arXiv subjects

P. V. Coveney

Publications and source records attributed to P. V. Coveney.

At least 19 recordsLinked to original sources

arXiv2022

Development and performance of a HemeLB GPU code for human-scale blood flow simulation

In recent years, it has become increasingly common for high performance computers (HPC) to possess some level of heterogeneous architecture - typically in the form of GPU accelerators. In some machines these are isolated within a dedicated partition, whilst in others they are integral to all compute nodes - often with multiple GPUs per node - and provide the majority of a machine's compute performance. In light of this trend, it is becoming essential that codes deployed on HPC are updated to execute on accelerator hardware. In this paper we introduce a GPU implementation of the 3D blood flow simulation code HemeLB that has been developed using CUDA C++. We demonstrate how taking advantage of NVIDIA GPU hardware can achieve significant performance improvements compared to the equivalent CPU only code on which it has been built whilst retaining the excellent strong scaling characteristics that have been repeatedly demonstrated by the CPU version. With HPC positioned on the brink of the exascale era, we use HemeLB as a motivation to provide a discussion on some of the challenges that many users will face when deploying their own applications on upcoming exascale machines.

cs.DC↗

arXiv2021

An efficient, localised approach for the simulation of elastic blood vessels using the lattice Boltzmann method

Many numerical studies of blood flow impose a rigid wall assumption due to the simplicity of its implementation compared to a full coupling to a solid mechanics model. In this paper, we present a localised method for incorporating the effects of elastic walls into blood flow simulations using the lattice Boltzmann method. We demonstrate that our approach is able to more accurately capture the flow behaviour expected in an elastic walled vessel than a rigid wall model and achieves this without a loss of computational performance. We also demonstrate that our approach can capture trends in wall shear stress distribution captured by fully coupled models in personalised vascular geometries.

physics.flu-dyn↗

arXiv2021

High fidelity blood flow in a patient-specific arteriovenous fistula

An arteriovenous fistula, created by artificially connecting segments of a patient's vasculature, is the preferred way to gain access to the bloodstream for kidney dialysis. The increasing power and availability of supercomputing infrastructure means that it is becoming more realistic to use simulations to help identify the best type and location of a fistula for a specific patient. We describe a 3D fistula model that uses the lattice Boltzmann method to simultaneously resolve blood flow in patient-specific arteries and veins. The simulations conducted here, comprising vasculatures of the whole forearm, demonstrate qualified validation against clinical data. Ongoing research to further encompass complex biophysics on realistic time scales will permit the use of human-scale physiological models for basic and clinical medicine.

physics.med-ph↗

arXiv2020

VECMAtk: A Scalable Verification, Validation and Uncertainty Quantification Toolkit for Scientific Simulations

We present the VECMA toolkit (VECMAtk), a flexible software environment for single and multiscale simulations that introduces directly applicable and reusable procedures for verification, validation (V&V), sensitivity analysis (SA) and uncertainty quantification (UQ). It enables users to verify key aspects of their applications, systematically compare and validate the simulation outputs against observational or benchmark data, and run simulations conveniently on any platform from the desktop to current multi-petascale computers. In this sequel to our paper on VECMAtk which we presented last year, we focus on a range of functional and performance improvements that we have introduced, cover newly introduced components, and applications examples from seven different domains such as conflict modelling and environmental sciences. We also present several implemented patterns for UQ/SA and V&V, and guide the reader through one example concerning COVID-19 modelling in detail.

cs.MS↗

arXiv2020

Towards Blood Flow in the Virtual Human: Efficient Self-Coupling of HemeLB

Many scientific and medical researchers are working towards the creation of a virtual human - a personalised digital copy of an individual - that will assist in a patient's diagnosis, treatment and recovery. The complex nature of living systems means that the development of this remains a major challenge. We describe progress in enabling the HemeLB lattice Boltzmann code to simulate 3D macroscopic blood flow on a full human scale. Significant developments in memory management and load balancing allow near linear scaling performance of the code on hundreds of thousands of computer cores. Integral to the construction of a virtual human, we also outline the implementation of a self-coupling strategy for HemeLB. This allows simultaneous simulation of arterial and venous vascular trees based on human-specific geometries.

physics.med-ph↗

arXiv2017

Scalable Quantum Simulation of Molecular Energies

We report the first electronic structure calculation performed on a quantum computer without exponentially costly precompilation. We use a programmable array of superconducting qubits to compute the energy surface of molecular hydrogen using two distinct quantum algorithms. First, we experimentally execute the unitary coupled cluster method using the variational quantum eigensolver. Our efficient implementation predicts the correct dissociation energy to within chemical accuracy of the numerically exact result. Second, we experimentally demonstrate the canonical quantum algorithm for chemistry, which consists of Trotterization and quantum phase estimation. We compare the experimental performance of these approaches to show clear evidence that the variational quantum eigensolver is robust to certain errors. This error tolerance inspires hope that variational quantum simulations of classically intractable molecules may be viable in the near future.

quant-ph↗

arXiv2012

Rheology of Lamellar Liquid Crystals in Two and Three Dimensions: A Simulation Study

