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At least 1,387 records · Page 77

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NASA NTRS1987

Reconstruction of coded aperture images

Balanced correlation method and the Maximum Entropy Method (MEM) were implemented to reconstruct a laboratory X-ray source as imaged by a Uniformly Redundant Array (URA) system. Although the MEM method has advantages over the balanced correlation method, it is computationally time consuming because of the iterative nature of its solution. Massively Parallel Processing, with its parallel array structure is ideally suited for such computations. These preliminary results indicate that it is possible to use the MEM method in future coded-aperture experiments with the help of the MPP.

Bielefeld, Michael J.↗

DOE OSTI2018

Stochastic Simulation of Complex Fluid Flows (Progress Report for period 07/01/2016 - 06/30/2018)

At a microscopic scale, fluids are composed of molecules whose positions and velocities are random. This gives rise to thermal fluctuations that span the whole range of scales from the microscopic through the mesoscopic, and even the macroscopic. The inclusion of thermal fluctuations is crucial in multi-scale models, which are an important theme in the research program of the DOE Office of Science, and in particular the ASCR Applied Mathematics program's priority focus area on modeling of complex systems involving processes that span vastly different time and/or length scales. In this five-year Early Career project, the PI Aleksandar Donev and collaborators developed computational algorithms for modeling complex fluid mixtures at small scales using a formulation based on fluctuating hydrodynamics. Novel computational methods were developed to model complex fluids with increasing physical complexity, starting from binary miscible and immiscible mixtures, going through multispecies non-reactive and reactive mixtures, and culminating with reactive electrolytes mixtures of neutral molecules and ions. In close collaboration with the group of John Bell at Lawrence Berkeley National Laboratory, the methods were implemented in a scalable computational framework suitable for modern parallel supercomputers, and made publicly available on github. A number of physical examples in which giant nonequilibrium fluctuations are improtant were studied, with a special focus on instabilities at a liquid-liquid interface driven by gravity, diffusion, reactions, and/or electric fields. The methods and codes developed in this project are expected to enable other novel applications in the DOE Basic Energy Sciences program, and engineering sciences more broadly.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

CarcSeq Measurement of Rat Mammary Cancer Driver Mutations and Relation to Spontaneous Mammary Neoplasia

Abstract The ability to deduce carcinogenic potential from subchronic, repeat dose rodent studies would constitute a major advance in chemical safety assessment and drug development. This study investigated an error-corrected NGS method (CarcSeq) for quantifying cancer driver mutations (CDMs) and deriving a metric of clonal expansion predictive of future neoplastic potential. CarcSeq was designed to interrogate subsets of amplicons encompassing hotspot CDMs applicable to a variety of cancers. Previously, normal human breast DNA was analyzed by CarcSeq and metrics based on mammary-specific CDMs were correlated with tissue donor age, a surrogate of breast cancer risk. Here we report development of parallel methodologies for rat. The utility of the rat CarcSeq method for predicting neoplastic potential was investigated by analyzing mammary tissue of 16-week-old untreated rats with known differences in spontaneous mammary neoplasia (Fischer 344, Wistar Han, and Sprague Dawley). Hundreds of mutants with mutant fractions ≥ 10−4 were quantified in each strain, most were recurrent mutations, and 42.5% of the nonsynonymous mutations have human homologs. Mutants in the mammary-specific target of the most tumor-sensitive strain (Sprague Dawley) showed the greatest nonsynonymous/synonymous mutation ratio, indicative of positive selection consistent with clonal expansion. For the mammary-specific target (Hras, Pik3ca, and Tp53 amplicons), median absolute deviation correlated with percentages of rats that develop spontaneous mammary neoplasia at 104 weeks (Pearson r = 1.0000, 1-tailed p = .0010). Therefore, this study produced evidence CarcSeq analysis of spontaneously occurring CDMs can be used to derive an early metric of clonal expansion relatable to long-term neoplastic outcome.

