git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@618 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -322,8 +322,8 @@ description:
 <TR ALIGN="center"><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">uniaxial</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A> 
+<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A> 
 </TD></TR></TABLE></DIV>
 
 <HR>

doc/boundary.html

@@ -43,10 +43,9 @@ commands.
 <P>The style <I>p</I> means the box is periodic, so that particles interact
 across the boundary, and they can exit one end of the box and re-enter
 the other end.  A periodic dimension can change in size due to
-constant pressure boundary conditions or volume rescaling (see the
+constant pressure boundary conditions or box deformation (see the <A HREF = "fix_npt.html">fix
-<A HREF = "fix_npt.html">fix npt</A> and <A HREF = "fix_volume_rescale.html">fix volume/rescale</A>
+npt</A> and <A HREF = "fix_deform.html">fix deform</A> commands).  The <I>p</I>
-commands).  The <I>p</I> style must be applied to both faces of a
+style must be applied to both faces of a dimension.
-dimension.
 </P>
 <P>The styles <I>f</I>, <I>s</I>, and <I>m</I> mean the box is non-periodic, so that
 particles do not interact across the boundary and do not move from one

doc/fix.html

@@ -103,9 +103,7 @@ made to the old fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
 <LI><A HREF = "fix_spring_self.html">fix spring/self</A> - spring from each atom to its origin
 <LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A> - temperature control by      velocity rescaling
 <LI><A HREF = "fix_tmd.html">fix tmd</A> - guide a group of atoms to a new configuration
-<LI><A HREF = "fix_uniaxial.html">fix uniaxial</A> - uniaxial straining of system while      preserving total volume
 <LI><A HREF = "fix_viscous.html">fix viscous</A> - viscous damping for granular simulations
-<LI><A HREF = "fix_volume_rescale.html">fix volume/rescale</A> - density control by      volume rescaling
 <LI><A HREF = "fix_wall_gran.html">fix wall/gran</A> - frictional wall(s) for      granular simulations
 <LI><A HREF = "fix_wall_lj93.html">fix wall/lj93</A> - Lennard-Jones 9-3 wall
 <LI><A HREF = "fix_wall_lj126.html">fix wall/lj126</A> - Lennard-Jones 12-6 wall

doc/pair_gayberne.html

@@ -68,12 +68,12 @@ commands:
 </P>
 <UL><LI>epsilon = well depth (energy units)
 <LI>sigma = minimum effective particle radii (distance units)
-<LI>a = ellipsoid radius in x dimension (distance units)
+<LI>epsilon_i_a = relative well depth of I for side-to-side interactions
-<LI>b = ellipsoid radius in y dimension (distance units)
+<LI>epsilon_i_b = relative well depth of I for face-to-face interactions
-<LI>c = ellipsoid radius in z dimension (distance units)
+<LI>epsilon_i_c = relative well depth of I for end-to-end interactions
-<LI>epsilon_a = relative well depth for side-to-side interactions
+<LI>epsilon_j_a = relative well depth of J for side-to-side interactions
-<LI>epsilon_b = relative well depth for face-to-face interactions
+<LI>epsilon_j_b = relative well depth of J for face-to-face interactions
-<LI>epsilon_c = relative well depth for end-to-end interactions
+<LI>epsilon_j_c = relative well depth of J for end-to-end interactions
 <LI>cutoff (distance units) 
 </UL>
 <P>The last coefficient is optional.  If not specified, the global
@@ -94,9 +94,9 @@ above.  The "shift yes" option currently cannot be used with this
 potential to shift energies to 0 at the cutoff due to the anisotropic
 dependence of the interaction.  Angular velocities are all set to zero
 initially.  The Gay-Berne potential does not become isotropic as r
-increases <A HREF = "#Everaers">(Everaers)</A>.  The distance of closest approach
+increases <A HREF = "#Everaers">(Everaers)</A>.  The distance-of-closest-approach
-approximation becomes less accurate as the shape of ellipsoids becomes
+approximation used by the code becomes less accurate as the shape of
-more dissimilar (high aspect ratio particles).
+ellipsoids becomes more dissimilar (high-aspect-ratio particles).
 </P>
 <P><B>Related commands:</B>
 </P>

doc/run.html

@@ -70,8 +70,7 @@ performed and you want a <A HREF = "fix.html">fix</A> command that ramps some va
 of runs and not just a single run.  Fixes in this category include
 <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_npt.html">fix npt</A>, <A HREF = "fix_langevin.html">fix
 langevin</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>,
-<A HREF = "fix_volume_rescale.html">fix volume/rescale</A>, <A HREF = "fix_deform.html">fix
+<A HREF = "fix_deform.html">fix deform</A>, and <A HREF = "fix_indent.html">fix indent</A>.  The
-deform</A>, and <A HREF = "fix_indent.html">fix indent</A>.  The
 <A HREF = "pair_style.html">pair_style soft</A> potential also ramps its
 coefficients in a similar way.
 </P>

doc/shape.html

@@ -48,14 +48,15 @@ longer in x than in y or z and with a circular cross-section in yz.
 Ellipsoids that are spherical can be defined by setting all 3 shape
 components the same.
 </P>
-<P>I can be specified in one of two ways.  An explicit numeric value can
+<P>The I index can be specified in one of two ways.  An explicit numeric
-be used, as in the 1st example above.  Or a wild-card asterik can be
+value can be used, as in the 1st example above.  Or a wild-card
-used to set the mass for multiple atom types.  This takes the form "*"
+asterik can be used to set the mass for multiple atom types.  This
-or "*n" or "n*" or "m*n".  If N = the number of atom types, then an
+takes the form "*" or "*n" or "n*" or "m*n".  If N = the number of
-asterik with no numeric values means all types from 1 to N.  A leading
+atom types, then an asterik with no numeric values means all types
-asterik means all types from 1 to n (inclusive).  A trailing asterik
+from 1 to N.  A leading asterik means all types from 1 to n
-means all types from n to N (inclusive).  A middle asterik means all
+(inclusive).  A trailing asterik means all types from n to N
-types from m to n (inclusive).
+(inclusive).  A middle asterik means all types from m to n
+(inclusive).
 </P>
 <P>A line in a data file that specifies shape uses the same format as the
 arguments of the shape command in an input script, except that no
@@ -63,7 +64,7 @@ wild-card asterik can be used.  For example, under the "Shapes"
 section of a data file, the line that corresponds to the 1st example
 above would be listed as
 </P>
-<PRE>1 1.0 
+<PRE>1 1.0 1.0 1.0 
 </PRE>
 <P><B>Restrictions:</B>
 </P>