Rectangular Full Packed Format for Cholesky's Algorithm: Factorization, Solution and Inversion

We describe a new data format for storing triangular, symmetric, and Hermitian matrices called RFPF (Rectangular Full Packed Format). The standard two dimensional arrays of Fortran and C (also known as full format) that are used to represent triangular and symmetric matrices waste nearly half of the storage space but provide high performance via the use of Level 3 BLAS. Standard packed format arrays fully utilize storage (array space) but provide low performance as there is no Level 3 packed BLAS. We combine the good features of packed and full storage using RFPF to obtain high performance via using Level 3 BLAS as RFPF is a standard full format representation. Also, RFPF requires exactly the same minimal storage as packed format. Each LAPACK full and/or packed triangular, symmetric, and Hermitian routine becomes a single new RFPF routine based on eight possible data layouts of RFPF. This new RFPF routine usually consists of two calls to the corresponding LAPACK full format routine and two calls to Level 3 BLAS routines. This means {\it no} new software is required. As examples, we present LAPACK routines for Cholesky factorization, Cholesky solution and Cholesky inverse computation in RFPF to illustrate this new work and to describe its performance on several commonly used computer platforms. Performance of LAPACK full routines using RFPF versus LAPACK full routines using standard format for both serial and SMP parallel processing is about the same while using half the storage. Performance gains are roughly one to a factor of 43 for serial and one to a factor of 97 for SMP parallel times faster using vendor LAPACK full routines with RFPF than with using vendor and/or reference packed routines

Features in the diffraction of a scalar plane wave from doubly-periodic Dirichlet and Neumann surfaces

The diffraction of a scalar plane wave from a doubly-periodic surface on which either the Dirichlet or Neumann boundary condition is imposed is studied by means of a rigorous numerical solution of the Rayleigh equation for the amplitudes of the diffracted Bragg beams. From the results of these calculations the diffraction efficiencies of several of the lowest order diffracted beams are calculated as functions of the polar and azimuthal angles of incidence. The angular dependencies of the diffraction efficiencies display features that can be identified as Rayleigh anomalies for both types of surfaces. In the case of a Neumann surface additional features are present that can be attributed to the existence of surface waves on such surfaces. Some of the results obtained through the use of the Rayleigh equation are validated by comparing them with results of a rigorous Green's function numerical calculation.Comment: 16 pages, 5 figure

Time-dependent radio emission from evolving jets

We investigated the time-dependent radiative and dynamical properties of light supersonic jets launched into an external medium, using hydrodynamic simulations and numerical radiative transfer calculations. These involved various structural models for the ambient media, with density profiles appropriate for galactic and extragalactic systems. The radiative transfer formulation took full account of emission, absorption, re-emission, Faraday rotation and Faraday conversion explicitly. High time-resolution intensity maps were generated, frame-by-frame, to track the spatial hydrodynamical and radiative properties of the evolving jets. Intensity light curves were computed via integrating spatially over the emission maps. We apply the models to jets in active galactic nuclei (AGN). From the jet simulations and the time-dependent emission calculations we derived empirical relations for the emission intensity and size for jets at various evolutionary stages. The temporal properties of jet emission are not solely consequences of intrinsic variations in the hydrodynamics and thermal properties of the jet. They also depend on the interaction between the jet and the ambient medium. The interpretation of radio jet morphology therefore needs to take account of environmental factors. Our calculations have also shown that the environmental interactions can affect specific emitting features, such as internal shocks and hotspots. Quantification of the temporal evolution and spatial distribution of these bright features, together with the derived relations between jet size and emission, would enable us to set constraints on the hydrodynamics of AGN and the structure of the ambient medium.Comment: 16 pages, 18 figures, MNRAS in press

Excited state quantum phase transitions in the bending spectra of molecules

European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 87208

A High Order Cartesian Grid, Finite Volume Method for Elliptic Interface Problems

