From f35b63f278c6dea268f4f55b22b7a693ce652a4b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 3 Sep 2015 00:14:17 +0000 Subject: [PATCH] '' git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13993 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/doc2/Manual.html.html | 4 ++-- doc/doc2/Section_errors.html | 2 +- doc/doc2/compute_rdf.html | 18 ++++++++++++------ 3 files changed, 15 insertions(+), 9 deletions(-) diff --git a/doc/doc2/Manual.html.html b/doc/doc2/Manual.html.html index 9063e77b65..fb577b7ecc 100644 --- a/doc/doc2/Manual.html.html +++ b/doc/doc2/Manual.html.html @@ -3,7 +3,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation

-

2 Sep 2015 version +

3 Sep 2015 version

Version info:

diff --git a/doc/doc2/Section_errors.html b/doc/doc2/Section_errors.html index 0e72c3dd08..699531acca 100644 --- a/doc/doc2/Section_errors.html +++ b/doc/doc2/Section_errors.html @@ -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. -
H matrix size has been exceeded: m_fill=%d H.m=%d\n +
H matrix size has been exceeded: m_fill=%d H.m=%d\\n
This is the size of the matrix. diff --git a/doc/doc2/compute_rdf.html b/doc/doc2/compute_rdf.html index c2af825cc2..7fcc6cd19e 100644 --- a/doc/doc2/compute_rdf.html +++ b/doc/doc2/compute_rdf.html @@ -45,8 +45,11 @@ interactions between atoms in the same bond, angle, or dihedral. This is the default setting for the special_bonds 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 command +those pairs will not be included in the RDF. This does not apply when +using long-range coulomb (coul/long, coul/msm, coul/wolf 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 rerun command to compute the RDF for snapshots in the dump file. The rerun script can use a special_bonds command that includes all pairs in the neighbor list. @@ -92,10 +95,13 @@ arguments are specified.

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 jtypeN were uniformly distributed. Thus it -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). +if atoms of type jtypeN were uniformly distributed. Thus it 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). The normalization +is corrected for finite size effects so that the large r limit for +a homogeneous liquid system of a single atom type becomes exactly 1.0 +(without the correction it would be (natoms-1)/natoms).

A coordination number coord(r) is also calculated, which is the number of atoms of type jtypeN within the current bin or closer, averaged