git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14348 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/compute_chunk_atom.html

@@ -136,7 +136,7 @@
 <li>chunk/atom = style name of this compute command</li>
 </ul>
 <pre class="literal-block">
-style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>type</em> or <em>molecule</em> or <em>compute/fix/variable</em>
+style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>bin/sphere</em> or <em>type</em> or <em>molecule</em> or <em>compute/fix/variable</em>
   <em>bin/1d</em> args = dim origin delta
     dim = <em>x</em> or <em>y</em> or <em>z</em>
     origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
@@ -149,6 +149,10 @@ style = <em>bin/1d</em> or <em>bin/2d</em> or <em>bin/3d</em> or <em>type</em> o
     dim = <em>x</em> or <em>y</em> or <em>z</em>
     origin = <em>lower</em> or <em>center</em> or <em>upper</em> or coordinate value (distance units)
     delta = thickness of spatial bins in dim (distance units)
+  <em>bin/sphere</em> args = xorig yorig zorig rmin rmax nrbin
+    xorig,yorig,zorig = center point of sphere
+    rmin,rmax = bin from radius rmin to rmax
+    nrbin = # of bins between rmin and rmax
   <em>type</em> args = none
   <em>molecule</em> args = none
   <em>compute/fix/variable</em> = c_ID, c_ID[I], f_ID, f_ID[I], v_name with no args

doc/compute_chunk_atom.txt

@@ -14,7 +14,7 @@ compute ID group-ID chunk/atom style args keyword values ... :pre
 
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 chunk/atom = style name of this compute command :l
-style = {bin/1d} or {bin/2d} or {bin/3d} or {type} or {molecule} or {compute/fix/variable}
+style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} or {compute/fix/variable}
   {bin/1d} args = dim origin delta
     dim = {x} or {y} or {z}
     origin = {lower} or {center} or {upper} or coordinate value (distance units)
@@ -27,6 +27,10 @@ style = {bin/1d} or {bin/2d} or {bin/3d} or {type} or {molecule} or {compute/fix
     dim = {x} or {y} or {z}
     origin = {lower} or {center} or {upper} or coordinate value (distance units)
     delta = thickness of spatial bins in dim (distance units)
+  {bin/sphere} args = xorig yorig zorig rmin rmax nrbin
+    xorig,yorig,zorig = center point of sphere
+    rmin,rmax = bin from radius rmin to rmax
+    nrbin = # of bins between rmin and rmax
   {type} args = none
   {molecule} args = none
   {compute/fix/variable} = c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name with no args

doc/fix_drude_transform.html

@@ -150,7 +150,7 @@ fix 1 all drude/transform/inverse
 <h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
 <p>Transform the coordinates of Drude oscillators from real to reduced
 and back for thermalizing the Drude oscillators as described in
-<a class="reference internal" href="#lamoureux"><span>(Lamoureux)</span></a> using a Nose-Hoover thermostat.  This fix is
+<a class="reference internal" href="tutorial_drude.html#lamoureux"><span>(Lamoureux)</span></a> using a Nose-Hoover thermostat.  This fix is
 designed to be used with the <a class="reference internal" href="tutorial_drude.html"><em>thermalized Drude oscillator model</em></a>.  Polarizable models in LAMMPS are
 described in <a class="reference internal" href="Section_howto.html#howto-25"><span>this Section</span></a>.</p>
 <p>Drude oscillators are a pair of atoms representing a single

doc/fix_langevin_drude.html

@@ -158,7 +158,7 @@ fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes
 </div>
 <div class="section" id="description">
 <h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
-<p>Apply two Langevin thermostats as described in <a class="reference internal" href="#jiang"><span>(Jiang)</span></a> for
+<p>Apply two Langevin thermostats as described in <a class="reference internal" href="tutorial_drude.html#jiang"><span>(Jiang)</span></a> for
 thermalizing the reduced degrees of freedom of Drude oscillators.
 This link describes how to use the <a class="reference internal" href="tutorial_drude.html"><em>thermalized Drude oscillator model</em></a> in LAMMPS and polarizable models in LAMMPS
 are discussed in <a class="reference internal" href="Section_howto.html#howto-25"><span>this Section</span></a>.</p>

doc/pair_thole.html

@@ -158,28 +158,30 @@ main pair style including Coulomb interactions, i.e. any pair style
 containing <em>coul/cut</em> or <em>coul/long</em> in its style name.</p>
 <p>The <em>thole</em> pair style computes the Coulomb interaction damped at
 short distances by a function</p>
-<p>begin{equation} T_{ij}(r_{ij}) = 1 - left( 1 +
-frac{s_{ij} r_{ij} }{2} right)
-exp left( - s_{ij} r_{ij} right) end{equation}</p>
+<div class="math">
+\[\begin{equation} T_{ij}(r_{ij}) = 1 - \left( 1 +
+\frac{s_{ij} r_{ij} }{2} \right)
+\exp \left( - s_{ij} r_{ij} \right) \end{equation}\]</div>
 <p>This function results from an adaptation to point charges
 <a class="reference internal" href="#noskov"><span>(Noskov)</span></a> of the dipole screening scheme originally proposed
-by <a class="reference internal" href="#thole"><span>Thole</span></a>. The scaling coefficient (s_{ij} ) is determined
-by the polarizability of the atoms, ( alpha_i ), and by a Thole
-damping parameter ( a ).  This Thole damping parameter usually takes
+by <a class="reference internal" href="#thole"><span>Thole</span></a>. The scaling coefficient <span class="math">\(s_{ij}\)</span> is determined
+by the polarizability of the atoms, <span class="math">\(\alpha_i\)</span>, and by a Thole
+damping parameter <span class="math">\(a\)</span>.  This Thole damping parameter usually takes
 a value of 2.6, but in certain force fields the value can depend upon
 the atom types. The mixing rule for Thole damping parameters is the
 arithmetic average, and for polarizabilities the geometric average
 between the atom-specific values.</p>
-<p>begin{equation} s_{ij} = frac{ a_{ij} }{
-(alpha_{ij})^{1/3} } = frac{ (a_i + a_j)/2 }{
-[(alpha_ialpha_j)^{1/2}]^{1/3} } end{equation}</p>
+<div class="math">
+\[\begin{equation} s_{ij} = \frac{ a_{ij} }{
+(\alpha_{ij})^{1/3} } = \frac{ (a_i + a_j)/2 }{
+[(\alpha_i\alpha_j)^{1/2}]^{1/3} } \end{equation}\]</div>
 <p>The damping function is only applied to the interactions between the
 point charges representing the induced dipoles on polarizable sites,
-that is, charges on Drude particles, ( q_{D,i} ), and opposite
-charges, ( -q_{D,i} ), located on the respective core particles
+that is, charges on Drude particles, <span class="math">\(q_{D,i}\)</span>, and opposite
+charges, <span class="math">\(-q_{D,i}\)</span>, located on the respective core particles
 (to which each Drude particle is bonded). Therefore, Thole screening
-is not applied to the full charge of the core particle ( q_i ), but
-only to the ( -q_{D,i} ) part of it.</p>
+is not applied to the full charge of the core particle <span class="math">\(q_i\)</span>, but
+only to the <span class="math">\(-q_{D,i}\)</span> part of it.</p>
 <p>The interactions between core charges are subject to the weighting
 factors set by the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command. The
 interactions between Drude particles and core charges or