Data model

This page gives an introduction to the data model used by OVITO to represent molecular structures and other particle-based datasets. Understanding the basic concepts of OVITO’s data model is important in order for you to work efficiently with the data analysis and visualization functions of the program, which operate on particle simulation data.

Particle properties

Particle properties are numeric values associated with the individual particles. They play a central role in the data model of OVITO and the way molecular and other structures are represented. Typical particle properties are the particle position, chemical type and velocity. The user can assign any number of additional properties to particles, either explicitly or as a result of computations performed by the program.

This general property concept is employed for other types of data elements as well, not only particles. For instance, the interatomic bonds may be associated with bond properties, e.g. bond type or color. Keep in mind that, while the following introduction focuses mainly on particles and their properties, the same principles apply also to other classes of data elements.

What’s a particle property?

Technically, an OVITO particle property is a uniform data array containing a numeric value for each particle in the system. All values are of the same data type, which may be scalar or vectorial. The length of the property array is always equal to the number of particles in the system.

Each property has a unique name, for example Position or Potential Energy. OVITO has a built-in list of commonly-used property names, which have a meaning to the program and a prescribed data layout, but you are free to define additional properties with user-defined names.

The Position particle property is special, because it is always present. Particles cannot exist without spatial coordinates. Other standard properties such as Color, Radius or Selection are optional. They may or may not be present. If they are not already loaded from the imported simulation file, you can add them within the program using various functions. The mentioned standard properties affect how OVITO renders the particles. By assigning values to these properties, you can control the visual appearance of the particles.

In OVITO, per-particle property values can have different data types (real or integer) and dimensionality (e.g. scalar, vector, tensor). The Position property, for instance, is a vector property with three components per particle, referred to as Position.X, Position.Y and Position.Z within OVITO’s user interface.

Inspecting properties

Data inspector displaying the table of particle properties

Standard properties such as Position, Particle Type and Velocity are typically initialized from the imported simulation file. Some file formats such as LAMMPS dump or the extended XYZ format can store an arbitrary number of extra data columns. These auxiliary attributes are automatically mapped to corresponding particle properties within OVITO.

To find out which properties are currently associated with the particles, you can open OVITO’s Data inspector panel, which is shown in the screenshot on the right. Alternatively, you can simply point the mouse cursor at some particle in the viewports to let OVITO display its property values in the status bar.

Assigning property values

OVITO provides a rich set of functions for modifying the properties of particles. These so-called modifiers will be introduced in more detail in a following section of this manual. But to already give you a first idea of the principle: The Assign color modifier function lets you assign a uniform color of your choice to all currently selected particles. It does that by setting the Color property of the particles to the given RGB value (if the Color property doesn’t exist yet, it is automatically created). The subset of currently selected particles is determined by the Selection particle property: Particles whose Selection property has a non-zero value are part of the current selection set, while particles for which Selection=0 are not selected.

Fittingly, OVITO provides a number of selection modifiers, which let you define a particle selection set by appropriately setting the values of the Selection property. For example, the Select type modifier takes the Particle Type property of each particle to decide whether or not to select that particle. It allows you to select all atoms of a particular chemical type, for example, and then perform some operation only on that subset of particles.

Another typical modifier is the Coordination analysis modifier. It computes the number of neighbors of each particle within a given cutoff range and stores the computation results in a new particle property named Coordination. Subsequently, you can refer to the values of this property, for example to select particles having a coordination number in a certain range or to color particles based on their coordination number (see Color coding modifier).

Of course it is possible to export the particle property values to an output file. OVITO supports a variety of output formats for that (see the data export section of this manual). For instance, the XYZ format is a simple table format supporting an arbitrary set of output columns.