Create bonds

Input:Output:

This modifier creates bonds between particles using a cutoff-based criterion.

The visual appearance of the generated bonds is controlled by the attached bonds display object.

Parameters

The modifier supports two different modes that determine how bonds are created between particles:

Uniform cutoff radius

Use this mode to create bonds between pairs of particles irrespective of their type.

Pair-wise cutoff radii

This mode gives you more control over which particle types get connected by bonds. The table lists all pair-wise combinations of particle types. Enter a cutoff distance into the third column to create bonds between pairs of particles of the given types.

Note that this mode is only available when the Particle Type property is defined.

Suppress inter-molecular bonds

If this option is active, bonds are only created between particles that belong to the same molecule, i.e. if their Molecule Identifier properties match. If the Molecule Identifier property is not defined at all, this option has no effect.

Lower cutoff

This parameter defines a lower cutoff, i.e. a minimum particle separation, for bonds to be created.

Technical background information

OVITO stores each bond generated by this modifier as a pair of particle indices. It makes sure that, if a particle is subsequently deleted, the dangling bonds are deleted too.

In addition to the two particle indices, OVITO stores a periodic shift vector with every bond. This shift vector indicates whether the bond crosses a periodic boundary of the simulation cell. The shift vector of bonds that do not cross a periodic boundary is (0,0,0). A bond that crosses a periodic cell boundary in the positive X direction, for instance, has the shift vector (1,0,0) and will be displayed as two half bonds.