Atualmente, existe uma variedade de arquiteturas disponíveis não apenas para a indústria, mas também para consumidores finais. Processadores multi-core tradicionais, GPUs, aceleradores, como o Xeon Phi, ou até mesmo processadores orientados para eficiência energética, como a família ARM, apresentam características arquiteturais muito diferentes. Essa ampla gama de características representa um desafio para os desenvolvedores de aplicações. Os desenvolvedores devem lidar com diferentes conjuntos de instruções, hierarquias de memória, ou até mesmo diferentes paradigmas de programação ao programar para essas arquiteturas. Para otimizar uma aplicação, é importante ter uma compreensão profunda de como ela se comporta em diferentes arquiteturas. Os trabalhos relacionados provaram ter uma ampla variedade de soluções. A maioria deles se concentrou em melhorar apenas o desempenho da memória. Outros se concentram no balanceamento de carga, na vetorização e no mapeamento de threads e dados, mas os realizam separadamente, perdendo oportunidades de otimização. Nesta dissertação de mestrado, foram propostas várias técnicas de otimização para melhorar o desempenho de uma aplicação de exploração sísmica real fornecida pela Petrobras, uma empresa multinacional do setor de petróleo. Os experimentos mostram que loop interchange é uma técnica útil para melhorar o desempenho de diferentes níveis de memória cache, melhorando o desempenho em até 5,3 e 3,9 nas arquiteturas Intel Broadwell e Intel Knights Landing, respectivamente. Ao alterar o código para ativar a vetorização, o desempenho foi aumentado em até 1,4 e 6,5 . O balanceamento de carga melhorou o desempenho em até 1,1 no Knights Landing. Técnicas de mapeamento de threads e dados também foram avaliadas, com uma melhora de desempenho de até 1,6 e 4,4 . O ganho de desempenho do Broadwell foi de 22,7 e do Knights Landing de 56,7 em comparação com uma versão sem otimizações, mas, no final, o Broadwell foi 1,2 mais rápido que o Knights Landing. / Nowadays, there are several different architectures available not only for the industry but also for final consumers. Traditional multi-core processors, GPUs, accelerators such as the Xeon Phi, or even energy efficiency-driven processors such as the ARM family, present very different architectural characteristics. This wide range of characteristics presents a challenge for the developers of applications. Developers must deal with different instruction sets, memory hierarchies, or even different programming paradigms when programming for these architectures. To optimize an application, it is important to have a deep understanding of how it behaves on different architectures. Related work proved to have a wide variety of solutions. Most of then focused on improving only memory performance. Others focus on load balancing, vectorization, and thread and data mapping, but perform them separately, losing optimization opportunities. In this master thesis, we propose several optimization techniques to improve the performance of a real-world seismic exploration application provided by Petrobras, a multinational corporation in the petroleum industry. In our experiments, we show that loop interchange is a useful technique to improve the performance of different cache memory levels, improving the performance by up to 5.3 and 3.9 on the Intel Broadwell and Intel Knights Landing architectures, respectively. By changing the code to enable vectorization, performance was increased by up to 1.4 and 6.5 . Load Balancing improved the performance by up to 1.1 on Knights Landing. Thread and data mapping techniques were also evaluated, with a performance improvement of up to 1.6 and 4.4 . We also compared the best version of each architecture and showed that we were able to improve the performance of Broadwell by 22.7 and Knights Landing by 56.7 compared to a naive version, but, in the end, Broadwell was 1.2 faster than Knights Landing.

