It the mol keyword is set to yes, then for every atom that is deleted, all other atoms in the same molecule will also be deleted. -This keyword is only used by the region style. It 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. +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 +each style. This means additional atoms may be deleted that are not +in the group or region, that are not required by the overlap cutoff +criterion, or that will create a higher fraction of porosity than was +requested.
Restrictions:
diff --git a/doc/delete_atoms.txt b/doc/delete_atoms.txt index 2d7eed9e7f..d646088683 100644 --- a/doc/delete_atoms.txt +++ b/doc/delete_atoms.txt @@ -83,11 +83,17 @@ 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 will also be deleted. -This keyword is only used by the {region} style. It 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. +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 +each style. This means additional atoms may be deleted that are not +in the group or region, that are not required by the overlap cutoff +criterion, or that will create a higher fraction of porosity than was +requested. [Restrictions:]