From c8b8adf8300b2a0687405a2e5423fe1b3f87dd7b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 6 Dec 2007 16:48:43 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1221 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/neigh_modify.html | 24 ++++++++++++++++++++++-- doc/neigh_modify.txt | 23 +++++++++++++++++++++-- 2 files changed, 43 insertions(+), 4 deletions(-) diff --git a/doc/neigh_modify.html b/doc/neigh_modify.html index 05f4cb551d..8afd1aa2e0 100644 --- a/doc/neigh_modify.html +++ b/doc/neigh_modify.html @@ -17,7 +17,7 @@

Examples: @@ -112,6 +115,19 @@ could potentially overflow the list. This threshhold is set by the one value which tells LAMMPS the maximum number of neighbor's one atom can have.

+

The binsize option allows you to specify what size of bins will be +used in neighbor list construction to sort and find neighboring atoms. +By default, for neighbor style bin, LAMMPS uses bins +that are 1/2 the size of the maximum pair cutoff. For neighbor style +multi, the bins are 1/2 the size of the minimum pair +cutoff. Typically these are good values values for minimizing the +time for neighbor list construction. This setting overrides the +default. If you make it too big, there is little overhead due to +looping over bins, but more atoms are checked. If you make it too +small, the optimal number of atoms is checked, but bin overhead goes +up. If you set the binsize to 0.0, LAMMPS will use the default +binsize of 1/2 the cutoff. +

Restrictions:

If the "delay" setting is non-zero, then it must be a multiple of the @@ -120,6 +136,10 @@ atom can have.

The exclude molecule option can only be used with atom styles that define molecule IDs.

+

The value of the page setting must be at least 10x larger than the +one setting. This insures neighbor pages are not mostly empty +space. +

Related commands:

neighbor, delete_bonds @@ -127,6 +147,6 @@ define molecule IDs.

Default:

The option defaults are delay = 10, every = 1, check = yes, exclude = -none, page = 100000, and one = 2000. +none, page = 100000, one = 2000, and binsize = 0.0.

diff --git a/doc/neigh_modify.txt b/doc/neigh_modify.txt index 86f99fc80d..7e9efa8120 100644 --- a/doc/neigh_modify.txt +++ b/doc/neigh_modify.txt @@ -13,7 +13,7 @@ neigh_modify command :h3 neigh_modify keyword values ... :pre one or more keyword/value pairs may be listed :ulb,l -keyword = {delay} or {every} or {check} or {exclude} or {page} or {one} +keyword = {delay} or {every} or {check} or {exclude} or {page} or {one} or {binsize} {delay} value = N N = delay building until this many steps since last build {every} value = M @@ -34,6 +34,8 @@ keyword = {delay} or {every} or {check} or {exclude} or {page} or {one} N = number of pairs stored in a single neighbor page {one} value = N N = max number of neighbors of one atom :pre + {binsize} value = size + size = bin size for neighbor list construction (distance units) :pre :ule [Examples:] @@ -107,6 +109,19 @@ could potentially overflow the list. This threshhold is set by the {one} value which tells LAMMPS the maximum number of neighbor's one atom can have. +The {binsize} option allows you to specify what size of bins will be +used in neighbor list construction to sort and find neighboring atoms. +By default, for "neighbor style bin"_neighbor.html, LAMMPS uses bins +that are 1/2 the size of the maximum pair cutoff. For "neighbor style +multi"_neighbor.html, the bins are 1/2 the size of the minimum pair +cutoff. Typically these are good values values for minimizing the +time for neighbor list construction. This setting overrides the +default. If you make it too big, there is little overhead due to +looping over bins, but more atoms are checked. If you make it too +small, the optimal number of atoms is checked, but bin overhead goes +up. If you set the binsize to 0.0, LAMMPS will use the default +binsize of 1/2 the cutoff. + [Restrictions:] If the "delay" setting is non-zero, then it must be a multiple of the @@ -115,6 +130,10 @@ If the "delay" setting is non-zero, then it must be a multiple of the The exclude molecule option can only be used with atom styles that define molecule IDs. +The value of the {page} setting must be at least 10x larger than the +{one} setting. This insures neighbor pages are not mostly empty +space. + [Related commands:] "neighbor"_neighbor.html, "delete_bonds"_delete_bonds.html @@ -122,4 +141,4 @@ define molecule IDs. [Default:] The option defaults are delay = 10, every = 1, check = yes, exclude = -none, page = 100000, and one = 2000. +none, page = 100000, one = 2000, and binsize = 0.0.