McKim, Karen L.↗

DOE OSTI2022

Source-to-Source Automatic Differentiation of OpenMP Parallel Loops

This article presents our work toward correct and efficient automatic differentiation of OpenMP parallel worksharing loops in forward and reverse mode. Automatic differentiation is a method to obtain gradients of numerical programs, which are crucial in optimization, uncertainty quantification, and machine learning. The computational cost to compute gradients is a common bottleneck in practice. For applications that are parallelized for multicore CPUs or GPUs using OpenMP, one also wishes to compute the gradients in parallel. Here, we propose a framework to reason about the correctness of the generated derivative code, from which we justify our OpenMP extension to the differentiation model. We implement this model in the automatic differentiation tool Tapenade and present test cases that are differentiated following our extended differentiation procedure. Performance of the generated derivative programs in forward and reverse mode is better than sequential, although our reverse mode often scales worse than the input programs.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1971

Analytical methods for performance evaluation of nonlinear filters.

In the investigation, the filtering problem is considered in the continuous time domain. The postulated simple suboptimal nonlinear filter structure closely parallels the structure of the Kalman-Bucy optimal linear filter algorithm. Two filter performance evaluation methods are developed based on the Kolmogorov equations for the transition density of Markov processes. The expansions in the approximations for the nonlinear system and observation functions are in effect carried out up to second-order terms in both methods. The description of the filter's performance is sought in terms of second-order statistics in both methods.

Bejczy, A. K.↗

DOE OSTI2017

Energy levels, oscillator strengths, line strengths, and transition probabilities in Si-like ions of La XLIII, Er LIV, Tm LV, and Yb LVI

Detailed calculations using the multi-configuration Dirac–Fock (MCDF) method are carried out for the lowest 64 fine-structure levels of the 3s{sup 2}3p{sup 2}, 3s{sup 2}3p3d, 3s3p{sup 3}, 3s3p{sup 2}3d, 3s{sup 2}3d{sup 2}, and 3p{sup 4} configurations in Si-like ions of La XLIII, Er LIV, Tm LV, and Yb LVI. Energies, oscillator strengths, wavelengths, line strengths, and radiative electric dipole transition rates are given for all ions. A parallel calculation using the many-body perturbation theory (MBPT) method is also carried out to assess the present energy levels accuracy. Comparisons are performed between these two sets of energy levels, as well as with other available results, showing that they are in good agreement with each other within 0.5%. These high accuracy results can be used to the modeling and the interpretation of astrophysical objects and fusion plasmas. - Highlights: • Energy levels and E1 transition rates of Si-like ions are presented. • Breit interaction and Quantum Electrodynamics effects are discussed. • Present results should be useful in the astrophysical application and plasma modeling.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2015

SU-C-304-03: Experimental Investigation On the Accuracy of Plastic Scintillation Dosimeters in Small Fields

Purpose: To investigate the accuracy of the Exradin W1 (SI) and of an “in-house” plastic scintillation dosimeter (CHUQ PSD) in small radiation fields. Methods: Output factor (OF) measurements with the W1 and CHUQ PSD were performed for field sizes of 0.5 x 0.5, 1 x 1 and 2 x 2 cm{sup 2}. Both detectors were placed parallel to the central axis (CAX) in water. The spectrum discrimination calibration method was performed in each set-up to account for the Cerenkov (CRV) signal created in the fiber. The OFs were compared to the expected field factors in water derived using i) Monte Carlo (MC) simulations of an accurate accelerator model and ii) microLion (PTW) and D1V diode (SI) OFs. MC-derived correction factors were applied to both the microLion and D1V OFs. For the CHUQ PSD the calibration was repeated in water (// CAX), solid water (perpendicular to CAX) and under a shielded configuration. The signal was collected using a spectrometer (wavelength range = 185–1100 nm). Spectral analysis was performed to evaluate potential changes of the spectral distributions under the various calibration set-up configurations. Results: The W1 OFs presented an over-response for the 0.5 x 0.5 cm{sup 2} in the range of 3 – 4.1% relative to the expected field factor. The CHUQ PSD presented an under-response in the range of 1.5 – 2.7%, without accounting for volume averaging. The CRV spectra under the various calibration procedures appeared similar to each other and only minor changes were observed to the respective OFs. Conclusion: The W1 and CHUQ PSD can be used in small fields down to a 1 x 1 cm{sup 2} field size. Discrepancies were encountered between the two detectors for the smallest field size of 0.5 x 0.5 cm{sup 2} with the CHUQ PSD exhibiting a closer agreement to the expected field factor. Funding sources: 1) Alexander S. Onassis Public Benefit Foundation in Greece and 2) CREATE Medical Physics Research Training Network grant of the Natural Sciences and Engineering Research Council, Grant number: 432290, RGPIN-2014-06475.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2018

