An implementation of the look-ahead Lanczos algorithm for non-Hermitian matrices, part 2

It is shown how the look-ahead Lanczos process (combined with a quasi-minimal residual QMR) approach) can be used to develop a robust black box solver for large sparse non-Hermitian linear systems. Details of an implementation of the resulting QMR algorithm are presented. It is demonstrated that the QMR method is closely related to the biconjugate gradient (BCG) algorithm; however, unlike BCG, the QMR algorithm has smooth convergence curves and good numerical properties. We report numerical experiments with our implementation of the look-ahead Lanczos algorithm, both for eigenvalue problem and linear systems. Also, program listings of FORTRAN implementations of the look-ahead algorithm and the QMR method are included

Development of a 3D Modal Neutron Code with the Finite Volume Method for the Diffusion and Discrete Ordinates Transport Equations. Application to Nuclear Safety Analyses

El principal objetivo de esta tesis es el desarrollo de un Método Modal para resolver dos ecuaciones: la Ecuación de la Difusión de Neutrones y la de las Ordenadas Discretas del Transporte de Neutrones. Además, este método está basado en el Método de Volúmenes Finitos para discretizar las variables espaciales. La solución de estas ecuaciones proporciona el flujo de neutrones, que está relacionado con la potencia que se produce en los reactores nucleares, por lo que es un factor fundamental para los Análisis de Seguridad Nuclear. Por una parte, la utilización del Método Modal está justificada para realizar análisis de inestabilidades en reactores. Por otra parte, el uso del Método de Volúmenes Finitos está justificado por la utilización de este método para resolver las ecuaciones termohidráulicas, que están fuertemente acopladas con la generación de energía en el combustible nuclear. En primer lugar, esta tesis incluye la definición de estas ecuaciones y los principales métodos utilizados para resolverlas. Además, se introducen los principales esquemas y características del Método de Volúmenes Finitos. También se describen los principales métodos numéricos para el Método Modal, que incluye tanto la solución de problemas de autovalores como la solución de Ecuaciones Diferenciales Ordinarias dependientes del tiempo. A continuación, se desarrollan varios algoritmos del Método de Volúmenes Finitos para el Estado Estacionario de la Ecuación de la Difusión de Neutrones. Se consigue desarrollar una formulación multigrupo, que permite resolver el problema de autovalores para cualquier número de grupos de energía, incluyendo términos de upscattering y de fisión en varios grupos de energía. Además, se desarrollan los algoritmos para realizar la computación en paralelo. La solución anterior es la condición inicial para resolver la Ecuación de Difusión de Neutrones dependiente del tiempo. En esta tesis se utiliza un Método Modal, que transforma el Sistema de Ecuaciones Diferenciales Ordinarias en uno de mucho menor tamaño, que se resuelve con el Método de la Matriz Exponencial. Además, se ha desarrollado un método rápido para estimar el flujo adjunto a partir del directo, ya que se necesita en el Método Modal. Por otra parte, se ha desarrollado un algoritmo que resuelve el problema de autovalores de la Ecuación del Transporte de Neutrones. Este algoritmo es para la formulación de Ordenadas Discretas y el Método de Volúmenes Finitos. En concreto, se han aplicado dos tipos de cuadraturas para las Ordenadas Discretas y dos esquemas de interpolación para el Método de Volúmenes Finitos. Finalmente, se han aplicado estos métodos a diferentes tipos de reactores nucleares, incluyendo reactores comerciales. Se han evaluado los valores de la constante de multiplicación y de la potencia, ya que son las variables fundamentales en los Análisis de Seguridad Nuclear. Además, se ha realizado un análisis de sensibilidad de diferentes parámetros como la malla y métodos numéricos. En conclusión, se obtienen excelentes resultados, tanto en precisión como en coste computacional.The main objective of this thesis is the development of a Modal Method to solve two equations: the Neutron Diffusion Equation and the Discrete Ordinates Neutron Transport Equation. Moreover, this method uses the Finite Volume Method to discretize the spatial variables. The solution of these equations gives the neutron flux, which is related to the power produced in nuclear reactors; thus, the neutron flux is a paramount variable in Nuclear Safety Analyses. On the one hand, the use of Modal Methods is justified because one uses them to perform instability analyses in nuclear reactors. On the other hand, it is worth using the Finite Volume Method because one uses it to solve thermalhydraulic equations, which are strongly coupled with the energy generation in the nuclear fuel. First, this thesis defines the equations mentioned above and the main methods to solve these equations. Furthermore, the thesis describes the major schemes and features of the Finite Volume Method. In addition, the author also introduces