git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15325 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/html/Section_commands.html

@@ -1410,8 +1410,8 @@ used if <a class="reference internal" href="Section_start.html#start-3"><span cl
 <td><a class="reference internal" href="dihedral_nharmonic.html"><span class="doc">nharmonic (o)</span></a></td>
 <td><a class="reference internal" href="dihedral_quadratic.html"><span class="doc">quadratic (o)</span></a></td>
 </tr>
-<tr class="row-even"><td><a class="reference internal" href="dihedral_table.html"><span class="doc">table (o)</span></a></td>
+<tr class="row-even"><td><a class="reference internal" href="dihedral_spherical.html"><span class="doc">spherical (o)</span></a></td>
-<td>&nbsp;</td>
+<td><a class="reference internal" href="dihedral_table.html"><span class="doc">table (o)</span></a></td>
 <td>&nbsp;</td>
 <td>&nbsp;</td>
 </tr>

doc/html/_sources/Section_commands.txt

@@ -764,7 +764,7 @@ used if :ref:`LAMMPS is built with the appropriate package <start_3>`.
 +---------------------------------------------------------+---------------------------------------+-------------------------------------------+-------------------------------------------+
 | :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>` | :doc:`fourier (o) <dihedral_fourier>` | :doc:`nharmonic (o) <dihedral_nharmonic>` | :doc:`quadratic (o) <dihedral_quadratic>` |
 +---------------------------------------------------------+---------------------------------------+-------------------------------------------+-------------------------------------------+
-| :doc:`table (o) <dihedral_table>`                       |                                       |                                           |                                           |
+| :doc:`spherical (o) <dihedral_spherical>`               | :doc:`table (o) <dihedral_table>`     |                                           |                                           |
 +---------------------------------------------------------+---------------------------------------+-------------------------------------------+-------------------------------------------+
 
 

doc/html/_sources/fix_deposit.txt

@@ -17,7 +17,7 @@ Syntax
 * M = insert a single atom or molecule every M steps
 * seed = random # seed (positive integer)
 * one or more keyword/value pairs may be appended to args
-* keyword = *region* or *id* or *global* or *local* or *near* or *attempt* or *rate* or *vx* or *vy* or *vz* or *mol* or *rigid* or *shake* or *units*
+* keyword = *region* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *mol* or *rigid* or *shake* or *units*
 .. parsed-literal::
 
      *region* value = region-ID
@@ -32,6 +32,9 @@ Syntax
        delta = lateral distance within which a neighbor is considered "nearby" (distance units)
      *near* value = R
        R = only insert atom/molecule if further than R from existing particles (distance units)
+     *gaussian* values = xmid ymid zmid sigma
+       xmid,ymid,zmid = center of the gaussian distribution (distance units)
+       sigma = width of gaussian distribution (distance units)
      *attempt* value = Q
        Q = attempt a single insertion up to Q times
      *rate* value = V
@@ -66,6 +69,7 @@ Examples
    fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
    fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
    fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice
+   fix 5 insert deposit 200 2 100 777 region disk gaussian 5.0 5.0 9.0 1.0 units box
 
 Description
 """""""""""
@@ -126,6 +130,11 @@ side = *in*\ .
    atoms" error.  Thus for triclinic boxes you should insure the
    specified region is wholly inside the simulation box.
 
+The locations of inserted particles are taken from uniform distributed
+random numbers, unless the *gaussian* keyword is used. Then the
+individual coordinates are taken from a gaussian distribution of
+width *sigma* centered on *xmid,ymid,zmid*\ .
+
 Individual atoms are inserted, unless the *mol* keyword is used.  It
 specifies a *template-ID* previously defined using the
 :doc:`molecule <molecule>` command, which reads files that define one or

