How to run scripts

OVITO’s scripting interface enables you to automate visualization and analysis tasks and to implement your own data manipulation and analysis algorithms. The scripting interface consists of a set of Python classes and functions that provide access to the program’s internal data model, data processing framework and visualization functions. For a new user, it can be somewhat confusing at first that the scripting capabilities can be used in multiple ways: On one hand, the graphical OVITO application contains an embedded Python interpreter, which lets you execute Python scripts in the context of the current interactive program session. Such scripts can operate on the currently loaded dataset and allow you to extend the capabilities of the graphical OVITO application. On the other hand, it is possible to execute automation scripts (batch scripts) from the system terminal without ever opening the OVITO application. This allows you to leverage the analysis and visualization capabilities of OVITO and build fully automated post-processing and visualization workflows. The following paragraphs provide brief overviews of these different ways of using OVITO’s scripting interface:

Batch scripts

Batch scripts are a way to integrate OVITO’s powerful data processing and visualization functions into custom workflows for post-processing of simulation data. Such script are typically executed from the system terminal using the ovitos script interpreter (not ovito!), which behaves similar to a standard Python interpreter and which will be introduced below. Batch scripts run non-interactively and without the graphical user interface, but they can leverage most program features that you already know from the interactive OVITO application, e.g. loading simulation data, setting up data pipelines, rendering pictures and animations, accessing computation results and exporting result data to an output file.

Macro scripts

The Run Script File function found in the File menu of OVITO lets you execute a Python script file within the running graphical user interface. The code statements will be executed in the context of the current program session and may invoke program functions just like a human user can. For example, your macro script may insert certain modifiers into the current data pipeline or export the data of the pipeline to an output file in a specific way.

This type of script is typically used to perform sequences of program actions that you need frequently. Instead of carrying them out by hand, you let the script invoke the actions for you, similar to an application macro. Note that OVITO offers the --script command line option, which lets you run a macro script right after application startup, for example to initialize the program session to a specific default state.

User-defined modifiers and viewport overlays

OVITO’s scripting interface also enables you to develop new kinds of modifiers that manipulate or analyze data in ways not covered by any of the built-in modifiers of the program. So-called Python script modifiers (see User-defined modifiers section) participate in the data pipeline system of OVITO and behave just like the built-in modifiers from a user’s perspective. A Python script modifier essentially is a callable Python function that you write. It is executed automatically and repeatedly by the system whenever the data pipeline gets evaluated.

Similar to modifiers, you can write custom viewport overlays. A Python script viewport overlay is a user-defined function that gets called by OVITO every time a viewport image is being rendered. This allows you to enrich images or movies rendered by OVITO with custom graphics or text and include additional information like scale bars or data plots dynamically generated from information in OVITO.

Note that Python script modifiers and Python viewport overlays can be used from within the graphical user interface as well as from non-interactive batch scripts. In the first case, the user actively inserts a Python modifier into the data pipeline and enters the code for the user-defined modifier function into the integrated code editor. In the latter case, the code of the custom modifier or overlay function is part of the batch script itself (see PythonScriptModifier class for an example).

OVITO’s Python interpreter

OVITO comes with a script interpreter named ovitos that can execute programs written in the standard Python language. The current version of this interpreter is compatible with the Python 3.6 language standard. You typically execute batch Python scripts from the terminal of your operating system using the ovitos script interpreter, which gets installed alongside 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 (look for ovitos.exe). It should not be confused with ovito, the main program providing the graphical 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 execute the script file from a Linux terminal as follows:

me@linux:~/ovito-3.0.0-x86_64/bin$ ./ovitos
Hello, this is OVITO 3.0.0

The ovitos script interpreter is a console program without a graphical user interface. This enables you to run scripts on remote machines or computing clusters that don’t possess a graphics display. ovitos behaves like a regular Python interpreter. Any command line arguments following the script’s name are passed 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 tells ovitos to load an .ovito state file before executing the script. This allows you to preload an existing data pipeline or visualization setup that you have previously prepared using the graphical version of OVITO. All actions of the script will subsequently be carried out in the context of this preloaded program state. This can save you programming work, because things like modifiers and the camera setup already get loaded from the state file and you don’t need to set them up programmatically in the batch script anymore.

Graphical mode

The -g command line option of the script interpreter starts a graphical program session and the script will be run in the context of OVITO’s main window. This allows you to follow your script commands as they are being executed. This is useful for debugging purposes if you want to visually check the outcome of your script’s action during the development phase. Keep in mind that the viewports will only show pipelines that are part of the current scene. Thus, it may be necessary to explicitly call Pipeline.add_to_scene() to make your imported data visible in this mode.

Number of CPU cores

OVITO uses all available processor cores by default to perform some computations. To explicitly restrict the program to a certain maximum 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, OVITO’s Python interpreter only includes 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 may fail, however, because such extensions may not be compatible with the build-time configuration of the embedded interpreter. In this case, it is recommended to build OVITO from source on your local system. 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 also accessible within OVITO and ovitos. Instructions how to build OVITO from the source code can be found in the user manual.

Using the ovito package from other Python interpreters

The ovito Python package can also be imported by Python scripts running in a standard Python interpreter other than ovitos. However, because the ovito module contains native extensions, it must be compiled specifically for the Python interpreter being used with. Since there is a chance that the binary extension module shipping with the prebuilt versions of OVITO is not compatible with your local Python interpreter, it may be necessary to build OVITO from source. In case you have multiple Python versions installed on your system, pay attention that OVITO is being built against the version that you will use for running scripts.

Once the graphical program and the ovito Python module have been successfully built, you should add the following directories from the build path to the PYTHONPATH environment variable, so that your Python interpreter can find the module:


Location of ovito package relative to build path:






© 2019, Alexander Stukowski.
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