arXiv subjects

Peter V. Coveney

Publications and source records attributed to Peter V. Coveney.

At least 73 records · Page 4Linked to original sources

arXiv2013

Analyzing and Modeling the Performance of the HemeLB Lattice-Boltzmann Simulation Environment

We investigate the performance of the HemeLB lattice-Boltzmann simulator for cerebrovascular blood flow, aimed at providing timely and clinically relevant assistance to neurosurgeons. HemeLB is optimised for sparse geometries, supports interactive use, and scales well to 32,768 cores for problems with ~81 million lattice sites. We obtain a maximum performance of 29.5 billion site updates per second, with only an 11% slowdown for highly sparse problems (5% fluid fraction). We present steering and visualisation performance measurements and provide a model which allows users to predict the performance, thereby determining how to run simulations with maximum accuracy within time constraints.

physics.comp-ph↗

arXiv2013

Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations

Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from desktops to petascale supercomputers, including combinations of these. Our work features two multiscale applications, in-stent restenosis and cerebrovascular bloodflow, which combine multiple existing single-scale applications to create a multiscale simulation. These applications can be efficiently coupled, deployed and executed on computers up to the largest (peta) scale, incurring a coupling overhead of 1 to 10% of the total execution time.

cs.DC↗

arXiv2012

Coalesced communication: a design pattern for complex parallel scientific software

We present a new design pattern for high-performance parallel scientific software, named coalesced communication. This pattern allows for a structured way to improve the communication performance through coalescence of multiple communication needs using two communication management components. We apply the design pattern to several simulations of a lattice-Boltzmann blood flow solver with streaming visualisation which engenders a reduction in the communication overhead of approximately 40%.

cs.DC↗

arXiv2007

Structural transitions and arrest of domain growth in sheared binary immiscible fluids and microemulsions

We investigate spinodal decomposition and structuring effects in binary immiscible and ternary amphiphilic fluid mixtures under shear by means of three dimensional lattice Boltzmann simulations. We show that the growth of individual fluid domains can be arrested by adding surfactant to the system, thus forming a bicontinous microemulsion. We demonstrate that the maximum domain size and the time of arrest depend linearly on the concentration of amphiphile molecules. In addition, we find that for a well defined threshold value of amphiphile concentration, the maximum domain size and time of complete arrest do not change. For systems under constant and oscillatory shear we analyze domain growth rates in directions parallel and perpendicular to the applied shear. We find a structural transition from a sponge to a lamellar phase by applying a constant shear and the occurrence of tubular structures under oscillatory shear. The size of the resulting lamellae and tubes depends strongly on the amphiphile concentration, shear rate and shear frequency.

cond-mat.soft↗

arXiv2006

Stress response and structural transitions in sheared gyroidal and lamellar amphiphilic mesophases: lattice-Boltzmann simulations

We report on the stress response of gyroidal and lamellar amphiphilic mesophases to steady shear simulated using a bottom-up lattice-Boltzmann model for amphiphilic fluids and sliding periodic (Lees-Edwards) boundary conditions. We study the gyroid per se (above the sponge-gyroid transition, of high crystallinity) and the molten gyroid (within such a transition, of shorter-range order). We find that both mesophases exhibit shear-thinning, more pronounced and at lower strain rates for the molten gyroid. At late times after the onset of shear, the skeleton of the crystalline gyroid becomes a structure of interconnected irregular tubes and toroidal rings, mostly oriented along the velocity ramp imposed by the shear, in contradistinction with free-energy Langevin-diffusion studies which yield a much simpler structure of disentangled tubes. We also compare the shear stress and deformation of lamellar mesophases with and without amphiphile when subjected to the same shear flow applied normal to the lamellae. We find that the presence of amphiphile allows (a) the shear stress at late times to be higher than in the case without amphiphile, and (b) the formation of rich patterns on the sheared interface, characterised by alternating regions of high and low curvature.

