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.

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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 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...

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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])