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 bonds display object attached to the modifier.

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 types if the pair separation is below the specified cutoff.

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 connect pairs of particles of the given types with bonds.

Note that is mode is only available if the Particle Type property is defined for particles.

No bonds between different molecules

If this option is active, bonds will only be created between particles that belong to the same molecule. Two particles belong to the same molecule if their Molecule Identifier property values are the same. If the Molecule Identifier property is not defined for the particles, this option has no effect.

Lower cutoff

This parameter allows to set a lower cutoff, i.e. a minimum length, for the 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.