Building Crystals and Slabs
***************************

AMSinput Crystal Surface Building structures Space group Supercell
Miller indices

In this tutorial we demonstrate the working of several tools that
combined give you great flexibility to build periodic structures.

If you are not interested in periodic structures (for example, if you
only use ADF), you can skip this tutorial.

The instruments at your disposal are:

* The crystal structures tool [image: CrystalTool][image].

* The predefined crystal structures in the database (via the search
  field).

* CIF file importer.

* Crystal builder from space group information.

* Super cell tool to enlarge the unit cell.

* Slice tool to cut out slabs from any crystal.

To use these tools you need to use AMSinput in periodic mode. For
example, by switching to the BAND mode, or by switching to DFTB or
Mopac and next changing the periodicity.

See also:

  More information about modeling crystals and slabs in AMS: see the
  Crystals and Surfaces tutorial.


The Crystal Structures Tool
===========================

If you are lucky your crystal structure is already included in
AMSinput. Most of the common structures are there. NaCl is one of
them.

   Start AMSinput (**SCM → New Input**) and switch from [image: ADFPanel][image] to [image: BANDPanel][image] (or to DFTB, and switch the periodicity to 'Bulk')
   Click on the snowflake-like pictogram [image: CrystalTool][image] on the toolbar.
   Select a **Cubic** lattice and then **NaCl**

   [image]

Next a builder menu will appear on the right-hand side, where you can
change the parameters of the structure, such as lattice constants

   [image]

In this case there is no need to change anything.

   Click **OK**
   **View → Periodic → Periodic View Type → Repeat Unit Cell**

   [image]

You can adjust the details like lattice constants by hand. For example
LiF: it has the same crystal structure as NaCl, but other elements and
a different lattice constant, namely 4.02:

   [image: CrystalTool][image] **→ Cubic → NaCl**
   Change the lattice constant and the elements as shown below
   Click **OK**

   [image]

The NaCl crystal structure will be replaced by the new LiF crystal
structure.

Some crystal structures have more parameters.

   [image: CrystalTool][image] **→ Tetragonal → Rutile**
   Click OK

   [image]

As you can see, it has two lattice parameters that need to be
specified. But now also the positions of the oxygens have a parameter
"x"

After clicking **OK** your screen will look like this

   [image]


The Crystal Structures Database
===============================

All crystal structures known to the crystal structures tool are also
available via the search tool.

Just as you can search for a molecule, you can search for a crystal.
So lets make NaCl again:

   **File → New**
   Click on the search icon, or press Cmd/ctrl-S
   Type 'NaCl' (without the quotes)

You should get a couple of matches:

   [image]

Select the NaCl crystal result (not the molecule!):

   Click on the 'NaCl' search result (in the Crystals section)

You now should have a NaCl crystal again.

Currently the structures of many simple crystals are included, as well
as a few complex structure (optimized by MOPAC). The zeolite
frameworks are also included as a starting point to make your zeolite
structure.


Crystal builder (from space group information)
==============================================

The structure database is very convenient but by necessity incomplete.
A more powerful approach is to build 3D crystals from the space group
information. Here we give an example on how to build TiO2 (Rutile)
again, now from its space group.

   Open the crystal builder:
   Click on [image: CrystalTool][image] **→ New From Space Group ...**

   [image]

And the following menu will appear on the right-hand side:

   [image]

Rutile has the symmetry of space group 136

   Enter **136** in the space group **Number** field, and press return/enter.
   Set the lattice parameters **a** to **4.59** and **b** to **2.96**
   Click on [image: AddButton][image] next to Coordinates, select **Ti** atom and **a** site
   Click on [image: AddButton][image] again,. Select **O** atom and **f** site, and set **x=0.3**

The final should look like this:

   [image]

   Press **Apply** and then **Close**

   [image]

In the toolbar there is another tool that may be of use: the star
button. Just like for molecules this button will try to detect the
symmetry of your system and make small changes to adjust to perfect
symmetry. It does this via spglib, see the help balloon for details.

   Click the Symmetrize button (the star in the toolbar)

You already had perfect symmetry, so nothing much changes. The
detected symmetry should be reported:

   [image]

You can view a larger part of the crystal and still see the unit cell
clearly:

   Right-click on the periodic display button (the 4 dots)
   Select: Repeat Unit Cell (Custom)
   In the dialog that pops up type 2 in the top-left cell (other elements will follow)
   Click OK
   Use ctrl/cmd-J and ctrl/cmd-K to make neighbor cells more or less transparent (or use the menu commands in the View menu)

This will give you a view like this:

   [image]


Slicer: building slabs, transform primitive to conventional cell
================================================================

The slicer is a very easy, yet powerful tool to make slabs from any
crystal structure. In this example we build a three layer slab of the
Cu(111) surface.

[image: CrystalTool][image] **→ Cubic → fcc** | Select fcc from the
"Cubic" crystals

The element and lattice constant are already correct for Cu.

   [image]

   Press "OK" to generate the Cu lattice
   **View → Periodic → Periodic View Type → Repeat Unit Cell** if needed

   [image]

Let us invoke the slicer tool to cut out the slab.

   Click on the [image: SliceTool][image] slice tool, *or* select [image: CrystalTool][image] **→ Generate Slab**.

The right side of the AMSinput window will show the Generate Slab
options.

If you hold your mouse over the Miller indices fields, you should get
a balloon that explains how to set the proper Miller indices.  In this
particular example we have the primitive unit cell of Cu, so first
**we need to convert to conventional unit cell**.

   Click on the **Convert to Conventional Cell** button.
   Set the number of layers to 3
   Set the Miller indices to "1, 1, 1"

   [image]

   Press **Generate Slab**

You will see (from the top), if the [image: PeriodicViewTool][image]
periodic view tool is activated,

   [image]

You may want to rotate it or select **View → View Direction → Along
X-axis** to convince yourself that it is a three layer slab.

   [image]

See also:

  More about primitive and conventional cells, and Surface unit cells
  and supercells.


Creating a supercell
====================

Quite often you want to use a larger unit cell. You can do this for
chains, slabs, and crystals, but we will demonstrate how it works for
a slab.

We will continue to work with the 3-layer Cu slab:

   Select the **Edit → Crystal → Generate Super Cell...** command

Thus invoking the Super Cell Tool

   [image]

Here you see how new lattice vectors are expressed in terms of old
ones. Because we have a slab this is a 2x2 matrix.

   Use the default (2 on the diagonal)
   Press OK

and you get a bigger unit cell with three atoms per layer:

   [image]

   Close AMSinput

See also: Surface unit cells and supercells
