LJGauss

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

Bases: LJGauss

Alchemical Lennard Jones Gauss 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.

LJGauss computes the Lennard-Jones Gauss force on all particles in the simulation state, with additional alchemical degrees of freedom:

\[U(r) = 1\ [\mathrm{energy}] \cdot \left[ \left ( \frac{1\ [\mathrm{length}]}{r} \right)^{12} - \left ( \frac{2\ [\mathrm{length}]}{r} \right)^{6} \right] - \alpha_{1}\epsilon \exp \left[ - \frac{\left(r - \alpha_{2}r_{0}\right)^{2}}{2 (\alpha_{3}\sigma)^{2}} \right],\]

where \(\alpha_i\) are the alchemical degrees of freedom.

Note

\(\alpha_i\) not accessed are set to 1.

Attention

hoomd.md.alchemy.pair.LJGauss does not support execution on GPUs.

Attention

hoomd.md.alchemy.pair.LJGauss does not support MPI parallel simulations.

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 LJGauss:

params

The potential parameters. The dictionary has the following keys:

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

  • sigma (float, required) - Gaussian width \(\sigma\) \([\mathrm{length}]\)

  • r0 (float, required) - Gaussian center \(r_0\) \([\mathrm{length}]\)

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

epsilon

Alchemical degrees of freedom for the potential parameter \(\epsilon\).

Type: AlchemicalDOFStore [tuple [particle_type, particle_type], AlchemicalDOF])

sigma

Alchemical degrees of freedom for the potential parameter \(\sigma\).

Type: AlchemicalDOFStore [tuple [particle_type, particle_type], AlchemicalDOF])

r0

Alchemical degrees of freedom for the potential parameter \(r_0\).

Type: AlchemicalDOFStore [tuple [particle_type, particle_type], AlchemicalDOF])