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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10698 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2013-08-30 19:31:44 +00:00
parent b0501ad7c7
commit afd85b2934
2 changed files with 30 additions and 34 deletions
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32
doc/compute_rdf.html
View File

@ -66,8 +66,8 @@ types represented by <I>jtypeN</I> are the distribution atom.
</P>
<P>Pairwise distances are generated by looping over a pairwise neighbor
list, just as they would be in a <A HREF = "pair_style.html">pair_style</A>
computation. The distance between two atoms I and J is included in
a specific histogram if the following criteria are met:
computation. The distance between two atoms I and J is included in a
specific histogram if the following criteria are met:
</P>
<UL><LI>atoms I,J are both in the specified compute group
<LI>the distance between atoms I,J is less than the maximum force cutoff
@ -85,12 +85,12 @@ 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).
</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 over atoms of type <I>itypeN</I>. This is calculated as the area-
or volume-weighted sum of g(r) values over all bins up to and including the
current bin, multiplied by the global average volume density of atoms of type
jtypeN.
<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
over atoms of type <I>itypeN</I>. This is calculated as the area- or
volume-weighted sum of g(r) values over all bins up to and including
the current bin, multiplied by the global average volume density of
atoms of type jtypeN.
</P>
<P>The simplest way to output the results of the compute rdf calculation
to a file is to use the <A HREF = "fix_ave_time.html">fix ave/time</A> command, for
@ -125,15 +125,13 @@ since processors (in parallel) don't know about atom coordinates for
atoms further away than that distance. If you want an RDF for larger
distances, you can use the <A HREF = "rerun.html">rerun</A> command to post-process
a dump file. The definition of g(r) used by LAMMPS is only appropriate
for characterizing atoms that are uniformly distributed
throughout the simulation cell. In such cases,
the coordination number is still correct and meaningful.
As an example, if a large simulation
cell contains only one atom of type <I>itypeN</I> and one of <I>jtypeN</I>,
then g(r) will register an arbitrarily large spike at whatever
distance they happen to be at, and zero everywhere else.
coord(r) will show a step change from zero to one at the location
of the spike in g(r).
for characterizing atoms that are uniformly distributed throughout the
simulation cell. In such cases, the coordination number is still
correct and meaningful. As an example, if a large simulation cell
contains only one atom of type <I>itypeN</I> and one of <I>jtypeN</I>, then g(r)
will register an arbitrarily large spike at whatever distance they
happen to be at, and zero everywhere else. coord(r) will show a step
change from zero to one at the location of the spike in g(r).
</P>
<P><B>Related commands:</B>
</P>

32
doc/compute_rdf.txt
View File

@ -63,8 +63,8 @@ types represented by {jtypeN} are the distribution atom.
Pairwise distances are generated by looping over a pairwise neighbor
list, just as they would be in a "pair_style"_pair_style.html
computation. The distance between two atoms I and J is included in
a specific histogram if the following criteria are met:
computation. The distance between two atoms I and J is included in a
specific histogram if the following criteria are met:
atoms I,J are both in the specified compute group
the distance between atoms I,J is less than the maximum force cutoff
@ -82,12 +82,12 @@ involves the count of {itypeN} atoms, the count of {jtypeN} 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).
A coordination number coord(r) is also calculated, which is the
number of atoms of type {jtypeN} within the current bin or closer,
averaged over atoms of type {itypeN}. This is calculated as the area-
or volume-weighted sum of g(r) values over all bins up to and including the
current bin, multiplied by the global average volume density of atoms of type
jtypeN.
A coordination number coord(r) is also calculated, which is the number
of atoms of type {jtypeN} within the current bin or closer, averaged
over atoms of type {itypeN}. This is calculated as the area- or
volume-weighted sum of g(r) values over all bins up to and including
the current bin, multiplied by the global average volume density of
atoms of type jtypeN.
The simplest way to output the results of the compute rdf calculation
to a file is to use the "fix ave/time"_fix_ave_time.html command, for
@ -122,15 +122,13 @@ since processors (in parallel) don't know about atom coordinates for
atoms further away than that distance. If you want an RDF for larger
distances, you can use the "rerun"_rerun.html command to post-process
a dump file. The definition of g(r) used by LAMMPS is only appropriate
for characterizing atoms that are uniformly distributed
throughout the simulation cell. In such cases,
the coordination number is still correct and meaningful.
As an example, if a large simulation
cell contains only one atom of type {itypeN} and one of {jtypeN},
then g(r) will register an arbitrarily large spike at whatever
distance they happen to be at, and zero everywhere else.
coord(r) will show a step change from zero to one at the location
of the spike in g(r).
for characterizing atoms that are uniformly distributed throughout the
simulation cell. In such cases, the coordination number is still
correct and meaningful. As an example, if a large simulation cell
contains only one atom of type {itypeN} and one of {jtypeN}, then g(r)
will register an arbitrarily large spike at whatever distance they
happen to be at, and zero everywhere else. coord(r) will show a step
change from zero to one at the location of the spike in g(r).
[Related commands:]