Quasi2D

The Quasi2D integrator implements Brownian Dynamics with Hydrodynamic Interactions for quasi-two-dimensional systems (periodic in two dimensions, confined in the third). This integrator is a wrapper around the UAMMD BDHI::Quasi2D integrator.

For more details on the underlying method, please refer to the UAMMD BDHI documentation.

  • type: BDHIDoublyPeriodic, Quasi2D

  • parameters:

    • timeStep: real: Time step \([time]\)

    • temperature: real: Temperature of the system \([energy]\)

    • viscosity: real: Viscosity of the fluid \([mass/(distance \cdot time)]\)

    • hydrodynamicRadius: real: Hydrodynamic radius of the particles \([distance]\) (optional, uses particle radius if not specified)

    • tolerance: real: Tolerance for the iterative solver (default: 1e-3)

Example:

"quasi2d":{
  "type":["BDHIDoublyPeriodic","Quasi2D"],
  "parameters":{
    "timeStep": 0.01,
    "temperature": 1.0,
    "viscosity": 1.0,
    "hydrodynamicRadius": 0.5,
    "tolerance": 1e-4
  }
}

Note

This integrator is suitable for systems with periodic boundary conditions in two dimensions and confinement in the third dimension.

Warning

This integrator assumes that particle masses and radii are defined in the particle data.