We present a higher-order finite volume method for solving elliptic PDEs with jump conditions on interfaces embedded in a 2D Cartesian grid. Second, fourth, and sixth order accuracy is demonstrated on a variety of tests including problems with high-contrast and spatially varying coefficients, large discontinuities in the source term, and complex interface geometries. We include a generalized truncation error analysis based on cell-centered Taylor series expansions, which then define stencils in terms of local discrete solution data and geometric information. In the process, we develop a simple method based on Green's theorem for computing exact geometric moments directly from an implicit function definition of the embedded interface. This approach produces stencils with a simple bilinear representation, where spatially-varying coefficients and jump conditions can be easily included and finite volume conservation can be enforced

Excited state quantum phase transitions in the bending spectra of molecules

We present an extension of the Hamiltonian of the two dimensional limit of the vibron model encompassing all possible interactions up to four-body operators. We apply this Hamiltonian to the modeling of the experimental bending spectrum of fourteen molecules. The bending degrees of freedom of the selected molecular species include all possible situations: linear, bent, and nonrigid equilibrium structures; demonstrating the flexibility of the algebraic approach, that allows for the consideration of utterly different physical cases with a general formalism and a single Hamiltonian. For each case, we compute predicted term values used to depict the quantum monodromy diagram, the Birge-Sponer plot, the participation ratio. We also show the bending energy functional obtained using the coherent --or intrinsic-- state formalism.Comment: 67 pages, 18 tables and 15 figure

Parallel unstructured solvers for linear partial differential equations

This thesis presents the development of a parallel algorithm to solve symmetric systems of linear equations and the computational implementation of a parallel partial differential equations solver for unstructured meshes. The proposed method, called distributive conjugate gradient - DCG, is based on a single-level domain decomposition method and the conjugate gradient method to obtain a highly scalable parallel algorithm. An overview on methods for the discretization of domains and partial differential equations is given. The partition and refinement of meshes is discussed and the formulation of the weighted residual method for two- and three-dimensions presented. Some of the methods to solve systems of linear equations are introduced, highlighting the conjugate gradient method and domain decomposition methods. A parallel unstructured PDE solver is proposed and its actual implementation presented. Emphasis is given to the data partition adopted and the scheme used for communication among adjacent subdomains is explained. A series of experiments in processor scalability is also reported. The derivation and parallelization of DCG are presented and the method validated throughout numerical experiments. The method capabilities and limitations were investigated by the solution of the Poisson equation with various source terms. The experimental results obtained using the parallel solver developed as part of this work show that the algorithm presented is accurate and highly scalable, achieving roughly linear parallel speed-up in many of the cases tested

Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia

Breeding practices adopted at different farms are aimed at maximizing the profitability of pig farming. In this work, we have analyzed the genetic diversity of Large White pigs in Russia. We compared genomes of historic and modern Large White Russian breeds using 271 pig samples. We have identified 120 candidate regions associated with the differentiation of modern and historic pigs and analyzed genomic differences between the modern farms. The identified genes were associated with height, fitness, conformation, reproductive performance, and meat quality

Parallel unstructured solvers for linear partial differential equations

This thesis presents the development of a parallel algorithm to solve symmetric systems of linear equations and the computational implementation of a parallel partial differential equations solver for unstructured meshes. The proposed method, called distributive conjugate gradient - DCG, is based on a single-level domain decomposition method and the conjugate gradient method to obtain a highly scalable parallel algorithm. An overview on methods for the discretization of domains and partial differential equations is given. The partition and refinement of meshes is discussed and the formulation of the weighted residual method for two- and three-dimensions presented. Some of the methods to solve systems of linear equations are introduced, highlighting the conjugate gradient method and domain decomposition methods. A parallel unstructured PDE solver is proposed and its actual implementation presented. Emphasis is given to the data partition adopted and the scheme used for communication among adjacent subdomains is explained. A series of experiments in processor scalability is also reported. The derivation and parallelization of DCG are presented and the method validated throughout numerical experiments. The method capabilities and limitations were investigated by the solution of the Poisson equation with various source terms. The experimental results obtained using the parallel solver developed as part of this work show that the algorithm presented is accurate and highly scalable, achieving roughly linear parallel speed-up in many of the cases tested.EThOS - Electronic Theses Online ServiceGBUnited Kingdo