Block Locally Optimal Preconditioned Eigenvalue Xolvers (BLOPEX) in hypre and PETSc

We describe our software package Block Locally Optimal Preconditioned Eigenvalue Xolvers (BLOPEX) publicly released recently. BLOPEX is available as a stand-alone serial library, as an external package to PETSc (``Portable, Extensible Toolkit for Scientific Computation'', a general purpose suite of tools for the scalable solution of partial differential equations and related problems developed by Argonne National Laboratory), and is also built into {\it hypre} (``High Performance Preconditioners'', scalable linear solvers package developed by Lawrence Livermore National Laboratory). The present BLOPEX release includes only one solver--the Locally Optimal Block Preconditioned Conjugate Gradient (LOBPCG) method for symmetric eigenvalue problems. {\it hypre} provides users with advanced high-quality parallel preconditioners for linear systems, in particular, with domain decomposition and multigrid preconditioners. With BLOPEX, the same preconditioners can now be efficiently used for symmetric eigenvalue problems. PETSc facilitates the integration of independently developed application modules with strict attention to component interoperability, and makes BLOPEX extremely easy to compile and use with preconditioners that are available via PETSc. We present the LOBPCG algorithm in BLOPEX for {\it hypre} and PETSc. We demonstrate numerically the scalability of BLOPEX by testing it on a number of distributed and shared memory parallel systems, including a Beowulf system, SUN Fire 880, an AMD dual-core Opteron workstation, and IBM BlueGene/L supercomputer, using PETSc domain decomposition and {\it hypre} multigrid preconditioning. We test BLOPEX on a model problem, the standard 7-point finite-difference approximation of the 3-D Laplacian, with the problem size in the range $10^5-10^8$.Comment: Submitted to SIAM Journal on Scientific Computin

Copper-doping effects in electronic structure and spectral properties of SmNi₅

The electronic structure and optical properties of the SmNi₅₋Cux (x = 0, 1, 2) compounds are studied. The band spectra of the studied intermetallics were calculated with LDA+U+SO method supplementing the local density approximation with a correction for strong electron interaction on the shell of the rare-earth element. Optical properties were studied by ellipsometry method in the wide wavelength range. It was found that the substitution of copper for nickel leads to local changes in the optical conductivity spectra. Both the spectroscopic measurements and theoretical calculations demonstrate the presence of a broad absorption band around 4 eV associated with the Cu 3d → Ni 3d electron transitions and increasing with the grown of copper content. The experimental dispersion curves of optical conductivity in the interband absorption region were interpreted using the results of the calculations

Fast Spectral Clustering of Data Using Sequential Matrix Compression

Spectral clustering has attracted much research interest in recent years since it can yield impressively good clustering results. Traditional spectral clustering algorithms first solve an eigenvalue decomposition problem to get the low-dimensional embedding of the data points, and then apply some heuristic methods such as k-means to get the desired clusters. However, eigenvalue decomposition is very time-consuming, making the overall complexity of spectral clustering very high, and thus preventing spectral clustering from being widely applied in large-scale problems. To tackle this problem, different from traditional algorithms, we propose a very fast and scalable spectral clustering algorithm called the sequential matrix compression (SMC) method. In this algorithm, we scale down the computational complexity of spectral clustering by sequentially reducing the dimension of the Laplacian matrix in the iteration steps with very little loss of accuracy. Experiments showed the feasibility and efficiency of the proposed algorithm. ? Springer-Verlag Berlin Heidelberg 2006.EI

Исходы новой коронавирусной инфекции COVID-19 у 68 пациентов с воспалительными заболеваниями кишечника