Computing resonant modes of accelerator cavities by solving nonlinear eigenvalue problems via rational approximation

Here, we present an efficient and reliable algorithm for solving a class of nonlinear eigenvalue problems arising from the modeling of particle accelerator cavities. The eigenvalue nonlinearity in these problems results from the use of waveguides to couple external power sources or to allow certain excited electromagnetic modes to exit the cavity. We use a rational approximation to reduce the nonlinear eigenvalue problem first to a rational eigenvalue problem. We then apply a special linearization procedure to turn the rational eigenvalue problem into a larger linear eigenvalue problem with the same eigenvalues, which can be solved by existing iterative methods. By using a compact scheme to represent both the linearized operator and the eigenvectors to be computed, we obtain a numerical method that only involves solving linear systems of equations of the same dimension as the original nonlinear eigenvalue problem. We refer to this method as a compact rational Krylov (CORK) method. We implemented the CORK method in the Omega3P module of the Advanced Computational Electromagnetic 3D Parallel (ACE3P) simulation suite and validated it by comparing the computed cavity resonant frequencies and damping Q factors of a small model problem to those obtained from a fitting procedure that uses frequency responses computed by another ACE3P module called S3P. We also used the CORK method to compute trapped modes damped in an ideal eight 9-cell SRF cavity cryomodule. This was the first time it was possible to compute these modes directly. The damping Q factors of the computed modes match well with those measured in experiments and the difference in resonant frequencies is within the range introduced by cavity imperfection. Therefore, the CORK method is an extremely valuable tool for computational cavity design.

43 PARTICLE ACCELERATORS↗

NASA NTRS1999

Parallelization of the Physical-Space Statistical Analysis System (PSAS)

Atmospheric data assimilation is a method of combining observations with model forecasts to produce a more accurate description of the atmosphere than the observations or forecast alone can provide. Data assimilation plays an increasingly important role in the study of climate and atmospheric chemistry. The NASA Data Assimilation Office (DAO) has developed the Goddard Earth Observing System Data Assimilation System (GEOS DAS) to create assimilated datasets. The core computational components of the GEOS DAS include the GEOS General Circulation Model (GCM) and the Physical-space Statistical Analysis System (PSAS). The need for timely validation of scientific enhancements to the data assimilation system poses computational demands that are best met by distributed parallel software. PSAS is implemented in Fortran 90 using object-based design principles. The analysis portions of the code solve two equations. The first of these is the "innovation" equation, which is solved on the unstructured observation grid using a preconditioned conjugate gradient (CG) method. The "analysis" equation is a transformation from the observation grid back to a structured grid, and is solved by a direct matrix-vector multiplication. Use of a factored-operator formulation reduces the computational complexity of both the CG solver and the matrix-vector multiplication, rendering the matrix-vector multiplications as a successive product of operators on a vector. Sparsity is introduced to these operators by partitioning the observations using an icosahedral decomposition scheme. PSAS builds a large (approx. 128MB) run-time database of parameters used in the calculation of these operators. Implementing a message passing parallel computing paradigm into an existing yet developing computational system as complex as PSAS is nontrivial. One of the technical challenges is balancing the requirements for computational reproducibility with the need for high performance. The problem of computational reproducibility is well known in the parallel computing community. It is a requirement that the parallel code perform calculations in a fashion that will yield identical results on different configurations of processing elements on the same platform. In some cases this problem can be solved by sacrificing performance. Meeting this requirement and still achieving high performance is very difficult. Topics to be discussed include: current PSAS design and parallelization strategy; reproducibility issues; load balance vs. database memory demands, possible solutions to these problems.

