ExpandedGaussian

class hoomd.md.pair.ExpandedGaussian(nlist, default_r_cut=None, default_r_on=0.0, mode='none')

Bases: Pair

Expanded Gaussian pair force.

Parameters:

  • nlist (hoomd.md.nlist.NeighborList) – Neighbor list.

  • default_r_cut (float) – Default cutoff radius \([\mathrm{length}]\).

  • default_r_on (float) – Default turn-on radius \([\mathrm{length}]\).

  • mode (str) – Energy shifting/smoothing mode.

ExpandedGaussian computes the radially-shifted Gaussian pair force should on every particle in the simulation state:

\[U(r) = \varepsilon \exp \left( -\frac{1}{2} \left( \frac{r-\Delta}{\sigma} \right)^2 \right)\]

Example:

nl = nlist.Cell()
expanded_gauss = pair.ExpandedGaussian(default_r_cut=3.0, nlist=nl)
expanded_gauss.params[("A", "A")] = dict(
    epsilon=1.0, sigma=1.0, delta=0.5
)
expanded_gauss.r_cut[("A", "B")] = 3.0

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 \(W_\mathrm{additional}\). 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...

Members inherited from Pair:

nlist

Neighbor list used to compute the pair force. Read more...

mode

Energy smoothing/cutoff mode. Read more...

r_cut

Cuttoff radius beyond which the energy and force are 0. Read more...

r_on

Radius at which the XPLOR smoothing function starts. Read more...

compute_energy()

Compute the energy between two sets of particles. Read more...

Members defined in ExpandedGaussian:

params

The expanded Gaussian potential parameters. The dictionary has the following keys:

  • epsilon (float, required) - energy parameter \(\varepsilon\) \([\mathrm{energy}]\)

  • sigma (float, required) - particle size \(\sigma > 0\) \([\mathrm{length}]\)

  • delta (float, required) - shift distance \(\delta\) \([\mathrm{length}]\)

Type: TypeParameter [tuple [particle_type, particle_type], dict]