Fluctuating Hydrodynamics

The group has recently created a github organization stochasticHydroTools with a number of repositories connected to our work on fluctuating hydrodynamics of particle suspensions.
  • The Fluctuating Immersed Boundary method can perform Brownian Dynamics of suspensions of colloids or elastic structures such as polymer chains in confined geometries, as described in the paper "Brownian Dynamics without Green's Functions", S. Delong, F. Balboa Usabiaga et al., J. Chem. Phys., 140, 134110, 2014 [ArXiv:1401.4198].
  • The RotationalDiffusion repository contains some simple python codes for performing Brownian Dynamics of rigid bodies in the presence of a single wall, as described in the paper "Brownian Dynamics of Confined Rigid Bodies", S. Delong and F. Balboa Usabiaga and A. Donev, 2015.
  • The GPU code fluam developed by collaborators Rafael Delgado-Buscalioni and Florencio Balboa implements compressible and incompressible staggered-grid fluctuating hydrodynamics for binary fluid mixtures and for particle suspensions. For incompressible hydrodynamics only periodic boundary conditions are supported because the code relies on FFT techniques for solving the Stokes equations.
  • The state-of-the-art parallel C++ Immersed Boundary Adaptive Mesh Refinement IBAMR framework developed and maintained by collaborator Boyce Griffith implements a stochastic stress tensor generator that can be used to implement fluctuating hydrodynamics for both binary fluid mixtures and for particle suspensions (presently only for neutrally buyoant particles). Full support for any combination of no-slip, slip and periodic boundary conditions is provided. You will need to download IBAMR first. See examples/IB/explicit/ex5 for an example that advects particles (markers) by thermal velocity fluctuations, and examples/navier_stokes/ex6 for an example that advects a scalar field (concentration or temperature) with thermal fluctuations in a Boussinesq model.
  • The IBAMR-based MixingIBAMR code  is an extension and improvement of  examples/navier_stokes/ex6 included in IBAMR, and contains example input files that we used for performing simulations of experimental measurements of giant fluctuations in binary fluid mixtures in microgravity and in Earth gravity. These simulations and the algorithms used are described in the papers "Multiscale temporal integrators for fluctuating hydrodynamics", S. Delong et al., Phys. Rev. E, 90, 063312, 2014 [ArXiv:1410.0240], with comparisons to experiments described in ArXiv:1410.6524 and ArXiv:1502.03693.
  • Parallel finite volume solvers for the compressible, incompressible, and low Mach number fluctuating hydrodynamic equations for fluid mixtures have been implemented in the Fortran binding of the BoxLib framework developed by the group of collaborator John Bell at LBNL. We are in the process of developing a module for staggered-grid low Mach hydrodynamics.

Immersed Boundary Method and CFD

Hard-Particle packing Codes

  1. Here are some old but still very efficient precompiled executables for generating packings of spheres, ellipsoids and super ellipsoids. These were developed during my Ph.D. research and you should consult my Ph.D. thesis if you plan to use them.
  2. If you wish to modify the codes yourself you should instead use the simpler but still reasonably efficient C++ sphere packing code.