cond-mat.soft↗

arXiv2004

Energy controlled insertion of polar molecules in dense fluids

We present a method to search low energy configurations of polar molecules in the complex potential energy surfaces associated with dense fluids. The search is done in the configurational space of the translational and rotational degrees of freedom of the molecule, combining steepest-descent and Newton-Raphson steps which embed information on the average sizes of the potential energy wells obtained from prior inspection of the liquid structure. We perform a molecular dynamics simulation of a liquid water shell which demonstrates that the method enables fast and energy-controlled water molecule insertion in aqueous environments. The algorithm finds low energy configurations of incoming water molecules around three orders of magnitude faster than direct random insertion. This method is an important step towards dynamic simulations of open systems and it may also prove useful for energy-biased ensemble average calculations of the chemical potential.

physics.chem-ph↗

arXiv2004

Detection and tracking of defects in the gyroid mesophase

Certain systems, such as amphiphile solutions or diblock copolymer melts, may assemble into structures called ``mesophases'', with properties intermediate between those of a solid and a liquid. These mesophases can be of very regular structure, but may contain defects and grain boundaries. Different visualization techniques such as volume rendering or isosurfacing of fluid density distributions allow the human eye to detect and track defects in liquid crystals because humans are easily capable of finding imperfections in repetitive spatial structures. However, manual data analysis becomes too time consuming and algorithmic approaches are needed when there are large amounts of data. We present and compare two different approaches we have developed to study defects in gyroid mesophases of amphiphilic ternary fluids. While the first method is based on a pattern recognition algorithm, the second uses the particular structural properties of gyroid mesophases to detect defects.

cond-mat.soft↗

arXiv2004

Symmetry-breaking in chiral polymerisation

We propose a model for chiral polymerisation and investigate its symmetric and asymmetric solutions. The model has a source species which decays into left- and right-handed types of monomer, each of which can polymerise to form homochiral chains; these chains are susceptible to `poisoning' by the opposite handed monomer. Homochiral polymers are assumed to influence the proportion of each type of monomer formed from the precursor. We show that for certain parameter values a positive feedback mechanism makes the symmetric steady-state solution unstable. The kinetics of polymer formation are then analysed in the case where the system starts from zero concentrations of monomer and chains. We show that following a long induction time, extremely large concentrations of polymers are formed for a short time, during this time an asymmetry introduced into the system by a random external perturbation may be massively amplified. The system then approaches one of the steady-state solutions described above.

physics.bio-ph↗

arXiv2004

Coarsening dynamics of ternary amphiphilic fluids and the self-assembly of the gyroid and sponge mesophases: lattice-Boltzmann simulations

By means of a three-dimensional amphiphilic lattice-Boltzmann model with short-range interactions for the description of ternary amphiphilic fluids, we study how the phase separation kinetics of a symmetric binary immiscible fluid is altered by the presence of the amphiphilic species. We find that a gradual increase in amphiphile concentration slows down domain growth, initially from algebraic, to logarithmic temporal dependence, and, at higher concentrations, from logarithmic to stretched-exponential form. In growth-arrested stretched-exponential regimes, at late times we observe the self-assembly of sponge mesophases and gyroid liquid crystalline cubic mesophases, hence confirming that (a) amphiphile-amphiphile interactions need not be long-ranged in order for periodically modulated structures to arise in a dynamics of competing interactions, and (b) a chemically-specific model of the amphiphile is not required for the self-assembly of cubic mesophases, contradicting claims in the literature. We also observe a structural order-disorder transition between sponge and gyroid phases driven by amphiphile concentration alone or, independently, by the amphiphile-amphiphile and the amphiphile-binary fluid coupling parameters. For the growth-arrested mesophases, we also observe temporal oscillations in the structure function at all length scales; most of the wavenumbers show slow decay, and long-term stationarity or growth for the others. We ascribe this behaviour to a combination of complex amphiphile dynamics leading to Marangoni flows.

