Absorbed

The Absorbed potential models particles that have been absorbed onto a surface, applying a harmonic restraint to keep them near their absorption point. This is useful for simulating irreversible adsorption or creating stable surface-bound particles.

\[\begin{split}U(\mathbf{r}) = \begin{cases} \frac{1}{2}K((x - x_0)^2 + (y - y_0)^2 + (z - z_0)^2) & \text{if particle is absorbed} \\ 0 & \text{otherwise} \end{cases}\end{split}\]

where:

• \(K\) is the spring constant of the harmonic restraint

• \(\mathbf{r} = (x, y, z)\) is the position of the particle

• \(\mathbf{r}_0 = (x_0, y_0, z_0)\) is the absorption point

The Absorbed potential is applied only to particles that were below the heightThreshold when the potential was first computed.

Note the strategy, playing with the common parameter startStep we can control the time when the particles are absorbed. For example we can wait for a structure to relax before it is absorbed.

---

• type: Surface, Absorbed

• parameters:

  • K: real: Spring constant of the harmonic restraint \([energy/distance^2]\)

  • heightThreshold: real: Height below which particles are considered absorbed \([distance]\)

Example:

"absorbed":{
  "type":["Surface","Absorbed"],
  "parameters":{
    "K": 100.0,
    "heightThreshold": 1.0
  }
}

Note

The Absorbed potential is applied only to particles that were below the heightThreshold when the potential was first computed. The absorption points are determined at this time and remain fixed throughout the simulation.

Warning

This potential determines the absorbed particles only once, when it is first computed. Ensure that your initial configuration is consistent with your intended absorption state.

Tip

The Absorbed potential can be used to model particles that are irreversibly bound to a surface while still allowing for some movement around their binding point.