Tether

class hoomd.md.bond.Tether

Bases: Bond

Tether bond force.

The tethered network is described in Refs. Gompper, G. & Kroll, D. M. Statistical Mechanics of Membranes and Surfaces 2nd edn (eds Nelson, D. R. et al.) 359-426 (World Scientific, 2004) and Noguchi, H. & Gompper, G., Phys. Rev. E 72 011901 (2005).

Tether computes forces, virials, and energies on all bonds in the simulation state with:

U(r)=Uatt(r)+Urep(r)U(r) = U_{\mathrm{att}}(r) + U_{\mathrm{rep}}(r)

where rr is the distance from one particle to the other in the bond.

Uatt(r)={kbexp⁡(1/(lc0−r)lmax−rr>lc00r≤lc0U_{\mathrm{att}}(r) = \begin{cases} k_b \frac{\exp(1/(l_{c0}-r)}{l_{max}-r} & r > l_{c0} \\ 0 & r \leq l_{c0} \\ \end{cases}
Urep(r)={kbexp⁡(1/(r−lc1)r−lminr<lc10r≥lc1U_{\mathrm{rep}}(r) = \begin{cases} k_b \frac{\exp(1/(r-l_{c1})}{r-l_{min}} & r < l_{c1}\\ 0 & r \ge l_{c1} \end{cases}
lmin<lc1<lc0<lmaxl_{min} < l_{c1} < l_{c0} < l_{max}

Examples:

bond_potential = bond.Tether()
bond_potential.params['A-A'] = dict(k_b=10.0, l_min=0.9, l_c1=1.2,
                                       l_c0=1.8, l_max=2.1)

Members inherited from AutotunedObject:

property kernel_parameters

Kernel parameters. Read more...

property is_tuning_complete

Check if kernel parameter tuning is complete. Read more...

tune_kernel_parameters()

Start tuning kernel parameters. Read more...

Members inherited from Force:

additional_energy

Additional energy term. Read more...

additional_virial

Additional virial tensor term WadditionalW_\mathrm{additional}. Read more...

cpu_local_force_arrays

Local force arrays on the CPU. Read more...

energies

Energy contribution UiU_i from each particle. Read more...

energy

The potential energy UU of the system from this force. Read more...

forces

The force F⃗i\vec{F}_i applied to each particle. Read more...

gpu_local_force_arrays

Local force arrays on the GPU. Read more...

torques

The torque τ⃗i\vec{\tau}_i applied to each particle. Read more...

virials

Virial tensor contribution WiW_i from each particle. Read more...

Members defined in Tether:

params

The parameter of the Tethering potential bonds. The dictionary has the following keys:

  • k_b (float, required) - bond stiffness [energy][\mathrm{energy}]

  • l_min (float, required) - minimum bond length [length][\mathrm{length}]

  • l_c1 (float, required) - cutoff distance of repulsive part [length][\mathrm{length}]

  • l_c0 (float, required) - cutoff distance of attractive part [length][\mathrm{length}]

  • l_max (float, required) - maximum bond length [length][\mathrm{length}]

Type:

TypeParameter[bond type, dict]