Chapter 17: Add And Move - Further Symmetry Related Commands
The PACK and ENCLOSURE commands already detailed allow the user to apply all of the symmetry operators in the spacegroup to the initial set of atoms in order to get a fully 'packed' result. In some cases however, the user may wish to apply only one symmetry operator or to apply ones that are not present in the spacegroup. The ADD and MOVE commands allow this.
The ADD command allows the user complete control over the
operator used to generate new atoms. The first task of the user
generate a list of those atoms to be used in the symmetry
later. One of the following sub-commands is required :-
Once the ADD list has been created the user must then supply
symmetry operators which will act on the atoms in this list to
the new atoms. The symmetry input is in two parts.
x y+1/2 z -0.333-x -y -z ETC
Decimal translations may come before or after the axis symbol. The fractions 1/2, 1/3, 1/4, 2/3, 1/6 and 5/6 are accepted by the program, but must appear after the x/y/z character. There must be spaces between the three parts but NO SPACES within the operator ie
X + 1/2 -Y Z
will produce an error as it is not possible to tell whether you mean X+1/2, -Y, Z or X, +1/2-Y, Z. This strict input syntax is used to eliminate any ambiguities.
TRANS Translations can also be applied if required. The translations are applied in unit cell fractions. The syntax is :-
TRANS x y z
ADD ATOMS C1 OPERATOR X+1/2 Y Z
or we could use
ADD ATOMS C1 TRANS 0.5 0 0
The OPERATOR and TRANS commands can be used together if required. We can apply a symmetry operator followed by a translation. This reduces the errors that may occur when trying to combine the two things into one symmetry operator.
The use of INITIAL versus ALL is illustrated below. Start with :-
ADD ALL TRANS 1 0 0
which gives us a molecule at x y z and another at x+1 y z. Follow this with :-
ADD ALL TRANS 0 1 0
and we get four molecules, x y z , x+1 y z , x+1 y+1 z and x y+1 z. Following it with :-
ADD INITIAL TRANS 0 1 0
Gives us three molecules, x y z, x+1 y z and x y+1 z.
The syntax for this command is identical to that for ADD.
the commands available are :-
The MOVE command applies a symmetry operator and/or a
all of the atoms held in the list defined by the
commands. Unlike ADD therefore, the same number of atoms are
the beginning and end of the operation.