git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2819 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_rigid.html

@@ -211,7 +211,7 @@ exclude
 </P>
 <P><B>Default:</B>
 </P>
-<P>The option defaults are force * 1 1 1 and torque * 1 1 1, meaning
+<P>The option defaults are force * on on on and torque * on on on meaning
 all rigid bodies are acted on by center-of-mass force and torque.
 </P>
 </HTML>

doc/fix_rigid.txt

@@ -202,6 +202,6 @@ exclude
 
 [Default:]
 
-The option defaults are force * 1 1 1 and torque * 1 1 1, meaning
+The option defaults are force * on on on and torque * on on on meaning
 all rigid bodies are acted on by center-of-mass force and torque.
 

doc/pair_gayberne.html

@@ -51,17 +51,20 @@ curvatures <A HREF = "#Everaers">(Everaers)</A>:
 <P>The variable names utilized as potential parameters are for the most
 part taken from <A HREF = "#Everaers">(Everaers)</A> in order to be consistent with
 its RE-squared potential fix.  Details on the upsilon and mu
-parameters are given <A HREF = "gbdoc">here</A>.  Use of this pair style requires
+parameters are given <A HREF = "gbdoc">here</A>.
-the NVE, NVT, or NPT fixes with the <I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix
-nve/asphere</A>) in order to integrate particle
-rotation.  Additionally, <A HREF = "atom_style.html">atom_style ellipsoid</A> should
-be used since it defines the rotational state of the ellipsoidal
-particles.
 </P>
 <P>More details of the Gay-Berne formulation are given in the references
 listed below and in <A HREF = "PDF/pair_gayberne_extra.pdf">this supplementary
 document</A>.
 </P>
+<P>Use of this pair style requires the NVE, NVT, or NPT fixes with the
+<I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
+order to integrate particle rotation.  Additionally, <A HREF = "atom_style.html">atom_style
+ellipsoid</A> should be used since it defines the
+rotational state of the ellipsoidal particles.  The size and shape of
+the ellipsoidal particles are defined by the <A HREF = "shape.html">shape</A>
+command.
+</P>
 <P>The following coefficients must be defined for each pair of atoms
 types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
 above, or in the data file or restart files read by the
@@ -81,6 +84,11 @@ commands, or by mixing as described below:
 <P>The last coefficient is optional.  If not specified, the global
 cutoff specified in the pair_style command is used.
 </P>
+<P>It is typical for the Gay-Berne potential to define <I>sigma</I> as the
+minimum of the 3 "shape" diameters for a I,I interaction, though this
+is not required.  Note that this is a different meaning for <I>sigma</I>
+than the <A HREF = "pair_resquared.html">pair_style resquared</A> potential uses.
+</P>
 <P>The epsilon_i and epsilon_j coefficients are actually defined for atom
 types, not for pairs of atom types.  Thus, in a series of pair_coeff
 commands, they only need to be specified once for each atom type.
@@ -149,7 +157,10 @@ to be specified in an input script that reads a restart file.
 </P>
 <P>This style is part of the "asphere" package.  It is only enabled if
 LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
-LAMMPS</A> section for more info.
+LAMMPS</A> section for more info.  You must also
+define a size and shape for each particle type via the
+<A HREF = "shape.html">shape</A> command which requires <A HREF = "atom_style.html">atom_style
+ellipsoid</A>.
 </P>
 <P>The Gay-Berne potential does not become isotropic as r increases
 <A HREF = "#Everaers">(Everaers)</A>.  The distance-of-closest-approach

doc/pair_gayberne.txt

@@ -48,17 +48,20 @@ curvatures "(Everaers)"_#Everaers:
 The variable names utilized as potential parameters are for the most
 part taken from "(Everaers)"_#Everaers in order to be consistent with
 its RE-squared potential fix.  Details on the upsilon and mu
-parameters are given "here"_gbdoc.  Use of this pair style requires
+parameters are given "here"_gbdoc.
-the NVE, NVT, or NPT fixes with the {asphere} extension (e.g. "fix
-nve/asphere"_fix_nve_asphere.html) in order to integrate particle
-rotation.  Additionally, "atom_style ellipsoid"_atom_style.html should
-be used since it defines the rotational state of the ellipsoidal
-particles.
 
 More details of the Gay-Berne formulation are given in the references
 listed below and in "this supplementary
 document"_PDF/pair_gayberne_extra.pdf.
 
+Use of this pair style requires the NVE, NVT, or NPT fixes with the
+{asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
+order to integrate particle rotation.  Additionally, "atom_style
+ellipsoid"_atom_style.html should be used since it defines the
+rotational state of the ellipsoidal particles.  The size and shape of
+the ellipsoidal particles are defined by the "shape"_shape.html
+command.
+
 The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
 above, or in the data file or restart files read by the
@@ -78,6 +81,11 @@ cutoff (distance units) :ul
 The last coefficient is optional.  If not specified, the global
 cutoff specified in the pair_style command is used.
 
+It is typical for the Gay-Berne potential to define {sigma} as the
+minimum of the 3 "shape" diameters for a I,I interaction, though this
+is not required.  Note that this is a different meaning for {sigma}
+than the "pair_style resquared"_pair_resquared.html potential uses.
+ 
 The epsilon_i and epsilon_j coefficients are actually defined for atom
 types, not for pairs of atom types.  Thus, in a series of pair_coeff
 commands, they only need to be specified once for each atom type.
@@ -146,7 +154,10 @@ This pair style can only be used via the {pair} keyword of the
 
 This style is part of the "asphere" package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_3 section for more info.
+LAMMPS"_Section_start.html#2_3 section for more info.  You must also
+define a size and shape for each particle type via the
+"shape"_shape.html command which requires "atom_style
+ellipsoid"_atom_style.html.
 