Background. COVID-19 is an infectious respiratory syndrome with a wide range of manifestations and outcomes. Patients with inflammatory bowel disease (IBD) generally have a higher risk of infection, especially if they receive immunosuppressive therapy. Aim to describe the manifestations of COVID-19 in patients with IBD and to determine the risk factors for severe COVID-19. Methods. The analysis included 68 patients with an established diagnosis of Crohns disease (CD) or ulcerative colitis and a confirmed new coronavirus infection. The diagnosis of coronavirus infection was established when SARS-CoV-2 was detected by PCR using nasopharyngeal smears, and computer tomography (CT) of the chest revealed inflammatory changes characteristic of coronavirus lung damage or high IgG and IgM titers based on the results of immunological blood analysis. Results. 68 patients with IBD and COVID-19 were observed in the Department of IBD, including 27 (39.7%) patients with CD, 41 (60.3%) patients with UC. Among patients diagnosed with pneumonia, 100 % of patients received therapy with thiopurines and infliximab. 8 (11.8%) patients were diagnosed with COVID-19 during hospitalization for a severe IBD attack. There was no statistically significant difference between UC and CD patients in terms of disease activity (p = 0.13) during the period of coronavirus infection. In 37 patients (26 UC, 11 BC) with pneumonia (100%), there was an exacerbation of IBD. Statistical significance was found between the development of more severe lung damage (CT 34) and IBD activity at the time of diagnosis of COVID-19 (p 0.001), the presence of comorbidities (p 0.001) and taking GCS (p 0.001) at the time of detection of COVID-19. However, the use of biological and immunosuppressive therapy was not associated with a higher risk of severe lung damage and the need for a ventilator. It was shown that the age of patients over 65 years was statistically correlated with the need for a ventilator (p = 0.02). Conclusion. The exacerbation of the disease, especially in elderly patients with comorbidities, the use of glucocorticosteroids was associated with negative consequences of COVID-19, while biological and immunosuppressant drugs used for the treatment of IBD did not have such a negative effect.Обоснование. COVID-19 это инфекционный респираторный синдром с широким спектром проявлений и исходов. Пациенты с воспалительными заболеваниями кишечника (ВЗК) имеют больший риск инфицирования SARS-CoV-2, в особенности если они получают иммуносупрессивную терапию. Цель исследования описать проявления COVID-19 у пациентов с ВЗК и определить факторы риска тяжелого течения COVID-19. Методы. В анализ были включены 68 пациентов c установленным диагнозом болезни Крона (БК) или язвенного колита (ЯК) и подтвержденной новой коронавирусной инфекцией. Диагноз коронавирусной инфекции устанавливался при выявлении SARS-CoV-2 методом ПЦР назофарингеальных мазков, выявлении при компьютерной томографии (КТ) органов грудной клетки воспалительных изменений, характерных для коронавирусного поражения легких, или высокого титра IgG и IgM по результатам иммунологического анализа крови. Результаты. 68 пациентов с ВЗК и COVID-19 наблюдались в отделении лечения Московского клинического научно-практического центра имени А.С. Логинова, из них 27 (39,7%) пациентов с БК, 41 (60,3%) пациент с ЯК. Не было выявлено статистически значимого различия между пациентами ЯК и БК в отношении активности заболевания (p = 0,13) в период коронавирусной инфекции. У 37 пациентов (26 с ЯК, 11 с БК) с пневмонией (100%) имелось обострение ВЗК. У 8 (11,8%) пациентов был диагностирован COVID-19 во время госпитализации по поводу тяжелой атаки ВЗК. Была выявлена статистическая значимость между развитием более тяжелого поражения легких (КТ 34) и активностью ВЗК на момент диагностирования COVID-19 (p 0,001), наличием сопутствующих заболеваний (p 0,001) и приемом ГКС (p 0,001) на момент выявления COVID-19. При этом применение биологической и иммуносупрессивной терапии не было связано с более высоким риском тяжелого поражения легких и потребностью в ИВЛ. Было показано, что возраст пациентов более 65 лет статистически коррелировал с потребностью в ИВЛ (p = 0,02). Заключение. Обострение заболевания, в особенности у пожилых пациентов с сопутствующей патологией, и прием глюкокортикостероидов имели зависимость с негативными последствиями COVID-19, в то время как препараты биологической и иммуносупрессорной терапии, применяемые для лечения ВЗК, не оказывали такого негативного влияния

