Make CIF File Defining Crystal Structure¶
|ATK/VNL: CIF Files Platforms: Links: Export CIFs, Export CIFs, GrapheneHydrocarbon In this tutorial you will learn how to define a new crystal structure by making a CIF file. This is an approach much easier than simply buliding the structure by hand.|
Crystallographic Information File (CIF) is a standard text file format for representing crystallographic information, promulgated by the International Union of Crystallography (IUCr). CIF was developed by the IUCr Working Party on Crystallographic Information in an effort sponsored by the IUCr Commission on Crystallographic Data and the IUCr Commission on Journals. Full specifications for the format are available at the IUCr website.
Description and Need¶
Imagine the following situation: you read an interesting scientific article about a particular crystal or other material (we are talking about periodic structures here, not molecules), and you would like to try simulating it in ATK/VNL - or some other software. However, it turns out the material in question is not included in the built-in crystal database in VNL, and you can’t find a CIF file for it anywhere. You do, however, have all necessary information in the article. What is then the approach for getting the structure into the Builder?
In some cases - also for use in other software packages - as it turns out, writing your own CIF file is not really that hard, and in many cases it’s a lot quicker than trying to build the structure by hand. This is because the CIF file only contains the symmetry-reduced basis, so even rather complicated cells can usually be described by just a few atom positions - and of course the corresponding symmetry operations. In the majority of cases it is however sufficient to just provide the spacegroup number of the Hermann-Mauguin symbol, since that uniquely defines the symmetry (perhaps combined with a setting or origin choice). This is the same information that you enter into the Crystal Builder.
Let us study an example based on a paper. That is, make CIF files for graphane, both in the boat and armchair configurations. The symmetry information we need can be found in Graphane: A two-dimensional hydrocarbon, by J. O. Sofo, A. S. Chaudhari and G. D. Barber, Phys. Rev. B 75, 153401 (2007) (also available as arXiv). Here are the relevant parameters:
Step 1: First we need a CIF file template. An easy way to make one is to export some simple structure from the Builder in VNL as a CIF file, but here is a very simple template:
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data_global _chemical_name 'New material' _cell_length_a 1.0 _cell_length_b 1.0 _cell_length_c 1.0 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _symmetry_space_group_name_H-M 'P 1' loop_ _atom_site_label _ atom_site_fract_x _atom_site_fract_y _atom_site_fract_z H 0 0 0
Step 2: Now we just need to take the symmetry information from the article and change the parameters. Thus we end up with the following CIF files for these graphane boat and chair configurations respectivelly:
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data_global _chemical_name 'Graphane boat' _cell_length_a 4.272 _cell_length_b 2.505 _cell_length_c 4.976 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _symmetry_space_group_name_H-M 'P m m n' loop_ _atom_site_label _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z C 4 f 0.8178 0 0.5636 H 4 f 0.7439 0 0.7717
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data_global _chemical_name 'Graphane - chair' _cell_length_a 2.516 _cell_length_b 2.516 _cell_length_c 4.978 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 120 _symmetry_space_group_name_H-M 'P -3 m 1' loop_ _atom_site_label _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z C 2 d 0.333333 0.666666 0.5419 H 2 d 0.333333 0.666666 0.7479
Step 3: Copy and paste the code you want in VNL’s Editor. Then save the file with an .cif extension. Dragging and dropping your .cif file on the Builder you can edit and study it!
It is of course possible to enter much more information in the CIF file, like the article reference and so on, but the information above is sufficient to fully define the structure, so that you now can perform calculations on this system. (In the example above we have actually also added the Wyckoff symbols for the atoms - this may come in handy later on!)