Yeung Man Yi = 多體量子系統問題 / 楊曼儀. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves [247-249]). / Text in English; abstracts in English and Chinese. / Yeung Man Yi = Duo ti liang zi xi tong wen ti / Yang Manyi. / Abstract --- p.i / Acknowledgment --- p.iii / Chapter I --- Computational Quantum Mechanics and Its Applications / 電算量子力學及其應用 --- p.1 / Chapter 1 --- Theoretical Methodology of Electronic Structures: Ab Initio Molecular Orbital Theory --- p.2 / Chapter 1.1 --- Molecular Hamiltonian --- p.2 / Chapter 1.2 --- Hartree Products --- p.5 / Chapter 1.3 --- Slater Determinants and Pauli Exclusion Principle --- p.6 / Chapter 1.4 --- Expansion of Total Electronic Energy in terms of Integrals over MOs --- p.8 / Chapter 1.5 --- Derivation of the Hartree-Fock Equations --- p.11 / Chapter 1.6 --- Orbital Energies and the Koopmans' Theorem --- p.14 / Chapter 1.7 --- AO Basic Sets --- p.17 / Chapter 1.7.1 --- Slater-Type Orbitals --- p.18 / Chapter 1.7.2 --- Gaussian Functions --- p.18 / Chapter 1.8 --- Self-Consistent Field Calculation --- p.19 / Chapter 1.9 --- Hartree-Fock Limit --- p.20 / Chapter 1.10 --- Electron Correlation --- p.20 / Chapter 1.10.1 --- Configuration Interaction --- p.20 / Chapter 1.10.2 --- Density Functional Theory --- p.21 / Chapter 2 --- Theoretical Investigation of Organic Light Emitting Molecules --- p.29 / Chapter 2.1 --- Introduction --- p.29 / Chapter 2.2 --- Methodology --- p.31 / Chapter 2.2.1 --- Theoretical Methodology --- p.31 / Chapter 2.2.2 --- Computational Methodology --- p.35 / Chapter 2.3 --- ADN series --- p.35 / Chapter 2.3.1 --- Molecular Structure --- p.36 / Chapter 2.3.2 --- Electronic Structure --- p.49 / Chapter 2.3.3 --- Absorption and Emission Energy --- p.55 / Chapter 2.3.4 --- Reorganization Energy --- p.56 / Chapter 2.3.5 --- Mobility --- p.57 / Chapter 2.3.6 --- Summary on ADN series --- p.66 / Chapter 2.4 --- XOT series --- p.67 / Chapter 2.4.1 --- Molecular Structure --- p.68 / Chapter 2.4.2 --- Electronic Structure --- p.89 / Chapter 2.4.3 --- Absorption and Emission Energy --- p.96 / Chapter 2.4.4 --- Reorganization Energy and Mobility --- p.98 / Chapter 2.4.5 --- Summary on XOT series --- p.100 / Chapter 2.5 --- KPA series --- p.102 / Chapter 2.5.1 --- Molecular Structure --- p.102 / Chapter 2.5.2 --- Electronic Structure --- p.123 / Chapter 2.5.3 --- Absorption and Emission Energy --- p.131 / Chapter 2.5.4 --- Reorganization Energy and Mobility --- p.131 / Chapter 2.5.5 --- Summary on KPA series --- p.133 / Chapter 2.6 --- NPA series --- p.136 / Chapter 2.6.1 --- Molecular Structure --- p.136 / Chapter 2.6.2 --- Electronic Structure --- p.160 / Chapter 2.6.3 --- Absorption and Emission Energy --- p.166 / Chapter 2.6.4 --- Reorganization Energy and Mobility --- p.167 / Chapter 2.6.5 --- Summary on NPA series --- p.169 / Chapter II --- Analytical Studies of Polarons and the Electron-Phonon Interaction / 極子與電子一聲子相互作用的解析研究 --- p.172 / Chapter 3 --- Study on Holstein Model Using Variational Approximation --- p.173 / Chapter 3.1 --- Holstein Hamiltonian --- p.173 / Chapter 3.2 --- Variational Transformation --- p.175 / Chapter 3.2.1 --- Lang-Firsov Transformation --- p.175 / Chapter 3.2.2 --- Squeezing Transformation --- p.177 / Chapter 3.3 --- Energy and Static Correlation Functions --- p.179 / Chapter 4 --- Study on Holstein Model Using Coupled-Cluster Method --- p.193 / Chapter 4.1 --- Approximation in the Coupled-Cluster Method --- p.193 / Chapter 4.2 --- Approach 1 --- p.195 / Chapter 4.2.1 --- The Zeroth and the First Levels --- p.195 / Chapter 4.2.2 --- Energies and Static Correlation Functions --- p.196 / Chapter 4.3 --- Approach 2 --- p.206 / Chapter 4.3.1 --- The Zeroth and the First Levels --- p.206 / Chapter 4.3.2 --- Energies and Static Correlation Functions --- p.210 / Chapter 4.4 --- Approach 3 --- p.225 / Chapter 4.4.1 --- The Zeroth and the First Levels --- p.226 / Chapter 4.4.2 --- Energies and Static Correlation Functions --- p.228 / Chapter 4.5 --- Comparison with the Variational Method --- p.243

