## How to Prepare an Input File for Surface Calculations

### September 11, 2013 Posted by Emre S. Tasci

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# How to Prepare an Input File for Surface Calculations

## Emre S. Tasci

Abstract

This how-to is intended to guide the reader during the preparation of the input file for an intended surface calculation study. Mainly VESTA software is used to manipulate and transform initial structure file along with some home brewed scripts to do simple operations such as translations.

# Description

# Tools

# Procedure

## Initial structural data

*Fm*3

*m*phase of the platinum carbide (PtC), reported by Zaoui & Ferhat[] as reproduced in BCS format in Table 1↓.

*Fm*3

*m*PtC (Figure 3↓).

## Constructing the Supercell

## Lattice Planes

*as long as one preserves the periodicities in the 3 axial directions*, they can be taken as large and in any convenient shape as allowed. A rectangular shaped such a unit cell, along with the outlying lattice plane parameters is presented in Figure 10↓ (the boundaries have been increased to [-2,5] in each direction for practicality).

## Trimming the new unit cell

## Transforming into the new unit cell

### A Word of caution

## Final Touch

*not*change as a side result. VASP format supports both notations so we export our structural data into VASP format (“File→Export Data…”, select “VASP” as the file format, then opt for “Write atomic coordinates as: Cartesian coordinates”).

*f*|

*z*= 0 =

*f*|

*z*= 1, meaning the atoms at the base and at the very top of the unit cell are the same (or “equivalent” from the interpretational side). If we had wanted the Pt atoms to be the ones forming the surface, then we would have made the transformation with the “-a+b,-1/2a-1/2b+c,a+b+c” matrix instead of “-a+b,-1/2a-1/2b+c,a+b+c+1/2”, so the half shift would amount the change in the order, and

*then*increase the c-lattice parameter size in the Cartesian coordinates notation (i.e., in the VASP file). The result of such a transformation is given in Figure 17↓.

# Alternative Ways

*in silico*is proposed. There are surely more direct and automated tools that achieve the same task. It has been brought to our attention that the commercial software package Accelrys Materials Studio [F] has an integrated tool called “Cleave Surface” which exactly serves for the same purpose discussed in this work. Since it is propriety software, it will not be further described here and we encourage the user to benefit from freely accessible software whenever possible.

# Conclusion

# Acknowledgements

# Appendix: Walkthru for PtC (111) Surface

- Open VESTA, (“File→New Structure”)
- “Unit Cell”:
- Space Group: 225 (F m -3 m)
- Lattice parameter a: 4.5 Å

- “Structure Parameters”:
- New→Symbol:C; Label:C; x,y,z=0.0
- New→Symbol:Pt; Label:Pt; x,y,z=0.5

- “Boundary..”
- x(min)=y(min)=z(min)=-2
- x(max)=y(max)=z(max)=5

- “Edit→Lattice Planes…”
- (hkl)=(111); d(Å)=9.09327
- (hkl)=(111); d(Å)=1.29904
- (hkl)=(-110); d(Å)=3.18198
- (hkl)=(-110); d(Å)=-3.18198
- (hkl)=(11-2); d(Å)=3.67423
- (hkl)=(11-2); d(Å)=-4.59279

(compare with Figure 10↑) - Select (“Select tool” – shortcut “s” key) and delete (shortcut “Del” key) all the atoms lying out of the area designated by the lattice planes.
- Select an “origin-atom” of a corner and the 3 “axe-atoms” in the edge of each direction of the unit cell, write down their fractional coordinates
- o(1,0,-1/2)
- a(0,1,-1/2)
- b(1/2,-1/2,1/2)
- c(2,1,1/2)

- Subtract the origin-atom coordinates from the rest and construct the transformation matrix accordingly
*P*= ⎡⎢⎢⎢⎣ − 1 − 121 1 − 121 011⎤⎥⎥⎥⎦ - Transform the initial unit cell with this matrix via TRANSTRU (http://www.cryst.ehu.es/cryst/transtru.html) (Figure 14↑)
- Save the resulting (low symmetry) structure as CIF, open it in VESTA, export it to VASP, select “Cartesian coordinates”
- Open the VASP file in an editor, increase the c-lattice parameter to a big value (e.g. 25.000) to introduce vacuum. Save it and open it in VESTA.

- “Unit Cell”:

# References

[1] Mois Ilia Aroyo, Juan Manuel Perez-Mato, Cesar Capillas, Eli Kroumova, Svetoslav Ivantchev, Gotzon Madariaga, Asen Kirov, and Hans Wondratschek. Bilbao crystallographic server: I. databases and crystallographic computing programs. Zeitschrift für Kristallographie, 221(1):1527, 01 2006. doi: 10.1524/zkri.2006.221.1.15.

[2] Mois I. Aroyo, Asen Kirov, Cesar Capillas, J. M. Perez-Mato, and Hans Wondratschek. Bilbao crystallographic server. ii. representations of crystallographic point groups and space groups. Acta Crystallographica Section A, 62(2):115128, Mar 2006. http://dx.doi.org/10.1107/S0108767305040286

[3] M I Aroyo, J M Perez-Mato, D Orobengoa, E Tasci, G De La Flor, and A Kirov. Crystallography online: Bilbao crystallographic server. Bulg Chem Commun, 43(2):183197, 2011.

[4] S. R. Hall, F. H. Allen, and I. D. Brown. The crystallographic information le (cif): a new standard archive file for crystallography. Acta Crystallographica Section A, 47(6):655685, Nov 1991.

[5] G. Kresse and J. Furthmüller. Ecient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys. Rev. B, 54:1116911186, Oct 1996.

[6] Koichi Momma and Fujio Izumi. VESTA3 for three-dimensional visualization of crystal, volumetric and morphology data. Journal of Applied Crystallography, 44(6):12721276, Dec 2011.

[7] A Zaoui and M Ferhat. Dynamical stability and high pressure phases of platinum carbide. Solid State Communications, 151(12):867869, 6 2011.

[8] Saulius Grazulis, Adriana Daskevic, Andrius Merkys, Daniel Chateigner, Luca Lutterotti, Miguel Quirós, Nadezhda R. Serebryanaya, Peter Moeck, Robert T. Downs, and Armel Le Bail. Crystallography open database (cod): an open-access collection of crystal structures and platform for world-wide collaboration. Nucleic Acids Research, 40(D1):D420D427, 2012.

[9] Alec Belsky, Mariette Hellenbrandt, Vicky Lynn Karen, and Peter Luksch. New developments in the inorganic crystal structure database (icsd): accessibility in support of materials research and design. Acta Crystallographica Section B, 58(3 Part 1):364369, Jun 2002.

[10] Springer, editor. The Landolt-Boernstein Database (http://www.springermaterials.com/navigation/). Springer Materials.

[11] Yongsheng Zhang. First-principles statistical mechanics approach to step decoration at solid surfaces . PhD thesis, Frei Universitat Berlin, 2008.

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