Larson, J. W.↗

DOE OSTI2021

Efficient quadrature rules for finite element discretizations of nonlocal equations

In this paper we design efficient quadrature rules for finite element discretizations of nonlocal diffusion problems with compactly supported kernel functions. Two of the main challenges in nonlocal modeling and simulations are the prohibitive computational cost and the nontrivial implementation of discretization schemes, especially in three-dimensional settings. In this work we circumvent both challenges by introducing a parametrized mollifying function that improves the regularity of the integrand, utilizing an adaptive integration technique, and exploiting parallelization. We first showthat the “mollified” solution converges to the exact one as the mollifying parameter vanishes, then we illustrate the consistency and accuracy of the proposed method on several two- and three-dimensional test cases. Furthermore, we demonstrate the good scaling properties of the parallel implementation of the adaptive algorithm and we compare the proposed method with recently developed techniques for efficient finite element assembly.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1999

MLP: A Parallel Programming Alternative to MPI for New Shared Memory Parallel Systems

Recent developments at the NASA AMES Research Center's NAS Division have demonstrated that the new generation of NUMA based Symmetric Multi-Processing systems (SMPs), such as the Silicon Graphics Origin 2000, can successfully execute legacy vector oriented CFD production codes at sustained rates far exceeding processing rates possible on dedicated 16 CPU Cray C90 systems. This high level of performance is achieved via shared memory based Multi-Level Parallelism (MLP). This programming approach, developed at NAS and outlined below, is distinct from the message passing paradigm of MPI. It offers parallelism at both the fine and coarse grained level, with communication latencies that are approximately 50-100 times lower than typical MPI implementations on the same platform. Such latency reductions offer the promise of performance scaling to very large CPU counts. The method draws on, but is also distinct from, the newly defined OpenMP specification, which uses compiler directives to support a limited subset of multi-level parallel operations. The NAS MLP method is general, and applicable to a large class of NASA CFD codes.

Taft, James R.↗

NASA NTRS1984

Transition and mixing in impulsively started jets and vortex rings

A new method is used to analyze transition in impulsively started jets and vortex rings. The method uses similarity variables to reduce the equations for unsteady particle paths to a quasi-autonomous system with the Reynolds number as a parameter. The flow pattern is represented in terms of the phase portrait of this system and the structure of the flow is defined by its critical points. Flow transition is examined in terms of bifurcations in the topology of the phase portrait which occur as the Reynolds number is increased. There is no assumption that the flow is parallel or that it is subjected to small disturbances. The method of analysis, through straightforward, is new and lies outside the usual small disturbance theory used to determine the stability of various profile shapes.

Cantwell, B. J.↗

NASA NTRS1992

SAPNEW: Parallel finite element code for thin shell structures on the Alliant FX-80

The finite element method has proven to be an invaluable tool for analysis and design of complex, high performance systems, such as bladed-disk assemblies in aircraft turbofan engines. However, as the problem size increase, the computation time required by conventional computers can be prohibitively high. Parallel processing computers provide the means to overcome these computation time limits. This report summarizes the results of a research activity aimed at providing a finite element capability for analyzing turbomachinery bladed-disk assemblies in a vector/parallel processing environment. A special purpose code, named with the acronym SAPNEW, has been developed to perform static and eigen analysis of multi-degree-of-freedom blade models built-up from flat thin shell elements. SAPNEW provides a stand alone capability for static and eigen analysis on the Alliant FX/80, a parallel processing computer. A preprocessor, named with the acronym NTOS, has been developed to accept NASTRAN input decks and convert them to the SAPNEW format to make SAPNEW more readily used by researchers at NASA Lewis Research Center.

