# Crystals and Surfaces¶

This tutorial covers, for **crystals**:

- Periodic crystals in AMSinput
- k-space sampling and convergence
- Lattice optimizations, with an example
- Overview of crystal properties in AMS

And for **surfaces**:

- Slabs vs. QM/MM in AMS
- Miller indices
- Create a surface slab in AMSinput
- Surface passivation, polar and nonpolar surfaces
- Surface relaxation, surface reconstruction
- Surface energy,
- Surface supercells, including matrix notation
- Adsorption sites and Adsorption energy calculations

Note

If you’re not familiar with AMSinput and AMSjobs, first go through the Getting Started and Building Crystals and Slabs tutorials, as well as some tutorial for your compute engine, like

- DFTB: Diamond Lattice Optimization and Phonons
- BAND: NiO and DFT+U
- Quantum ESPRESSO: Geometry and Lattice Optimization
- VASP: TiO2 surface relaxation
- ReaxFF: Water on an aluminum surface

To run the PLAMS python scripts, first go through the Python Scripting With PLAMS tutorial.

In this tutorial, Zn atoms are colored brown for improved contrast (the default color is white). Learn how to change the default color of atoms.

## 3D-periodic crystals¶

This tutorial covers only **3D-periodic crystals** and their surfaces.
Quasicrystals (aperiodic crystals) are not covered.

### Files¶

AMSinput can import and export coordinates in many different file formats, including **.cif** and **.pdb** files.
Select **File → Import coordinates** or **File → Export coordinates**.

When exporting to **.xyz** format, AMS also writes the lattice vectors into the file.

### Unit cells¶

In AMS, a 3D-periodic crystal can be represented as a periodic repetition of some
**unit cell**. This is known as **periodic boundary conditions** (PBC). The
unit cell is defined by three **lattice vectors**.

There are infinitely many choices of unit cells. The two most important ones are:

- The
**primitive cell**, which is the smallest possible unit cell (containing only one lattice point), and - The
**conventional cell**, which follows guidelines outlined by the International Union for Crystallography.

For example, copper is a cubic closed-packed (ccp) metal with a face-centered cubic (fcc) lattice. The primitive and conventional cells are:

Cu unit cell | # lattice points | # atoms | angles between lattice vectors |
---|---|---|---|

primitive | 1 | 1 | non-orthogonal |

conventional | 4 | 4 | orthogonal (90°) |

- Download and import
`Cu_ccp_primitive.xyz`

into AMSinput

In **AMSinput** you can switch between primitive and conventional cells. Select
**→ To Conventional Cell**, or **→ To Primitive
Cell**. View the lattice vectors and lattice parameters under **Model → Lattice**.

All other possible unit cells can be generated as supercells from the primitive
cell. Select **→ Generate Super Cell**.

You can also view some of the periodic images of the system, without generating a supercell. Click the periodic view tool.

For many crystals, the primitive and conventional unit cells are identical.

Note

The conventional Cu unit cell contains 4 lattice points in a
*crystallographic* sense. AMS does not recognize that all 4 Cu atoms at the
lattice points are identical, but would treat them independently (at an
increased computational cost compared to the primitive cell).

Tip

In AMSinput, select **View → Periodic → Show Lattice Vectors** and **Show Lattice Vector Labels** to see the lattice vectors.
Select **View → Periodic → Show Unit Cell** to highlight the unit cell.

### When to use primitive cell, conventional cell, or supercell¶

- Always use the
**primitive cell**for**electronic or phonon band structure calculations**. (For the calculation of phonon band structures, you should use the primitive cell but*also*specify the size of the supercell used internally by AMS). - Always use the
**conventional cell**when**creating a surface (slab) from Miller indices**. - Use some suitable
**supercell**when you do not have a perfect crystal, for example if you want to introduce a**defect**like a vacancy. The size of the supercell then determines the defect concentration. Supercells can also be used for approximately modeling**amorphous solids**, if atoms are displaced from their crystal positions.

### Lattice vectors and lattice parameters¶

A unit cell in AMS is represented by three **lattice vectors** \(\vec{a}\),
\(\vec{b}\), and \(\vec{c}\).

In crystallography it is more common to describe crystal structures with six
**lattice parameters**: \(a, b, c, \alpha, \beta, \gamma\), where

- \(a, b, c\) are the
**lengths**of the three lattice vectors - \(\alpha\) is the angle between \(\vec{b}\) and \(\vec{c}\)
- \(\beta\) is the angle between \(\vec{a}\) and \(\vec{c}\)
- \(\gamma\) is the angle between \(\vec{a}\) and \(\vec{b}\)

In AMSinput, go to **Model → Lattice** to see the lattice vectors and lattice
parameters (see Fig. 7). You can also edit them, but make sure to tick the **Adjust atoms
when changing lattice vectors** box if you want the fractional coordinates to
stay the same (if you want the atoms to move when you change the lattice).

In AMSinput, you can also select **View → Properties** to see the **density**.

### Fractional coordinates¶

The positions of the atoms can either be expressed in

- Cartesian coordinates in angstrom (default in AMS), or
- Fractional coordinates (in the basis of the lattice vectors), which are common in crystallography

Toggle between Cartesian and fractional coordinates in AMSinput, by going to the **Model →
Coordinates** panel, and tick the **Use fractional coordinates** checkbox.

