Importing data

To open a simulation file from your local hard disk, choose FileOpen Local File from the menu. OVITO will detect the format of the file automatically. See the table below for a list of supported formats. The program can read compressed files that have a .gz suffix (only formats that are text-based).

Simulation time sequences

OVITO can load a sequence of snapshots of a simulation. The following scenarios are supported:

Multiple files containing one frame each:

This is the default scenario, and the program tries to automatically recognize sequences of files after you loaded a first file by looking for others in the same directory with a similar name. OVITO replaces the last number in the filename (if there is any) with the wildcard character * to generate a search pattern and find other files in the same directory belonging to the animation sequence. For instance, if you initially opened the file anim1c_5000.dump, OVITO generates the search pattern anim1c_*.dump to find all matching frames such as anim1c_0.dump, anim1c_1000.dump, anim1c_2000.dump, etc. It is possible to manually adjust the search pattern in the Frame sequence panel if the one generated by OVITO does not fit.

A single file containing multiple frames:

The LAMMPS dump and the XYZ formats can store multiple simulation frames in a single file. By default, OVITO loads only the first frame from a file to save time. You have to explicitly tell OVITO to look for additional frames by checking the File contains multiple timesteps option in the import settings panel. OVITO will then scan the file for the contained animation frames and display them in the time line at the bottom of the main window.

Multiple files containing multiple frames each:

To load multiple files, each containing multiple simulation frames, take the following steps: First open the first file from the sequence. Then activate the File contains multiple timesteps option. Finally, edit the wildcard pattern in the Frame sequence panel to include the '*' wildcard character to let OVITO find all matching files in the directory.

Importing files from remote computers

OVITO has a built-in SSH client to directly access files on remote machines. This is useful when working with simulation data stored on parallel computing clusters without having to copy them over to the local computer first. To open a simulation file from a remote machine, choose FileOpen Remote File from the menu.

In the current version, OVITO does not allow browsing directories on remote machines. That means you have to specify the full path of a remote file directly. The format of remote paths follows the URL scheme

    sftp://user@hostname/path/filename

Where sftp:// is the file access protocol (Secure File Transfer Protocol), user the login for the remote machine, hostname the name of the remote machine, and /path/filename the path to the 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 OVITO is quit. OVITO makes a temporary copy of remote files on the local computer before loading them to speed up subsequent accesses to simulation frames. The local copies are kept until you quit OVITO or press the Reload button in the import file panel.

Use the command line

When starting OVITO from a terminal, you can directly specify a file to be loaded. This works with both local and remote files:

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

Supported file formats

OVITO can read particle data and molecular dynamics output 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. Only the atomic style is supported.

XYZ

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

This format does not store simulation box dimensions. OVITO takes the axis-aligned bounding box of particles as the simulation box.

POSCAR

File format used by the ab initio simulation package VASP.

IMD

File format used by the molecular dynamics code IMD.

CFG

File format used by the AtomEye software.

PARCAS

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

NetCDF

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

Triangle meshes can be read in the following format:

File formatDescription
VTK

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