From dd589582e852fc1032949435d5a74788daf0fab2 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 21 Aug 2008 14:03:21 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2091 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/communicate.html | 16 +++++++++------- doc/communicate.txt | 16 +++++++++------- doc/neighbor.html | 26 ++++++++++++-------------- doc/neighbor.txt | 26 ++++++++++++-------------- 4 files changed, 42 insertions(+), 42 deletions(-) diff --git a/doc/communicate.html b/doc/communicate.html index 7e161bc7f6..8914e83247 100644 --- a/doc/communicate.html +++ b/doc/communicate.html @@ -59,14 +59,14 @@ specified group) will still migrate to new processors as they move. The group specified with this option must also be specified via the atom_modify first command.

-

The cutoff option allows you to set a ghost cutoff distance which is -the distance from the borders of a processor's sub-domain at which +

The cutoff option allows you to set a ghost cutoff distance, which +is the distance from the borders of a processor's sub-domain at which ghost atoms are acquired from other processors. By default the ghost -cutoff = the neighbor cutoff = the pairwise force cutoff + the -neighbor skin. See the neighbor command for more -information about the skin distance. If the specified Rcut is greater -than the neighbor cutoff, then extra ghost atoms will be acquired. If -it is smaller, the ghost cutoff is set to the neighbor cutoff. +cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. See +the neighbor command for more information about the +skin distance. If the specified Rcut is greater than the neighbor +cutoff, then extra ghost atoms will be acquired. If it is smaller, +the ghost cutoff is set to the neighbor cutoff.

These are simulation scenarios in which it may be useful to set a ghost cutoff > neighbor cutoff: @@ -107,5 +107,7 @@ find the needed atoms.

Default:

The default settings are style = single, group = all, cutoff = 0.0. +The cutoff default of 0.0 means that effectively ghost cutoff = +neighbor cutoff = pairwise force cutoff + neighbor skin.

diff --git a/doc/communicate.txt b/doc/communicate.txt index 3e73375daf..5fb23aa91d 100644 --- a/doc/communicate.txt +++ b/doc/communicate.txt @@ -52,14 +52,14 @@ specified group) will still migrate to new processors as they move. The group specified with this option must also be specified via the "atom_modify first"_atom_modify.html command. -The {cutoff} option allows you to set a ghost cutoff distance which is -the distance from the borders of a processor's sub-domain at which +The {cutoff} option allows you to set a ghost cutoff distance, which +is the distance from the borders of a processor's sub-domain at which ghost atoms are acquired from other processors. By default the ghost -cutoff = the neighbor cutoff = the pairwise force cutoff + the -neighbor skin. See the "neighbor"_neighbor.html command for more -information about the skin distance. If the specified Rcut is greater -than the neighbor cutoff, then extra ghost atoms will be acquired. If -it is smaller, the ghost cutoff is set to the neighbor cutoff. +cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. See +the "neighbor"_neighbor.html command for more information about the +skin distance. If the specified Rcut is greater than the neighbor +cutoff, then extra ghost atoms will be acquired. If it is smaller, +the ghost cutoff is set to the neighbor cutoff. These are simulation scenarios in which it may be useful to set a ghost cutoff > neighbor cutoff: @@ -100,3 +100,5 @@ find the needed atoms. [Default:] The default settings are style = single, group = all, cutoff = 0.0. +The cutoff default of 0.0 means that effectively ghost cutoff = +neighbor cutoff = pairwise force cutoff + neighbor skin. diff --git a/doc/neighbor.html b/doc/neighbor.html index 135a53fba6..46dd94148d 100644 --- a/doc/neighbor.html +++ b/doc/neighbor.html @@ -26,21 +26,19 @@ neighbor 2.0 nsq

Description:

This command sets parameters that affect the building of pairwise -neighbor lists. All atom pairs within a cutoff distance equal to the -their force cutoff plus the skin distance are stored in the list. -Typically, the larger the skin distance, the less often neighbor lists -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 the default values below. +neighbor lists. All atom pairs within a neighbor cutoff distance +equal to the their force cutoff plus the skin distance are stored in +the list. Typically, the larger the skin distance, the less often +neighbor lists 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 the +default values below.

-

Even if pairwise neighbor lists are not used in a simulation (e.g. a -pair potential is not defined), the skin distance may still determine -how often atoms migrate to new processors due to atom motion and -should thus be set appropriately. This is because atoms migrate on -the same timestep that neighbor lists are built. See the various -settings of the neigh_modify command which control when -neighbor lists are built, based on atom movement via the "check yes" -option. +

The skin distance is also used to determine how often atoms migrate +to new processors if the check option of the +neigh_modify command is set to yes. Atoms are +migrated (communicated) to new processors on the same timestep that +neighbor lists are re-built.

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 diff --git a/doc/neighbor.txt b/doc/neighbor.txt index 9d3532dee2..33488e247e 100644 --- a/doc/neighbor.txt +++ b/doc/neighbor.txt @@ -23,21 +23,19 @@ neighbor 2.0 nsq :pre [Description:] This command sets parameters that affect the building of pairwise -neighbor lists. All atom pairs within a cutoff distance equal to the -their force cutoff plus the {skin} distance are stored in the list. -Typically, the larger the skin distance, the less often neighbor lists -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 the default values below. +neighbor lists. All atom pairs within a neighbor cutoff distance +equal to the their force cutoff plus the {skin} distance are stored in +the list. Typically, the larger the skin distance, the less often +neighbor lists 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 the +default values below. -Even if pairwise neighbor lists are not used in a simulation (e.g. a -pair potential is not defined), the skin distance may still determine -how often atoms migrate to new processors due to atom motion and -should thus be set appropriately. This is because atoms migrate on -the same timestep that neighbor lists are built. See the various -settings of the "neigh_modify"_neigh_modify command which control when -neighbor lists are built, based on atom movement via the "check yes" -option. +The {skin} distance is also used to determine how often atoms migrate +to new processors if the {check} option of the +"neigh_modify"_neigh_modify command is set to {yes}. Atoms are +migrated (communicated) to new processors on the same timestep that +neighbor lists are re-built. 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