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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13994 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
2015-09-03 00:14:29 +00:00
parent f35b63f278
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doc/compute_rdf.html
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@ -166,8 +166,11 @@ interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a>
command, and means those pairwise interactions do not appear in the
neighbor list. Because this fix uses the neighbor list, it also means
those pairs will not be included in the RDF. One way to get around
this, is to write a dump file, and use the <a class="reference internal" href="rerun.html"><em>rerun</em></a> command
those pairs will not be included in the RDF. This does not apply when
using long-range coulomb (<em>coul/long</em>, <em>coul/msm</em>, <em>coul/wolf</em> or similar.
One way to get around this would be to set special_bond scaling factors
to very tiny numbers that are not exactly zero (e.g. 1.0e-50). Another
workaround is to write a dump file, and use the <a class="reference internal" href="rerun.html"><em>rerun</em></a> command
to compute the RDF for snapshots in the dump file. The rerun script
can use a <a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command that includes all
pairs in the neighbor list.</p>
@ -209,10 +212,13 @@ one individual histogram, due to the way the <em>itypeN</em> and <em>jtypeN</em>
arguments are specified.</p>
<p>The g(r) value for a bin is calculated from the histogram count by
scaling it by the idealized number of how many counts there would be
if atoms of type <em>jtypeN</em> were uniformly distributed. Thus it
involves the count of <em>itypeN</em> atoms, the count of <em>jtypeN</em> atoms, the
volume of the entire simulation box, and the volume of the bin&#8217;s thin
shell in 3d (or the area of the bin&#8217;s thin ring in 2d).</p>
if atoms of type <em>jtypeN</em> were uniformly distributed. Thus it involves
the count of <em>itypeN</em> atoms, the count of <em>jtypeN</em> atoms, the volume
of the entire simulation box, and the volume of the bin&#8217;s thin shell
in 3d (or the area of the bin&#8217;s thin ring in 2d). The normalization
is corrected for finite size effects so that the large <em>r</em> limit for
a homogeneous liquid system of a single atom type becomes exactly 1.0
(without the correction it would be (natoms-1)/natoms).</p>
<p>A coordination number coord(r) is also calculated, which is the number
of atoms of type <em>jtypeN</em> within the current bin or closer, averaged
over atoms of type <em>itypeN</em>. This is calculated as the area- or