the major methods used in the Modal Method, which include the methods used to solve the eigenvalue problem, as well as those used to solve the time dependent Ordinary Differential Equations. Next, the author develops several algorithms of the Finite Volume Method applied to the Steady State Neutron Diffusion Equation. In addition, the thesis includes an improvement of the multigroup formulation, which solves problems involving upscattering and fission terms in several energy groups. Moreover, the author optimizes the algorithms to do calculations with parallel computing. The previous solution is used as initial condition to solve the time dependent Neutron Diffusion Equation. The author uses a Modal Method to do so, which transforms the Ordinary Differential Equations System into a smaller system that is solved by using the Exponential Matrix Method. Furthermore, the author developed a computationally efficient method to estimate the adjoint flux from the forward one, because the Modal Method uses the adjoint flux. Additionally, the thesis also presents an algorithm to solve the eigenvalue problem of the Neutron Transport Equation. This algorithm uses the Discrete Ordinates formulation and the Finite Volume Method. In particular, the author uses two types of quadratures for the Discrete Ordinates and two interpolation schemes for the Finite Volume Method. Finally, the author tested the developed methods in different types of nuclear reactors, including commercial ones. The author checks the accuracy of the values of the crucial variables in Nuclear Safety Analyses, which are the multiplication factor and the power distribution. Furthermore, the thesis includes a sensitivity analysis of several parameters, such as the mesh and numerical methods. In conclusion, excellent results are reported in both accuracy and computational cost.El principal objectiu d'esta tesi és el desenvolupament d'un Mètode Modal per a resoldre dos equacions: l'Equació de Difusió de Neutrons i la de les Ordenades Discretes del Transport de Neutrons. A més a més, este mètode està basat en el Mètode de Volums Finits per a discretitzar les variables espacials. La solució d'estes equacions proporcionen el flux de neutrons, que està relacionat amb la potència que es produïx en els reactors nuclears; per tant, el flux de neutrons és un factor fonamental en els Anàlisis de Seguretat Nuclear. Per una banda, la utilització del Mètode Modal està justificada per a realitzar anàlisis d'inestabilitats en reactors. Per altra banda, l'ús del Mètode de Volums Finits està justificat per l'ús d'este mètode per a resoldre les equacions termohidràuliques, que estan fortament acoblades amb la generació d'energia en el combustible nuclear. En primer lloc, esta tesi inclou la definició d'estes equacions i els principals mètodes utilitzats per a resoldre-les. A més d'això, s'introduïxen els principals esquemes i característiques del Mètode de Volums Finits. Endemés, es descriuen els principals mètodes numèrics per al Mètode Modal, que inclou tant la solució del problema d'autovalors com la solució d'Equacions Diferencials Ordinàries dependents del temps. A continuació, es desenvolupa diversos algoritmes del Mètode de Volums Finits per a l'Estat Estacionari de l'Equació de Difusió de Neutrons. Es conseguix desenvolupar una formulació multigrup, que permetre resoldre el problema d'autovalors per a qualsevol nombre de grups d'energia, incloent termes d' upscattering i de fissió en diversos grups d'energia. A més a més, es desenvolupen els algoritmes per a realitzar la computació en paral·lel. La solució anterior és la condició inicial per a resoldre l'Equació de Difusió de Neutrons dependent del temps. En esta tesi s'utilitza un Mètode Modal, que transforma el Sistema d'Equacions Diferencials Ordinàries en un problema de menor tamany, que es resol amb el Mètode de la Matriu Exponencial. Endemés, s'ha desenvolupat un mètode ràpid per a estimar el flux adjunt a partir del directe, perquè es necessita en el Mètode Modal. Per altra banda, s'ha desenvolupat un algoritme que resol el problema d'autovalors de l'Equació de Transport de Neutrons. Este algoritme és per a la formulació d'Ordenades Discretes i el Mètode de Volums Finits. En concret, s'han aplicat dos tipos de quadratures per a les Ordenades Discretes i dos esquemes d'interpolació per al Mètode de Volums Finits. Finalment, s'han aplicat estos mètodes a diversos tipos de reactors nuclears, incloent reactors comercials. S'han avaluat els valor de la constat de multiplicació i de la potència, perquè són variables fonamentals en els Anàlisis de Seguretat Nuclear. Endemés, s'ha realitzat un anàlisi de sensibilitat de diversos paràmetres com la malla i mètodes numèrics. En conclusió, es conseguix obtenir excel·lents resultats, tant en precisió com en cost computacional.Bernal García, Á. (2018). Development of a 3D Modal Neutron Code with the Finite Volume Method for the Diffusion and Discrete Ordinates Transport Equations. Application to Nuclear Safety Analyses [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/112422TESI

