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Peter V. Coveney

Publications and source records attributed to Peter V. Coveney.

At least 55 records · Page 3Linked to original sources

Ordering of Trotterization: Impact on Errors in Quantum Simulation of Electronic Structure

Trotter-Suzuki decompositions are frequently used in the quantum simulation of quantum chemistry. They transform the evolution operator into a form implementable on a quantum device, while incurring an error---the Trotter error. The Trotter error can be made arbitrarily small by increasing the Trotter number. However, this increases the length of the quantum circuits required, which may be impractical. It is therefore desirable to find methods of reducing the Trotter error through alternate means. The Trotter error is dependent on the order in which individual term unitaries are applied. Due to the factorial growth in the number of possible orderings with respect to the number of terms, finding an optimal strategy for ordering Trotter sequences is difficult. In this paper, we propose three ordering strategies, and assess their impact on the Trotter error incurred. Initially, we exhaustively examine the possible orderings for molecular hydrogen in a STO-3G basis. We demonstrate how the optimal ordering scheme depends on the compatibility graph of the Hamiltonian, and show how it varies with increasing bond length. We then use 44 molecular Hamiltonians to evaluate two strategies based on coloring their incompatibility graphs, while considering the properties of the obtained colorings. We find that the Trotter error for most systems involving heavy atoms, using a reference magnitude ordering, is less than 1 kcal/mol. Relative to this, the difference between ordering schemes can be substantial, being approximately on the order of millihartrees. The coloring-based ordering schemes are reasonably promising, however further work is required. Finally, we consider ordering strategies based on the norm of the Trotter error operator, including an iterative method for generating the new error operator terms added upon insertion of a term into an ordered Hamiltonian.

quant-ph↗

HEMELB Acceleration and Visualization for Cerebral Aneurysms

A weakness in the wall of a cerebral artery causing a dilation or ballooning of the blood vessel is known as a cerebral aneurysm. Optimal treatment requires fast and accurate diagnosis of the aneurysm. HemeLB is a fluid dynamics solver for complex geometries developed to provide neurosurgeons with information related to the flow of blood in and around aneurysms. On a cost efficient platform, HemeLB could be employed in hospitals to provide surgeons with the simulation results in real-time. In this work, we developed an improved version of HemeLB for GPU implementation and result visualization. A visualization platform for smooth interaction with end users is also presented. Finally, a comprehensive evaluation of this implementation is reported. The results demonstrate that the proposed implementation achieves a maximum performance of 15,168,964 site updates per second, and is capable of speeding up HemeLB for deployment in hospitals and clinical investigations.

physics.comp-ph↗

A comparison of the Bravyi-Kitaev and Jordan-Wigner transformations for the quantum simulation of quantum chemistry

The ability to perform classically intractable electronic structure calculations is often cited as one of the principal applications of quantum computing. A great deal of theoretical algorithmic development has been performed in support of this goal. Most techniques require a scheme for mapping electronic states and operations to states of and operations upon qubits. The two most commonly used techniques for this are the Jordan-Wigner transformation and the Bravyi-Kitaev transformation. However, comparisons of these schemes have previously been limited to individual small molecules. In this paper we discuss resource implications for the use of the Bravyi-Kitaev mapping scheme, specifically with regard to the number of quantum gates required for simulation. We consider both small systems which may be simulatable on near-future quantum devices, and systems sufficiently large for classical simulation to be intractable. We use 86 molecular systems to demonstrate that the use of the Bravyi-Kitaev transformation is typically at least approximately as efficient as the canonical Jordan-Wigner transformation, and results in substantially reduced gate count estimates when performing limited circuit optimisations.

quant-ph↗

Big Data: the End of the Scientific Method?

