Particles for multiphysics simulations

The simulation of the motion of interacting particles is a deceivingly simple, yet powerful and natural, method for exploring physical systems as diverse as planetary dark matter and proteins, unsteady separated flows, and plasmas. Particles can be viewed as objects carrying a physical property of a system, that is being simulated through the evolution of th trajectories and the evolution of the properties carried by the particles.

Lagrangian descriptions of discrete and continuum systems

Simulations of continuum and molecular phenomena can be formulated by following the motion of interacting particles that carry the physical properties of the flow. In a continuum, these properties can be macroscopic, e.g. density, momentum, vorticity,… for a discrete system, such as atoms, we will consider mass, velocity and electric charge.

Molecular Dynamics of water and Carbon Nanotubes

Particle Laden Flow Simulations Using Particles

Continuum systems, particle methods and computational challenges

We study Lagrangian, multiresolution, particle methods for the simulation of continuous systems with an empahsis on fluid mechanics applications. Particle methods, such as Smoothed Particle Hydrodynamics (SPH) and Vortex Methods (VM) enjoy the inherent robustness and adaptivity of Lagrangian methods. At the same time though, uncontrolled particle distortion leads to degraded accuracy and the computation of of spatial differential operators on the particles is highly inefficient. For these reasons, we develop hybrid particle-mesh methodologies which periodically reinitialize the particle positions through high order, moment conserving interpolation and use the mesh for efficient computations of differential operators.

Remeshed particle methods: lost adaptivity?

Our hybrid particle-mesh approach also allows consistent formulations for adaptivity, such as multiresolution analysis. We have developed the Particle-Wavelet Method, a variant which combines the versatility and efficiency of grid-based Wavelet collocation methods while retaining the virtues of a particle method.

left: Principle of wavelet based adaptation in 2D: after the data is compressed on a regular grid, particles are created with appropriate core sizes. middle and right: Particle-Wavelet method as extended to the simulation of transport problems on implicit geometries: the particles adapt to small scales in both the function and the geometry on which it is defined.

 

Discrete particle methods : challenges and lessons from continuum simulations

We develop molecular dynamics (MD) for the simulation of flows at the atomistic scale and Dissipative Particle Dynamics (DPD) methods for the simulations of flows at mesoscopic scales. In these simualtions we employ Fast Poisson solvers that have been developed for related continuum simulations. Additional challenges involve simulations for non-periodic boundaries and the coupling of atomistic-continuum simulations. We develop a systematic framework for the simulation of hybrid atomistic-continuum systems. The underlying idea is to use each method for a particular part of the domain depending on the flow physics that is being simulated. Applications involve : flows in nanodevices and flows of biological interest such as those in small arteries and in biosensors.

People: Philippe Chatelain, Michael Bergdorf, Jens Honore Walther, Diego Rossinelli, Evangelos Kotsalis, Alvaro Foletti

Collaborators: Anthony Leonard (Caltech), Georges-Henri Cottet (Grenoble), Richard Jaffe (NASA Ames)

Funding: ETHZ, Swiss National Science Foundation

Student Projects:

  • GPGPU: Particle-Mesh Operations for 3D Domains
  • Fast Solvers for Complex Geometries

Publications

2007

  • A. M. Altenhoff, J. H. Walther, and P. Koumoutsakos, “A stochastic boundary forcing for dissipative particle dynamics,” J. Comput. Phys., vol. 225, iss. 1, p. 1125–1136, 2007.

BibTeX

@article{altenhoff2007a,
author = {Adrian M. Altenhoff and Jens H. Walther and Petros Koumoutsakos},
doi = {10.1016/j.jcp.2007.01.015},
journal = {{J. Comput. Phys.}},
month = {jul},
number = {1},
pages = {1125--1136},
publisher = {Elsevier {BV}},
title = {A stochastic boundary forcing for dissipative particle dynamics},
url = {https://cse-lab.seas.harvard.edu/files/cse-lab/files/research_numerics_discrete_continuum_simulations_2007_1.pdf},
volume = {225},
year = {2007}
}

Abstract

The method of dissipative particle dynamics (DPD) is an effective, coarse grained model of the hydrodynamics of complex fluids. DPD simulations of wall-bounded flows are however often associated with spurious fluctuations of the fluid properties near the wall. We present a novel stochastic boundary forcing for DPD simulations of wall-bounded flows, based on the identification of fluctuations in simulations of the corresponding homogeneous system at equilibrium. The present method is shown to enforce accurately the no-slip boundary condition, while minimizing spurious fluctuations of material properties, in a number of benchmark problems. (c) 2007 Elsevier Inc. All rights reserved.

  • P. Chatelain, G. -H. Cottet, and P. Koumoutsakos, “Particle mesh hydrodynamics for astrophysics simulations,” Int. J. Mod. Phys. C, vol. 18, iss. 04, p. 610–618, 2007.

BibTeX

@article{chatelain2007a,
author = {Chatelain, P. and Cottet, G.-H. and Koumoutsakos, P.},
doi = {10.1142/s0129183107010851},
journal = {{Int. J. Mod. Phys. C}},
month = {apr},
number = {04},
pages = {610--618},
publisher = {World Scientific Pub Co Pte Lt},
title = {Particle Mesh Hydrodynamics for Astrophysics Simulations},
url = {https://cse-lab.seas.harvard.edu/files/cse-lab/files/research_numerics_dcs_2007_2.pdf},
volume = {18},
year = {2007}
}

Abstract

We present a particle method for the simulation of three dimensional compressible hydrodynamics based on a hybrid Particle-Mesh discretization of the governing equations. The method is rooted on the regularization of particle locations as in remeshed Smoothed Particle Hydrodynamics (rSPH). The rSPH method was recently introduced to remedy problems associated with the distortion of computational elements in SPH, by periodically re-initializing the particle positions and by using high order interpolation kernels. In the PMH formulation, the particles solely handle the convective part of the compressible Euler equations. The particle quantities are then interpolated onto a mesh, where the pressure terms are computed. PMH, like SPH, is free of the convection CFL condition while at the same time it is more efficient as derivatives are computed on a mesh rather than particle-particle interactions. PMH does not detract from the adaptive character of SPH and allows for control of its accuracy. We present simulations of a benchmark astrophysics problem demonstrating the capabilities of this approach.

