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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10890 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2013-10-30 14:40:51 +00:00
parent 46d431811d
commit 166d6df67e
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13
doc/compute_coord_atom.html
View File

@ -60,6 +60,19 @@ time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.
</P>
<P>IMPORTANT NOTE: If you have a bonded system, then the settings of
<A HREF = "special_bonds.html">special_bonds</A> command can remove pairwise
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 coordination count. One way
to get around this, is to write a dump file, and use the
<A HREF = "rerun.html">rerun</A> command to compute the coordination 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.
</P>
<P><B>Output info:</B>
</P>
<P>If single <I>type1</I> keyword is specified (or if none are specified),

13
doc/compute_coord_atom.txt
View File

@ -57,6 +57,19 @@ time the calculation is performed (i.e. each time a snapshot of atoms
is dumped). Thus it can be inefficient to compute/dump this quantity
too frequently.
IMPORTANT NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the "special_bonds"_special_bonds.html
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 coordination count. One way
to get around this, is to write a dump file, and use the
"rerun"_rerun.html command to compute the coordination for snapshots
in the dump file. The rerun script can use a
"special_bonds"_special_bonds.html command that includes all pairs in
the neighbor list.
[Output info:]
If single {type1} keyword is specified (or if none are specified),

12
doc/compute_rdf.html
View File

@ -39,6 +39,18 @@ defined by the <A HREF = "pair_style.html">pair_style</A> command. The bins are
uniform size in radial distance. Thus a single bin encompasses a thin
shell of distances in 3d and a thin ring of distances in 2d.
</P>
<P>IMPORTANT NOTE: If you have a bonded system, then the settings of
<A HREF = "special_bonds.html">special_bonds</A> command can remove pairwise
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
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.
</P>
<P>The <I>itypeN</I> and <I>jtypeN</I> arguments are optional. These arguments
must come in pairs. If no pairs are listed, then a single histogram
is computed for g(r) between all atom types. If one or more pairs are

12
doc/compute_rdf.txt
View File

@ -36,6 +36,18 @@ defined by the "pair_style"_pair_style.html command. The bins are of
uniform size in radial distance. Thus a single bin encompasses a thin
shell of distances in 3d and a thin ring of distances in 2d.
IMPORTANT NOTE: If you have a bonded system, then the settings of
"special_bonds"_special_bonds.html command can remove pairwise
interactions between atoms in the same bond, angle, or dihedral. This
is the default setting for the "special_bonds"_special_bonds.html
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 "rerun"_rerun.html command
to compute the RDF for snapshots in the dump file. The rerun script
can use a "special_bonds"_special_bonds.html command that includes all
pairs in the neighbor list.
The {itypeN} and {jtypeN} arguments are optional. These arguments
must come in pairs. If no pairs are listed, then a single histogram
is computed for g(r) between all atom types. If one or more pairs are