We argue that the boldest claims of Big Data are in need of revision and toning-down, in view of a few basic lessons learned from the science of complex systems. We point out that, once the most extravagant claims of Big Data are properly discarded, a synergistic merging of BD with big theory offers considerable potential to spawn a new scientific paradigm capable of overcoming some of the major barriers confronted by the modern scientific method originating with Galileo. These obstacles are due to the presence of nonlinearity, nonlocality and hyperdimensions which one encounters frequently in multiscale modelling.

cs.GL↗

Multiscale Computing in the Exascale Era

We expect that multiscale simulations will be one of the main high performance computing workloads in the exascale era. We propose multiscale computing patterns as a generic vehicle to realise load balanced, fault tolerant and energy aware high performance multiscale computing. Multiscale computing patterns should lead to a separation of concerns, whereby application developers can compose multiscale models and execute multiscale simulations, while pattern software realises optimized, fault tolerant and energy aware multiscale computing. We introduce three multiscale computing patterns, present an example of the extreme scaling pattern, and discuss our vision of how this may shape multiscale computing in the exascale era.

cs.DC↗

A Distributed Multi-agent Market Place for HPC Compute Cycle Resource Trading

Computer simulation is finding a role in an increasing number of scientific disciplines, concomitant with the rise in available computing power. Realizing this inevitably requires access to computational power beyond the desktop, making use of clusters, supercomputers, data repositories, networks and distributed aggregations of these resources. Accessing one such resource entails a number of usability and security problems; when multiple geographically distributed resources are involved, the difficulty is compounded. This presents the user with the problem of how to gain access to suitable resources to run their workloads as they need them. In this paper we present our solutions to this problem, a resource trading platform that allows users to purchase access to resources within a distributed e-infrastructure. We present the implementation of this Resource Allocation Market Place as a distributed multi-agent system, and show how it provides a highly flexible, efficient tool to schedule workflows across high performance computing resources.

cs.DC↗

An automated multiscale ensemble simulation approach for vascular blood flow

Cerebrovascular diseases such as brain aneurysms are a primary cause of adult disability. The flow dynamics in brain arteries, both during periods of rest and increased activity, are known to be a major factor in the risk of aneurysm formation and rupture. The precise relation is however still an open field of investigation. We present an automated ensemble simulation method for modelling cerebrovascular blood flow under a range of flow regimes. By automatically constructing and performing an ensemble of multiscale simulations, where we unidirectionally couple a 1D solver with a 3D lattice-Boltzmann code, we are able to model the blood flow in a patient artery over a range of flow regimes. We apply the method to a model of a middle cerebral artery, and find that this approach helps us to fine-tune our modelling techniques, and opens up new ways to investigate cerebrovascular flow properties.

cs.DC↗

Interface deformations affect the orientation transition of magnetic ellipsoidal particles adsorbed at fluid-fluid interfaces

Manufacturing new soft materials with specific optical, mechanical and magnetic properties is a significant challenge. Assembling and manipulating colloidal particles at fluid interfaces is a promising way to make such materials. We use lattice-Boltzmann simulations to investigate the response of magnetic ellipsoidal particles adsorbed at liquid-liquid interfaces to external magnetic fields. We provide further evidence for the first-order orientation phase transition predicted by Bresme and Faraudo [Journal of Physics: Condensed Matter 19 (2007), 375110]. We show that capillary interface deformations around the ellipsoidal particle significantly affect the tilt-angle of the particle for a given dipole-field strength, altering the properties of the orientation transition. We propose scaling laws governing this transition, and suggest how to use these deformations to facilitate particle assembly at fluid-fluid interfaces.

cond-mat.soft↗

Detachment Energies of Spheroidal Particles from Fluid-Fluid Interfaces

The energy required to detach a single particle from a fluid-fluid interface is an important parameter for designing certain soft materials, for example, emulsions stabilised by colloidal particles, colloidosomes designed for targeted drug delivery, and bio-sensors composed of magnetic particles adsorbed at interfaces. For a fixed particle volume, prolate and oblate spheroids attach more strongly to interfaces because they have larger particle-interface areas. Calculating the detachment energy of spheroids necessitates the difficult measurement of particle-liquid surface tensions, in contrast with spheres, where the contact angle suffices. We develop a simplified detachment energy model for spheroids which depends only on the particle aspect ratio and the height of the particle centre of mass above the fluid-fluid interface. We use lattice Boltzmann simulations to validate the model and provide quantitative evidence that the approach can be applied to simulate particle-stabilized emulsions, and highlight the experimental implications of this validation.

cond-mat.soft↗

Weighted decomposition in high-performance lattice-Boltzmann simulations: are some lattice sites more equal than others?