We present large scale computer simulations of the nonlinear bulk rheology of lamellar phases (smectic liquid crystals) at moderate to large values of the shear rate (Peclet numbers 10-100), in both two and three dimensions. In two dimensions we find that modest shear rates align the system and stabilise an almost regular lamellar phase, but high shear rates induce the nucleation and proliferation of defects, which in steady state is balanced by the annihilation of defects of opposite sign. The critical shear rate at onset of this second regime is controlled by thermodynamic and kinetic parameters; we offer a scaling analysis that relates the critical shear rate to a critical "capillary number" involving those variables. Within the defect proliferation regime, the defects may be partially annealed by slowly decreasing the applied shear rate; this causes marked memory effects, and history-dependent rheology. Simulations in three dimensions show instead shear-induced ordering even at the highest shear rates studied here. This suggests that the critical shear rate shifts markedly upward on increasing dimensionality. This may in part reflect the reduced constraints on defect motion, allowing them to find and annihilate each other more easily. Residual edge defects in the 3D aligned state mostly point along the flow velocity, an orientation impossible in two dimensions.

cond-mat.soft↗

arXiv2012

Confined Cubic Blue Phases under Shear

We study the behaviour of confined cubic blue phases under shear flow via lattice Boltzmann simulations. We focus on the two experimentally observed phases, blue phase I and blue phase II. The disinclination network of blue phase II continuously breaks and reforms under shear, leading to an oscillatory stress response in time. The oscillations are only regular for very thin samples. For thicker samples, the shear leads to a "stick-slip" motion of part of the network along the vorticity direction. Blue phase I responds very differently: its defect network undergoes seemingly chaotic rearrangements under shear, irrespective of system size.

cond-mat.soft↗

arXiv2010

Formal Modelling of a Usable Identity Management Solution for Virtual Organisations

This paper attempts to accurately model security requirements for computational grid environments with particular focus on authentication. We introduce the Audited Credential Delegation (ACD) architecture as a solution to some of the virtual organisations identity management usability problems. The approach uses two complementary models: one is state based, described in Z notation, and the other is event-based, expressed in the Process Algebra of Hoare's Communicating Sequential Processes (CSP). The former will be used to capture the state of the WS and to model back-end operations on it whereas the latter will be used to model behavior, and in particular, front-end interactions and communications. The modelling helps to clearly and precisely understand functional and security requirements and provide a basis for verifying that the system meets its intended requirements.

cs.SE↗

arXiv2007

Prediction of the functional properties of ceramic materials from composition using artificial neural networks

We describe the development of artificial neural networks (ANN) for the prediction of the properties of ceramic materials. The ceramics studied here include polycrystalline, inorganic, non-metallic materials and are investigated on the basis of their dielectric and ionic properties. Dielectric materials are of interest in telecommunication applications where they are used in tuning and filtering equipment. Ionic and mixed conductors are the subjects of a concerted effort in the search for new materials that can be incorporated into efficient, clean electrochemical devices of interest in energy production and greenhouse gas reduction applications. Multi-layer perceptron ANNs are trained using the back-propagation algorithm and utilise data obtained from the literature to learn composition-property relationships between the inputs and outputs of the system. The trained networks use compositional information to predict the relative permittivity and oxygen diffusion properties of ceramic materials. The results show that ANNs are able to produce accurate predictions of the properties of these ceramic materials which can be used to develop materials suitable for use in telecommunication and energy production applications.

cond-mat.mtrl-sci↗

arXiv2007

A hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules

We present a hybrid computational method for simulating the dynamics of macromolecules in solution which couples a mesoscale solver for the fluctuating hydrodynamics (FH) equations with molecular dynamics to describe the macromolecule. The two models interact through a dissipative Stokesian term first introduced by Ahlrichs and Dünweg [J. Chem. Phys. {\bf 111}, 8225 (1999)]. We show that our method correctly captures the static and dynamical properties of polymer chains as predicted by the Zimm model. In particular, we show that the static conformations are best described when the ratio $\fracσ{b}=0.6$, where $σ$ is the Lennard-Jones length parameter and $b$ is the monomer bond length. We also find that the decay of the Rouse modes' autocorrelation function is better described with an analytical correction suggested by Ahlrichs and Dünweg. Our FH solver permits us to treat the fluid equation of state and transport parameters as direct simulation parameters. The expected independence of the chain dynamics on various choices of fluid equation of state and bulk viscosity is recovered, while excellent agreement is found for the temperature and shear viscosity dependence of centre of mass diffusion between simulation results and predictions of the Zimm model. We find that Zimm model approximations start to fail when the Schmidt number $Sc \lessapprox 30$. Finally, we investigate the importance of fluid fluctuations and show that using the preaveraged approximation for the hydrodynamic tensor leads to around 3% error in the diffusion coefficient for a polymer chain when the fluid discretization size is greater than $50Å$.