 The Gay-Berne potential does not become isotropic as r increases
 "(Everaers)"_#Everaers.  The distance-of-closest-approach

doc/pair_resquared.html

@@ -28,7 +28,7 @@ pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0
 <A HREF = "#Everaers">(Everaers)</A>, <A HREF = "#Babadi">(Babadi)</A> between pairs of
 ellipsoidal and/or spherical Lennard-Jones particles.  For ellipsoidal
 interactions, the potential considers the ellipsoid as being comprised
-of small spheres of size sigma. LJ particles are a single sphere of
+of small spheres of size sigma.  LJ particles are a single sphere of
 size sigma.  The distinction is made to allow the pair style to make
 efficient calculations of ellipsoid/solvent interactions.
 </P>
@@ -39,9 +39,9 @@ in <A HREF = "PDF/pair_resquared_extra.pdf">this supplementary document</A>.
 <I>asphere</I> extension (e.g. <A HREF = "fix_nve_asphere.html">fix nve/asphere</A>) in
 order to integrate particle rotation.  Additionally, <A HREF = "atom_style.html">atom_style
 ellipsoid</A> should be used since it defines the
-rotational state of the ellipsoidal particles and the
+rotational state of the ellipsoidal particles.  The size and shape of
-<A HREF = "shape.html">shape</A> command should be used to specify ellipsoid
+the ellipsoidal particles are defined by the <A HREF = "shape.html">shape</A>
-diameters.
+command.
 </P>
 <P>The following coefficients must be defined for each pair of atoms
 types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
@@ -59,6 +59,14 @@ commands:
 <LI>epsilon_j_c = relative well depth of type J for end-to-end interactions
 <LI>cutoff (distance units) 
 </UL>
+<P>The last coefficient is optional.  If not specified, the global
+cutoff specified in the pair_style command is used.
+</P>
+<P>As described above, <I>sigma</I> is the size of the small spheres which are
+integrated over to create the potential.  Note that this is a
+different meaning for <I>sigma</I> than the <A HREF = "pair_gayberne.html">pair_style
+gayberne</A> potential uses.
+</P>
 <P>The parameters used depend on the type of the interacting particles,
 i.e. ellipsoid or LJ sphere.  The type of particle is determined by
 the diameters specified with the <A HREF = "shape.html">shape</A> command.  LJ
@@ -173,7 +181,10 @@ command</A>.
 </P>
 <P>This style is part of the "asphere" package.  It is only enabled if
 LAMMPS was built with that package.  See the <A HREF = "Section_start.html#2_3">Making
-LAMMPS</A> section for more info.
+LAMMPS</A> section for more info.  You must also
+define a size and shape for each particle type via the
+<A HREF = "shape.html">shape</A> command which requires <A HREF = "atom_style.html">atom_style
+ellipsoid</A>.
 </P>
 <P>The distance-of-closest-approach approximation used by LAMMPS becomes 
 less accurate when high-aspect ratio ellipsoids are used.

doc/pair_resquared.txt

@@ -25,7 +25,7 @@ Style {resquared} computes the RE-squared anisotropic interaction
 "(Everaers)"_#Everaers, "(Babadi)"_#Babadi between pairs of
 ellipsoidal and/or spherical Lennard-Jones particles.  For ellipsoidal
 interactions, the potential considers the ellipsoid as being comprised
-of small spheres of size sigma. LJ particles are a single sphere of
+of small spheres of size sigma.  LJ particles are a single sphere of
 size sigma.  The distinction is made to allow the pair style to make
 efficient calculations of ellipsoid/solvent interactions.
 
@@ -36,9 +36,9 @@ Use of this pair style requires the NVE, NVT, or NPT fixes with the
 {asphere} extension (e.g. "fix nve/asphere"_fix_nve_asphere.html) in
 order to integrate particle rotation.  Additionally, "atom_style
 ellipsoid"_atom_style.html should be used since it defines the
-rotational state of the ellipsoidal particles and the
+rotational state of the ellipsoidal particles.  The size and shape of
-"shape"_shape.html command should be used to specify ellipsoid
+the ellipsoidal particles are defined by the "shape"_shape.html
-diameters.
+command.
 
 The following coefficients must be defined for each pair of atoms
 types via the "pair_coeff"_pair_coeff.html command as in the examples
@@ -56,6 +56,14 @@ epsilon_j_b = relative well depth of type J for face-to-face interactions
 epsilon_j_c = relative well depth of type J for end-to-end interactions
 cutoff (distance units) :ul
 
+The last coefficient is optional.  If not specified, the global
+cutoff specified in the pair_style command is used.
+
+As described above, {sigma} is the size of the small spheres which are
+integrated over to create the potential.  Note that this is a
+different meaning for {sigma} than the "pair_style
+gayberne"_pair_gayberne.html potential uses.
+
 The parameters used depend on the type of the interacting particles,
 i.e. ellipsoid or LJ sphere.  The type of particle is determined by
 the diameters specified with the "shape"_shape.html command.  LJ
@@ -170,7 +178,10 @@ command"_run_style.html.
 
 This style is part of the "asphere" package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
-LAMMPS"_Section_start.html#2_3 section for more info.
+LAMMPS"_Section_start.html#2_3 section for more info.  You must also
+define a size and shape for each particle type via the
+"shape"_shape.html command which requires "atom_style
+ellipsoid"_atom_style.html.
 
 The distance-of-closest-approach approximation used by LAMMPS becomes 
 less accurate when high-aspect ratio ellipsoids are used.