You may also specify fractional coordinates in the text input file.

### Rotation of lattice vectors relative to cartesian axes¶

The components of the lattice vectors are cartesian (xyz) coordinates in **angstroms**.

The lattice vectors can be rotated in an infinite number of ways relative to the cartesian axes.
**In AMS it does in general not matter how the lattice vectors are rotated**. However, some other programs or file
formats, which use the lattice parameters \(a, b, c, \alpha, \beta,
\gamma\) may require that some convention is followed.
Two common conventions are

- \(\vec{c}\) is parallel to
*z*, and \(\vec{b}\) lies in the*yz*plane. - \(\vec{a}\) is parallel to
*x*, and \(\vec{b}\) lies in the*xy*plane.

In AMSinput, you can rotate the lattice vectors to follow the above conventions
under **Model → Lattice**. Tick the **Adjust atoms when changing lattice
vectors**, and press the **Align c to z-axis** or **Align a to x-axis**
buttons.

Note

ReaxFF runs slightly faster if the the first convention is used.

## k-space sampling¶

With DFTB, BAND, Quantum ESPRESSO, and VASP via AMS, you must specify some k-point sampling for periodic calculations. ReaxFF, ForceField, and MLPotential do not use k-points.

In **DFTB and BAND**, you can specify the k-space quality
using the values `GammaOnly`

, `Basic`

, `Normal`

, `Good`

,
`VeryGood`

, and `Excellent`

. You can also manually specify the number of k-points along each reciprocal lattice vector, or for highly symmetric systems use a Symmetric k-space grid.

In **Quantum ESPRESSO** and **VASP via AMS**, you must manually specify the dimensions of the Monkhorst-Pack grid.

The required amount of k-points depends on the material and size of the unit cell:

**Metals**require many k-points**Insulators, semiconductors**, and**molecular crystals**typically require fewer k-points**Small unit cells**require many k-points**Large unit cells**and**supercells**require fewer k-points

To determine suitable k-point settings for your method and system, you should
do a **k-point convergence study** in which you systematically increase the
quality of the k-space sampling until the quantity that you are interested in
(e.g., energy or lattice parameter) is converged. See Example: lattice optimization of wurtzite ZnO with DFTB
for an example.

Note

The `NumericalQuality`

keyword for BAND affects the k-space sampling.

Tip

**If possible, avoid comparing energies calculated with nonidentical k-space
sampling**. For example, if you create a supercell from the primitive cell
and introduce an interstitial defect, calculate the insertion energy with respect to the energy
of the nondefective *supercell*, not with respect to a multiple of the
energy of the primitive cell. See also: Surface energy calculations.

See also

## Lattice optimization¶

### Run a lattice optimization¶

It is common in computational chemistry to **optimize the lattice vectors** of
a crystal before constructing a supercell or surface. It is **necessary** to
first optimize the lattice before calculating phonons or the elastic tensor.

In AMSinput, select **Task → Geometry optimization** on the main panel, and
then on the **Details → Geometry optimization** panel tick the **Optimize
lattice** checkbox.

You can also set the **maximum number of iterations**.

Warning

ReaxFF is not reliable for lattice optimizations of small crystal unit cells. For ReaxFF we recommend creating a larger supercell (at least 8x8x8 angstrom) before running a lattice optimization.

### Convergence criteria for lattice optimizations¶

Four convergence criteria are considered:

- The maximum gradient (atomic force) component
- The root-mean-square of the gradient (atomic force) components
- The maximum displacement from one step to the next
- The maximum stress energy per atom

The first three are defined as for normal geometry optimizations.

The **maximum stress energy per atom** is used as a convergence criterion for
the components of the stress tensor. It is the
maximum value of the matrix `stress_tensor * cell_volume / number_of_atoms`

.

In AMSinput, **change the convergence criteria** on the **Details → Geometry Optimization** panel.

### Tips for lattice optimizations¶

**Have dense (good) k-point grids**, if you use BAND, DFTB, Quantum ESPRESSO, or VASP. The quality of a k-point grid depends on the lattice, and during a lattice optimization the lattice changes. Therefore make sure that the quality is better than normal.**BAND can be quite slow for lattice optimizations**. Consider optimizing the lattice with Quantum ESPRESSO, and then switch back to BAND.**To only allow isotropic scaling of the unit cell**, go to*Model → Geometry Constraints and PES Scan*, and tick the off-diagonal (*xy*,*xz*, and*yz*) checkboxes under*Freeze Strain*and the diagonal (*xx*,*yy*, and*zz*) checkboxes under*Equal Strain*.**To optimize the lattice under external pressure**, go to*Details → Geometry Optimization*and set the*Pressure*.

### Example: lattice optimization of wurtzite ZnO with DFTB¶

This example uses the znorg-0-1 DFTB parameter set. You can also run the example with ForceField (UFF), BAND, or Quantum ESPRESSO.

ZnO crystallizes in the hexagonal wurtzite structure, for which *a* = *b*, *α* = *β* = 90°, and *γ* = 120°.

