git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9369 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/dump.html

@@ -454,22 +454,21 @@ defined with an atom style of <I>dipole</I>.  They give the orientation of
 the atom's point dipole moment.  The <I>mu</I> attribute gives the
 magnitude of the atom's dipole moment.
 </P>
-<P>The <I>radius</I> and <I>diameter</I> attributes are specific to extended
-spherical particles that have a finite size, such as those defined
-with an atom style of <I>sphere</I>.
+<P>The <I>radius</I> and <I>diameter</I> attributes are specific to spherical
+particles that have a finite size, such as those defined with an atom
+style of <I>sphere</I>.
 </P>
 <P>The <I>omegax</I>, <I>omegay</I>, and <I>omegaz</I> attributes are specific to
-extended spherical or aspherical particles that have an angular
-velocity.  Only certain atom styles, such as <I>sphere</I> define this
-quantity.
+finite-size spherical particles that have an angular velocity.  Only
+certain atom styles, such as <I>sphere</I> define this quantity.
 </P>
 <P>The <I>angmomx</I>, <I>angmomy</I>, and <I>angmomz</I> attributes are specific to
-extended aspherical particles that have an angular momentum.  Only
+finite-size aspherical particles that have an angular momentum.  Only
 the <I>ellipsoid</I> atom style defines this quantity.
 </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.
+<P>The <I>tqx</I>, <I>tqy</I>, <I>tqz</I> attributes are for finite-size particles that
+can sustain a rotational torque due to interactions with other
+particles.
 </P>
 <P>The <I>spin</I>, <I>eradius</I>, <I>ervel</I>, and <I>erforce</I> attributes are for
 particles that represent nuclei and electrons modeled with the

doc/dump.txt

@@ -442,22 +442,21 @@ defined with an atom style of {dipole}.  They give the orientation of
 the atom's point dipole moment.  The {mu} attribute gives the
 magnitude of the atom's dipole moment.
 
-The {radius} and {diameter} attributes are specific to extended
-spherical particles that have a finite size, such as those defined
-with an atom style of {sphere}.
+The {radius} and {diameter} attributes are specific to spherical
+particles that have a finite size, such as those defined with an atom
+style of {sphere}.
 
 The {omegax}, {omegay}, and {omegaz} attributes are specific to
-extended spherical or aspherical particles that have an angular
-velocity.  Only certain atom styles, such as {sphere} define this
-quantity.
+finite-size spherical particles that have an angular velocity.  Only
+certain atom styles, such as {sphere} define this quantity.
 
 The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
-extended aspherical particles that have an angular momentum.  Only
+finite-size aspherical particles that have an angular momentum.  Only
 the {ellipsoid} atom style defines this quantity.
 
-The {tqx}, {tqy}, {tqz} attributes are for extended spherical or
-aspherical particles that can sustain a rotational torque due
-to interactions with other particles.
+The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that
+can sustain a rotational torque due to interactions with other
+particles.
 
 The {spin}, {eradius}, {ervel}, and {erforce} attributes are for
 particles that represent nuclei and electrons modeled with the

doc/fix_langevin.html

@@ -93,11 +93,10 @@ a Gaussian random number) for speed.
 <P>Note that unless you use the <I>omega</I> or <I>angmom</I> keywords, the
 thermostat effect of this fix is applied to only the translational
 degrees of freedom for the particles, which is an important
-consideration if extended spherical or aspherical particles, which
-have rotational degrees of freedom, are being thermostatted.  The
-translational degrees of freedom can also have a bias velocity removed
-from them before thermostatting takes place; see the description
-below.
+consideration for finite-size particles, which have rotational degrees
+of freedom, are being thermostatted.  The translational degrees of
+freedom can also have a bias velocity removed from them before
+thermostatting takes place; see the description below.
 </P>
 <P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
 performs Nose/Hoover thermostatting AND time integration, this fix

doc/fix_langevin.txt

@@ -81,11 +81,10 @@ a Gaussian random number) for speed.
 Note that unless you use the {omega} or {angmom} keywords, the
 thermostat effect of this fix is applied to only the translational
 degrees of freedom for the particles, which is an important
-consideration if extended spherical or aspherical particles, which
-have rotational degrees of freedom, are being thermostatted.  The
-translational degrees of freedom can also have a bias velocity removed
-from them before thermostatting takes place; see the description
-below.
+consideration for finite-size particles, which have rotational degrees
+of freedom, are being thermostatted.  The translational degrees of
+freedom can also have a bias velocity removed from them before
+thermostatting takes place; see the description below.
 