cond-mat.soft↗

arXiv2006

Fluctuating hydrodynamic modelling of fluids at the nanoscale

A good representation of mesoscopic fluids is required to combine with molecular simulations at larger length and time scales (De Fabritiis {\it et. al}, Phys. Rev. Lett. 97, 134501 (2006)). However, accurate computational models of the hydrodynamics of nanoscale molecular assemblies are lacking, at least in part because of the stochastic character of the underlying fluctuating hydrodynamic equations. Here we derive a finite volume discretization of the compressible isothermal fluctuating hydrodynamic equations over a regular grid in the Eulerian reference system. We apply it to fluids such as argon at arbitrary densities and water under ambient conditions. To that end, molecular dynamics simulations are used to derive the required fluid properties. The equilibrium state of the model is shown to be thermodynamically consistent and correctly reproduces linear hydrodynamics including relaxation of sound and shear modes. We also consider non-equilibrium states involving diffusion and convection in cavities with no-slip boundary conditions.

physics.flu-dyn↗

arXiv2006

The Application Hosting Environment: Lightweight Middleware for Grid-Based Computational Science

Grid computing is distributed computing performed transparently across multiple administrative domains. Grid middleware, which is meant to enable access to grid resources, is currently widely seen as being too heavyweight and, in consequence, unwieldy for general scientific use. Its heavyweight nature, especially on the client-side, has severely restricted the uptake of grid technology by computational scientists. In this paper, we describe the Application Hosting Environment (AHE) which we have developed to address some of these problems. The AHE is a lightweight, easily deployable environment designed to allow the scientist to quickly and easily run legacy applications on distributed grid resources. It provides a higher level abstraction of a grid than is offered by existing grid middleware schemes such as the Globus Toolkit. As a result the computational scientist does not need to know the details of any particular underlying grid middleware and is isolated from any changes to it on the distributed resources. The functionality provided by the AHE is `application-centric': applications are exposed as web services with a well-defined standards-compliant interface. This allows the computational scientist to start and manage application instances on a grid in a transparent manner, thus greatly simplifying the user experience. We describe how a range of computational science codes have been hosted within the AHE and how the design of the AHE allows us to implement complex workflows for deployment on grid infrastructure.

physics.comp-ph↗

arXiv2006

Multiscale modelling of liquids with molecular specificity

The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the full molecular nature of the system where it is of interest and coarse-graining it elsewhere. This is made possible by coupling molecular dynamics with a mesoscopic description of realistic liquids based on Landau's fluctuating hydrodynamics. We show that our scheme correctly couples hydrodynamics and that fluctuations, at both the molecular and continuum levels, are thermodynamically consistent. Hybrid simulations of sound waves in bulk water and reflected by a lipid monolayer are presented as illustrations of the scheme.

physics.flu-dyn↗

arXiv2006

Coupled applications on distributed resources

Coupled models are set to become increasingly important in all aspects of science and engineering as tools with which to study complex systems in an integrated manner. Such coupled, hybrid simulations typically communicate data between the component models of which they are comprised relatively infrequently, and so a Grid is expected to present an ideal architecture on which to run them. In the present paper, we describe a simple, flexible and extensible architecture for a two-component hybrid molecular-continuum coupled model (hybrid MD). We discuss its deployment on distributed resources and the extensions to the RealityGrid computational-steering system to handle coupled models.

physics.comp-ph↗

arXiv2006

A stochastic Trotter integration scheme for dissipative particle dynamics

In this article we show in details the derivation of an integration scheme for the dissipative particle dynamic model (DPD) using the stochastic Trotter formula [De Fabritiis et al., Physica A, 361, 429 (2006)]. We explain some subtleties due to the stochastic character of the equations and exploit analyticity in some interesting parts of the dynamics. The DPD-Trotter integrator demonstrates the inexistence of spurious spatial correlations in the radial distribution function for an ideal gas equation of state. We also compare our numerical integrator to other available DPD integration schemes.

cond-mat.soft↗

arXiv2006

Emergence of rheological properties in lattice Boltzmann simulations of gyroid mesophases

We use a lattice Boltzmann (LB) kinetic scheme for modelling amphiphilic fluids that correctly predicts rheological effects in flow. No macroscopic parameters are included in the model. Instead, three-dimensional hydrodynamic and rheological effects are emergent from the underlying particulate conservation laws and interactions. We report evidence of shear thinning and viscoelastic flow for a self-assembled gyroid mesophase. This purely kinetic approach is of general importance for the modelling and simulation of complex fluid flows in situations when rheological properties cannot be predicted {\em a priori}.

cond-mat.soft↗

arXiv2005

Efficient numerical integrators for stochastic models

The efficient simulation of models defined in terms of stochastic differential equations (SDEs) depends critically on an efficient integration scheme. In this article, we investigate under which conditions the integration schemes for general SDEs can be derived using the Trotter expansion. It follows that, in the stochastic case, some care is required in splitting the stochastic generator. We test the Trotter integrators on an energy-conserving Brownian model and derive a new numerical scheme for dissipative particle dynamics. We find that the stochastic Trotter scheme provides a mathematically correct and easy-to-use method which should find wide applicability.

physics.comp-ph↗