Theory and computation of covariant Lyapunov vectors

Lyapunov exponents are well-known characteristic numbers that describe growth rates of perturbations applied to a trajectory of a dynamical system in different state space directions. Covariant (or characteristic) Lyapunov vectors indicate these directions. Though the concept of these vectors has been known for a long time, they became practically computable only recently due to algorithms suggested by Ginelli et al. [Phys. Rev. Lett. 99, 2007, 130601] and by Wolfe and Samelson [Tellus 59A, 2007, 355]. In view of the great interest in covariant Lyapunov vectors and their wide range of potential applications, in this article we summarize the available information related to Lyapunov vectors and provide a detailed explanation of both the theoretical basics and numerical algorithms. We introduce the notion of adjoint covariant Lyapunov vectors. The angles between these vectors and the original covariant vectors are norm-independent and can be considered as characteristic numbers. Moreover, we present and study in detail an improved approach for computing covariant Lyapunov vectors. Also we describe, how one can test for hyperbolicity of chaotic dynamics without explicitly computing covariant vectors.Comment: 21 pages, 5 figure

First experimental results obtained using the highpower free electron laser at the siberian center for photochemical research

The first lasing near the wavelength of 140 µm was achieved in April 2003 using a high-power free electron laser (FEL) constructed at the Siberian Center for Photochemical Research. In this paper we briefly describe the design of the FEL driven by an accelerator–recuperator. Characteristics of the electron beam and terahertz laser radiation, obtained in the first experiments, are also presented in the paper.У Сибірському центрі фотохімічних досліджень навесні 2003 року отримана генерація випромінювання з довжиною хвилі 140 мкм на потужному лазері на вільних електронах (ЛВЕ). У роботі коротко описана конструкція ЛВЕ на базі прискорювача рекуператора і представлені результати вимірювання деяких параметрів електронного пучка і терагерцового випромінювання.В Сибирском центре фотохимических исследований весной 2003 года получена генерация излучения с длиной волны 140 мкм на мощном лазере на свободных электронах (ЛСЭ). В работе кратко описана конструкция ЛСЭ на базе ускорителя рекуператора и представлены результаты измерения некоторых параметров электронного пучка и терагерцового излучения

Constraints on the cosmic expansion history from GWTC–3

We use 47 gravitational wave sources from the Third LIGO–Virgo–Kamioka Gravitational Wave Detector Gravitational Wave Transient Catalog (GWTC–3) to estimate the Hubble parameter H(z), including its current value, the Hubble constant H0. Each gravitational wave (GW) signal provides the luminosity distance to the source, and we estimate the corresponding redshift using two methods: the redshifted masses and a galaxy catalog. Using the binary black hole (BBH) redshifted masses, we simultaneously infer the source mass distribution and H(z). The source mass distribution displays a peak around 34 M⊙, followed by a drop-off. Assuming this mass scale does not evolve with the redshift results in a H(z) measurement, yielding ${H}_{0}={68}_{-8}^{+12}\,\mathrm{km}\ \,\ {{\rm{s}}}^{-1}\,{\mathrm{Mpc}}^{-1}$ (68% credible interval) when combined with the H0 measurement from GW170817 and its electromagnetic counterpart. This represents an improvement of 17% with respect to the H0 estimate from GWTC–1. The second method associates each GW event with its probable host galaxy in the catalog GLADE+, statistically marginalizing over the redshifts of each event's potential hosts. Assuming a fixed BBH population, we estimate a value of ${H}_{0}={68}_{-6}^{+8}\,\mathrm{km}\ \,\ {{\rm{s}}}^{-1}\,{\mathrm{Mpc}}^{-1}$ with the galaxy catalog method, an improvement of 42% with respect to our GWTC–1 result and 20% with respect to recent H0 studies using GWTC–2 events. However, we show that this result is strongly impacted by assumptions about the BBH source mass distribution; the only event which is not strongly impacted by such assumptions (and is thus informative about H0) is the well-localized event GW190814