Importing data

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

Loading a data file creates a new visual object in the three-dimensial scene to display the data. This object maintains a reference to the original source file, and it is possible to reload the data from the external file or to replace the source data with a different file later on. The "External File" panel, which is shown in the screenshot below, contains a toolbar with corresponding command buttons. Switching to a another input file is useful if you have set up a visualization or a data filtering sequence and now want to re-use it on a different simulation dataset.

Simulation sequences

Figure 1. The External File panel

The External File panel


OVITO can load and display animated simulation trajectories. The following scenarios are supported:

Series of files, each containing one frame:

This is the default scenario. The program tries to automatically recognize sequences of files in a directory by looking for other files with a similar name as the one you picked. To this end, OVITO replaces the last number (if any) in the filename with the wildcard character * to generate a search pattern and find other files in the same directory belonging to the time series. For instance, if you load the file anim1c_5000.dump, OVITO generates 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 change the search pattern afterwards if the one generated by OVITO does not fit (see the screenshot on the right).

Single file containing multiple frames:

The LAMMPS dump and the XYZ file formats can store multiple simulation timesteps in one file. By default, OVITO loads only the first frame from the file to save time. You have to explicitly tell OVITO to look for additional frames by checking the File contains time series option highlighted in the screenshot. OVITO will then quickly scan the entire file to find all simulation frames.

Series of files, each containing several frames:

To load multiple files, each one containing multiple simulation frames, follow these steps: Load the first file from the sequence. Then check the File contains time series option. Finally, edit the file pattern to include the '*' wildcard character to let OVITO find all other matching files in the directory.

Separate topology and trajectory files:

Some MD simulation codes work with separate topology and trajectory files. The topology file contains the static definitions of atoms, types, bonds, etc. while the trajectory file contains the trajectories of motion computed by the simulation code. In such case, load the topology file in OVITO first (e.g. a LAMMPS data file). The apply the Load trajectory modifier to the dataset to load the time-dependent atomic positions from the trajectory file (e.g. a LAMMPS dump file).

OVITO displays a timeline and a slider control at the bottom of main window when a simulation sequence is loaded, which allows you to jump between frames. Note that OVITO only loads the currently displayed simulation frame into memory to avoid running out of memory in the case of large datasets and/or long trajectories.

Importing files from remote computers

OVITO comes with a built-in SSH client to directly access files on remote machines. This capability is useful when working with simulation data stored on remote HPC clusters and saves you from transferring the data to your local desktop computer first. To open a simulation file on a remote machine, choose FileLoad Remote File from the menu.

OVITO currently does not allow you to browse directories on remote machines. That means you have to directly specify the full path to a remote file as an URL of the form:

    sftp://user@hostname/path/filename

Where sftp:// is the file access protocol (Secure File Transfer Protocol), user the SSH login name on the remote machine, hostname the name of the remote machine, and /path/filename the simulation file to import. It is possible to specify a non-standard port number by appending :portnumber to the hostname.

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

Using the command line

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

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

Supported file formats

OVITO can read particle datasets in the following formats:

File formatDescription
LAMMPS dump

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

LAMMPS data

File format used by the LAMMPS molecular dynamics code.

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.

POSCAR / XDATCAR / CHGCAR

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

IMD

File format used by the molecular dynamics code IMD.

CFG

File format used by the AtomEye visualization program.

PARCAS

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

NetCDF

Binary format for molecular dynamics data based on the standard NetCDF container. There exists an extension module for LAMMPS that adds NetCDF output.

PDB

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

FHI-aims

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

GSD/HOOMD

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

CASTEP

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

OVITO can load triangle meshes (polygonal data) in the following format:

File formatDescription
VTK

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