Cerius2 Builders

4       Interface Builder

The C²·Interface Builder module is used for constructing models of a crystal interface between two different crystals or a twin or defect within a crystal. The C²·Interface Builder module aids in simulating experimental data such as high-resolution transmission electron microscopy images of interfaces (C²·HRTEM module) and in visualizing epitaxy and structural relationships between crystalline particles in contact.

This chapter contains information on:

About the interface builder

Creating an interface

Creating a periodic model from an interface

For information about	See
Loading and saving interface structure files.	The discussion of loading and saving structure files in Cerius2 Modeling Environment.
Building crystals.	Crystal Builder.
Building surfaces.	Surface Builder.
Microscopy.	Cerius2 Analytical Instruments.

The sequence of steps for using the C²·Interface Builder module is shown below. These steps are described in more detail later in the chapter.

1.   Define the right side of the interface--Specify the crystal model, Miller plane, match vector, match point, and dimensions of the right side of the interface.

2.   Define the left side of the interface--Specify the crystal model, Miller plane, match vector, match point, and dimensions of the left side of the interface.

3.   Build the interface--Specify the interfacial separation and the various atom bonding and superposition criteria. When the interface is built, the two planes are oriented so that the projections of their match points are coincident and their match vectors are parallel.

4.   Edit the interface (optional)--After the interface has been built, you have another opportunity to automatically remove superimposed atoms. You may also do manual editing.

5.   Create a periodic structure (optional)--For some applications, you may want to create a crystal or a surface model from the nonperiodic interface model. You can do this with the Crystal Builder or Surface Builder module.

Controls belonging to the C²·Interface Builder module are contained on the INTERFACE BUILDER card, which is located by default on the BUILDERS 1 deck of cards. To access the INTERFACE BUILDER card, click its name to bring it to the front of the deck of cards, which should now look like this:

Creating an interface

This section includes information on:

Defining the sides of the interface

Building the interface

Editing the interface after it is build

The starting model(s)

For each side, you need to specify a crystal model from which to take the interface. The model is chosen from the Interface Model pulldown (the left and right control panels contain the same set of controls), which show only crystal models that are suitable for use with the interface builder. The model needs to be chosen first.

Usually the crystal used for the left side is different from the crystal for the right side. However, to model a fault or twinning in a crystal, you use the same crystal for both sides of the interface.

The interface plane

The interface Plane itself is specified by the Miller indices h, k, and l. The convention is that the vector coming out of the built interface (that is, towards the other side) is normal to the interface plane. For the right side of the interface, the vector normal to the Miller plane points in the negative x direction. For the left side of the interface, this vector points in the positive x direction.

You also need to specify a Depth for the interface side. This is the thickness of the slab that is taken from the crystal to form the interface model and may be thought of as the amount of pure crystal on the back side of the interface.

Match point

The Match Point specifies a point in crystal fractional coordinates that should match the match point of the other crystal. The match point is also the origin of the interface slab to be cut from the crystal. If the interface separation is zero, the match points coincide. If not, their projections normal to the interface planes coincide.

Match vector

For each crystal, a match vector must be defined as the First Side of Interface Mesh. Because the two interface planes must be oriented with their match vectors parallel, the match vector and match point together define the relative orientations of the two planes. The match vector is given in the u, v, w fractional coordinate system of the crystal, and the interface builder checks that the vector is indeed in the interface plane. When the interface is built, this vector lies along the z axis.

You may want to preserve some periodicity in the direction of the match vector. This is particularly true if you want to put the interface into a 2D or 3D periodic box. If you enter a value in the multiplication (by) entry box to the right of the entry box for specifying the u, v, w coordinates of the first side of the interface, the unit vector length multiplied by this value is the length of the side. Because lattice vectors are necessarily along periodicities in the crystal structure, using an integer multiplication factor ensures a good repeat along the match direction.

Mesh shape

Two methods are available for specifying the shape of the two interface planes: ORTHOGONAL (the edges of the interface plane meet at right angles, which gives a square or rectangle) and VECTOR (the interface may be a parallelogram). The two sides of the interface need not be the same shape or specified by the same method.

• For the orthogonal method, you must define two edges for each interface: one being the match vector and the other perpendicular to the match vector in the plane of the interface (along the y axis), using the First Side of Interface Mesh and Second Side of Interface Mesh entry boxes.

• The vector method enables you to specify an interface that is a parallelogram. The first vector is the match vector (First Side of Interface Mesh entry box). The second vector (Second Side of Interface Mesh entry box) must also be in the interface plane, and its length can be given explicitly in angstroms or as a multiple of the unit vector.

Constructing the starting model

Load or build one or two crystals from which the interface is to be constructed.

Decide on the Miller planes, one for each side, that you will use to form the interface. You may find it helpful to view the planes using the facilities of the Crystal Visualization or the Crystal Facetting control panels of the Crystal Builder module. For detailed information, please see Crystal Builder.

Accessing the tools

Open the Interface Right Side control panel by selecting the Right Side menu item from the INTERFACE BUILDER card. Alternatively, if you have the Interface Building control panel (see Accessing the tools) open, click its Right Side... pushbutton.

Open the Interface Left Side control panel by selecting the Left Side menu item from the INTERFACE BUILDER card. Alternatively, if you have the Interface Building control panel (Accessing the tools) open, click its Left Side... pushbutton.

Beginning the process

From the Interface Model pulldown, select the crystal to be used to generate a side of the interface.

