3) Creating CIF file (Crystallographic Information File)

CIF file is a file describing the crystallographic information of the material you want to model with DFT. As you can see from the “Quantum Espresso (input file sections)”page, you have to change the format of the CIF file into the QE input file and then do the other processes and modeling on that.

On this page, I will try to introduce some important parts in the CIF file, that you need to have accurately.

Source: https://compmatphys.epotentia.com/

After downloading the NaCl cif file and open it with a text editor, you’ll see many differnt sections.

  • _cell_angle_alpha 90
    _cell_angle_beta 90
    _cell_angle_gamma 90
    _cell_length_a 5.64056
    _cell_length_b 5.64056
    _cell_length_c 5.64056

These are the basic parameters to know just the shape of the unit cell. length of the edges and the angle between them. Here the 90 degrees show the shape is cubic.

  • _symmetry_space_group_name_H-M    ‘F m -3 m’

another one, not necessary but useful it is. it is Herman-Mauguin notation. If you dont know, dont worry.

  • _space_group_IT_number   225

this the Ref number of this space group. (International table of crystallography)

all crystals have these names and numbers, but as I said don’t worry if you don’t know them.

  • symmetry information is also given in the file, the long X Y Z section.

 

  • The important section is the position of the atoms. There is a block named “Loop_”:
    loop_
    _atom_site_label
    _atom_site_fract_x
    _atom_site_fract_y
    _atom_site_fract_z
    Na 0.00000 0.00000 0.00000
    Cl 0.50000 0.50000 0.50000

In that example, it is a simple format. It could also consist of different labels and parameters like and symmterical data. Your CIF file should include these numbers and labes as well, to make sure your DFT is working efficiently.

In this example, a and b are for the Wyckoff symbol (about the symmetry). By knowing this and the positions of first Na and Cl, we can tell where the others are.

To find out the Wyckoff positions for the given space group we can use the website:
www.cryst.ehu.es (Biblao crystallography server)

go to space group symmetry >> wyckpos >> choose >>
as you see for this crystal the spacegroup number and name is 225 Fm-3m. by clicking on it the Wyckoff position is written. for Na and Cl:

4 b m-3m
(1/2,1/2,1/2)
4 a m-3m
(0,0,0)

If an article mentions the structure and the space group name, we can go to the mentioned site and find the other Wyckoff positions and numbers. For example for TiO2- the space group name is Pnma, and if the positions of the first atoms of Ti, O1 and O2 are given, we can go to the site and find the other numbers.

If we don’t have the symmetrical information of the crystal, like a picture of NaCL crystal, we can create the CIF file ourselves and put the position of all the atoms inside. In this situation the space group name should be P1, the most asymmetrical space group on the Bilbao website. It means we aill put the position of the all the atoms and not use the symmterical properties.

_symmetry_space_group_name_H-M      ‘P 1’
_symmetry_Int_Tables_number      1

You can see that the position of all the atoms are given here. But for DFT we need to give those dat as well to make sure the calculation is efficient and take less time.



How to give or find the symmetrical properties of a given crystal with P1 space group

 

Let say you haven’t found the CIF file for your crystal and you had to create it yourself. If you go to https://compmatphys.epotentia.com/topic/whats-in-a-cif/ you can download a template file for that.

After creating your crystal you can visualize it in software like VESTA, XCRYSDEN, etc. or on an online website like Bilbao Crsytallophic server. (structure utility >>> Visualize)

Another problem with handmade CIF file, could be the lack of symmetric information. As we can put the space group name as P1 which is for crystal with just the information of the position of its atoms without symmetric info. This is not a problem for visualization but DFT codes can benefit a lot from symmetrical information of crystals.

To find the symmetrical properties:

For this we need to google “Stokes Findsym” and open this website:
https://stokes.byu.edu/iso/findsym.php

This website finds the spacegroup by giving the position of atoms in unit cells. But you have to make sure your CIF file is standard. To make sure your CIF file is standard, go back to the Bilbao site and visualize your CIF. Then download the visualized new CIF file from the bottom of the page. This new CIF file is written a little bit different to the original one.

The new CIF is now readable with the Findsym site. (Browse >>>> upload the new CIF>>> press ok. At the bottom press ok

In the output, starting from the # cif file section, the data is not complete with all the symmetry information. You can copy that paste it into a text file and save it as ***.cif.


Note: in some cases that the space group number is low or there are low symmetrical properties, Findsym will add some line and information to the cif file that can cause an error. To solve this you can refer to this page of “online course on Computational Materials Physics”, by Prof. Stefaan Cottenier. It gives you the necessary information regarding crystal with space groups like P1.