Cerius2 Builders

3       Surface Builder

The C²·Surface Builder module is used for constructing 2D-periodic structures by cleaving a plane from a crystal or by placing atoms and fragments within a suitable 2D-surface cell.

Surface models are required for calculations with some modules, for example, the C²·LEED/RHEED module. For calculations using other modules, you can convert surface structures into large nonperiodic superstructures to represent the surface.

The C²·Surface Builder module also helps to visualize surfaces within crystal models that were built with the C²·Crystal Builder module.

This chapter contains information on:

Building and unbuilding surfaces

Displaying surfaces

For information about	See
Loading and saving surface structure files.	The discussion of loading and saving structure files in Cerius2 Modeling Environment.
Surface file formats.	The discussion of Cerius2 structure files in Cerius2 Modeling Environment.
Building crystals.	Crystal Builder.
Building interfaces from surfaces.	Interface Builder.
Diffraction from surfaces.	Cerius2 Analytical Instruments.

Cleaving a surface from a crystal

Building a surface from a nonperiodic model

Building a surface by adding atoms

Changing surface lattice vectors

Creating a surface superstructure

Unbuilding a surface

The C²·Surface Builder builds surfaces in which a basic surface unit is repeated using a 2D periodic cell. Many similarities exist between the Crystal Builder module, which builds 3D structures, and the Surface Builder module, which builds 2D structures.

You can also use the surface builder to convert surfaces into superstructures and superlattices.

Any surface can be unbuilt, converting the surface to one cell of a nonperiodic model. All unit cell information is lost.

General procedure

You can build surfaces in two basic ways:

• Specify a surface as a slab within a crystal and a thickness for the slab to be cleaved out (cleave-from-crystal method, see Cleaving a surface from a crystal).

• Specify a 2D unit cell and add nonperiodic models (Building a surface from a nonperiodic model) or atoms (Building a surface by adding atoms) to it (build-from-atoms method).

The MSI and CSSR file formats are the only formats that save 2D models, that is, they include the 2D unit cell information. However, once the surface has been converted into a nonperiodic superstructure, any of the file formats used for nonperiodic models can be used to save the structure.

Accessing the tools

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

Cleaving a surface from a crystal

Constructing the starting model

Build (see Building and unbuilding crystals) or load a crystal model to serve as the starting structure. This model must be loaded into the current Cerius² session, but need not be the current model.

Accessing the tools

Select the Cleave Crystal Surface menu item on the SURFACE BUILDER card to open the Cleave Crystal Surface control panel.

Open the Surface Box control panel by clicking the More... pushbutton on the Cleave Crystal Surface control panel.

Beginning the process

Choose the desired crystal model from the model pulldown near the top of the Cleave Crystal Surface control panel. This assures that the surface is cut from the correct crystal.

Choose the appropriate Cleave Rule. If you want the surface to be cleaved on an atom-by-atom basis, ignoring bonds, use the ATOMIC rule. If you want Cerius² to try to maintain whole molecules, choose the DEFAULT or MOLECULAR rule. For more information about cleave rules, see the on-screen help.

From the face to have dangling bonds popup, select how you want dangling bonds to be handled. All the bonding that was present in the crystal model is transferred to the surface model. Additionally, you can use this popup to control whether to display the bonds to atoms that are not included in the surface. These connected atoms appear in the surface model as dummy X atoms. You may view them, but they do not affect calculations. (However, you can select them all by element and change them, for instance, to hydrogens.)

Specifying the surface slab

Enter the Miller indices for the slab in the Direction entry box.

When the Miller indices have been specified, the surface builder selects two vectors, U and V, in the plane of the slab to be the basis vectors for the surface. These are two of the set of shortest lattice vectors lying in the plane. Use the Direction, U, and V entry boxes on the Surface Box control panel to set the shape and position of the cleaving slab with respect to the crystal.

Set the thickness of the surface slab by entering a value in one of the Depth entry boxes (in terms of angstroms for the left entry box or number of cells for the right entry box) in the Cleave Crystal Surface control panel. The thickness of the slab in number of cells refers to the crystallographic d-spacing. For example, when you slice the (1 1 0) plane, the depth of one unit cell is 1 X d(1 1 0).

