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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13993 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
2015-09-03 00:14:17 +00:00
parent a3017bc092
commit f35b63f278
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4
doc/doc2/Manual.html.html
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@ -3,7 +3,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="2 Sep 2015 version">
<META NAME="docnumber" CONTENT="3 Sep 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<P><CENTER><H3>LAMMPS Documentation
</H3></CENTER>
<CENTER><H4>2 Sep 2015 version
<CENTER><H4>3 Sep 2015 version
</H4></CENTER>
<H4>Version info:
</H4>

2
doc/doc2/Section_errors.html
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@ -10604,7 +10604,7 @@ feature is disabled by using 'pair_modify table 0'.
computes a temperature on a different group of atoms than the fix
itself operates on. This is probably not what you want to do.
<DT><I>H matrix size has been exceeded: m_fill=%d H.m=%d\n</I>
<DT><I>H matrix size has been exceeded: m_fill=%d H.m=%d\\n</I>
<DD>This is the size of the matrix.

18
doc/doc2/compute_rdf.html
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@ -45,8 +45,11 @@ interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the <A HREF = "special_bonds.html">special_bonds</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 HREF = "rerun.html">rerun</A> command
those pairs will not be included in the RDF. This does not apply when
using long-range coulomb (<I>coul/long</I>, <I>coul/msm</I>, <I>coul/wolf</I> 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 HREF = "rerun.html">rerun</A> command
to compute the RDF for snapshots in the dump file. The rerun script
can use a <A HREF = "special_bonds.html">special_bonds</A> command that includes all
pairs in the neighbor list.
@ -92,10 +95,13 @@ 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 <I>jtypeN</I> were uniformly distributed. Thus it
involves the count of <I>itypeN</I> atoms, the count of <I>jtypeN</I> atoms, the
volume of the entire simulation box, and the volume of the bin's thin
shell in 3d (or the area of the bin's thin ring in 2d).
if atoms of type <I>jtypeN</I> were uniformly distributed. Thus it involves
the count of <I>itypeN</I> atoms, the count of <I>jtypeN</I> atoms, the volume
of the entire simulation box, and the volume of the bin's thin shell
in 3d (or the area of the bin's thin ring in 2d). The normalization
is corrected for finite size effects so that the large <I>r</I> 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 <I>jtypeN</I> within the current bin or closer, averaged