 IMPORTANT NOTE: Unlike the "fix nvt"_fix_nh.html command which
 performs Nose/Hoover thermostatting AND time integration, this fix

doc/fix_nph_sphere.html

@@ -29,8 +29,8 @@ fix 2 water nph/sphere aniso 0.0 0.0 1000.0 dilate partial
 <P><B>Description:</B>
 </P>
 <P>Perform constant NPH integration to update position, velocity, and
-angular velocity each timestep for extended spherical particles in the
-group using a Nose/Hoover pressure barostat.  P is pressure; H is
+angular velocity each timestep for finite-size spherical particles in
+the group using a Nose/Hoover pressure barostat.  P is pressure; H is
 enthalpy.  This creates a system trajectory consistent with the
 isenthalpic ensemble.
 </P>

doc/fix_nph_sphere.txt

@@ -26,8 +26,8 @@ fix 2 water nph/sphere aniso 0.0 0.0 1000.0 dilate partial :pre
 [Description:]
 
 Perform constant NPH integration to update position, velocity, and
-angular velocity each timestep for extended spherical particles in the
-group using a Nose/Hoover pressure barostat.  P is pressure; H is
+angular velocity each timestep for finite-size spherical particles in
+the group using a Nose/Hoover pressure barostat.  P is pressure; H is
 enthalpy.  This creates a system trajectory consistent with the
 isenthalpic ensemble.
 

doc/fix_npt_sphere.html

@@ -29,8 +29,8 @@ fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partia
 <P><B>Description:</B>
 </P>
 <P>Perform constant NPT integration to update position, velocity, and
-angular velocity each timestep for extended spherical particles in the
-group using a Nose/Hoover temperature thermostat and Nose/Hoover
+angular velocity each timestep for finite-sizex spherical particles in
+the group using a Nose/Hoover temperature thermostat and Nose/Hoover
 pressure barostat.  P is pressure; T is temperature.  This creates a
 system trajectory consistent with the isothermal-isobaric ensemble.
 </P>

doc/fix_npt_sphere.txt

@@ -26,8 +26,8 @@ fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partia
 [Description:]
 
 Perform constant NPT integration to update position, velocity, and
-angular velocity each timestep for extended spherical particles in the
-group using a Nose/Hoover temperature thermostat and Nose/Hoover
+angular velocity each timestep for finite-sizex spherical particles in
+the group using a Nose/Hoover temperature thermostat and Nose/Hoover
 pressure barostat.  P is pressure; T is temperature.  This creates a
 system trajectory consistent with the isothermal-isobaric ensemble.
 

doc/fix_nve_sphere.html

@@ -38,7 +38,7 @@ fix 1 all nve/sphere update dipole
 <P><B>Description:</B>
 </P>
 <P>Perform constant NVE integration to update position, velocity, and
-angular velocity for extended spherical particles in the group each
+angular velocity for finite-size spherical particles in the group each
 timestep.  V is volume; E is energy.  This creates a system trajectory
 consistent with the microcanonical ensemble.
 </P>

doc/fix_nve_sphere.txt

@@ -29,7 +29,7 @@ fix 1 all nve/sphere update dipole :pre
 [Description:]
 
 Perform constant NVE integration to update position, velocity, and
-angular velocity for extended spherical particles in the group each
+angular velocity for finite-size spherical particles in the group each
 timestep.  V is volume; E is energy.  This creates a system trajectory
 consistent with the microcanonical ensemble.
 

doc/fix_nvt_sphere.html

@@ -27,9 +27,9 @@ fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2
 <P><B>Description:</B>
 </P>
 <P>Perform constant NVT integration to update position, velocity, and
-angular velocity each timestep for extended spherical particles in the
-group using a Nose/Hoover temperature thermostat.  V is volume; T is
-temperature.  This creates a system trajectory consistent with the
+angular velocity each timestep for finite-size spherical particles in
+the group using a Nose/Hoover temperature thermostat.  V is volume; T
+is temperature.  This creates a system trajectory consistent with the
 canonical ensemble.
 </P>
 <P>This fix differs from the <A HREF = "fix_nh.html">fix nvt</A> command, which

doc/fix_nvt_sphere.txt

@@ -24,9 +24,9 @@ fix 1 all nvt/sphere temp 300.0 300.0 100.0 drag 0.2 :pre
 [Description:]
 
 Perform constant NVT integration to update position, velocity, and
-angular velocity each timestep for extended spherical particles in the
-group using a Nose/Hoover temperature thermostat.  V is volume; T is
-temperature.  This creates a system trajectory consistent with the
+angular velocity each timestep for finite-size spherical particles in
+the group using a Nose/Hoover temperature thermostat.  V is volume; T
+is temperature.  This creates a system trajectory consistent with the
 canonical ensemble.
 
