Simulation cell

The Simulation cell data object defines the geometry of the simulation domain in two or three dimensions, including boundary conditions (PBC flags). The simulation cell loaded from the imported simulation file can be found in the Data source section of the pipeline editor (see screenshot).

Note: Additionally, the upper section of the pipeline editor shows a second item labeled Simulation cell, which is the corresponding visual element. This visual element controls how the simulation cell appears in rendered images.

If the imported simulation file does not specify cell dimensions, OVITO automatically generates an ad-hoc simulation cell that encloses all particles in an axis-aligned bounding box.

Dimensionality

OVITO supports both 2D and 3D datasets. The dimensionality is automatically detected during file import but can be manually adjusted in the Simulation cell panel.

In 2D mode, the Z-coordinates of particles and the third simulation cell vector are ignored in most calculations.

Boundary conditions

The periodic boundary condition (PBC) flags determine whether OVITO applies periodicity when performing calculations. Where possible, OVITO reads or infers these flags from the imported simulation file. If needed, you can manually override these flags in the Simulation cell panel.

Cell geometry

The shape of the simulation cell is defined by three vectors forming a parallelepiped and an origin point, which represents one corner of the cell.

The Simulation cell panel found under the Data source section always displays the original shape information from the imported simulation file. To modify the simulation cell vectors, use the Affine transformation modifier in the data pipeline.