doc/html/fix_deposit.html

@@ -139,7 +139,7 @@
 <li>M = insert a single atom or molecule every M steps</li>
 <li>seed = random # seed (positive integer)</li>
 <li>one or more keyword/value pairs may be appended to args</li>
-<li>keyword = <em>region</em> or <em>id</em> or <em>global</em> or <em>local</em> or <em>near</em> or <em>attempt</em> or <em>rate</em> or <em>vx</em> or <em>vy</em> or <em>vz</em> or <em>mol</em> or <em>rigid</em> or <em>shake</em> or <em>units</em></li>
+<li>keyword = <em>region</em> or <em>id</em> or <em>global</em> or <em>local</em> or <em>near</em> or <em>gaussian</em> or <em>attempt</em> or <em>rate</em> or <em>vx</em> or <em>vy</em> or <em>vz</em> or <em>mol</em> or <em>rigid</em> or <em>shake</em> or <em>units</em></li>
 </ul>
 <pre class="literal-block">
 <em>region</em> value = region-ID
@@ -154,6 +154,9 @@
   delta = lateral distance within which a neighbor is considered &quot;nearby&quot; (distance units)
 <em>near</em> value = R
   R = only insert atom/molecule if further than R from existing particles (distance units)
+<em>gaussian</em> values = xmid ymid zmid sigma
+  xmid,ymid,zmid = center of the gaussian distribution (distance units)
+  sigma = width of gaussian distribution (distance units)
 <em>attempt</em> value = Q
   Q = attempt a single insertion up to Q times
 <em>rate</em> value = V
@@ -184,6 +187,7 @@
 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">3</span> <span class="nb">all</span> <span class="n">deposit</span> <span class="mi">1000</span> <span class="mi">2</span> <span class="mi">100</span> <span class="mi">29494</span> <span class="n">region</span> <span class="n">myblock</span> <span class="n">local</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="n">units</span> <span class="n">box</span>
 <span class="n">fix</span> <span class="mi">2</span> <span class="n">newatoms</span> <span class="n">deposit</span> <span class="mi">10000</span> <span class="mi">1</span> <span class="mi">500</span> <span class="mi">12345</span> <span class="n">region</span> <span class="n">disk</span> <span class="n">near</span> <span class="mf">2.0</span> <span class="n">vz</span> <span class="o">-</span><span class="mf">1.0</span> <span class="o">-</span><span class="mf">0.8</span>
 <span class="n">fix</span> <span class="mi">4</span> <span class="n">sputter</span> <span class="n">deposit</span> <span class="mi">1000</span> <span class="mi">2</span> <span class="mi">500</span> <span class="mi">12235</span> <span class="n">region</span> <span class="n">sphere</span> <span class="n">vz</span> <span class="o">-</span><span class="mf">1.0</span> <span class="o">-</span><span class="mf">1.0</span> <span class="n">target</span> <span class="mf">5.0</span> <span class="mf">5.0</span> <span class="mf">0.0</span> <span class="n">units</span> <span class="n">lattice</span>
+<span class="n">fix</span> <span class="mi">5</span> <span class="n">insert</span> <span class="n">deposit</span> <span class="mi">200</span> <span class="mi">2</span> <span class="mi">100</span> <span class="mi">777</span> <span class="n">region</span> <span class="n">disk</span> <span class="n">gaussian</span> <span class="mf">5.0</span> <span class="mf">5.0</span> <span class="mf">9.0</span> <span class="mf">1.0</span> <span class="n">units</span> <span class="n">box</span>
 </pre></div>
 </div>
 </div>
@@ -239,6 +243,10 @@ tilted box, then an insertion will likely fail, leading to a &#8220;lost
 atoms&#8221; error.  Thus for triclinic boxes you should insure the
 specified region is wholly inside the simulation box.</p>
 </div>
+<p>The locations of inserted particles are taken from uniform distributed
+random numbers, unless the <em>gaussian</em> keyword is used. Then the
+individual coordinates are taken from a gaussian distribution of
+width <em>sigma</em> centered on <em>xmid,ymid,zmid</em>.</p>
 <p>Individual atoms are inserted, unless the <em>mol</em> keyword is used.  It
 specifies a <em>template-ID</em> previously defined using the
 <a class="reference internal" href="molecule.html"><span class="doc">molecule</span></a> command, which reads files that define one or

doc/src/Section_commands.txt

@@ -1078,6 +1078,7 @@ package"_Section_start.html#start_3.
 "fourier (o)"_dihedral_fourier.html,
 "nharmonic (o)"_dihedral_nharmonic.html,
 "quadratic (o)"_dihedral_quadratic.html,
+"spherical (o)"_dihedral_spherical.html,
 "table (o)"_dihedral_table.html :tb(c=4,ea=c)
 
 :line

doc/src/fix_deposit.txt

@@ -19,7 +19,7 @@ type = atom type to assign to inserted atoms (offset for moleclue insertion) :l
 M = insert a single atom or molecule every M steps :l
 seed = random # seed (positive integer) :l
 one or more keyword/value pairs may be appended to args :l
-keyword = {region} or {id} or {global} or {local} or {near} or {attempt} or {rate} or {vx} or {vy} or {vz} or {mol} or {rigid} or {shake} or {units} :l
+keyword = {region} or {id} or {global} or {local} or {near} or {gaussian} or {attempt} or {rate} or {vx} or {vy} or {vz} or {mol} or {rigid} or {shake} or {units} :l
   {region} value = region-ID
     region-ID = ID of region to use as insertion volume
   {id} value = {max} or {next}
@@ -32,6 +32,9 @@ keyword = {region} or {id} or {global} or {local} or {near} or {attempt} or {rat
     delta = lateral distance within which a neighbor is considered "nearby" (distance units)
   {near} value = R
     R = only insert atom/molecule if further than R from existing particles (distance units)
+  {gaussian} values = xmid ymid zmid sigma
+    xmid,ymid,zmid = center of the gaussian distribution (distance units)
+    sigma = width of gaussian distribution (distance units)
   {attempt} value = Q
     Q = attempt a single insertion up to Q times
   {rate} value = V
@@ -61,7 +64,8 @@ keyword = {region} or {id} or {global} or {local} or {near} or {attempt} or {rat
 
 fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
 fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
-fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice :pre
+fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice
+fix 5 insert deposit 200 2 100 777 region disk gaussian 5.0 5.0 9.0 1.0 units box :pre
 
 [Description:]
 
@@ -119,6 +123,11 @@ tilted box, then an insertion will likely fail, leading to a "lost
 atoms" error.  Thus for triclinic boxes you should insure the
 specified region is wholly inside the simulation box.
 
+The locations of inserted particles are taken from uniform distributed
+random numbers, unless the {gaussian} keyword is used. Then the
+individual coordinates are taken from a gaussian distribution of
+width {sigma} centered on {xmid,ymid,zmid}.
+
 Individual atoms are inserted, unless the {mol} keyword is used.  It
 specifies a {template-ID} previously defined using the
 "molecule"_molecule.html command, which reads files that define one or