Input file formats

OVITO can read the following file formats:

Format name

Description

Data type(s)

LAMMPS data

File format used by the LAMMPS molecular dynamics code.

particles, bonds, angles, dihedrals, impropers

LAMMPS dump

File format used by the LAMMPS LAMMPS molecular dynamics code. OVITO supports both text-based and binary dump files.

particles

LAMMPS dump local

File format written by the dump local command of LAMMPS. OVITO’s Load trajectory modifier can read varying bond topology and per-bond quantities from such files generated in reactive molecular dynamics simulations.

bonds

ReaxFF bonds

File format written by the LAMMPS fix reax/c/bonds command and the original ReaxFF code of Adri van Duin. OVITO’s Load trajectory modifier can read the bond topology, bond order and atomic charges dumped during ReaxFF molecular dynamics simulations.

bonds

XYZ

Simple column-based text format for particle data, which is documented here. OVITO can read the extended XYZ format, which supports arbitrary sets of particle data columns, and can store additional information such as the simulation cell geometry and boundary conditions.

particles

POSCAR / XDATCAR / CHGCAR

File formats used by the ab initio simulation package VASP. OVITO can import atomistic configurations and also charge density fields from CHGCAR files.

particles, voxel grids

Gromacs GRO

Coordinate file format used by the GROMACS simulation code.

particles

Gromacs XTC

Trajectory file format used by the GROMACS simulation code.

particles

CFG

File format used by the AtomEye visualization program.

particles

NetCDF

Binary format for molecular dynamics data following the AMBER format convention. NetCDF files are produced by the LAMMPS dump netcdf command.

particles

CIF

Crystallographic Information File format as specified by the International Union of Crystallography (IUCr). Parser supports only small-molecule crystal structures.

particles

PDB

Protein Data Bank (PDB) files.

particles

PDBx/mmCIF

The PDBx/mmCIF format stores macromolecular structures and is used by the Worldwide Protein Data Bank.

particles

Quantum Espresso

Input data format used by the Quantum Espresso electronic-structure calculation code.

particles

FHI-aims

Geometry and log-file formats used by the ab initio simulation package FHI-aims.

particles

GSD/HOOMD

Binary molecular dynamics format written by the HOOMD-blue code. See GSD (General Simulation Data) format.

particles, bonds

CASTEP

File format used by the CASTEP ab initio code. OVITO can read the .cell, .md and .geom formats.

particles

XSF

File format used by the XCrySDen program.

particles, voxel grids

Cube

File format used by the Gaussian simulation package. Specifications of the format can be found here and here.

particles, voxel grids

IMD

File format used by the molecular dynamics code IMD.

particles

DL_POLY

File format used by the molecular simulation package DL_POLY.

particles

GALAMOST

XML-based file format used by the GALAMOST molecular dynamics code.

particles, bonds

VTK (legacy format)

File format used by the Visualization Toolkit (VTK) and the software ParaView. The format is described here. The file reader currently supports only ASCII-based files containing PolyData and UnstructuredGrid data with triangular cells.

triangle meshes

VTI (VTK ImageData)

XML-based file format used by the Visualization Toolkit (VTK) and the software ParaView. The format is described here. The file reader currently supports only a subset of the full format specification and is geared towards files written by the Aspherix simulation code.

voxel grids

VTP (VTK PolyData)

XML-based file format used by the Visualization Toolkit (VTK) and the software ParaView. The format is described here. The file reader currently supports only a subset of the full format specification and is geared towards mesh geometry and particle data files written by the Aspherix simulation code. VTK PolyData blocks consisting of triangle strips or polygons are imported as surface meshes by OVITO. PolyData consisting of vertices only are imported as a set of particles.

surface meshes, particles

VTM (VTK MultiBlock)

XML-based file format used by the Visualization Toolkit (VTK) and the software ParaView. VTK multiblock data files are meta-files that point to a list of VTK XML files, which will all be loaded by OVITO as a single data collection.

any

PVD (ParaView data file)

XML-based file format used by the software ParaView, which describes a trajectory formed by a sequence of individual data files. The file format is described here.

any

OBJ

Common text-based format for storing triangle mesh geometry (see here).

triangle meshes

STL

Another popular format for storing triangle mesh geometry (see here).

triangle meshes

PARCAS

Binary file format written by the MD code Parcas developed in K. Nordlund’s group at University of Helsinki.

particles

ParaDiS

File format of the ParaDiS discrete dislocation dynamics code.

dislocation lines

oxDNA

Configuration/topology file format used by the oxDNA simulation code for coarse-grained DNA models.

particles, bonds