 This fix differs from the "fix nvt"_fix_nh.html command, which

doc/fix_store_state.html

@@ -43,10 +43,10 @@
       fx,fy,fz = forces on atoms
       q = atom charge
       mux,muy,muz = orientation of dipolar atom
-      radius = radius of extended spherical particle
-      omegax,omegay,omegaz = angular velocity of extended particle
-      angmomx,angmomy,angmomz = angular momentum of extended particle
-      tqx,tqy,tqz = torque on extended particles
+      radius = radius of spherical particle
+      omegax,omegay,omegaz = angular velocity of spherical particle
+      angmomx,angmomy,angmomz = angular momentum of aspherical particle
+      tqx,tqy,tqz = torque on finite-size 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
       f_ID = per-atom vector calculated by a fix with ID

doc/fix_store_state.txt

@@ -36,10 +36,10 @@ input = one or more atom attributes :l
       fx,fy,fz = forces on atoms
       q = atom charge
       mux,muy,muz = orientation of dipolar atom
-      radius = radius of extended spherical particle
-      omegax,omegay,omegaz = angular velocity of extended particle
-      angmomx,angmomy,angmomz = angular momentum of extended particle
-      tqx,tqy,tqz = torque on extended particles
+      radius = radius of spherical particle
+      omegax,omegay,omegaz = angular velocity of spherical particle
+      angmomx,angmomy,angmomz = angular momentum of aspherical particle
+      tqx,tqy,tqz = torque on finite-size 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
       f_ID = per-atom vector calculated by a fix with ID

doc/fix_temp_berendsen.html

@@ -38,11 +38,11 @@ thermostat <A HREF = "#Berendsen">(Berendsen)</A>, which rescales their velociti
 every timestep.
 </P>
 <P>The thermostat is applied to only the translational degrees of freedom
-for the particles, which is an important consideration if extended
-spherical or aspherical particles which have rotational degrees of
-freedom are being thermostatted with this fix.  The translational
-degrees of freedom can also have a bias velocity removed from them
-before thermostatting takes place; see the description below.
+for the particles, which is an important consideration for finite-size
+particles which have rotational degrees of freedom are being
+thermostatted with this fix.  The translational degrees of freedom can
+also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
 </P>
 <P>The desired temperature at each timestep is a ramped value during the
 run from <I>Tstart</I> to <I>Tstop</I>.  The <I>Tdamp</I> parameter is specified in

doc/fix_temp_berendsen.txt

@@ -30,11 +30,11 @@ thermostat "(Berendsen)"_#Berendsen, which rescales their velocities
 every timestep.
 
 The thermostat is applied to only the translational degrees of freedom
-for the particles, which is an important consideration if extended
-spherical or aspherical particles which have rotational degrees of
-freedom are being thermostatted with this fix.  The translational
-degrees of freedom can also have a bias velocity removed from them
-before thermostatting takes place; see the description below.
+for the particles, which is an important consideration for finite-size
+particles which have rotational degrees of freedom are being
+thermostatted with this fix.  The translational degrees of freedom can
+also have a bias velocity removed from them before thermostatting
+takes place; see the description below.
 
 The desired temperature at each timestep is a ramped value during the
 run from {Tstart} to {Tstop}.  The {Tdamp} parameter is specified in

doc/pair_gayberne.html

@@ -200,7 +200,7 @@ diameter.
 <P>This pair style requires that atoms be ellipsoids as defined by the
 <A HREF = "atom_style.html">atom_style ellipsoid</A> command.
 </P>
-<P>Particles acted on by the potential can be extended aspherical or
+<P>Particles acted on by the potential can be finite-size aspherical or
 spherical particles, or point particles.  Spherical particles have all
 3 of their shape parameters equal to each other.  Point particles have
 all 3 of their shape parameters equal to 0.0.

doc/pair_gayberne.txt

@@ -195,7 +195,7 @@ diameter.
 This pair style requires that atoms be ellipsoids as defined by the
 "atom_style ellipsoid"_atom_style.html command.
 
-Particles acted on by the potential can be extended aspherical or
+Particles acted on by the potential can be finite-size aspherical or
 spherical particles, or point particles.  Spherical particles have all
 3 of their shape parameters equal to each other.  Point particles have
 all 3 of their shape parameters equal to 0.0.

doc/pair_resquared.html

@@ -214,7 +214,7 @@ LAMMPS</A> section for more info.
 <P>This pair style requires that atoms be ellipsoids as defined by the
 <A HREF = "atom_style.html">atom_style ellipsoid</A> command.
 </P>
-<P>Particles acted on by the potential can be extended aspherical or
+<P>Particles acted on by the potential can be finite-size aspherical or
 spherical particles, or point particles.  Spherical particles have all
 3 of their shape parameters equal to each other.  Point particles have
 all 3 of their shape parameters equal to 0.0.

doc/pair_resquared.txt

@@ -209,7 +209,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 This pair style requires that atoms be ellipsoids as defined by the
 "atom_style ellipsoid"_atom_style.html command.
 
-Particles acted on by the potential can be extended aspherical or
+Particles acted on by the potential can be finite-size aspherical or
 spherical particles, or point particles.  Spherical particles have all
 3 of their shape parameters equal to each other.  Point particles have
 all 3 of their shape parameters equal to 0.0.