A Parallel Iterative Method for Computing Molecular Absorption Spectra

We describe a fast parallel iterative method for computing molecular absorption spectra within TDDFT linear response and using the LCAO method. We use a local basis of "dominant products" to parametrize the space of orbital products that occur in the LCAO approach. In this basis, the dynamical polarizability is computed iteratively within an appropriate Krylov subspace. The iterative procedure uses a a matrix-free GMRES method to determine the (interacting) density response. The resulting code is about one order of magnitude faster than our previous full-matrix method. This acceleration makes the speed of our TDDFT code comparable with codes based on Casida's equation. The implementation of our method uses hybrid MPI and OpenMP parallelization in which load balancing and memory access are optimized. To validate our approach and to establish benchmarks, we compute spectra of large molecules on various types of parallel machines. The methods developed here are fairly general and we believe they will find useful applications in molecular physics/chemistry, even for problems that are beyond TDDFT, such as organic semiconductors, particularly in photovoltaics.Comment: 20 pages, 17 figures, 3 table

Algorithms for Large Scale Problems in Eigenvalue and Svd Computations and in Big Data Applications

As ”big data” has increasing influence on our daily life and research activities, it poses significant challenges on various research areas. Some applications often demand a fast solution of large, sparse eigenvalue and singular value problems; In other applications, extracting knowledge from large-scale data requires many techniques such as statistical calculations, data mining, and high performance computing. In this dissertation, we develop efficient and robust iterative methods and software for the computation of eigenvalue and singular values. We also develop practical numerical and data mining techniques to estimate the trace of a function of a large, sparse matrix and to detect in real-time blob-filaments in fusion plasma on extremely large parallel computers. In the first work, we propose a hybrid two stage SVD method for efficiently and accurately computing a few extreme singular triplets, especially the ones corresponding to the smallest singular values. The first stage achieves fast convergence while the second achieves the final accuracy. Furthermore, we develop a high-performance preconditioned SVD software based on the proposed method on top of the state-of-the-art eigensolver PRIMME. The method can be used with or without preconditioning, on parallel computers, and is superior to other state-of-the-art SVD methods in both efficiency and robustness. In the second study, we provide insights and develop practical algorithms to accomplish efficient and accurate computation of interior eigenpairs using refined projection techniques in non-Krylov iterative methods. By analyzing different implementations of the refined projection, we propose a new hybrid method to efficiently find interior eigenpairs without compromising accuracy. Our numerical experiments illustrate the efficiency and robustness of the proposed method. In the third work, we present a novel method to estimate the trace of matrix inverse that exploits the pattern correlation between the diagonal of the inverse of the matrix and that of some approximate inverse. We leverage various sampling and fitting techniques to fit the diagonal of the approximation to that of the inverse. Our method may serve as a standalone kernel for providing a fast trace estimate or as a variance reduction method for Monte Carlo in some cases. An extensive set of experiments demonstrate the potential of our method. In the fourth study, we provide first results on applying outlier detection techniques to effectively tackle the fusion blob detection problem on extremely large parallel machines. We present a real-time region outlier detection algorithm to efficiently find and track blobs in fusion experiments and simulations. Our experiments demonstrated we can achieve linear time speedup up to 1024 MPI processes and complete blob detection in two or three milliseconds

