To load a simulation file from your local computer in OVITO, select
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.
OVITO can load and animate simulation trajectories that consist of a sequence of 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_*.dumpto find all matching frames (e.g.
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 automatically detects when the imported file contains more than one frame and loads them as an animation sequence. For some file types, e.g. XYZ and LAMMPS dump, this is indicated by the Contains multiple timesteps checkbox highlighted in the screenshot. Note that OVITO typically keeps only the data of a single frame in memory at a time. Subsequent frames are loaded into memory only when needed, for example if you play back the animation or move the time slider.
- Separate topology and trajectory files:
Some MD simulation codes work with separate topology and trajectory files. The topology file contains the static definition of atoms, types, bonds, etc. while the trajectory file stores the motion trajectories and other time-dependent data computed by the simulation code. In such a case, you should open 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 on the fly merge both pieces of information -the static topology and the trajectory data- 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→ 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:
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 visualize them side by side in one picture. Or you can visualize the same input data in multiple ways, either side by side or superimposed on each other, using several different data pipelines. To do this, either use the Add to scene" option. All data pipelines in the current scene are listed in the drop-down box at the top of the command panel (see screenshot). This box selects the pipeline that is currently displayed in the pipeline editor beneath it.→ function to duplicate the currently selected pipeline, or simply invoke the → function repeatedly to load multiple datasets into the same scene. When OVITO asks you whether to replace the already loaded dataset, pick the "
Tip: You can reposition objects in the three-dimensional scene using the Move and Rotate tools found in the upper toolbar. This is useful if you want to 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 format||Description||Data type|
File format used by the LAMMPS molecular dynamics code. OVITO supports both text-based and binary dump files.
File format used by the LAMMPS molecular dynamics code.
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.
|particles, voxel grid|
File format used by the molecular dynamics code IMD.
File format used by the AtomEye visualization program.
File format used by the molecular simulation package DL_POLY.
Binary file format written by the MD code Parcas developed in K. Nordlund's group at University of Helsinki.
Protein Data Bank (PDB) files (experimental support).
Geometry and log-file formats used by the ab initio simulation package FHI-aims.
File format used by the XCrySDen program.
|particles, voxel grid|
|Cube||particles, voxel grid|
XML-based file format used by the GALAMOST molecular dynamics code.
Input data format used by the Quantum Espresso electronic-structure calculation code.
Format used by the Visualization Toolkit (VTK). This text-based format is documented here. Note that OVITO supports only triangular cells.
Common text-based format for storing triangle mesh geometry (see here).
Another popular format for storing triangle mesh geometry (see here). Note that OVITO supports only STL files in ASCII format.
File format of the ParaDiS discrete dislocation dynamics code.