Export XYZ, CIF, CAR, VASP Files in VNL

VNL: File handling

Platforms:
Links: VASP, VASPfiles, Import Files
File types: XYZ, CIF, CAR, VASP

In this tutorial, you will learn how to build a configuration
in VNL and export it for use in another program.
eATK

Built-in export filters

Molecular Structures

For molecular structures, you can directly export the geometry in an XYZ file, via the menu File‣Export configuration in the builder_icon Builder. Choose the XYZ format under Files of type, enter the file name, and save the file.

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Crystal Structures

A similar approach is possible for exporting periodic structures (crystals, nanotubes, etc) to CIF or CAR files.

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Exporting from scripts

The function nlprint is also a convenient tool for exporting structures:

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 nlprint(configuration)

Include this line in a script (referring to the correct variable for the structure), and pipe the output to a file when you run it:

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 atkpython script.py > file.xyz

There will be a few lines in the file file.xyz that you need to remove, but the format of the coordinate list is proper XYZ. If the structure is a twoprobe_icon two-probe or bulk_icon bulk configuration, there will be some additional information about the unit cell too.

Note

The XYZ file format is a chemical file format. There is no formal standard and several variations exist, but a typical XYZ format specifies the molecule geometry by giving the number of atoms with Cartesian coordinates that will be read on the first line, a comment on the second, and the lines of atomic coordinates in the following lines. The file format is used in computational chemistry programs for importing and exporting geometries. The units are generally in Angstroms. Some variations include using atomic numbers instead of atomic symbols, or skipping the comment line. Files using the XYZ format conventionally have the .xyz extension.

Note

CAR stands for Component Application Resource. The CAR files contain information about the assets that are available for a software application being run on the Brew Mobile Platform. This platform is used to operate applications on a variety of mobile phones. The CAR files are compiled into a binary BAR file. This file is automatically loaded when the application is run.

The .car file extension is also used for AtHome Assistant files, Biosym chemical modeler input files, NeoBook Cartoon image format files, CAR Archive compressed archive files, CardMaker card files, Carnivores Ice Age resource files, Design-Your-CD data files and Railroad Tycoon 3 car properties files.

Note

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. Many computer programs for molecular viewing are compatible with this format, including Jmol.

Note

VASP is a fileformat/extension used by VASP. VASP software uses a relatively large number of input and output files:

INCAR CONTCAR DOSCAR XDATCAR PCDAT EIGENVAL
STOPCAR POSCAR PROOUT TMPCAR OSZICAR WAVECAR
stout IBZKPT ELFCAR CHG PROCAR CHGCAR
POTCAR KPOINTS LOCPOT EXHCAR DOSCAR  

You can find more details about their content on the VASP website.