Import XYZ, CIF, CAR, VASP Files in VNL

VNL: File handling

Platforms:
Links: Export Files
File types: XYZ, CIF, CAR, VASP(POSCAR)

In this tutorial, you will learn how to import
configuration files from other programs.
iATK

Drag and Drop

In the simplest case, all you actually have to do is to drop the file itself on one of the instruments in VNL, typically the builder_icon Builder (for editing the structure), or the viewer_icon Viewer (for just visualizing the structure).

snap3

Importing structures in a script

It is also possible to import and use external files directly in a script:

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 molecule = nlread('myfile.xyz')[0]

Note that “nlread” returns a list, normally only with one element, hence the [0]. The file formats are recognized by the extensions, so the same principle would apply to CIF, CAR, or POSCAR files alike. Here is another way to use the XYZ format, if you prefer to just copy/paste the coordinate list

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 h2o = MoleculeConfiguration(xyz_format=
     """3
     water
     O   0.000 0.000 0.0
     H   0.757 0.586 0.0
     H  -0.757 0.586 0.0""")

Note that the format must be that of a real XYZ file, with the two first lines specifying the number of atoms, and the comment/title. For more details, see the manual entry for the MolecularConfiguration class.

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 at the VASP website.