From 1c320484e355f6d7fb4b3dee8b1639319cc8cbd4 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 20 Aug 2008 14:56:12 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2076 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/neighbor.html | 26 ++++++++++++++++++-------- doc/neighbor.txt | 26 ++++++++++++++++++-------- doc/set.html | 28 ++++++++++++++++++++++++++-- doc/set.txt | 28 ++++++++++++++++++++++++++-- 4 files changed, 88 insertions(+), 20 deletions(-) diff --git a/doc/neighbor.html b/doc/neighbor.html index f1a7446f74..8b24a4929d 100644 --- a/doc/neighbor.html +++ b/doc/neighbor.html @@ -33,13 +33,6 @@ need to be built, but more pairs must be checked for possible force interactions every timestep. The default value for skin depends on the choice of units for the simulation (see below).

-

For simulations without pairwise interactions (see "pair_style none" -command), and just bonded interactions, you still need to set the -neighbor skin distance. Pairwise neighbor lists will not be formed -but the skin distance also determines which atoms are communicated -from nearby processors, so it should be slightly large enough that all -bond, angle, etc atoms are acquired. -

The style value selects what algorithm is used to build the list. The bin style creates the list by binning which is an operation that scales linearly with N/P, the number of atoms per processor where N = @@ -71,7 +64,24 @@ the pairwise list and the number of times neighbor lists were built are printed to the screen and log file. See this section for details.

-

Restrictions: none +

Restrictions: +

+

For simulations without pairwise interactions (see "pair_style none" +command), but that include bonded interactions, you still need to set +the neighbor skin distance. Pairwise neighbor lists will not be +formed, but the pair cutoff (0.0 in this case) plus the skin distance +is the range at which atoms are communicated from nearby processors. +This needs to be large enough that atoms in the same bond, angle, etc +as an atom owned by a processor are acquired. What distance is +appropriate depends on the newton bond setting. For +newton bond off, the distance needs to be the furthest distance +between any two atoms in the bond, angle, etc. E.g. the distance +between the 1-4 atoms in a dihedral. For newton bond on, the distance +is between the central atom in the bond, angle, etc and any other +atom. E.g. the distance between the 2-4 atoms in a dihedral. +

+

The same logic applies to systems that include bonded interactions and +a pairwise cutoff shorter than the distances just described.

Related commands:

diff --git a/doc/neighbor.txt b/doc/neighbor.txt index 937793022e..9a04488d4c 100644 --- a/doc/neighbor.txt +++ b/doc/neighbor.txt @@ -30,13 +30,6 @@ need to be built, but more pairs must be checked for possible force interactions every timestep. The default value for {skin} depends on the choice of units for the simulation (see below). -For simulations without pairwise interactions (see "pair_style none" -command), and just bonded interactions, you still need to set the -neighbor skin distance. Pairwise neighbor lists will not be formed -but the skin distance also determines which atoms are communicated -from nearby processors, so it should be slightly large enough that all -bond, angle, etc atoms are acquired. - The {style} value selects what algorithm is used to build the list. The {bin} style creates the list by binning which is an operation that scales linearly with N/P, the number of atoms per processor where N = @@ -68,7 +61,24 @@ the pairwise list and the number of times neighbor lists were built are printed to the screen and log file. See "this section"_Section_start.html#2_7 for details. -[Restrictions:] none +[Restrictions:] + +For simulations without pairwise interactions (see "pair_style none" +command), but that include bonded interactions, you still need to set +the neighbor skin distance. Pairwise neighbor lists will not be +formed, but the pair cutoff (0.0 in this case) plus the skin distance +is the range at which atoms are communicated from nearby processors. +This needs to be large enough that atoms in the same bond, angle, etc +as an atom owned by a processor are acquired. What distance is +appropriate depends on the "newton bond"_newton.html setting. For +newton bond off, the distance needs to be the furthest distance +between any two atoms in the bond, angle, etc. E.g. the distance +between the 1-4 atoms in a dihedral. For newton bond on, the distance +is between the central atom in the bond, angle, etc and any other +atom. E.g. the distance between the 2-4 atoms in a dihedral. + +The same logic applies to systems that include bonded interactions and +a pairwise cutoff shorter than the distances just described. [Related commands:] diff --git a/doc/set.html b/doc/set.html index 1c439ad155..ac034cd732 100644 --- a/doc/set.html +++ b/doc/set.html @@ -13,7 +13,7 @@

Syntax:

-
set style ID keyword value ... 
+
set style ID keyword values ...