From c8bbcb34de08370a523b0efab54640f7b19ddc2b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 27 Jun 2014 23:44:32 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12159 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/delete_atoms.html | 13 +++++++------ doc/delete_atoms.txt | 13 +++++++------ doc/group.html | 17 +++++++++-------- doc/group.txt | 17 +++++++++-------- 4 files changed, 32 insertions(+), 28 deletions(-) diff --git a/doc/delete_atoms.html b/doc/delete_atoms.html index 3effb64590..f7e7f3558f 100644 --- a/doc/delete_atoms.html +++ b/doc/delete_atoms.html @@ -90,12 +90,13 @@ number of atoms in the system. This is not done for molecular systems has already been assigned.

It the mol keyword is set to yes, then for every atom that is -deleted, all other atoms in the same molecule (i.e. with the same -molecule ID) will also be deleted. This is a way to insure that -entire molecules are deleted instead of only a subset of atoms in the -molecule which will typically lead to errors because of bond, angle, -or dihedral interactions stored by remaining atoms which reference -deleted atoms. +deleted, all other atoms in the same molecule (with the same molecule +ID) will also be deleted. This is not done for atoms with molecule ID += 0, since it is assumed to flag isolated atoms that are not part of +molecules. This is a way to insure that entire molecules are deleted +instead of only a subset of atoms in the molecule which will typically +lead to errors because of bond, angle, or dihedral interactions stored +by remaining atoms which reference deleted atoms.

IMPORTANT NOTE: The molecule deletion operation in invoked after all individual atoms have been deleted using the rules described above for diff --git a/doc/delete_atoms.txt b/doc/delete_atoms.txt index 0c82ce374b..ba1ef9aeaf 100644 --- a/doc/delete_atoms.txt +++ b/doc/delete_atoms.txt @@ -82,12 +82,13 @@ number of atoms in the system. This is not done for molecular systems has already been assigned. It the {mol} keyword is set to {yes}, then for every atom that is -deleted, all other atoms in the same molecule (i.e. with the same -molecule ID) will also be deleted. This is a way to insure that -entire molecules are deleted instead of only a subset of atoms in the -molecule which will typically lead to errors because of bond, angle, -or dihedral interactions stored by remaining atoms which reference -deleted atoms. +deleted, all other atoms in the same molecule (with the same molecule +ID) will also be deleted. This is not done for atoms with molecule ID += 0, since it is assumed to flag isolated atoms that are not part of +molecules. This is a way to insure that entire molecules are deleted +instead of only a subset of atoms in the molecule which will typically +lead to errors because of bond, angle, or dihedral interactions stored +by remaining atoms which reference deleted atoms. IMPORTANT NOTE: The molecule deletion operation in invoked after all individual atoms have been deleted using the rules described above for diff --git a/doc/group.html b/doc/group.html index c100bd70b1..16b1b32b69 100644 --- a/doc/group.html +++ b/doc/group.html @@ -176,14 +176,15 @@ variables are current when they are evaluated between runs.

The include style with its arg molecule adds atoms to a group that have the same molecule ID as atoms already in the group. The molecule -ID = 0 is ignored in this operation, since it assumed to represent -atoms that are not part of molecules. An example of where this -operation is useful is if the region style has been used previously -to add atoms to a group that are within a geometric region. If -molecules straddle the region boundary, then atoms outside the region -that are part of molecules with atoms inside the region will not be in -the group. Using the group command a 2nd time with include molecule -will add those atoms that are outside the region to the group. +ID = 0 is ignored in this operation, since it is assumed to flag +isolated atoms that are not part of molecules. An example of where +this operation is useful is if the region style has been used +previously to add atoms to a group that are within a geometric region. +If molecules straddle the region boundary, then atoms outside the +region that are part of molecules with atoms inside the region will +not be in the group. Using the group command a 2nd time with include +molecule will add those atoms that are outside the region to the +group.

IMPORTANT NOTE: The include molecule operation is relatively expensive in a parallel sense. This is because it requires diff --git a/doc/group.txt b/doc/group.txt index 8d7d0db0db..3a889fda39 100644 --- a/doc/group.txt +++ b/doc/group.txt @@ -172,14 +172,15 @@ variables are current when they are evaluated between runs. The {include} style with its arg {molecule} adds atoms to a group that have the same molecule ID as atoms already in the group. The molecule -ID = 0 is ignored in this operation, since it assumed to represent -atoms that are not part of molecules. An example of where this -operation is useful is if the {region} style has been used previously -to add atoms to a group that are within a geometric region. If -molecules straddle the region boundary, then atoms outside the region -that are part of molecules with atoms inside the region will not be in -the group. Using the group command a 2nd time with {include molecule} -will add those atoms that are outside the region to the group. +ID = 0 is ignored in this operation, since it is assumed to flag +isolated atoms that are not part of molecules. An example of where +this operation is useful is if the {region} style has been used +previously to add atoms to a group that are within a geometric region. +If molecules straddle the region boundary, then atoms outside the +region that are part of molecules with atoms inside the region will +not be in the group. Using the group command a 2nd time with {include +molecule} will add those atoms that are outside the region to the +group. IMPORTANT NOTE: The {include molecule} operation is relatively expensive in a parallel sense. This is because it requires