Obtaining a good load balance is a significant challenge in scaling up lattice-Boltzmann simulations of realistic sparse problems to the exascale. Here we analyze the effect of weighted decomposition on the performance of the HemeLB lattice-Boltzmann simulation environment, when applied to sparse domains. Prior to domain decomposition, we assign wall and in/outlet sites with increased weights which reflect their increased computational cost. We combine our weighted decomposition with a second optimization, which is to sort the lattice sites according to a space filling curve. We tested these strategies on a sparse bifurcation and very sparse aneurysm geometry, and find that using weights reduces calculation load imbalance by up to 85%, although the overall communication overhead is higher than some of our runs.

cs.DC↗

Assembling Ellipsoidal Particles at Fluid Interfaces using Switchable Dipolar Capillary Interactions

The fabrication of novel soft materials is an important scientific and technological challenge. We investigate the response of magnetic ellipsoidal particles adsorbed at fluid-fluid interfaces to external magnetic fields. By exploiting previously discovered first-order orientation phase transitions we show how to switch on and off dipolar capillary interactions between particles, leading to the formation of distinctive self-assembled structures and allowing dynamic control of the bottom-up fabrication of reconfigurable novel-structured materials

cond-mat.soft↗

Impact of blood rheology on wall shear stress in a model of the middle cerebral artery

Perturbations to the homeostatic distribution of mechanical forces exerted by blood on the endothelial layer have been correlated with vascular pathologies including intracranial aneurysms and atherosclerosis. Recent computational work suggests that in order to correctly characterise such forces, the shear-thinning properties of blood must be taken into account. To the best of our knowledge, these findings have never been compared against experimentally observed pathological thresholds. In the current work, we apply the three-band diagram (TBD) analysis due to Gizzi et al. to assess the impact of the choice of blood rheology model on a computational model of the right middle cerebral artery. Our results show that, in the model under study, the differences between the wall shear stress predicted by a Newtonian model and the well known Carreau-Yasuda generalized Newtonian model are only significant if the vascular pathology under study is associated with a pathological threshold in the range 0.94 Pa to 1.56 Pa, where the results of the TBD analysis of the rheology models considered differs. Otherwise, we observe no significant differences.

cs.CE↗

Computer simulations reveal complex distribution of haemodynamic forces in a mouse retina model of angiogenesis

There is currently limited understanding of the role played by haemodynamic forces on the processes governing vascular development. One of many obstacles to be overcome is being able to measure those forces, at the required resolution level, on vessels only a few micrometres thick. In the current paper, we present an in silico method for the computation of the haemodynamic forces experienced by murine retinal vasculature (a widely used vascular development animal model) beyond what is measurable experimentally. Our results show that it is possible to reconstruct high-resolution three-dimensional geometrical models directly from samples of retinal vasculature and that the lattice-Boltzmann algorithm can be used to obtain accurate estimates of the haemodynamics in these domains. We generate flow models from samples obtained at postnatal days (P) 5 and 6. Our simulations show important differences between the flow patterns recovered in both cases, including observations of regression occurring in areas where wall shear stress gradients exist. We propose two possible mechanisms to account for the observed increase in velocity and wall shear stress between P5 and P6: i) the measured reduction in typical vessel diameter between both time points, ii) the reduction in network density triggered by the pruning process. The methodology developed herein is applicable to other biomedical domains where microvasculature can be imaged but experimental flow measurements are unavailable or difficult to obtain.

cs.CE↗

Deformability-based red blood cell separation in deterministic lateral displacement devices - a simulation study

We show, via three-dimensional immersed-boundary-finite-element-lattice-Boltzmann simulations, that deformability-based red blood cell (RBC) separation in deterministic lateral displacement (DLD) devices is possible. This is due to the deformability-dependent lateral extension of RBCs and enables us to predict a priori which RBCs will be displaced in a given DLD geometry. Several diseases affect the deformability of human cells. Malaria-infected RBCs or sickle cells, for example, tend to become stiffer than their healthy counterparts. It is therefore desirable to design microfluidic devices which can detect those diseases based on the cells' deformability fingerprint, rather than preparing samples using expensive and time-consuming biochemical preparation steps. Our findings should be helpful in the development of new methods for sorting cells and particles by deformability.