One of the central tasks for biomolecular modeling is to develop accurate and computationally cheap methods. In this dissertation, we present the development of a brand new polarizable force field—Polarizable Simulations with Second order Interaction Model (POSSIM) involving electrostatic polarization. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second-order approximation of the full-scale induced point dipole polarization formalism. POSSIM force field has been extended to include parameters for small molecules serving as models for peptide and protein side-chains. Parameters have been fitted to permit reproducing many-body energies, gas-phase dimerization energies and geometries and liquid-phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters have been employed in further development of the POSSIM fast polarizable force field for proteins. The POSSIM framework has been expanded to include a complete polarizable force field for proteins. Most of the parameter fitting was done to high-level quantum mechanical data. Conformational geometries and energies for dipeptides have been reproduced within average errors of ca. 0.5 kcal/mol for energies of the conformers (for the electrostatically neutral residues) and 9.7º for key dihedral angles. We have also validated this force field by simulating an elastin-like polypeptide GVG(VPGVG)3 in aqueous solution. Elastin-like peptides with the (VPGVG)n motif are known to exhibit anomalous behavior of their radius of gyration that increases when temperature is lowered (the so called inverse temperature transition). We have simulated the system with the OPLS-AA and POSSIM force fields and demonstrated that our newly developed polarizable POSSIM parameters permit to capture the experimentally observed decrease of the radius of gyration with increasing temperature, while the fixed-charges OPLS-AA ones do not. Furthermore, our fitting of the force field parameters for the peptides and proteins has been streamlined compared with the previous generation of the complete polarizable force field and relied more on transferability of parameters for non-bonded interactions (including the electrostatic component). The resulting deviations from the quantum mechanical data are similar to those achieved with the previous generation, thus the technique is robust and the parameters are transferable. At the same time, the number of parameters used in this work was noticeably smaller than that of the previous generation of our complete polarizable force field for proteins, thus the transferability of this set can be expected to be greater and the danger of force field fitting artifacts is lower. Therefore, we believe that this force field can be successfully applied in a wide variety of applications to proteins and protein-ligand complexes.

Molecular simulation is applied to understanding the behaviour of alkane liquids with the eventual goal of being able to predict the viscosity of an arbitrary alkane mixture from first principles. Such prediction would have numerous scientific and industrial applications, as alkanes are the largest component of fuels, lubricants, and waxes; furthermore, they form the backbones of a myriad of organic compounds. This dissertation details the creation of a potential, a model for how the atoms and molecules in the simulation interact, based on a systematic approximation of the quantum mechanical potential energy surface using machine learning. This approximation has the advantage of producing forces and energies of nearly quantum mechanical accuracy at a tiny fraction of the usual cost. It enables accurate simulation of the large systems and long timescales required for accurate prediction of properties such as the density and viscosity. The approach is developed and tested on methane, the simplest alkane, and investigations are made into potentials for longer, more complex alkanes. The results show that the approach is promising and should be pursued further to create an accurate machine learning potential for the alkanes. It could even be extended to more complex molecular liquids in the future.

No description available.

