Importing data

To open a simulation file from your local hard disk, choose FileLoad File from the menu. OVITO detects the format of the selected file automatically. See the table below for a list of supported formats. Compressed files with a .gz suffix can be opened directly.

After loading and displaying the data from the selected file, OVITO opens the file import panel as shown in the screenshot below. At the top of this settings panel you find a row of command buttons. The left-most button, for example, allows you to select a new input file and replace the currently loaded data. This is useful if you have already set up a sequence of data modification or analysis steps and now want to re-use it with a different simulation dataset.

Hint: Everytime you import a new simulation dataset, OVITO automatically adjusts the visible region in the viewports to show the entire simulation box. If you want to suppress the automatic zoom and keep the current view settings when loading a new file, use the Create Camera function from the viewport menu first.

Simulation sequences

Figure 1. The External File panel

The External File panel


OVITO can load sequences of simulation snapshots (time series). 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 consecutive file series. For instance, if you initially 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 edit the search pattern 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 as shown in the screenshot. OVITO will then quickly scan the entire file to find all frames of the time series.

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.

When a time series was loaded, OVITO displays a timeline with a slider control at the bottom of main window, which allows you to jump between frames. Note that OVITO loads only the simulation frame currently displayed in the viewports into memory to keep memory usage at a minimum. Every time you jump between simulation frames the program will load the requested data from the external file(s) on demand.

Importing files from remote computers

OVITO has 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 of a remote file. The format follows the standard URL scheme:

    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 OVITO is quit. 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

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

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

Basic support for Protein Data Bank (PDB) files.

FHI-aims

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

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.