Periodic

class hoomd.md.dihedral.Periodic

Bases: Dihedral

Periodic dihedral force.

Periodic computes forces, virials, and energies on all dihedrals in the simulation state with:

$$U(\phi) = \frac{1}{2}k \left( 1 + d \cos\left(n \phi - \phi_0 \right) \right)$$

Examples:

harmonic = dihedral.Periodic()
harmonic.params["A-A-A-A"] = dict(k=3.0, d=-1, n=3, phi0=0)
harmonic.params["A-B-C-D"] = dict(k=100.0, d=1, n=4, phi0=math.pi / 2)

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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...

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Members inherited from Force:

additional_energy

Additional energy term. Read more...

additional_virial

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

cpu_local_force_arrays

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

energies

Energy contribution $U_i$ from each particle. Read more...

energy

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

forces

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

gpu_local_force_arrays

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

torques

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

virials

Virial tensor contribution $W_i$ from each particle. Read more...

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Members defined in Periodic:

params

The parameter of the harmonic bonds for each dihedral type. The dictionary has the following keys:

• k (float, required) - potential constant $k$ $[\mathrm{energy}]$

• d (float, required) - sign factor $d$

• n (int, required) - angle multiplicity factor $n$

• phi0 (float, required) - phase shift $\phi_0$ $[\mathrm{radians}]$

Type:

TypeParameter [dihedral type, dict]