**3.**Set**Model**to**SCC-DFTB**.**4.**Set**Parameter directory**to**DFTB.org/znorg-0-1****5.**Set**K-space**to**Good**.**7.**Select**Optimize lattice**:**Yes**.**8.**Run the job with**File → Run**, and save with the name**zno_lattopt.ams**.**9.**When the job has finished, AMSinput will ask whether to update the coordinates. Select**Yes, New job**.**10.**View the new lattice vectors and lattice parameters under**Model → Lattice**.**11.**Export your structure to .xyz format:**File → Export coordinates → .xyz**. Save it with the name`ZnO_optimized_znorg.xyz`

.**12.***Optional:*switch to AMSjobs (**SCM → Jobs**), select your job, and build a spreadsheet summary with**Tools → Build spreadsheet**.

Table 3 gives the *a* and *c* lattice parameters for different
k-space qualities. This is an example of a **k-point convergence test**.

k-space | a (Å) |
c (Å) |
---|---|---|

Basic | 3.281 | 5.425 |

Normal | 3.295 | 5.347 |

Good | 3.290 | 5.375 |

Very Good | 3.289 | 5.375 |

Tip

k-point convergence tests can be scripted with the PLAMS Python module.
Download a `PLAMS python script`

and `xyz file`

to generate the above table.

## Solid-state properties¶

**Band gap**with BAND/DFTB/QE: The one-electron gap is printed towards the end of the logfile for DFTB and BAND calculations. The one-electron gap can also be extracted from band structure calculations, which include all high-symmetry k-points.**Electronic density of states (DOS)**with BAND/DFTB/QE: On the Main panel, tick the*Calculate DOS*checkbox. This also calculates the partial DOS, PDOS.**Electronic band structure**with BAND/DFTB/QE: On the Main panel, tick the*Calculate band structure*checkbox. Band structures are usually calculated for the primitive cell. To create a custom path through the Brillouin zone, go to*Properties → Band Structure*.**Phonon dispersion curves and phonon DOS**:*Properties → Phonons and Elastic tensor → Phonons*. First optimize the lattice! See the Diamond lattice optimization and phonons tutorial.**Bulk modulus, Shear modulus, Young’s modulus, Elastic tensor**:*Properties → Phonons and Elastic tensor → Elastic tensor*. First optimize the lattice with tight convergence criteria.**Stress-strain curve, yield point**: See the Snapping Polyacetylene Chain tutorial.**Thermal expansion coefficient**: Run well-equilibrated NPT molecular dynamics simulations at several different temperatures: See the Thermal expansion coefficients of thermoset polymers tutorial.**Atomization energy**and**lattice energy**: See Bond energy calculations.

## Surface models in computational chemistry¶

There are two main ways of representing surfaces in atomistic modeling:

- A
**slab model**, which is periodic in the lateral directions. It can also be periodic in the surface normal direction, in which case a**vacuum gap**separates the slabs (a repeated slab model). The AMS engines**BAND, DFTB,**and**ReaxFF**can be modeled with 2-dimensional periodicity and do not require a vacuum gap.**Quantum ESPRESSO**and**VASP via AMS**require a vacuum gap (3-dimensional periodicity). - An
**embedded cluster (QM/MM)**, in which a piece of the surface is modeled at a high level of theory (e.g. DFT), and the rest at a lower level of theory (force field or point charges).**ADF, BAND, and DFTB**can be used for this type of surface model. Combining different engines in QM/MM is done via the**Hybrid**engine.

The rest of this tutorial only covers **slab models**, which are the most common type of surface model. For more details about QM/MM, see the Inorganic linker in organic framework tutorial.

Tip

AMS includes a Microkinetics module for modeling reactions on surfaces.

Engine | 2D slab | 3D slab (vacuum gap) | QM/MM |
---|---|---|---|

ADF | ❌ | ❌ | ✔ (QM) |

BAND | ✔ | ✔ | ✔ (QM) |

DFTB | ✔ | ✔ | ✔ (QM, MM) |

ForceField | ✔ | ✔ | ✔ (MM) |

ReaxFF | ✔ | ✔ | ✔ (MM) |

ML Potential | ❌ | ✔ | ❌ |

Quantum ESPRESSO | ❌ | ✔ | ❌ |

VASP via AMS | ❌ | ✔ | ❌ |

## Miller indices¶

### Surface Miller indices¶

Surfaces are often defined based on **Miller indices**. A surface plane is denoted **(hkl)**.

The Miller indices give the **inverse** fractional intercepts along the lattice vectors in
the **conventional unit cell**. If an index is 0, the surface lateral plane is
parallel to that direction. A negative index is denoted by a bar.

**Example 1**: The Cu(100) surface is parallel to the second and third lattice vectors of Cu in the conventional unit cell.

**Example 2**: The Cu(111) surface is formed by the plane slicing all lattice vectors of the Cu conventional unit cell at the maximum coordinates for the unit cell.

**Example 3**: The Cu(511) surface is formed by the plane slicing the second and third lattice vectors of the Cu conventional unit cell at the maximum coordinates for the unit cell, but slicing the first vector at one fifth. This forms a **stepped surface**.

For **hexagonal crystals** (e.g. Zn or ZnO), four Miller indices (hkil) are often used. The third index (i) is then redundant: h + k + i = 0.

