Importing data

To load a simulation file from your local computer in OVITO, select FileLoad File from the menu or use the corresponding button in the toolbar. OVITO detects the format of the file automatically (see supported formats below). Compressed text-based files having a .gz suffix can be directly read by OVITO.

The imported data will appear in the viewports as a new visual object in the three-dimensional scene and also as an entry in the "Data source" section of the pipeline editor as indicated in the screenshot on the right. Note that the program maintains a link to the original file on disk from which it obtained the data. Selecting the data source entry in the pipeline editor opens the "External File" panel, which is also visible in the screenshot. This panel manages the link to the external data file. The tool buttons at the top of the panel let you reload the data from the input file in case it was changed by an external program, or you can pick a different file as data source if desired. As you will see, switching the input file is sometimes useful if you have set up a complex data analysis pipeline and want to re-use it on a different input dataset later on.

Simulation sequences

OVITO can load and animate simulation trajectories that consist of a sequence of snapshots or frames. The following scenarios are supported by the software:

Series of files:

When importing a new file, the program automatically tries to detect if it is part of a numbered sequence of files with similar names. To this end, OVITO replaces the last number (if any) in the filename you picked with the wildcard character * to generate a search pattern, which is used to look in the same directory for other files belonging to the same sequence. For instance, if you imported a file named anim1c_5000.dump, OVITO will generate the search pattern anim1c_*.dump to find all matching frames (e.g. anim1c_0.dump, anim1c_1000.dump, anim1c_2000.dump, etc). It is possible to manually adjust this search pattern afterwards in case the generated one is not adequate. The corresponding input field is highlighted in the screenshot.

File containing multiple frames:

OVITO will automatically detect when the imported file contains multiple frames and loads them as an animation sequence. For some file types, such as XYZ and LAMMPS dump files, this mode is indicated by the Contains multiple timesteps check box highlighted in the screenshot. Note that OVITO typically keeps only a single frame at a time in memory. Other frames are loaded from the source data file only as needed, for example if you play back the animation or move the time slider.

Separate files for topology and trajectories:

Some MD simulation codes work with separate topology and trajectory files. The topology file stores the static definition of atoms, types, bonds, etc. while the trajectory file contains just the motion trajectories computed by the simulation. In such a case, you should load the topology file first (e.g. a LAMMPS data file). Then use the Load trajectory modifier to load the time-dependent atomic positions from the separate trajectory file (e.g. a LAMMPS dump file). This modifier will merge both pieces of information, the static topology and the trajectories, on the fly into a single time-dependent dataset.

OVITO will display a timeline and a time slider at the bottom of main window when a simulation sequence with more than one frame was loaded. Find out more about OVITO's animation functions in the Animation section of this manual.

Importing files from remote computers

OVITO comes with a built-in SSH client for accessing files on remote machines. It can save you from transferring data stored in remote locations, for example on HPC clusters, to your local desktop computer first. To open a simulation file stored on a remote machine, select FileLoad Remote File from the menu.

The current program version doe not let you browse directories on remote machines. That means you have to specify the full path of the remote file as an URL of the form:

    sftp://user@hostname/path/filename

Where sftp:// is the remote file access protocol, user the SSH login name on the remote machine, hostname the name of the remote machine, and /path/filename the full path to the simulation file to import.

When OVITO connects to the remote machine, it will ask for the login password or the passphrase for the private key to be used for authentication. Once established, the SSH connection is kept alive until the end of the program session. OVITO makes a temporary copy of the remote file on the local computer before loading the data into memory to speed up subsequent accesses to simulation frames. The local file copies are cached until the end of the program session or until you hit Reload in the External File panel.

Using the command line

If you launch OVITO from a terminal, you can directly specify a file to load. This works for local and remote files:

    ovito /path/filename
    ovito sftp://hostname/path/filename
       

Visualizing multiple datasets

OVITO allows you to load several datasets and show them side by side in one picture, and it allows you to load the same file more than once in order to visualize the data in several different ways for comparison. To do this, simply invoke the FileLoad File function from the menu repeatedly. When OVITO asks you whether to replace the already loaded dataset or not, pick the "Add to scene" option. All loaded datasets (more precisely, all data pipelines that are part of the scene) are listed in the drop-down box at the top of the command panel (see screenshot). This drop-down box switches the pipeline that is currently shown in the pipeline editor.

Tip: You can reposition each object in the three-dimensional scene as desired using the Move and Rotate tools found in the upper toolbar. In this way you can visualize multiple datasets in juxtaposition.

Supported file formats

OVITO provides file readers for a variety of input formats, in particular data formats written by molecular dynamics and other atomistic simulation codes. In addition, it can load, process and visualize other types of data, for example triangle meshes and voxel data grids.

File formatDescriptionData type
LAMMPS dump

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

particles
LAMMPS data

File format used by the LAMMPS molecular dynamics code.

particles, bonds
XYZ

A simple column-based text format, which is documented here.

The basic XYZ format does not contain simulation cell information. OVITO takes the axis-aligned bounding box of particles as the simulation box in this case. The program also supports the extended XYZ format, which includes information on the simulation cell, boundary conditions, and per-particle fields.

particles
POSCAR / XDATCAR / CHGCAR

File formats used by the ab initio simulation package VASP. OVITO can read and visualize charge density data from CHGCAR files.

particles, voxel grid
IMD

File format used by the molecular dynamics code IMD.

particles
CFG

File format used by the AtomEye visualization program.

particles
PARCAS

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

particles
NetCDF

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

particles
PDB

Protein Data Bank (PDB) files (experimental support).

particles, bonds
FHI-aims

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

particles
GSD/HOOMD

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

particles
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 grid
Cube

File format used by the Gaussian simulation package. A description of the format can be found here.

particles, voxel grid
VTK

Format used by the Visualization Toolkit (VTK). This text-based format is documented here. Note that OVITO supports only triangular cells.

triangle mesh