Running scripts

OVITO’s scripting interface enables you to automate visualization and analysis tasks and to extend the program (e.g. by adding your own data modification or analysis functions). The following sections provide a short overview of the different ways scripting can used in OVITO – and how OVITO’s capabilities can be leveraged from scripts:

Invoking program functions

Scripts can invoke program functions, similar to what a human user does in the graphical interface. For example, you can write a Python script file and execute it within the context of the current program session using the Run Script File function from the Scripting menu of OVITO. Such a macro script can insert new modifiers into the current data pipeline, access the results of the pipeline and export the data to an output file. Typically, such a macro script operates on data that is already loaded in the current OVITO program session.


More commonly, however, you want to fully automate processing or visualization tasks from beginning to end: (1) loading input data, (2) processing or analyzing it, (3) saving results to disk. Such a batch script is executed from the terminal using the external ovitos script interpreter, which works like a normal Python interpreter and which will be introduced below. This approach can be used, for instance, to process a large number of simulation snapshots right on the computing cluster where the data is stored.

Extending OVITO: User-defined modifiers

OVITO’s scripting framework also gives you the possibility to develop new kinds of modifiers that manipulate or analyze simulation data in ways not covered by any of the built-in modifiers of the program. So-called Python script modifiers (see Writing new modifiers section) participate in the data pipeline system of OVITO and behave like the built-in modifiers from a user’s perspective. A Python script modifier essentially is a callable Python function, which you write. It is executed automatically by the system whenever the data pipeline it has been inserted into gets evaluated.

Extending OVITO: User-defined viewport overlays

Similar to scripted modifiers, you can also write custom viewport overlays. A Python script overlay is a user-defined function that gets called by OVITO every time an interactive viewport is repainted or an image is rendered. This allows you to enrich images or movies rendered by OVITO with custom graphics or text, e.g., to include additional information like scale bars or data plots with information dynamically computed by OVITO.

Note that Python script modifiers and Python viewport overlays can be used both from within the graphical user interface and from non-interactive batch scripts. In the first case, the user inserts the Python modifier in the graphical interface of OVITO and enters the function code in the integrated code editor. In the second case, the custom modifier or overlay function is embedded in the batch script (see PythonScriptModifier class for an example).

OVITO’s Python interpreter

OVITO comes with a script interpreter, which can execute programs written in the Python language. The current version of OVITO is compatible with the Python 3.4 language standard. You typically execute batch Python scripts from the terminal of your operating system using the ovitos script interpreter that is installed along with OVITO:

ovitos [-o file] [-g] [] [args...]

The ovitos program is located in the bin/ subdirectory of OVITO for Linux, in the directory of OVITO for macOS, and in the main application directory on Windows systems. It should not be confused with ovito, the graphical program with the interative user interface.

Let’s use a text editor to write a simple Python script file named

import ovito
print("Hello, this is OVITO %i.%i.%i" % ovito.version)

We can then execute the script from a Linux terminal as follows:

me@linux:~/ovito-2.9.0-x86_64/bin$ ./ovitos
Hello, this is OVITO 2.9.0

By default, the ovitos script interpreter displays only console output and no graphical output. This allows running OVITO scripts on remote machines or computing clusters that don’t possess a graphics display. The ovitos program behaves like a standard Python interpreter. Any command line arguments following the script’s name are passed on to the script via the sys.argv variable. Furthermore, it is possible to start an interactive interpreter session by running ovitos without any arguments.

Preloading program state

The -o command line option lets ovitos load an .ovito state file before executing the script. This allows you to preload an existing visualization setup that you have previously prepared with the graphical version of OVITO and saved to a .ovito file. This can save you programming work, because modifiers, parameters and the camera setup get already loaded from the state file and don’t need to be set up programatically in the batch script anymore.

Activate graphical mode

The -g command line option opens graphical program session. Then OVITO’s main window is shown and you can follow your script’s actions as they are being executed. This is useful, for instance, if you want to visually check the outcome of your script’s action during the development phase.

Number of parallel threads

OVITO uses all available processor cores by default to perform computations. To restrict OVITO to a certain number of parallel threads, use the --nthreads command line parameter, e.g. ovitos --nthreads 1

Third-party Python modules

The embedded script interpreter of OVITO is a preconfigured version of the standard CPython interpreter with the ovito Python package included. This makes it possible to run scripts both within the graphical program OVITO as well as through the ovitos command line interpreter. However, the ovitos interpreter includes only the NumPy, matplotlib, and PyQt5 packages as preinstalled extensions.

If you want to call other third-party Python modules from your OVITO scripts, it may be possible to install them in the ovitos interpreter using the normal pip or setuptools mechanisms (e.g., run ovitos -m pip install <package> to install a module via pip).

Installing Python extensions that include native code (e.g. Scipy) in the embedded interpreter will likely fail, however. It is recommended to build OVITO from source on your local system in this case. The graphical program as well as ovitos will then make use of your system’s standard Python installation. This makes all modules that are installed in your system interpreter accessible within OVITO and ovitos as well. How to build OVITO from source is described on this page.

Using the ovito package from other Python interpreters

The ovito Python package can also be imported by Python scripts running in an external Python interpreter, not ovitos. However, because this module contains native extensions, it must be compiled specifically for the Python interpreter being used. Since there is a chance that the binary extension module shipped with the prebuilt version of OVITO is not compatible with your local Python interpreter, it might be necessary to build OVITO from source. In case you have multiple Python interpreters installed on your system, make sure OVITO is being linked against the version that you are going to run your scripts with.

Once the graphical program and the ovito Python module have been successully built, you should add the following directory to the PYTHONPATH, so that the Python interpreter can find it:

Platform: Location of ovito package relative to build path:
Windows plugins/python/
Linux lib/ovito/plugins/python/