LBsoft: A parallel open-source software for simulation of colloidal systems

We present LBsoft, an open-source software developed mainly to simulate the hydro-dynamics of colloidal systems based on the concurrent coupling between lattice Boltzmann methods for the fluid and discrete particle dynamics for the colloids. Such coupling has been developed before, but, to the best of our knowledge, no detailed discussion of the programming issues to be faced in order to attain efficient implementation on parallel architectures, has ever been presented to date. In this paper, we describe in detail the underlying multi-scale models, their coupling procedure, along side with a description of the relevant input variables, to facilitate third-parties usage. The code is designed to exploit parallel computing platforms, taking advantage also of the recent AVX-512 instruction set. We focus on LBsoft structure, functionality, parallel implementation, performance and availability, so as to facilitate the access to this computational tool to the research community in the field. The capabilities of LBsoft are highlighted for a number of prototypical case studies, such as pickering emulsions, bicontinuous systems, as well as an original study of the coarsening process in confined bijels under shear.

[1]  R. Mezzenga,et al.  Understanding foods as soft materials , 2005, Nature materials.

[2]  A. Ladd,et al.  Lubrication corrections for lattice-Boltzmann simulations of particle suspensions. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[3]  Tuomo Rossi,et al.  Comparison of implementations of the lattice-Boltzmann method , 2008, Comput. Math. Appl..

[4]  RESEARCH NOTE An improved leap-frog rotational algorithm , 1997 .

[5]  F. Jansen,et al.  From bijels to Pickering emulsions: a lattice Boltzmann study. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[6]  Martin T. Dove,et al.  DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism , 2006 .

[7]  Roberto Piazza,et al.  Soft Matter: The stuff that dreams are made of , 2011 .

[8]  Danna Zhou,et al.  d. , 1934, Microbial pathogenesis.

[9]  D. C. Rapaport,et al.  Multi-million particle molecular dynamics: II. Design considerations for distributed processing , 1991 .

[10]  William Smith,et al.  Molecular dynamics on hypercube parallel computers , 1991 .

[11]  A. Ladd,et al.  Lattice-Boltzmann Simulations of Particle-Fluid Suspensions , 2001 .

[12]  I. Tiselj,et al.  Lattice Boltzmann Method , 2022, Advanced Computational Techniques for Heat and Mass Transfer in Food Processing.

[13]  Gerhard Wellein,et al.  Comparison of different propagation steps for lattice Boltzmann methods , 2011, Comput. Math. Appl..

[14]  Molecular Dynamics Simulation of Spinodal Decomposition in Three-Dimensional Binary Fluids. , 1996, Physical review letters.

[15]  Vincent Heuveline,et al.  THE OPENLB PROJECT: AN OPEN SOURCE AND OBJECT ORIENTED IMPLEMENTATION OF LATTICE BOLTZMANN METHODS , 2007 .

[16]  Peter V. Coveney,et al.  HemeLB: A high performance parallel lattice-Boltzmann code for large scale fluid flow in complex geometries , 2008, Comput. Phys. Commun..

[17]  Ulrich Rüde,et al.  Optimization and Profiling of the Cache Performance of Parallel Lattice Boltzmann Codes in 2 D and 3 D ∗ , 2003 .

[18]  G. Gonnella,et al.  Pattern study of thermal phase separation for binary fluid mixtures , 2011 .

[19]  D. J. Tildesley,et al.  Large Scale Molecular Dynamics on Parallel Computers using the Link-cell Algorithm , 1991 .

[20]  Ulrich Rüde,et al.  Massively Parallel Algorithms for the Lattice Boltzmann Method on NonUniform Grids , 2015, SIAM J. Sci. Comput..

[21]  Jens Harting,et al.  Effects of nanoparticles and surfactant on droplets in shear flow , 2012, 1201.6562.

[22]  Michael E. Cates,et al.  Bijels: a new class of soft materials , 2008 .

[23]  Ruddy Brionnaud,et al.  Solution to industry benchmark problems with the lattice-Boltzmann code XFlow , 2012 .

