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