cond-mat.soft↗

arXiv2004

Self-assembly of the gyroid cubic mesophase: lattice-Boltzmann simulations

We present the first simulations of the self-assembly kinetics of the gyroid cubic mesophase using a Boltzmann transport method. No macroscopic parameters are included in the model and three-dimensional hydrodynamics is emergent from the microscopic conservation laws. The self-assembly arise from local inter-particle interactions in an initially homogeneous, phase segregating binary fluid with dispersed amphiphile. The mixture evolves in discrete time according to the dynamics of a set of coupled Boltzmann-BGK equations on a lattice. We observe a transient microemulsion phase during self-assembly, the structure function peaks and direct-space imaging unequivocally identifying the gyroid at later times. For larger lattices, highly ordered subdomains are separated by grain boundaries. Relaxation towards the ordered equilibrium structure is very slow compared to the diffusive and microemulsion-assembling transients, the structure function oscillating in time due to a combination of Marangoni effects and long-time-scale defect dynamics.

cond-mat.soft↗

arXiv2004

Large-scale grid-enabled lattice-Boltzmann simulations of complex fluid flow in porous media and under shear

Well designed lattice-Boltzmann codes exploit the essentially embarrassingly parallel features of the algorithm and so can be run with considerable efficiency on modern supercomputers. Such scalable codes permit us to simulate the behaviour of increasingly large quantities of complex condensed matter systems. In the present paper, we present some preliminary results on the large scale three-dimensional lattice-Boltzmann simulation of binary immiscible fluid flows through a porous medium derived from digitised x-ray microtomographic data of Bentheimer sandstone, and from the study of the same fluids under shear. Simulations on such scales can benefit considerably from the use of computational steering and we describe our implementation of steering within the lattice-Boltzmann code, called LB3D, making use of the RealityGrid steering library. Our large scale simulations benefit from the new concept of capability computing, designed to prioritise the execution of big jobs on major supercomputing resources. The advent of persistent computational grids promises to provide an optimal environment in which to deploy these mesoscale simulation methods, which can exploit the distributed nature of compute, visualisation and storage resources to reach scientific results rapidly; we discuss our work on the grid-enablement of lattice-Boltzmann methods in this context.

physics.comp-ph↗

arXiv2003

Three-dimensional lattice-Boltzmann simulations of critical spinodal decomposition in binary immiscible fluids

We use a modified Shan-Chen, noiseless lattice-BGK model for binary immiscible, incompressible, athermal fluids in three dimensions to simulate the coarsening of domains following a deep quench below the spinodal point from a symmetric and homogeneous mixture into a two-phase configuration. We find the average domain size growing with time as $t^γ$, where $γ$ increases in the range $0.545 < γ< 0.717$, consistent with a crossover between diffusive $t^{1/3}$ and hydrodynamic viscous, $t^{1.0}$, behaviour. We find good collapse onto a single scaling function, yet the domain growth exponents differ from others' works' for similar values of the unique characteristic length and time that can be constructed out of the fluid's parameters. This rebuts claims of universality for the dynamical scaling hypothesis. At early times, we also find a crossover from $q^2$ to $q^4$ in the scaled structure function, which disappears when the dynamical scaling reasonably improves at later times. This excludes noise as the cause for a $q^2$ behaviour, as proposed by others. We also observe exponential temporal growth of the structure function during the initial stages of the dynamics and for wavenumbers less than a threshold value.

cond-mat.soft↗

arXiv2002

Galilean-Invariant Lattice-Boltzmann Models with H-Theorem

We demonstrate that the requirement of galilean invariance determines the choice of H function for a wide class of entropic lattice Boltzmann models for the incompressible Navier-Stokes equations. The required H function has the form of the Burg entropy for D=2, and of a Tsallis entropy with q=1-2/D for D>2, where D is the number of spatial dimensions. We use this observation to construct a fully explicit, unconditionally stable, galilean invariant, lattice-Boltzmann model for the incompressible Navier-Stokes equations, for which attainable Reynolds number is limited only by grid resolution.

cond-mat.stat-mech↗

arXiv2001

Three dimensional hydrodynamic lattice-gas simulations of domain growth and self-assembly in binary immiscible and ternary amphiphilic fluids