Kamat, Manohar P.↗

NASA NTRS1995

Newton-Krylov-Schwarz: An implicit solver for CFD

Newton-Krylov methods and Krylov-Schwarz (domain decomposition) methods have begun to become established in computational fluid dynamics (CFD) over the past decade. The former employ a Krylov method inside of Newton's method in a Jacobian-free manner, through directional differencing. The latter employ an overlapping Schwarz domain decomposition to derive a preconditioner for the Krylov accelerator that relies primarily on local information, for data-parallel concurrency. They may be composed as Newton-Krylov-Schwarz (NKS) methods, which seem particularly well suited for solving nonlinear elliptic systems in high-latency, distributed-memory environments. We give a brief description of this family of algorithms, with an emphasis on domain decomposition iterative aspects. We then describe numerical simulations with Newton-Krylov-Schwarz methods on aerodynamics applications emphasizing comparisons with a standard defect-correction approach, subdomain preconditioner consistency, subdomain preconditioner quality, and the effect of a coarse grid.

Cai, Xiao-Chuan↗

DOE OSTI2015

Flux tube train model for local turbulence simulation of toroidal plasmas

A new simulation method for local turbulence in toroidal plasmas is developed by extending the conventional idea of the flux tube model. In the new approach, a train of flux tubes is employed, where flux tube simulation boxes are serially connected at each end along a field line so as to preserve a symmetry of the local gyrokinetic equations for image modes in an axisymmetric torus. Validity of the flux tube train model is confirmed against the toroidal ion temperature gradient turbulence for a case with a long parallel correlation of fluctuations, demonstrating numerical advantages over the conventional method in the time step size and the symmetry-preserving property.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2014

Simulation of confined magnetohydrodynamic flows with Dirichlet boundary conditions using a pseudo-spectral method with volume penalization

A volume penalization approach to simulate magnetohydrodynamic (MHD) flows in confined domains is presented. Here the incompressible visco-resistive MHD equations are solved using parallel pseudo-spectral solvers in Cartesian geometries. The volume penalization technique is an immersed boundary method which is characterized by a high flexibility for the geometry of the considered flow. In the present case, it allows to use other than periodic boundary conditions in a Fourier pseudo-spectral approach. The numerical method is validated and its convergence is assessed for two- and three-dimensional hydrodynamic (HD) and MHD flows, by comparing the numerical results with results from literature and analytical solutions. The test cases considered are two-dimensional Taylor–Couette flow, the z-pinch configuration, three dimensional Orszag–Tang flow, Ohmic-decay in a periodic cylinder, three-dimensional Taylor–Couette flow with and without axial magnetic field and three-dimensional Hartmann-instabilities in a cylinder with an imposed helical magnetic field. Finally, we present a magnetohydrodynamic flow simulation in toroidal geometry with non-symmetric cross section and imposing a helical magnetic field to illustrate the potential of the method.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Metallization and stringing for back-contact solar cells

Metallization and stringing methods for back-contact solar cells, and resulting solar cells, are described. In an example, in one embodiment, a method involves aligning conductive wires over the back sides of adjacent solar cells, wherein the wires are aligned substantially parallel to P-type and N-type doped diffusion regions of the solar cells. The method involves bonding the wires to the back side of each of the solar cells over the P-type and N-type doped diffusion regions. The method further includes cutting every other one of the wires between each adjacent pair of the solar cells.

Terao, Akira↗

NASA NTRS1994

Parallel aeroelastic computations for wing and wing-body configurations

The objective of this research is to develop computationally efficient methods for solving fluid-structural interaction problems by directly coupling finite difference Euler/Navier-Stokes equations for fluids and finite element dynamics equations for structures on parallel computers. This capability will significantly impact many aerospace projects of national importance such as Advanced Subsonic Civil Transport (ASCT), where the structural stability margin becomes very critical at the transonic region. This research effort will have direct impact on the High Performance Computing and Communication (HPCC) Program of NASA in the area of parallel computing.

Byun, Chansup↗