DPStokes

The DPStokes integrator implements Brownian Dynamics with Hydrodynamic Interactions for doubly periodic systems using the Doubly Periodic Stokes (DPStokes) method. This integrator is a wrapper around the UAMMD DPStokesSlab_ns::DPStokesIntegrator.

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

type: BDHIDoublyPeriodic, DPStokes
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 \([distance]\)
- nx, ny: int: Number of grid points in x and y directions
- nz: int: Number of grid points in z direction (optional)
- Lx, Ly: real: Box size in x and y directions \([distance]\)
- H: real: Height of the simulation box \([distance]\)
- w: real: Width of the Gaussian kernel \([distance]\)
- beta: real: Regularization parameter for the Gaussian kernel (optional)
- alpha: real: Regularization parameter for the wall (optional)
- w_d: real: Width of the Gaussian kernel for the derivative (optional)
- beta_d: real: Regularization parameter for the derivative kernel (optional)
- alpha_d: real: Regularization parameter for the wall derivative (optional)
- mode: string: Wall mode (“none”, “bottom”, or “slit”)
- tolerance: real: Tolerance for the iterative solver (default: 1e-7)

Example:

"dpstokes":{
  "type":["BDHIDoublyPeriodic","DPStokes"],
  "parameters":{
    "timeStep": 0.01,
    "temperature": 1.0,
    "viscosity": 1.0,
    "hydrodynamicRadius": 0.5,
    "nx": 64,
    "ny": 64,
    "Lx": 32.0,
    "Ly": 32.0,
    "H": 10.0,
    "w": 0.5,
    "mode": "slit",
    "tolerance": 1e-6
  }
}

Note

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

Warning

This integrator requires that the particle group contains all particles in the system.