GroupTheory`

GTClusterManipulate

GTClusterManipulate[cluster]

manipulates a cluster in different ways. The manipulation is controlled by the option GOMethod.

Details and Options

The command GTCluster generates a spherical cluster. For the discussion of several problems a modification of this basic cluster is necessary. GTClusterManipulate allows a series of manipulations. The command can be easily extended with other manipulations.
The following option can be given:
GOMethod "Help" Presents all implemented manipulations.

Examples

open allclose all

Basic Examples (1)

First load the package:

Load the database and extract the the structure for Barium titanate.

Generate the cluster.

Now the cluster can be plotted:

Now a surface will be created. In this process it is assumed, that the z-axis is the surface normal.

Options (14)

GOMethod (14)

Several manipulations are controlled by a keyword only, but other have to be accompanied by some detailed information to perform the action.

"Help"

The help option allows to get an overview of all implemented manipulations.

"AddAtoms"

Atoms can be added to the cluster.

In this plot the colors from ElementData are used. We can also provide our own color scheme.

Note, we have to order the colors with respect to the alphabetical order of the atoms.

"CutPlane"

A plane is defined by the normal vector of the plane and one point lying in the plane.

"CutSphere"

A spherical cluster is cut out of the cluster around a given position.

After cutting out the new sphere, it might be translated such, the the center of the cluster becomes the origin. In the original cluster a Ti atom was in the center of the cluster. Now an O atom is located in the center of the smaller cluster.

"Project"

The atoms in the cluster will be projected to the plane z=0. Here, the atoms in the slab will be projected. Several atoms might be projected to the same position in the z=0 plane

Generate a slab (see explanation to "Slab")

"RemoveAtoms"

Single atoms can be removed from the cluster.

"RemoveType"

Atoms of a special type will be removed from the cluster. Here, the Ba atoms will be removed from the cluster with surface.

"Rotate"

The whole cluster will be rotated. The rotation can be defined in two ways. First, a list of two vectors is given. The first vector will be transformed to the second vector. Second, a scalar and a vector is given. The scalar represents the rotation angle and the vector defines the rotation axis. We take a small cluster to demonstrate the action. To see better what happens, the coordinate system is drawn. Also the direction which should be the new z-axis is marked.

We want to rotate the 〈110〉 direction to the z-axis, to get a Ba atom on the z-axis

In another mode the cluster can be rotated by a given angle around a given axis.

"SelectType"

Atoms of a special type will be selected from the cluster. Only those atoms will be shown. Here, Ti atoms will be selected from the cluster with surface.

"Slab"

A certain number of layers will be cut out of the cluster. This needs a cluster surface. The layers are counted for z<=0.

"Surface"

A surface will be created.

"SymmetryElement"

While Rotate allows a rotation by an arbitrary angle, SymmetryElement applies a symmetry element of a certain point group. The cluster has not to be invariant under this operation.