O presente trabalho apresenta o estudo das propriedades da condensação de Bose-Einstein e da superfluidez em um sistema bosônico disposto em um arranjo unidimensional de potenciais periódicos em formato de anel. O Hamiltoniano efetivo usual em termos dos operadores de campo é implementado na representação construída em termos das funções de Bloch da primeira banda e o problema é resolvido por meio da sua diagonalização através de métodos numéricos. No limite de hopping pequeno, este modelo é essencialmente equivalente à representação usual do modelo de Bose-Hubbard, mas incorpora efeitos adicionais através das energias de Bloch de partícula independente e dos elementos da matriz de dois corpos na situação em que o hopping é grande [19]. Através da inclusão de rotação no sistema, as energias de partícula independente são forçadas a depender da velocidade angular. Isto implica, correspondentemente, uma dependência da velocidade angular nas funções de onda de partícula independente e nos resultados de muitos corpos obtidos através da diagonalização do Hamiltoniano. Com o objetivo de estudar a superfluidez, o critério de dois fluidos é empregado e através de resultados numéricos obtêm-se a variação da fração de superfluido com o quadrado da velocidade angular. Ainda, considera-se aqui uma expressão perturbativa para o parâmetro inercial do sistema expresso em termos das excitações do sistema sem rotação, o que permite relacionar as energias do sistema com rotação com aquelas do sistema sem rotação. Isto é particularmente interessante para obter a fração de superfluido em termos da informação espectral do sistema sem rotação. Resultados semelhantes podem ser encontrados através da definição de superfluido baseada na resposta do sistema a uma variação de fase, imposta através de condições de contorno torcidas [30, 33], mas com a diferença de que os desenvolvimentos aqui não fazem uso da hipótese do modo condensado. De maneira geral, os resultados numéricos obtidos indicam, que pelo menos para este sistema, as frações de superfluido e condensado são quantidades sem relação direta, sugerindo então que mesmo para sistemas gasosos diluídos a idéia de que a superfluidez é uma consequência da condensação de Bose-Einstein deve ser considerada com mais cuidado. / In this work we study the properties of Bose-Einstein condensation and superfluidity in a finite bosonic system in a 1-dimensional ring with a periodic potential under rotation. The usual field effective Hamiltonian is implemented in a representation constructed in terms of the first band Bloch functions and the problem is solved by numeric diagonalization. In the limit of small hopping, this model is essentially equivalent to the quasi-momentum representation of the usual Bose-Hubbard model but incorporates additional effects via Bloch single particle energies and two-body matrix elements in the case of large hopping [19]. By including rotation in the system we force the single particle energies to be a function of the angular velocity. This implies a corresponding angular velocity dependence of the single particle wavefunctions and many-body diagonalization results. In order to study superfluidity, we consider the two fluid criterion. Numerical results for the superfluid fraction involving the change of in rinsic ground state energy with the square of the angular velocity are obtained. We also consider a perturbative expression for the system inertial parameter expressed in terms of the excitation spectrum of the non rotating system, which enables us to relate the energies in the rotating system to the ones in the system without rotation. This is particularly interesting for obtaining superfluid fraction in terms of spectral information of the non rotating system. Similar results can be found by using the definition of superfluid fraction based on the response of the system to a phase variation imposed by means of twisted boundary conditions [30, 33], but with the difference that our developments do not assume the hypothesis of a condensate mode. Our numerical results indicate that in this system condensate and superfluid fractions are quite unrelated in terms of parameter values, indicating that even for dilute gases the concept that superfluidity is a consequence of Bose-Einstein condensation should be considered more carefully.