For **hexagonal crystals with a rhombohedral lattice** (e.g. α-Al_{2}O_{3} or calcite CaCO_{3}), the Miller indices can refer to either the rhombohedral primitive cell or the hexagonal conventional cell. You need to know which convention is used; when publishing or communicating with others, you should explicitly state which convention you use.

### Crystal directions¶

**A direction in a crystal is written as [hkl]**, and denotes the linear
combination \(h\vec{a} + k\vec{b} + l\vec{c}\).

This direction is **not necessarily** perpendicular to the plane (hkl). **Example**:
in a monoclinic cell with α = γ = 90° and β > 90°, the [001] direction
is parallel to \(\vec{c}\) which is not perpendicular to the (001) plane;
the (001) plane is parallel to both \(\vec{a}\) and \(\vec{b}\).

For hexagonal lattices, crystal directions can either be given using three indices as above, or a special four-index [hkil] notation. How to convert between the two types of notation is described in materials science or crystallography text books.

AMSinput and the other GUI modules do not show crystal directions.

Note

Crystal directions are almost always given with respect to the **conventional cell**.

## Generate a slab with AMSinput¶

**4.**Miller indices`5`

,`1`

,`1`

**5.**Number of layers: 10**6.****Generate slab**

This will generate a Cu(511) slab as in Fig. 12. See also the Building Crystals and Slabs tutorial.

The slab is rotated such that the **surface normal direction** is parallel to *z*.

If you have the , , , or
panel active, the **periodicity** will be automatically changed to **Slab** (2D). For
the other engines, 3D periodicity (**Bulk**) is retained, and a vacuum gap is introduced.
View the lattice parameters under **Model → Lattice**.

Note

When the periodicity is set to **Slab**, the \(\vec{a}\) and \(\vec{b}\) surface lattice vectors
must lie in the *xy* plane. View the lattice vectors under **Model → Lattice**.

Tip

If the surface unit cell is hexagonal (examples: Cu(111) and ZnO(0001)), the angle
\(\gamma\) between the \(\vec{a}\) and \(\vec{b}\) lattice
vectors may become 60°. It is more common to use an angle of 120°. You can
change the angle under **Model → Lattice**, or use the **→ To Conventional Cell** tool.

## Surface terminations¶

The above definition of (hkl) Miller indices was based on intercepts in the
conventional unit cell, but **any** plane that is parallel to that plane is
*also* a (hkl) surface, but with a potentially different surface termination.

In AMSinput, **→ Generate Slab**, you can click on an atom before
generating the slab to slice through that atom.

In general, you should carefully look at the generated surface structure to see if it is reasonable.

**Example**. Import `ZnO_wurtzite.xyz`

. Generate 3 layers of a ZnO(0001) (for hexagonal crystals, ignore the
third index so type in `0`

, `0`

, `1`

). First generate the slab with the Zn(1) atom
selected, then with the O(3) atom selected. The surface terminations are
different. In the first case, the surface atoms become 3-coordinated, which is
favorable. In the second case, the surface atoms become 1-coordinated, which
is much less stable.

Similarly, you can generate “good” and “bad” terminations of the ZnO(\(10\bar{1}0\)) surface.

Tip

**Create a thicker slab than you need**, and manually remove atoms until the
surface terminations are correct. **Double-check your stoichiometry** under
*View → Properties*, or by **Select → Select All**.

## What makes a good slab model¶

In general when creating a slab, you would like to

**Retain the stoichiometry**. Example: a ZnO slab should ideally contain the same number of Zn as O atoms (just like in the bulk).**Maximize the coordination numbers**of the surface atoms (see Surface terminations)**Have identical “top” and “bottom” sides**: This may not be possible for all crystals or surfaces (example: a slab exposing Zn-terminated ZnO(0001) at the “top” side will necessarily expose the O-terminated ZnO(\(000\bar{1}\)) surface at the bottom side, see Fig. 13 d)

Sometimes it is very difficult to create ideal slabs, especially if the crystal
contains **composite ions like carbonate, nitrate, sulfate, or phosphate**.

## Surface passivation¶

**Surface passivation** is often accomplished by adding **H atoms** that are coordinated by the surface atoms. Such H atoms can passivate **dangling bonds**.

**Example**: The diamond(100) surface is terminated by two-coordinated sp^{3} C atoms. This is very unstable. By passivating the surface with H, the dangling bonds at the surface become passivated.

Tip

Between steps 5 and 6 you can get the primitive surface unit cell with **→Convert To Primitive Cell**.

Note

The **Add Hydrogens** function does not add H atoms to the most
energetically favored positions. Randomly move the H atoms a little, and perform
a geometry optimization, to find more suitable positions for the H atoms.

Note

The **Add Hydrogens** function does not work for all chemical elements. For
some elements, you need to add the H atoms manually.

## Surface relaxation¶

A geometry optimization of a surface will typically give the result that the surface atoms relax away from the positions of a bulk-truncated crystal. For example, the surface atoms may move closer to the subsurface atoms.

Surface relaxation can also happen for atoms in the subsurface layers.