To specify how the interface slab is sliced from the crystal, choose ATOMIC or MOLECULAR from the Cleave popup, as desired or appropriate for your crystal. MOLECULAR means that the interface is built by cutting complete molecules from the crystal. ATOMIC means that it is built by cutting atoms from the crystal regardless of how they form molecules. The MOLECULAR option can cause atoms to end up outside the volume strictly defined as the interface slab, in particular within the space between the two sides of the interface after it is built.

Specifying the interface slab

Enter the Miller indices of the interface Plane.

Specify the Depth or thickness (in angstroms) of the slab that will form the interface.

Enter the match vector for the interface side in the First Side of Interface Mesh entry box. If you attempt to input a vector that is not in the Miller plane, a warning is displayed in the text window.

Specify the length of the slab along the match vector in angstroms or in terms of the number of lattice vectors, using one of the entry boxes to the right of the First Side of Interface Mesh entry box.

To specify the general shape of the interface mesh, choose ORTHOGONAL or VECTOR from the Mesh popup:

• If you have chosen an ORTHOGONAL mesh shape, enter a value for the length of the side perpendicular to the first vector, in the Second Side of Interface Mesh entry box.

• If you have chosen a VECTOR mesh shape, enter a vector and a length to define the second side of the interface, using the Second Side of Interface Mesh entry box and either of the two entry boxes to its right.

Tip

Additional information

Please see the on-screen help for additional information about the controls in all the panels mentioned here.

Building the interface

How it works

The interface is built from the two sides specified in the Interface Left Side and Interface Right Side control panels. The build operation takes place in the current workspace, which must be empty. The original crystals are not affected by the interface building.

The interface is built so that the normals of the left and right Miller planes face each other. The relative positions of the faces are governed by the match vector (First Side of Interface Mesh) and the Match Point specified in the Interface Left Side and Interface Right Side control panels and by the Interfacial Separation, which is specified in the Interface Building control panel. The match vector is aligned with the z axis.

Various bonding and atom options can be specified before building. For example, you can specify whether you want to calculate bonding upon building or whether and how superimposed atoms are removed.

Accessing the tools

After defining the interface sides as described above (Specifying the sides of the interface), open the Interface Building control panel by selecting the Interface Building menu item on the INTERFACE BUILDER card.

Specifying build parameters

Set the size of the gap between the interface planes (the Interfacial Separation) in angstroms. The effects of various values are:

• 0 Å--No interfacial separation between the left and right sides, likely resulting in superimposed atoms in the interface.

• > 0-1.5 Å--This much separation may lead to bonding across the interface if the Calculate bonds on building box is checked.

• > 2 Å--This much separation between the two sides is suitable for visualization purposes.

Set the dangling bonds popup according to how you would like dangling bonds to be displayed. They may be omitted altogether (NEITHER), drawn on the LEFT or RIGHT side only, or drawn on BOTH sides of the interface. Dangling bonds are a representation of bonds that existed in the crystal across the cleave face of the interface. The atom that is not in the cleaved set is replaced by a dummy atom. Use of this option gives an indication of the bonding patterns that may be required across the interface.

When the Remove superimposed atoms box is checked, atom pairs at the interface that are superimposed (within the Superimposition tolerance) are replaced by one atom from the interface side specified by the Keep atoms popup. Any bonds to the removed atom are transferred to the retained atom.

After the build parameters have been specified, make an existing empty model space current or open a new empty model space.

Building the interface

Click the BUILD INTERFACE pushbutton. The new interface is built in the current (empty) model space.

Additional information

Please see the on-screen help for additional information about the controls in all the panels mentioned here.

Editing the interface after it is build

Note

Accessing the tools

Open the Edit Interface control panel by selecting the Edit Interface menu item from the INTERFACE BUILDER card.

Cleaning up the interface

With the interface in the current model window, click the REMOVE DUPLICATES pushbutton. The Superimposition tolerance entry box on the Interface Building control panel also controls the tolerance for duplication here.

Additional information

Please see the on-screen help for additional information about the controls in all the panels mentioned here.

Creating a periodic model from an interface

Creating a crystal from an interface

Creating a surface from an interface

When an interface is built, it is oriented in a way that makes creating a periodic model from the interface model straightforward.

In addition, the crystal and surface cell parameters are set so that building a crystal or surface from an interface model puts the interface in a reasonable plane and assigns default cell or mesh parameters that match the dimensions of the right side of the interface. This enables you to extend interfaces, particularly those where the two sides match. For example, this is necessary for performing HRTEM simulations on an interface, because HRTEM calculations can be applied only to crystal models.

Creating a crystal from an interface

Accessing the tools

Open the Crystal Building control panel by selecting the Crystal Building menu item from the CRYSTAL BUILDER card.

Building the crystal

Set various parameters as desired (see Crystal Builder).

Click the BUILD CRYSTAL pushbutton. The interface appears correctly placed in a 3D unit cell.

Additional information

Please see the on-screen help for additional information about the controls in all the panels mentioned here.

Creating a surface from an interface

Accessing the tools

Open the Building From Atoms control panel by selecting the Building From Atoms menu item from the SURFACE BUILDER card.

Click the Cell Parameters... pushbutton to open the Surface Cell Parameters control panel.

Beginning the process

Notice that the u, v, and cell parameters in the Surface Cell Parameters control panel are defaulted to the dimensions of the right side of the interface.

Building the surface

Set various parameters as desired (see Surface Builder).

On the Building From Atoms control panel, click the BUILD SURFACE pushbutton. The interface appears correctly placed in a 2D surface cell.

Additional information

Please see the on-screen help for additional information about the controls in all the panels mentioned here.