom-ID shapex shapey shapez quatw quati quatj quatk 
+
+
          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 
+
        
+
      • example: 
+
+
          12 3 17 29 
+
        
+
+
      
+
      The Ellipsoids section must appear if atom_style
+ellipsoid 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.
+
      
+
      
+
 
      EndBondTorsion Coeffs section:
 
      
 
      • one line per dihedral type 
diff --git a/doc/read_data.txt b/doc/read_data.txt
index ec7a5d85d9..52af541f96 100644
--- a/doc/read_data.txt
+++ b/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
-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
diff --git a/doc/set.html b/doc/set.html
index ebbe56870e..5bda7a4db6 100644
--- a/doc/set.html
+++ b/doc/set.html
@@ -141,23 +141,25 @@ 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
-have 3 shape paraeters whicha are used to specify the aspect ratios of
-an ellipsoidal particle, which is oriented by default with its x-axis
-along the simulation box's x-axis, and similarly for y and z.  If this
-body is rotated (via the right-hand rule) by an angle theta around a
-unit rotation vector (a,b,c), then the quaternion that represents its
-new orientation is given by (cos(theta/2), a*sin(theta/2),
-b*sin(theta/2), c*sin(theta/2)).  The theta and a,b,c values are the
-arguments to the quat keyword.  LAMMPS normalizes the quaternion in
-case (a,b,c) was not specified as a unit vector.  For 2d systems, the
-a,b,c values are ignored, since a rotation vector of (0,0,1) is the
-only valid choice.
+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.
+xy plane are generated.  As with keyword quat, 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
 must be finite-size spheres as defined by the atom_style
@@ -172,13 +174,13 @@ particles must be aspherical ellipsoids as defined by the read_data command.
 
        
-
        Keyword mas sets the mass of all selected particles.  The
-particles must have a per-atom mass attribute, as defined by the
+
        Keyword mass sets the mass of all selected particles.  The particles
+must have a per-atom mass attribute, as defined by the
 atom_style command.  See the "mass" command for how
 to set mass values on a per-type basis.
 
        
@@ -189,7 +191,7 @@ to set mass values on a per-type basis.  If the atom has a radius
 attribute (see atom_style sphere) 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) and its shape parameters are non-zero.
+ellipsoid) and its 3 shape parameters are non-zero.
 Otherwise the mass is set to the density value directly.
 
        
 
        Keyword volume sets the volume of all selected particles.