To quantify the surface relaxation, you can

- in
**AMSmovie**, go to**View → Coordinates**to see how the coordinates of the atoms change during a geometry optimization, **SCM → KFbrowser**, select**File → Expert mode**, view the input coordinates (in bohr) under**InputMolecule → Coords**, and the final coordinates (in bohr) under**Molecule → Coords**.- view the input and final coordinates in a spreadsheet summary (
**Tools → Build spreadsheet**in**AMSjobs**).

## Surface reconstruction¶

A surface reconstruction is a significant structural change at the surface compared to the bulk.

**Example 1**: The Si(100) surface forms a (2×1) reconstruction in which the
surface atoms form rows of dimers (not found in the bulk). (2×2) and *c*(4×2)
reconstructions are also possible. Download a `PLAMS python script`

to
run the jobs shown below, and visualize the DOS in AMSdos (**SCM → Dos**).

**Example 2**: The polar Zn-terminated ZnO(0001) surface can form quite large
triangular pits and islands ↗, which help to stabilize the surface because the
stoichiometry of the pits and islands is different from the bulk stoichoimetry. See also: Polar and non-polar surfaces.

## Polar and non-polar surfaces¶

Nonpolar surfaces are the most common and are typically more stable than polar surfaces. For ionic compounds, some surfaces are polar.

A surface is polar if the formal dipole
moment perpendicular to the slab grows with the slab thickness. Here, the *formal
dipole moment* is calculated based on the formal charges of the ions. The growing dipole moment
gives a diverging energy as the slab thickness increases.

Nevertheless, polar surfaces can form in real life, as they are stabilized in some manner.

In calculations, a polar surface slab exposes two different polar surfaces, one on the “top” side and one on the “bottom” side. For example, the Zn-terminated ZnO(0001) at the top and the O-terminated ZnO(\(000\bar{1}\)) at the bottom (Fig. 13 d).

### Polar surface stabilization mechanisms¶

A polar surface can be stabilized by

- A change in stoichiometry, e.g., vacancies or other defects
- Adsorption
- charge transfer from one side of the slab to the other ↗, potentially leading to surface metallization. This is common in electronic structure calculations but uncommon in experiment.
- for thin slabs, the entire crystal structure might change ↗.

**Example**: ZnO(0001) and ZnO(\(000\bar{1}\))

ZnO(0001) can be stabilized by, for example

- 1/4 surface Zn vacancies, or
- 1/2 ML OH adsorption

ZnO(\(000\bar{1}\)) can be stabilized by, for example,

- 1/4 surface O vacancies, or
- 1/2 ML H adsorption

**1.**Download and extract`polar_stabilization.zip`

**2.**Import`clean_good.xyz`

in AMSinput**5.**Set**Parameter directory**to**DFTB.org/znorg-0-1**.**6.**Run the job (it may require a few hundred SCC cycles)**7.**View results in AMSdos:**SCM → Dos****8.**To view the partial DOS from only a few atom, select the atoms in the AMSdos window**9.**View the DOS for the top layer, a middle layer, and the bottom layer**10.**Repeat steps 2-9 for`vacancies_good.xyz`

and`adsorbates_good.xyz`

Fig. 18 a shows the DFTB-calculated DOS for a **clean
ZnO(0001) slab** (terminated as in Fig. 13 d). The positions of the bands shift when going from the top to the bottom layer. The conduction band at the Zn-terminated side overlaps with the
valence band on the O-terminated side, giving rise to charge transfer and
**surface metallization**. Because of this, the SCC (or SCF for DFT calculations) can be **difficult to converge**.

Fig. 18 b and c show the DFTB-calculated DOS after
vacancy or adsorption stabilization. In these cases, there is no surface
metallization and the ZnO slab remains a **semiconductor**.

Note

Ideal (unstabilized) polar surfaces can be difficult to converge in DFT and DFTB calculations. Always try to stabilize the surface via change in stoichoimetry or adsorption.

If you use **VASP via AMS**, you can use pseudo-atoms with a fractional number
of electrons by selecting the corresponding POTCAR files. Such pseudo-atoms are
sometimes used to passivate polar surfaces, but it is also possible to use real
elements, like H, with some suitable stoichiometry.

## Surface unit cells and supercells¶

Just like a crystal, a surface also has a primitive unit cell (containing only one lattice point). In surface-science-style calculations, it is common to use a surface supercell. By creating a supercell, the coverage of adsorbates can be fine-tuned.

### Create a conventional surface unit cell¶

When you generate a slab in **AMSinput**, you may not always get the conventional
surface unit cell. To get the conventional surface unit cell, select
**→ To Conventional Cell**. For the primitive surface unit cell, select **→ To Primitive Cell**.

Note

For surfaces, the primitive and conventional cells only differ for centered rectangular lattices.

**Example: The Cu(111) surface**

**1.**Import`Cu_ccp_primitive.yz`

**2.****→ To Conventional Cell**. Note: this generates the conventional cell of the bulk Cu crystal, which is needed for the slab generation.**4.**Type Miller indices`1`

,`1`

,`1`

**5.**Number of layers: 5**6.****Generate slab**. The generated slab has 4 atoms in the top layer. (This is not the conventional surface cell)**7.****→ To Conventional Cell**. The slab now has only 1 atom in the top layer.**This is the conventional Cu(111) surface unit cell**for a 5-layers-thick slab. See also Fig. 19

Tip

On the **Model → Lattice** page, tick the **Adjust atoms when changing
lattice** checkbox and rotate the surface lattice vectors so that
\(\vec{a}\) is parallel to *x*.

