Atomsk - Supported File Formats

Supported file formats

File conversion can be achieved very easily with Atomsk. Just call the program with the name of the file you want to convert, and the output format:

atomsk <inputfile> <format>

The file formats supported by Atomsk appear in the table below. To put it simple, Atomsk can convert from any YES in the "Input" column to any YES in the "Output" column. Click on a format name in the first column to display a page detailing its specification, how Atomsk deals with it, the possible restrictions, and examples showing how to convert from or to this format. Please read these pages carefully.

Format or extension (Code)	Input	Output
Visualization software
cfg (AtomEye)	[all]	[all]
dd (ddplot)		(mode ddplot only)
vesta (VESTA)	[occ,f]	[occ,f]
xsf (XCrySDen)	[f]	[f]
Ab initio software packages
ABINIT	[type]	[type]
COORAT (MBPP)
CRYSTAL
POSCAR (VASP format)	[fix]	[fix]
OUTCAR (VASP format)	[f] (mode one-in-all only)
pw (Quantum Espresso input file)	[f,fix]	[f,fix]
out (Quantum Espresso output file)	[f] (mode one-in-all only)
fdf (SIESTA)	[type]	[type]
xv (SIESTA)	[v]	[v]
Classical force-field software packages
bop (BOP)	[fix]	[fix]
bx (BOPfox)	[fix, µ]	[fix, µ]
CONFIG (DL_POLY)	[f,v]	[f,v]
gin (GULP)	[fix,occ,q,bsrad,v]	[fix,occ,q,bsrad,v]
imd (IMD)	[type,v]	[type,v]
lmc (LAMMPS custom dump file)	[all]
lmp (LAMMPS data file)	[type,v]	[f,q,type,v]
mol (MOLDY)
xmd (XMD)	[type,v]	[type,v]
Electron microscopy image simulation software packages
cel (Dr Probe)	[occ,Tvib]	[occ,Tvib]
cfg (QSTEM)	[all]	[all]
jems (JEMS)	[occ,Tvib,abs]	[occ,Tvib,abs]
Other data types
atsk (Atomsk binary format)	[all]	[all]
cif (Crystallographic Information File)	[q,occ,Tvib]	[q,occ,Tvib]
csv (Comma-Separated Values)		[all]
dat (columns of data)		[all]
pdb (Protein Data Bank)	[q,occ]	[q,occ]
str (PDFFIT structure file)	[occ,Tvib]	[occ,Tvib]
xyz/exyz/sxyz (general purpose format)	[all]	[all]

For each format, the Input and Output columns also indicate [in square brackets] the auxiliary properties that, if they exist, can be read or written by Atomsk:

[all] means that all auxiliary properties are read (or written) regardless of their names or number;
[abs] stands for absorption coefficients;
[bsrad] stands for breathing shell radius (for ionic core-shell model);
[f] stands for forces (fx,fy,fz)
[fix] stands for fixed (or "frozen") atoms (fixx, fixy, fixz);
[occ] stands for the site occupancies;
[q] stands for the electric charges of ions (and shells);
[Tvib] stands for thermal vibration (Debye-Waller) parameters;
[type] stands for "atom types" used by some formats;
[v] stands for atom velocities (vx,vy,vz);

When nothing is specified then it means that no auxiliary property is read or written in that format. Note that all auxiliary properties are not transferable from one format to another, so some properties may be lost during conversion. For instance if atom charges, velocities and forces are read from an LMC file, then when converted to CFG they will all be written, but when converted to XSF only the forces will be written.

If the output file is "NULL" then no output is produced at all. If the output file is "-" then the output is sent to the standard output (stdout, usually the screen) instead of into a file, and verbosity is set to zero (no other message is displayed on screen, except for warning and error messages).

Some modes and options may create new auxiliary properties, or update existing ones. Refer to the page of each of these for more information. For removing auxiliary properties one can use the option -rmprop.

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