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