### Create a supercell¶

From the conventional surface cell, it is common to create supercells, either to accommodate surface reconstructions or overlayers (adlayers, adsorbed layers) of some particular structure.

Supercells are often described using either **Wood’s notation** (not supported by AMSinput) or **matrix notation** (supported by AMSinput).

**Wood’s notation** gives supercell’s lattice vector lengths as multiples of
the original lattice lengths, together with any applied rotation. This notation
can only be used if the angle γ between the lattice vector does not change when
creating the supercell.

**Examples of Wood’s notation**:

- Cu(100) (2×1)
- Cu(100) (√2×√2)-R45°
- Cu(111) (√3×√3)-R30°

In AMSinput, you cannot specify supercells using Wood’s notation but must
instead use **matrix notation**, which works for any supercell (potentially allowing the angle γ to change).
See Fig. 19.
The above three examples would translate to

- Cu(100) \(\begin{pmatrix}2 & 0 \\ 0 & 1\end{pmatrix}\)
- Cu(100) \(\begin{pmatrix}1 & 1 \\ 1 & -1\end{pmatrix}\)
- Cu(111) \(\begin{pmatrix}2 & 1 \\ -1 & 1\end{pmatrix}\)

In AMSinput, select **→ Generate supercell** and enter the supercell matrix.

For **hexagonal** surfaces, like Cu(111) or ZnO(0001), γ = 120°. It is often
more convenient to work with a supercell in which γ = 90°, especially if the
purpose is to construct a large slab for a molecular dynamics simulation.

**Convert hexagonal (γ = 120°) surface unit cell to rectangular (γ = 90°) supercell**:

- Cu(111) \(\begin{pmatrix}1 & 0 \\ 1 & 2\end{pmatrix}\)

Tip

Hexagonal *bulk* crystals (e.g., wurtzite ZnO) can similarly be converted to an orthorhombic supercell. The matrix is then
\(\begin{pmatrix}1 & 0 & 0 \\ 1 & 2 & 0 \\ 0 & 0 & 1\end{pmatrix}\)

## Surface energy calculations¶

The **surface energy** \(E^{\text{surf}}\) gives the energy required to form a surface, per unit surface area.

In a slab calculation with two identical surfaces, the slab energy \(E^\text{slab}\) can be divided into a “bulk” contribution and a “surface” contribution:

where \(n^\text{slab}\) is the number of formula units in the slab unit cell,
\(n^\text{bulk}\) is the number of formula units in the bulk unit cell, *A* is the
surface area, and \(E^{\text{surf}}\) is the surface energy. The factor 2 appears because the slab exposes two surfaces.

**Surface energy method 1 (recommended)**

- Plot \(E^\text{slab}\) vs. \(n^\text{slab}\) for progressively thicker slabs,
- Fit a straight line through the datapoints,
- Extract \(E^{\text{surf}}\) from the intercept with the y-axis (at 0 “thickness”, \(n^\text{slab} = 0\)).

In this way, \(E^{\text{bulk}}\) is not needed explicitly (but corresponds to the slope of the plot), and the k-point sampling is identical for each slab thickness. This means that the k-points in the surface calculation do not need to be extremely accurately converged.

**Surface energy method 2**

The above equation can be rearranged to give

\(E^{\text{surf}}\) can be calculated using this equation for a thick slab. This requires that \(E^{\text{bulk}}\) be calculated explicitly. Both \(E^{\text{slab}}\) and \(E^{\text{bulk}}\) must be very well converged with respect to k-point sampling, and \(E^{\text{bulk}}\) must be calculated for a very carefully converged (optimized) lattice.

Note

It is easiest to calculate the surface energy for slabs constructed from the
**optimized** bulk lattice parameters, so that there is no strain the
surface-lateral direction.

If your intention is to model a surface of a bulk crystal, then **do not
optimize the lattice of the slab**. Optimize the lattice of the **bulk**,
and use that to construct the slab.

If your intention is to model a **thin film**, you can consider optimizing the lattice of the slab.

### Example: Surface energy of ZnO(\(10\bar{1}0\))¶

This ZnO(\(10\bar{1}0\)) surface energy example uses DFTB and the `ZnO_optimized_znorg.xyz`

file from the
lattice optimization example. You can
also run these calculations with BAND, ForceField (UFF), ReaxFF, Quantum
ESPRESSO, or VASP via AMS. Use the same method that you used when generating
`ZnO_optimized_znorg.xyz`

.

**1.**Import`ZnO_optimized_znorg.xyz`

into AMSinput**3.**Set**Parameter directory**to**DFTB.org/znorg-0-1****4.**Set**Kspace**to**Normal****5.**Set**Task**to**Geometry Optimization**. On the**Details → Geometry Optimization**panel, make sure that*Optimize lattice*is**not**activated.**7.****Miller indices**`1`

,`0`

,`0`

(for hexagonal crystals, ignore the third Miller index \(\bar{1}\)).**8.****Number of layers**: 4 (in this case the number of “double”-layers)**10.**Press the**Generate Slab**button.**11.**On the**Model → Lattice**panel, note the**surface area**\(|\vec{a} \times \vec{b}|\) = 17.68 Å².**11.**Save and run the job.**12.**Repeat the above steps for a few other thicknesses (number of layers).