2006

  • I. F. Sbalzarini, J. H. Walther, M. Bergdorf, S. E. Hieber, E. M. Kotsalis, and P. Koumoutsakos, “PPM – a highly efficient parallel particle–mesh library for the simulation of continuum systems,” J. Comput. Phys., vol. 215, iss. 2, p. 566–588, 2006.

BibTex

@article{sbalzarini2006c,
author = {I.F. Sbalzarini and J.H. Walther and M. Bergdorf and S.E. Hieber and E.M. Kotsalis and P. Koumoutsakos},
doi = {10.1016/j.jcp.2005.11.017},
journal = {{J. Comput. Phys.}},
month = {jul},
number = {2},
pages = {566--588},
publisher = {Elsevier {BV}},
title = {{PPM} {\textendash} A highly efficient parallel particle{\textendash}mesh library for the simulation of continuum systems},
url = {https://cse-lab.seas.harvard.edu/files/cse-lab/files/research_numerics_dcs_2006.pdf},
volume = {215},
year = {2006}
}

Abstract

This paper presents a highly efficient parallel particle-mesh (PPM) library, based on a unifying particle formulation for the simulation of continuous systems. In this formulation, the grid-free character of particle methods is relaxed by the introduction of a mesh for the reinitialization of the particles, the computation of the field equations, and the discretization of differential operators. The present utilization of the mesh does not detract from the adaptivity, the efficient handling of complex geometries, the minimal dissipation, and the good stability properties of particle methods. The coexistence of meshes and particles, allows for the development of a consistent and adaptive numerical method, but it presents a set of challenging parallelization issues that have hindered in the past the broader use of particle methods. The present library solves the key parallelization issues involving particle-mesh interpolations and the balancing of processor particle loading, using a novel adaptive tree for mixed domain decompositions along with a coloring scheme for the particle-mesh interpolation. The high parallel efficiency of the library is demonstrated in a series of benchmark tests on distributed memory and on a shared-memory vector architecture. The modularity of the method is shown by a range of simulations, from compressible vortex rings using a novel formulation of smooth particle hydrodynamics, to simulations of diffusion in real biological cell organelles. The present library enables large scale simulations of diverse physical problems using adaptive particle methods and provides a computational tool that is a viable alternative to mesh-based methods.

2005

  • M. Bergdorf, G. Cottet, and P. Koumoutsakos, “Multilevel adaptive particle methods for convection-diffusion equations,” Multiscale Model. Sim., vol. 4, iss. 1, p. 328–357, 2005.

BibTeX

@article{bergdorf2005a,
author = {Michael Bergdorf and Georges-Henri Cottet and Petros Koumoutsakos},
doi = {10.1137/040602882},
journal = {{Multiscale Model. Sim.}},
month = {jan},
number = {1},
pages = {328--357},
publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})},
title = {Multilevel Adaptive Particle Methods for Convection-Diffusion Equations},
url = {https://cse-lab.seas.harvard.edu/files/cse-lab/files/research_numerics_dcs_2005_1.pdf},
volume = {4},
year = {2005}
}

Abstract

We present novel multilevel particle methods with extended adaptivity in areas where increased resolution is required. We present two complementary approaches as inspired by r-adaptivity and adaptive mesh refinement (AMR) concepts introduced infinite difference and finite element schemes. For the r-adaptivity a new class of particle-based mapping functions is introduced, while the particle AMR method uses particle remeshing in overlapping domains as a key element. The advantages and drawbacks of the proposed particle methods are illustrated based on results from the solution of one-dimensional convection-diffusion equations, while the extension of the method to higher dimensions is demonstrated in simulations of the inviscid evolution of an elliptical vortex.

  • P. Koumoutsakos, “Multicscale flow simulations using particles,” Annu. Rev. Fluid Mech., vol. 37, iss. 1, p. 457–487, 2005.

BibTeX

@article{koumoutsakos2005a,
author = {Petros Koumoutsakos},
doi = {10.1146/annurev.fluid.37.061903.175753},
journal = {{Annu. Rev. Fluid Mech.}},
month = {jan},
number = {1},
pages = {457--487},
publisher = {Annual Reviews},
title = {Multicscale Flow Simulations using Particles},
url = {https://cse-lab.seas.harvard.edu/files/cse-lab/files/research_numerics_dcs_2005_2.pdf},
volume = {37},
year = {2005}
}

Abstract

Flow simulations are one of the archetypal multiscale problems. Simulations of turbulent and unsteady separated flows have to resolve a multitude of interacting scales, whereas molecular phenomena determine the structure of shocks and the validity of the no-slip boundary condition. Particle simulations of continuum and molecular phenomena can be formulated by following the motion of interacting particles that carry the physical properties of the flow. In this article we review Lagrangian, multiresolution, particle methods such as vortex methods and smooth particle hydrodynamics for the simulation of continuous flows and molecular dynamics for the simulation of flows at the atomistic scale. We review hybrid molecular-continuum simulations with an emphasis on the computational aspects of the problem. We identify the common computational characteristics of particle methods and discuss their properties that enable the formulation of a systematic framework for multiscale flow simulations.