Extending the reach of algorithms for the calculation of molecular vibronic spectra

Theoretical spectroscopy is an important field of chemistry that can help extract useful information about the properties of a molecule from experimental spectral data. Ab initio calculations of molecular spectra can be performed and compared against experimental data to determine the validity of various calculated molecular properties. Unfortunately, the computational cost of these spectral simulations rises quickly with the number of atoms in the molecule of interest. As a result, current techniques for simulating molecular spectra are often limited for use with only the smallest of molecules. The main purpose of this work is to develop new computational tools in an effort to extend the reach of current state-of-the-art spectral simulation algorithms and allow for the spectroscopic study of larger molecules than is currently feasible. The calculation of vibronic spectra requires the solution of the time-independent Schrödinger equation to obtain the vibronic energy levels of a molecule and their corresponding transition intensities. When the Born-Oppenheimer approximation is applicable for the solution of the time-independent Schrödinger equation, the vibrational energy levels of a molecule can be easily determined analytically, if the harmonic approximation is used. What remains, then, for a spectral simulation, is the calculation of the transition intensities associated with each energy level. Under the harmonic approximation, the transition intensities (also known as Franck-Condon factors) can be calculated via a set of recurrence equations developed by Doktorov, Malkin, and Manko. The implementation of these recurrence equations, though, can be computationally intensive for medium-to-large molecules, especially for finite-temperature simulations. In this work, I present a new algorithm for the calculation of Franck-Condon factors via the Doktorov recurrence equations that achieves significantly better computational performance than existing implementations, with speedups of roughly thirty times on a single processor. When the Born-Oppenheimer approximation is not applicable, vibronic coupling effects must be accounted for to achieve an accurate spectral simulation. A common approach for treating vibronic coupling effects is to solve the time-independent Schrödinger equation using a model Hamiltonian developed by Köppel, Domcke, and Cederbaum (KDC). Using the KDC approach, the problem of solving the Schrödinger equation becomes a problem of solving for the eigenstates of a large, sparse matrix. The computational difficulty of this problem is then dependent on the size of the matrix. Unfortunately, the size of the matrix at hand grows exponentially with the number of vibrational modes of the molecule of interest, and matrix dimensions can easily reach upwards of one billion and beyond. In an attempt to make tractable problems involving very large matrices, I present in this work a distributed-memory parallelization strategy for the KDC approach. The resulting parallel algorithm achieves impressive parallel scalability and has been used to study several previously intractable spectroscopic problems. I conclude this work by presenting ab initio calculations and spectral simulations for the molecule trans-1,3-butadiene. The spectroscopy of butadiene has been studied by expermentalists and theorist alike, but a complete KDC spectral model has yet to be achieved due in part to the large size of the resulting matrices. Using the newly-developed parallel algorithm described above, I am able to present spectra from simulations using the most complete KDC model for butadiene to date and discuss what these results may tell us about butadiene’s electronic structure.Computational Science, Engineering, and Mathematic

ブロック赤黒順序付けによるPoissonソルバーの並列化とParticie-in-Cellプラズマシミュレーションへの応用

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