Cameron Manual

Chapter 17: Add And Move - Further Symmetry Related Commands

: 17.1: ADD; 17.2: EXAMPLES; 17.3: MOVE

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.

17.1: ADD

The ADD command allows the user complete control over the symmetry operator used to generate new atoms. The first task of the user is to generate a list of those atoms to be used in the symmetry generation later. One of the following sub-commands is required :-

ATOMS
The names of atoms to be included in the pack list are specified here. Element names can also be used if required.

ALL
ALL refers to the atoms that are in the current list. If any atoms have been generated by previous PACK , ENCLOSURE or ADD commands then these will all go into the list.

INITIAL
ADD INITIAL means that the only atoms to go into the ADD list are those that were initially input.

GROUP
This is followed by a group name. The group must have been previously been defined by the command DEFGROUP.

Once the ADD list has been created the user must then supply the symmetry operators which will act on the atoms in this list to generate the new atoms. The symmetry input is in two parts.

OPERATOR The symmetry operator may be input in decimal or fractional form eg

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

17.2: EXAMPLES

To generate an atom at x+1/2 y z from an atom at x y z we can use

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.

17.3: MOVE

The syntax for this command is identical to that for ADD. Therefore the commands available are :-

ATOMS

ALL

GROUP

INITIAL
Which must be followed one (or both) of :-

OPERATOR

TRANS

The MOVE command applies a symmetry operator and/or a translation to all of the atoms held in the list defined by the ATOMS/ALL/GROUP/INITIAL commands. Unlike ADD therefore, the same number of atoms are present at the beginning and end of the operation.