Estudamos as excitações de baixa energia, presentes em um gás de bosons homogêneo, de spin nulo, sujeitos a uma interação de dois corpos repulsiva e a temperatura zero, utilizando a aproximação gaussiana, que consiste num caso particular de aproximação de campo médio. As equações dinâmicas resultantes foram linearizadas ao redor da solução estática de Hartree-Fock-Bogoliubov. Obtivemos uma banda contínua e limitada inferiormente, além de um segundo ramo discreto, que define um limite inferior para as excitações e que, ao contrário do resultado proveniente do tratamento de Hartree-Fock-Bogoliubov, possui um comportamento linear sem gap com respeito ao momento da excitação no limite de grandes comprimentos de onda, ou seja, possui uma equação de dispersão do tipo fônon. Discutimos também a forma através da qual é possível gerar desvios do equilíbrio, vinculados aos estados excitados, e concluímos haver restrições sobre os possíveis desvios das grandezas características em campo médio gaussiano, quando tais desvios são gerados por transformações infinitesimais unitárias de um corpo tomadas até primeira ordem. / We study low-lying excitations of a spinless, homogeneous bose gas, with repulsive interaction, at zero temperature, in terms of a gaussian mean field approximation. The dynamical equations of this approximation have been linearized in small displacements from the well known static Hartree-Fock-Bogoliubov solution. We obtain a gapped continous band of excitations above a discrete branch with phonon behavior at large wavelengths. We also discuss the allowed forms of excitations and conclude that restrictions exist for the allowed deviations of the general set of gaussian mean field parameters, when they are generated in first orders by infinitesimal unitary transformations.

Cette étude est motivée par les besoins réels de calcul dans la physique des réacteurs. Notre objectif est de concevoir les algorithmes parallèles, y compris en proposant efficaces noyaux algébriques linéaires et méthodes numériques parallèles.Dans un environnement many-cœurs en mémoire partagée tel que le système Intel Many Integrated Core (MIC), la parallélisation efficace d'algorithmes est obtenue en termes de parallélisme des tâches à grain fin et parallélisme de données. Pour la programmation des tâches, deux principales stratégies, le partage du travail et vol de travail ont été étudiées. A des fins de généralité et de réutilisation, nous utilisons des interfaces de programmation parallèle standard, comme OpenMP, Cilk/Cilk+ et TBB. Pour vectoriser les tâches, les outils disponibles incluent Cilk+ array notation, pragmas SIMD, et les fonctions intrinsèques. Nous avons évalué ces techniques et proposé un noyau efficace de multiplication matrice-vecteur dense. Pour faire face à une situation plus complexe, nous proposons d'utiliser le modèle hybride MPI/OpenMP pour la mise en œuvre de noyau multiplication matrice-vecteur creux. Nous avons également conçu un modèle de performance pour modéliser les performances sur MICs et ainsi guider l'optimisation. En ce qui concerne la résolution de systèmes linéaires, nous avons proposé un solveur parallèle évolutif issue de méthodes Monte Carlo. Cette méthode présente un degré de parallélisme abondant, qui s’adapte bien à l'architecture multi-coeurs. Pour répondre à certains des goulots d'étranglement fondamentaux de ce solveur, nous proposons un modèle d'exécution basée sur les tâches qui résout complètement ces problèmes. / This study is driven by the real computational needs coming from different fields of reactor physics, such as neutronics or thermal hydraulics, where the eigenvalue problem and resolution of linear system are the key challenges that consume substantial computing resources. In this context, our objective is to design and improve the parallel computing techniques, including proposing efficient linear algebraic kernels and parallel numerical methods. In a shared-memory environment such as the Intel Many Integrated Core (MIC) system, the parallelization of an algorithm is achieved in terms of fine-grained task parallelism and data parallelism. For scheduling the tasks, two main policies, the work-sharing and work-stealing was studied. For the purpose of generality and reusability, we use common parallel programming interfaces, such as OpenMP, Cilk/Cilk+, and TBB. For vectorizing the task, the available tools include Cilk+ array notation, SIMD pragmas, and intrinsic functions. We evaluated these techniques and propose an efficient dense matrix-vector multiplication kernel. In order to tackle a more complicated situation, we propose to use hybrid MPI/OpenMP model for implementing sparse matrix-vector multiplication. We also designed a performance model for characterizing performance issues on MIC and guiding the optimization. As for solving the linear system, we derived a scalable parallel solver from the Monte Carlo method. Such method exhibits inherently abundant parallelism, which is a good fit for many-core architecture. To address some of the fundamental bottlenecks of this solver, we propose a task-based execution model that completely fixes the problems.