cond-mat.soft↗

Distributed Multiscale Computing with MUSCLE 2, the Multiscale Coupling Library and Environment

We present the Multiscale Coupling Library and Environment: MUSCLE 2. This multiscale component-based execution environment has a simple to use Java, C++, C, Python and Fortran API, compatible with MPI, OpenMP and threading codes. We demonstrate its local and distributed computing capabilities and compare its performance to MUSCLE 1, file copy, MPI, MPWide, and GridFTP. The local throughput of MPI is about two times higher, so very tightly coupled code should use MPI as a single submodel of MUSCLE 2; the distributed performance of GridFTP is lower, especially for small messages. We test the performance of a canal system model with MUSCLE 2, where it introduces an overhead as small as 5% compared to MPI.

cs.DC↗

Rheology of Cubic Blue Phases

We study the behaviour of cubic blue phases under shear flow via lattice Boltzmann simulations. We focus on the two experimentally observed phases, Blue Phase I (BPI) and Blue Phase II (BPII). The disclination network of Blue Phase II continuously breaks and reforms under steady shear, leading to an oscillatory stress response in time. For larger shear rates, the structure breaks up into a Grandjean texture with a cholesteric helix lying along the flow gradient direction. Blue Phase I leads to a very different response. Here, oscillations are only possible for intermediate shear rates -- very slow flow causes a transition of the initially ordered structure into an amorphous network with an apparent yield stress. Larger shear rates lead to another amorphous state with different structure of the defect network. For even larger flow rates the same break-up into a Grandjean texture as for Blue Phase II is observed. At the highest imposed flow rates both cubic blue phases adopt a flow-aligned nematic state. Our results provide the first theoretical investigation of sheared blue phases in large systems, and are relevant to understanding the bulk rheology of these materials.

cond-mat.soft↗

Choice of boundary condition for lattice-Boltzmann simulation of moderate Reynolds number flow in complex domains

Modeling blood flow in larger vessels using lattice-Boltzmann methods comes with a challenging set of constraints: a complex geometry with walls and inlet/outlets at arbitrary orientations with respect to the lattice, intermediate Reynolds number, and unsteady flow. Simple bounce-back is one of the most commonly used, simplest, and most computationally efficient boundary conditions, but many others have been proposed. We implement three other methods applicable to complex geometries (Guo, Zheng and Shi, Phys Fluids (2002); Bouzdi, Firdaouss and Lallemand, Phys. Fluids (2001); Junk and Yang Phys. Rev. E (2005)) in our open-source application \HemeLB{}. We use these to simulate Poiseuille and Womersley flows in a cylindrical pipe with an arbitrary orientation at physiologically relevant Reynolds (1--300) and Womersley (4--12) numbers and steady flow in a curved pipe at relevant Dean number (100--200) and compare the accuracy to analytical solutions. We find that both the Bouzidi-Firdaouss-Lallemand and Guo-Zheng-Shi methods give second-order convergence in space while simple bounce-back degrades to first order. The BFL method appears to perform better than GZS in unsteady flows and is significantly less computationally expensive. The Junk-Yang method shows poor stability at larger Reynolds number and so cannot be recommended here. The choice of collision operator (lattice Bhatnagar-Gross-Krook vs.\ multiple relaxation time) and velocity set (D3Q15 vs.\ D3Q19 vs.\ D3Q27) does not significantly affect the accuracy in the problems studied.

physics.comp-ph↗

Survey of Multiscale and Multiphysics Applications and Communities

Multiscale and multiphysics applications are now commonplace, and many researchers focus on combining existing models to construct combined multiscale models. Here we present a concise review of multiscale applications and their source communities. We investigate the prevalence of multiscale projects in the EU and the US, review a range of coupling toolkits they use to construct multiscale models and identify areas where collaboration between disciplines could be particularly beneficial. We conclude that multiscale computing has become increasingly popular in recent years, that different communities adopt very different approaches to constructing multiscale simulations, and that simulations on a length scale of a few metres and a time scale of a few hours can be found in many of the multiscale research domains. Communities may receive additional benefit from sharing methods that are geared towards these scales.

cs.OH↗