The simulation cell information loaded from the input file is displayed in this control panel (see screenshot). If the input file does not contain any cell information, an orthogonal bounding box is automatically generated by OVITO to enclose all loaded particles.
The dimensionality setting determines whether the particle system is 2- or 3-dimensional. In mode "2D", the z-coordinates of particles and the third simulation cell vector will be ignored during most computations performed by OVITO.
The periodic boundary condition (PBC) flags control whether OVITO should perform calculation within a periodic domain or not. If possible, OVITO tries to read these flags from the input data file, but you can manually change them later on if needed.
The simulation cell dimensions and the coordinates of the cell's origin are read from input data file if possible. If not, the cell geometry is dynamically computed by OVITO to form a bounding box around all particles. You can override the cell vectors manually. However, all changes will be reset whenever OVITO reloads the input data file. To permanently change the simulation cell geometry, you can use the Affine Transformation modifier. It allows to change the cell vectors to prescribed values, irrespective of the current input cell geometry.
You can control the visual appearance of the simulation cell by opening the simulation cell display panel.