To display the cleaving slab on the crystal model before splitting it from the crystal (as a yellow dashed line, click the Display Surface Box check box. The contents of the cleaving slab become the basis for the surface model.

Adjust the position of the slab by entering an Origin for the cleaving slab (with respect to the crystal coordinates) or by using the six Move box arrows on the Surface Box control panel. You can also move the slab with the Move box perpendicular arrows in the Cleave Crystal Surface control panel. The position of the cleaving box is instantly updated in the model window, so long as the Display Surface Box check box in the Cleave Crystal Surface control panel is checked.

Cleaving the surface

Now open a new, empty model space (see Cerius² Modeling Environment to review how to do this) to contain the surface model. Click the CLEAVE pushbutton on the Cleave Crystal Surface control panel. The cleaved surface appears in the current model space.

Caution

Additional information

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

Building a surface from a nonperiodic model

The surface is built in the yz plane, with the v surface vector coincident with the z axis. You should position the model roughly where you want it to be when the surface is built. (See the discussion of moving and manipulating models in Cerius² Modeling Environment.)

Constructing the starting model

Load or build a nonperiodic model. See Cerius² Modeling Environment for information on building, saving, and loading models.

Accessing the tools

Select the Building From Atoms menu item on the SURFACE BUILDER card to open the Building From Atoms control panel.

Open the Surface Build Preferences control panel by clicking the Preferences... pushbutton on the Building From Atoms control panel.

Open the Surface Cell Parameters control panel by clicking the Cell Parameters... pushbutton in the Building From Atoms control panel.

Beginning the process

In the Surface Build Preferences control panel, set the Visualization style to ORIGINAL.

If you want bonds across unit cell boundaries and between symmetry copies of atoms to be calculated automatically, assure that the Automatically calculate bonds check box in the Surface Build Preferences control panel is checked (see the discussion of bond calculation criteria in Cerius² Modeling Environment).

Important

Specifying the unit surface cell

Enter the dimensions of the surface cell in the u, v, and entry boxes of the Surface Cell Parameters control panel. (The choice of coordinate system has no effect until after the surface is built.) However, choosing an unsuitable 2D cell may lead to many atoms' overlapping and, consequently, many bonds across cell boundaries.

Building the surface

Click the BUILD SURFACE pushbutton in the Building From Atoms control panel. The surface cell appears in the model window.

As needed, readjust the position of the model with respect to the surface cell using keyboard-mouse combinations and/or items in the Move pulldown (on the main control panel's menu bar) and the Sketcher control panel (see Cerius² Modeling Environment for details).

At this stage, you may want to redisplay the surface according to one of the other visualization styles. Choose a new Visualization style with the popup in the Surface Build Preferences control panel:

• The DEFAULT option is suitable for most surfaces. All bonded fragments (molecules) are translated so that their centers of geometry lie within the unit cell. Networks are displayed so that, in the repeat direction of the network, atoms fit into the cell. Bonded fragments or atoms that lie on a cell faces or edge are repeated on the opposite face or edge.

• The ONE-CELL option means to translate each atom into the surface cell. No repeats are shown, resulting in exactly one cell's worth of atoms being shown.

• The ORIGINAL option makes atoms appear exactly where they were originally defined. No extra translations are added, so atoms may appear outside the unit cell.

Tip

Additional information

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

Building a surface by adding atoms

Beginning the process

Begin with an empty model space.

Accessing the tools

Select the Building From Atoms menu item on the SURFACE BUILDER card to open the Building From Atoms control panel.

Open the Surface Cell Parameters control panel by clicking the Cell Parameters... pushbutton in the Building From Atoms control panel.

Open the Add Atom control panel by clicking the Add Atoms... pushbutton on the Building From Atoms control panel. Alternatively, select the Build/Add Atom... menu item in the main Visualizer control panel.

