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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) YES [all] YES [all]
dd (ddplot) NO YES (mode ddplot only)
vesta (VESTA) YES [occ,f] YES [occ,f]
xsf (XCrySDen) YES [f] YES [f]
Ab initio software packages
COORAT (MBPP) YES YES
POSCAR (VASP format) YES [fix] YES [fix]
pw (Quantum Espresso input file) YES [f,fix] YES [f,fix]
out (Quantum Espresso output file) YES [f] (mode one-in-all only) NO
xv (SIESTA) YES [v] YES [v]
Classical force-field software packages
bop (BOP) YES [fix] YES [fix]
CONFIG (DL_POLY) YES [f,v] YES [f,v]
gin (GULP) YES [fix,occ,q,bsrad,v] YES [fix,occ,q,bsrad,v]
imd (IMD) YES [type,v] YES [type,v]
lmc (LAMMPS custom dump file) YES [all] NO
lmp (LAMMPS data file) YES [type,v] YES [f,q,type,v]
mol (MOLDY) YES YES
xmd (XMD) YES [type,v] YES [type,v]
Electron microscopy image simulation software packages
cel (Dr Probe) YES [occ,Tvib] YES [occ,Tvib]
cfg (QSTEM) YES [all] YES [all]
jems (JEMS) YES [occ,Tvib,abs] YES [occ,Tvib,abs]
Other data types
atsk (Atomsk binary format) YES [all] YES [all]
cif (Crystallographic Information File) YES [q,occ,Tvib] YES [q,occ,Tvib]
str (PDFFIT structure file) YES [occ,Tvib] YES [occ,Tvib]
pdb (Protein Data Bank) YES [q,occ] YES [q,occ]
xyz/exyz/sxyz (general purpose format) YES [all] YES [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:

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.

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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