bond

Bond force classes apply a force and virial on every particle in the simulation state commensurate with the potential energy:

$$U_\mathrm{bond} = \sum_{(j,k) \in \mathrm{bonds}} U_{jk}(r)$$

Each bond is defined by an ordered pair of particle tags in the hoomd.State member bond_group. HOOMD-blue does not construct bond groups, users must explicitly define bonds in the initial condition.

In the bond group (j,k), $r$ is the length of the bond between the particle positions $r= |\mathrm{minimum\_image}(\vec{r}_k - \vec{r}_j)|$.

Bond force classes assign 1/2 of the potential energy to each of the particles in the bond group:

$$U_i = \frac{1}{2} \sum_{(j,k) \in \mathrm{bonds}} U_{jk}(r) [i=j \lor i=k]$$

and similarly for virials.

Classes

• Bond
• FENEWCA
• Harmonic
• Table
• Tether