Now, tabulate the slab energies \(E^{\text{slab}}\) for each thickness. To get the energy, either

**SCM → Jobs**, select the job,**Job → Edit Comments**, in the*Results*dropdown menu choose*Energy*, click**Set as Default**, click**Save**, select**View → Comments**.**SCM → Output**, use the bottom search box to search for`calculation results`

. The energy is printed directly below.**SCM → KFbrowser**,*File → Related files → dftb.rkf*,**AMS results → Energy**.**SCM → Jobs**, select all jobs for the different thicknesses,**Tools → Build spreadsheet**, click the**Do It**button.

Using **method 1**, fit a straight line through the datapoints, as in Fig. 20.

The intercept = \(2AE^\text{surf}\), where *A* = 17.68 Å² for all slabs.
**The surface energy becomes**

If **method 2** is used for the thickest slab with Normal k-space sampling,
\(E^{\text{surf}}\) becomes 1.04 J/m^{2}. When reoptimizing the thickest slab with
Good k-space sampling, \(E^{\text{surf}}\) instead becomes 1.31 J/m^{2}, which is the
same number we found above using method 1.

Tip

Download PLAMS python scripts to `set up and run`

and
`postprocess`

jobs that
generate the surface energy graph and numbers. See also: the
Python Scripting With PLAMS tutorial.

Tip

Calculate the surface energy of ZnO(\(11\bar{2}0\)) using method 1 and method 2 with
SCC-DFTB znorg-0-1. Answer: \(E^{\text{surf}}\) = 1.39 J/m^{2}.

### Surface energy vs. cleavage energy¶

The **cleavage energy** is the energy required to create a slab from the bulk.
If the slab exposes two identical surfaces, the cleavage energy is double the
surface energy.

For example, you can only calculate the cleavage energy of the combined Zn-terminated ZnO(0001) and O-terminated ZnO(\(000\bar{1}\)) surfaces, and not the individual surface energies.

## Adsorption¶

### Adsorption on surfaces in AMSinput¶

You can place an adsorbate on a surface (substrate) in arbitrary conformations by rotating and translating the molecule.

Some surfaces have high-symmetry adsorption sites, like **ontop**, **bridge**, or **hollow** sites.

### Example: ontop, bridge, fcc hollow and hcp hollow sites on Cu(111)¶

`Download Cu_111_4l_H2O.xyz`

, or create a 4-layer Cu(111) (5x5) surface supercell from the conventional Cu unit cell and add a water molecule somewhere on top of it.

For easier visualization, we will color the 2nd Cu layer **green**, and the 3rd Cu layer **yellow**.

**1.**In AMSinput,**View → View Direction → Along x-axis****2.****Atoms → Details (Color, Radius, Mass, …)****3.**Select an atom in the 2nd Cu layer. On the right hand side, click the brown “Color” rectangle for this atom.**4.**Change the color to green**5.**Select all atoms in the 2nd Cu layer**6.**Right-click on the**green**rectangle from before. This colors all atoms in the 2nd layer green.**7.**Repeat steps 3-6 for the 3rd Cu layer, and color it yellow.**8.****View → View Direction → Along z-axis**

This is what it looks like from the side and from the top:

**1.****Edit → Tune Geometry****2.**Select the water molecule and click the**⬭**label to the right of**Atoms to move**.**3.**Select three atoms in the top Cu layer and click the**⬭**label to the right of**Plane**.**4.**Set**Distance to plane**to 2.5 angstrom, and choose**to closest atom**.**5.**•**Ontop**: Select one Cu atom in the top layer•**Bridge**: Select two neighboring Cu atoms in the top layer•**fcc hollow**: Select three neighboring Cu atoms in the top layer that surround a yellow (third-layer) atom when viewed from above.•**hcp hollow**: Select three neighboring Cu atoms in the top layer that surround a green (second-layer) atom when viewed from above.**6.**Click the**⬭**label to the right of**Above atoms**.**7.**Click the**Move**button. This moves the adsorbate to the chosen adsorption site.

Tip

In the **Tune Geometry** window you can also

**Translate atoms, direction**: translate the*Atoms to move*a certain**distance**along a certain**direction**. Use the**⬭**label to define the direction from selected atoms. Click the ◀ ▶ buttons to move the atom.**Translate atoms, target**: translate the*Atoms to move*towards a certain**target position**. Use the**⬭**label to define the target position based on the currently selected atom. Click the ◀ ▶ buttons to move the atom.**Rotate atoms**: rotate the*Atoms to move*around a certain**axis**(vector) that goes through a**center**(position). For example, set*Angle*to 20°,*axis*to`0`

,`0`

,`1`

, and*center*to`0`

,`0`

,`0`

. to rotate the*Atoms to move*around the z axis in steps of 20°.

If you place the mouse cursor over an input field, you will get more information in a help balloon.

### Adsorption energy¶

The **adsorption energy** \(\Delta E^\text{ads}\) is the binding energy of a molecule (adsorbate) on a surface:

All energies on the right hand side are calculated for **geometry-optimized systems**.
With the above equation, a positive adsorption energy implies exothermic
adsorption. **A different sign convention can also be used**:

With this equation, a negative adsorption energy implies exothermic adsorption.