We simulate the dynamics of phase assembly in binary immiscible fluids and ternary microemulsions using a three-dimensional hydrodynamic lattice gas approach. For critical spinodal decomposition we perform the scaling analysis in reduced variables introduced by Jury et al. and Kendon et al. We find a late-stage scaling exponent consistent with the inertial regime. However, as observed with the previous lattice-gas model of Appert et al. our data does not fall in the same range of reduced length and time as that of Kendon et al. For off-critical binary spinodal decomposition we observe a reduction of the effective exponent with the volume fraction of the minority phase. However, the n=1/3 Lifshitz-Slyzov-Wagner droplet coalescence exponent is not observed. Adding a sufficient number of surfactant particles to a critical quench of binary immiscible fluids produces a ternary bicontinuous microemulsion. We observe a change in scaling behaviour from algebraic to logarithmic growth for amphiphilic fluids in which the domain growth is not arrested. For formation of a microemulsion where the domain growth is halted we find a stretched exponential growth law provides the best fit to the data.

cond-mat.soft↗

arXiv2001

Three dimensional hysdrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic flow through porous media

We report the results of a study of multiphase flow in porous media. A Darcy's law for steady multiphase flow was investigated for both binary and ternary amphiphilic flow. Linear flux-forcing relationships satisfying Onsager reciprocity were shown to be a good approximation of the simulation data. The dependence of the relative permeability coefficients on water saturation was investigated and showed good qualitative agreement with experimental data. Non-steady state invasion flows were investigated, with particular interest in the asymptotic residual oil saturation. The addition of surfactant to the invasive fluid was shown to significantly reduce the residual oil saturation.

cond-mat.soft↗

arXiv2001

Lattice-Boltzmann simulations of self-assembly of a binary amphiphilic fluid into ordered bicontinuous cubic and lamellar phases

We report the first results of our three-dimensional, mesoscopic, amphiphilic lattice-Boltzmann model, which has been used to simulate the dynamics of self-assembly of ordered cubic and lamellar phases in binary water-surfactant systems. Our results provide insight into the mechanism of ordering of such mesophases in terms of various molecular forces acting between water and surfactant molecules and the mechanism driving the transition from the lamellar to the cubic phase.

cond-mat.soft↗

arXiv2000

A lattice-Boltzmann model for interacting amphiphilic fluids

We develop our recently proposed lattice-Boltzmann method for the non-equilibrium dynamics of amphiphilic fluids (Chen, Boghosian, Coveney and Nekovee, Proc. Roy. Soc. London A, 456, 1431 (2000).) Our method maintains an orientational degree of freedom for the amphiphilic species and models fluid interactions at a microscopic level by introducing self-consistent mean-field forces between the particles into the lattice-Boltzmann dynamics, in a way that is consistent with kinetic theory. We present the results of extensive simulations in two dimensions which demonstrate the ability of our model to capture the correct phenomenology of binary and ternary amphiphilic fluids.

cond-mat.soft↗

arXiv2000

Two-dimensional hydrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic fluid flow through porous media

The behaviour of two dimensional binary and ternary amphiphilic fluids under flow conditions is investigated using a hydrodynamic lattice gas model. After the validation of the model in simple cases (Poiseuille flow, Darcy's law for single component fluids), attention is focussed on the properties of binary immiscible fluids in porous media. An extension of Darcy's law which explicitly admits a viscous coupling between the fluids is verified, and evidence of capillary effects are described. The influence of a third component, namely surfactant, is studied in the same context. Invasion simulations have also been performed. The effect of the applied force on the invasion process is reported. As the forcing level increases, the invasion process becomes faster and the residual oil saturation decreases. The introduction of surfactant in the invading phase during imbibition produces new phenomena, including emulsification and micellisation. At very low fluid forcing levels, this leads to the production of a low-resistance gel, which then slows down the progress of the invading fluid. At long times (beyond the water percolation threshold), the concentration of remaining oil within the porous medium is lowered by the action of surfactant, thus enhancing oil recovery. On the other hand, the introduction of surfactant in the invading phase during drainage simulations slows down the invasion process -- the invading fluid takes a more tortuous path to invade the porous medium -- and reduces the oil recovery (the residual oil saturation increases).

cond-mat.soft↗