This thesis, divided into two parts, is concerned with the analysis of spectral and dynamical characteristics of certain quantum spin systems in the presence of either I) quenched disorder, or II) dynamical noise. In the first part, the quantum random energy model (QREM), a mean-field spin glass model with a many-body localisation transition, is studied. In Chapter 2, we attempt a diagrammatic perturbative analysis of the QREM from the ergodic side, proceeding by analogy to the single-particle theory of weak localisation. Whilst we are able to describe diffusion, the analogy breaks down and a description of the onset of localisation in terms of quantum corrections quickly becomes intractable. Some progress is possible by deriving a quantum kinetic equation, namely the relaxation of the one-spin reduced density matrix is determined, but this affords little insight and extension to two-spin quantities is difficult. We change our approach in Chapter 3, studying instead a stroboscopic version of the model using the formalism of quantum graphs. Here, an analytic evaluation of the form factor in the diagonal approximation is possible, which we find to be consistent with the universal random matrix theory (RMT) result in the ergodic regime. In Chapter 4, we replace the QREM's transverse field with a random kinetic term and present a diagrammatic calculation of the average density of states, exact in the large-N limit, and interpret the result in terms of the addition of freely independent random variables. In the second part, we turn our attention to noisy quantum spins. Chapter 5 is concerned with noninteracting spins coupled to a common stochastic field; correlations arising from the common noise relax only due to the spins' differing precession frequencies. Our key result is a mapping of the equation of motion of n-spin correlators onto the (integrable) non-Hermitian Richardson-Gaudin model, enabling exact calculation of the relaxation rate of correlations. The second problem, addressed in Chapter 6, is that of the dynamics of operator moments in a noisy Heisenberg model; qualitatively different behaviour is found depending on whether or not the noise conserves a component of spin. In the case of nonconserving noise, we report that the evolution of the second moment maps onto the Fredrickson-Andersen model - a kinetically constrained model originally introduced to describe the glass transition. This facilitates a rigorous study of operator spreading in a continuous-time model, providing a complementary viewpoint to recent investigations of random unitary circuits.

Estudamos as excitações de baixa energia, presentes em um gás de bosons homogêneo, de spin nulo, sujeitos a uma interação de dois corpos repulsiva e a temperatura zero, utilizando a aproximação gaussiana, que consiste num caso particular de aproximação de campo médio. As equações dinâmicas resultantes foram linearizadas ao redor da solução estática de Hartree-Fock-Bogoliubov. Obtivemos uma banda contínua e limitada inferiormente, além de um segundo ramo discreto, que define um limite inferior para as excitações e que, ao contrário do resultado proveniente do tratamento de Hartree-Fock-Bogoliubov, possui um comportamento linear sem gap com respeito ao momento da excitação no limite de grandes comprimentos de onda, ou seja, possui uma equação de dispersão do tipo fônon. Discutimos também a forma através da qual é possível gerar desvios do equilíbrio, vinculados aos estados excitados, e concluímos haver restrições sobre os possíveis desvios das grandezas características em campo médio gaussiano, quando tais desvios são gerados por transformações infinitesimais unitárias de um corpo tomadas até primeira ordem. / We study low-lying excitations of a spinless, homogeneous bose gas, with repulsive interaction, at zero temperature, in terms of a gaussian mean field approximation. The dynamical equations of this approximation have been linearized in small displacements from the well known static Hartree-Fock-Bogoliubov solution. We obtain a gapped continous band of excitations above a discrete branch with phonon behavior at large wavelengths. We also discuss the allowed forms of excitations and conclude that restrictions exist for the allowed deviations of the general set of gaussian mean field parameters, when they are generated in first orders by infinitesimal unitary transformations.