Specifying the unit surface cell

Enter the dimensions of the surface cell in the u, v, and entry boxes of the Surface Cell Parameters control panel. (The choice of coordinate system has no effect until after the surface is built.)

Building the surface

Click the BUILD SURFACE pushbutton in the Building From Atoms control panel. The surface cell appears in the model window.

Adding atoms

Choose the surface fractional (UVd) or Cartesian (XYZ) coordinate system from the popup in the Add Atom control panel.

For each atom, you need to enter an element type and x, y, z coordinates (Cartesian) or U, V, d coordinates (surface fractional). The x, y, z, and d coordinates are in angstroms, and U and V in fractional coordinates. You may also want to specify other options for the atom: Hybridization, a nonzero Charge, Occupancy, Name, and isotropic and/or anisotropic temperature factors. Click the ADD ATOM pushbutton after each atom has been specified. The new atom appears in the model window.

If you make a mistake and want to remove an atom, you can delete it using the UNDO pushbutton. You can also delete selected atoms with items in the Edit menu on the main Visualizer control panel.

Additional information

Please see the on-screen help for additional information about the controls in all the panels mentioned here. For additional information about the Add Atom control panel, see the discussion of build operations in Cerius² Modeling Environment.

Changing surface lattice vectors

How it works

The effect of lattice alteration on atom position depends on the coordinate type you want to fix:

• If the Cartesian coordinates of the atoms remain fixed, the model conformation remains the same, although gaps or bad contacts may result.

• If the fractional coordinates of the atoms remain fixed, then, for example, an atom in the middle of the surface remains in the middle, but the model conformation is distorted by rescaling.

Open the Surface Cell Parameters control panel by selecting the Cell Parameters menu item from the SURFACE BUILDER card or by clicking the Cell Parameters... pushbutton on the Building From Atoms control panel.

Changing the lattice vectors

Make the surface model that you want to edit be current.

Use the Surface Cell Parameters control panel to choose which coordinate system to fix: CARTESIAN or FRACTIONAL.

Use the u, v, and entry boxes and/or the sliders to enter new dimensions for the U and V surface vectors and for the angle between the vectors.

Additional information

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

Creating a surface superstructure

• To introduce disorder into a surface structure, generate a superlattice from a block of surface cells, then selectively edit the superlattice.

• To perform calculations on a surface using Cerius² modules that do not explicitly accept 2D-periodic surface models, generate a large nonperiodic superstructure from the surface cells.

Open the Surface Visualization control panel by clicking the Visualization menu item on the SURFACE BUILDER card. Alternatively, click the Visualization... menu item on the Building From Atoms control panel.

Open the Building From Atoms control panel (by selecting the Building From Atoms menu item on the SURFACE BUILDER card) or the Cleave Crystal Surface control panel (by selecting the Cleave Crystal Surface menu item on the SURFACE BUILDER card).

Size of the new structure

Use the Surface Cell Display Range controls in the Surface Visualization control panel to display the number of surface cells that you want included in the superstructure or superlattice.

Creating a superlattice

To create one large periodic surface structure (a superlattice) from the displayed atoms, click the Periodic Superlattice action button in the Cleave Crystal Surface or Building From Atoms control panel.

Creating a nonperiodic superstructure

Alternatively, to create a nonperiodic superstructure from the displayed atoms, click the Non-periodic Superstructure action button in either panel.

Caution

Additional information

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

Unbuilding a surface

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

Unbuilding a surface

To return the model to its nonperiodic asymmetric unit, deleting all symmetry copies of atoms and the surface cell, click the UNBUILD SURFACE pushbutton to return the surface model to a nonperiodic model.

Additional information

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

Displaying surfaces

Accessing the tools

Open the Surface Visualization control panel by selecting the Visualization menu item from the SURFACE BUILDER card. Alternatively, click the Visualization... pushbutton on the Building From Atoms control panel.

Display range

Enter the number of surface cells to be displayed along the U and V directions.

Click the ENTER pushbutton, and a block of surface units of the prescribed dimensions is displayed in the model window.

Additional information

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