When reporting adsorption energies, always specify the equation that you used to calculate them.

### Basis set superposition error with BAND¶

In BAND, if your basis set is not large enough, the adsorption may become
artificially stable from the basis set superposition error (BSSE). **The best way
to address BSSE is to increase the size of the basis set**. Alternatively, you
can also apply the counterpoise correction.

DFTB, Quantum ESPRESSO, VASP via AMS, and the other engines do not show any BSSE.

**Example**: water molecule adsorption on ZnO(\(10\bar{1}0\)).

The figure below shows calculated adsorption energies with and without counterpoise correction. Each geometry was optimized with the corresponding basis set, and the counterpoise correction was applied to final slab+mol system.

Basis set | Counterpoise correction (kcal/mol) |
---|---|

DZ | 3.69 |

DZP | 3.00 |

TZP | 1.31 |

TZ2P | 1.15 |

QZ4P | 0.14 |

### In-cell approach for adsorption energies with ReaxFF¶

In ReaxFF, the electronegativity equalization method (EEM) is used to determine the charges on the atoms, which in turn determine the Coulomb energy contribution to the total energy.

In an isolated molecule, charge can only be redistributed among the atoms in the molecule. Similarly, for an isolated slab, charge can only be redistributed among the atoms in the slab.

In the combined slab+molecule system, there is more freedom to redistribute the charge, potentially lowering the energy and giving more stable adsorption. This issue is similar to the basis set superposition error.

**For ReaxFF calculations**, it is therefore an option to use the **in-cell approach**:

where the first term is calculated for a system where the slab and molecule are placed far apart in the same cell (“in-cell”), see Fig. 23 d. In this way, for both systems on the right hand side, the charges have the same freedom to redistribute.

A different sign convention can also be used:

**Example:** H_{2}O adsorption on ZnO(\(10\bar{1}0\)). (3×2) supercell, 5
double-layers thick, constructed from bulk lattice parameters *a* = 3.28
Å, *c* = 5.28 Å. Download `a PLAMS python script calculating these numbers`

.

kcal/mol | |
---|---|

E^{slab} |
-10331.25 |

E^{mol} |
-248.85 |

E^{slab} + E^{mol} |
-10580.11 |

E^{slab+mol widely separated} |
-10590.11 |

E^{slab+mol} |
-10606.43 |

E^{ads} (standard) |
-26.3 |

E^{ads} (in-cell) |
-16.3 |

The difference in adsorption energy between the two approaches is 10 kcal/mol, which stems from the fact that

This energy difference gets larger for larger supercells and thicker slabs, see Fig. 25

Tip

Keep the in-cell approach in mind when creating training sets for ReaxFF parametrization.

### One-sided vs. two-sided adsorption¶

A slab exposes two surfaces, and adsorbates can either be added to both surfaces or only one.

For Quantum ESPRESSO and VASP, double-sided adsorption can prevent the formation of a dipole moment across the vacuum gap. The other engines support 2D periodicity for which there is no vacuum gap.

### Fixing the central and/or bottom layers of the slab¶

It is common to **fix the positions** of either the central or the bottom layers of the slab.

When relaxing a clean (without adsorbates) slab, it is a good idea to relax
either all atoms, or to keep the central layers fixed. In this way, both the top and bottom
sides of the slab relax. This **relaxed** slab can then be used for

- one-sided adsorption (relaxing everything or fixing the central and bottom layers),
- double-sided adsorption (relaxing everything or fixing the central layers).

**Even in the case of one-sided adsorption (on the top surface) it is good to
have a relaxed bottom surface** when using DFTB, BAND, Quantum ESPRESSO, or
VASP. This will help SCF convergence and give a “cleaner” DOS (compare
Fig. 16 and Fig. 17),
especially for covalent or ionic materials. For metals the effect is smaller.

In AMSinput, select the atoms that you would like to keep fixed. On the **Model
→ Geometry Constrained and PES Scan** panel, click the plus button
next to *selected atoms (fix positions)*.

**Example**: See the TiO2 surface relaxation tutorial.

## Solid-solid and solid-liquid interfaces¶

### Solid-solid interfaces¶

A solid/solid interface (heterojunction) under periodic boundary conditions corresponds to a slab of material A adsorbed onto a slab of material B.

A crystalline interface can be written as **A(hkl) || B(h’k’l’) with A[uvw] ||
B[u’v’w’]**, where the first part specifies which crystal planes that are
parallel, and the second part specifies a crystal direction in A in the (hkl) plane that is
parallel to a crystal direction in B in the (h’k’l’) plane.

The lattice vectors of the slab models of the two materials must match exactly (coincidence site lattice). Two materials usually have very different crystal structures, so to create such a model, supercells that are possibly strained or rotated need to be created, before adsorbing one slab on top of the other.

### Solid-liquid interfaces¶

Solid/liquid interfaces can easily be created in AMSinput. Create a slab, and select **Edit → Builder**.

Note

The builder will create a solid/liquid interface under 3D periodic boundary conditions.

For more details, see the Water on an aluminum surface tutorial.