[24]  Jeffrey S. Racine,et al.  The Cygwin tools: a GNU toolkit for Windows , 2000 .

[25]  William Schroeder,et al.  The Visualization Toolkit: An Object-Oriented Approach to 3-D Graphics , 1997 .

[26]  Anthony J. C. Ladd,et al.  Lattice-Boltzmann methods for suspensions of solid particles , 2015 .

[27]  P V Coveney,et al.  Structural transitions and arrest of domain growth in sheared binary immiscible fluids and microemulsions. , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[28]  David P. Lockard,et al.  Evaluation of PowerFLOW for Aerodynamic Applications , 2002 .

[29]  Peter V. Coveney,et al.  LB3D: A parallel implementation of the Lattice-Boltzmann method for simulation of interacting amphiphilic fluids , 2017, Comput. Phys. Commun..

[30]  I. Pagonabarraga,et al.  Inertial effects in three-dimensional spinodal decomposition of a symmetric binary fluid mixture: a lattice Boltzmann study , 2001, Journal of Fluid Mechanics.

[31]  P S Clegg,et al.  Bicontinuous emulsions stabilized solely by colloidal particles. , 2007, Nature materials.

[32]  Bruce D. Jones,et al.  Multiphase lattice Boltzmann simulations for porous media applications , 2014, Computational Geosciences.

[33]  William Gropp,et al.  Parallel computing and domain decomposition , 1992 .

[34]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[35]  Richard L. Anderson,et al.  DL_MESO: highly scalable mesoscale simulations , 2013 .

[36]  Erlend Magnus Viggen,et al.  The Lattice Boltzmann Method , 2017 .

[37]  Wolfgang J. Paul,et al.  A special purpose parallel computer for molecular dynamics: motivation, design, implementation, and application , 1987 .

[38]  A. Ladd Numerical simulations of particulate suspensions via a discretized Boltzmann equation. Part 1. Theoretical foundation , 1993, Journal of Fluid Mechanics.

[39]  D. C. Rapaport,et al.  Multi-million particle molecular dynamics: III. Design considerations for data-parallel processing , 1993 .

[40]  S. Succi The Lattice Boltzmann Equation , 2018, Oxford Scholarship Online.

[41]  Utkarsh Ayachit,et al.  The ParaView Guide: A Parallel Visualization Application , 2015 .

[42]  J. Harting,et al.  Direct Assembly of Magnetic Janus Particles at a Droplet Interface. , 2017, ACS nano.

[43]  D. d'Humières,et al.  Two-relaxation-time Lattice Boltzmann scheme: About parametrization, velocity, pressure and mixed boundary conditions , 2008 .

[44]  William Smith,et al.  Molecular dynamics on distributed memory (MIMD) parallel computers , 1993 .

[45]  Frederica Darema,et al.  The SPMD Model : Past, Present and Future , 2001, PVM/MPI.

[46]  C. Aidun,et al.  Direct analysis of particulate suspensions with inertia using the discrete Boltzmann equation , 1998, Journal of Fluid Mechanics.

[47]  A. Ladd Numerical simulations of particulate suspensions via a discretized Boltzmann equation. Part 2. Numerical results , 1993, Journal of Fluid Mechanics.

[48]  I. Pagonabarraga,et al.  Colloidal Jamming at Interfaces: A Route to Fluid-Bicontinuous Gels , 2005, Science.

[49]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[50]  Dmitri Rozmanov,et al.  Robust rotational-velocity-Verlet integration methods. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[51]  Ignacio Pagonabarraga,et al.  LUDWIG: A parallel Lattice-Boltzmann code for complex fluids , 2001 .

[52]  David Fincham,et al.  Leapfrog Rotational Algorithms , 1992 .

[53]  F. Toschi,et al.  Surface roughness-hydrophobicity coupling in microchannel and nanochannel flows. , 2006, Physical review letters.

[54]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

[55]  R W Hockney,et al.  Computer Simulation Using Particles , 1966 .

[56]  Yu Chen,et al.  Lattice Boltzmann simulation of capillary interactions among colloidal particles , 2008, Comput. Math. Appl..