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At least 757 records · Page 42

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DOE OSTI2019

ECP Milestone Memo WBS 2.3.4.13 ECP/VTK-m FY18Q4 [MS-18/09-10] Dynamic Types / Rendering Topologies STDA05-16

The STDA05-16 milestone comprises the following 3 distinct deliverables. OpenMP VTK-m currently supports three types of devices: serial CPU, TBB, and CUDA. To run algorithms on multicore CPU-type devices (such as Xeon and Xeon Phi), TBB is required. However, there are known issues with integrating a software product using TBB with another one using OpenMP. Therefore, we will add an OpenMP device to the VTK-m software. When engaged, this device will run parallel algorithms using OpenMP directives. This will mesh more nicely with other code also using OpenMP. Rendering Topological Entities VTK-m currently supports surface rendering by tessellation of data structures,and rendering the resulting triangles. We will extend current functionality to include face, edge, and point rendering. Better Dynamic Types Impl For the best efficiency across all platforms, VTK-m algorithms use static typing with C++ templates. However, many libraries like VTK, ParaView, and Visit use dynamic types with virtual functions because data types often cannot be determined at compile time. We have an interface in VTK-m to merge these two typing mechanisms by generating all possible combinations of static types when faced with a dynamic type. Although this mechanism works, it generates very large executables and takes a very long time to compile. As we move forward, it is clear that these problems will get worse and become infeasible at exascale. We will rectify the problem by introducing some level of virtual methods, which require only a single code path, within VTK-m algorithms. This first milestone produces a design document to propose an approach to the new system.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Extending PETSc's Composable Hierarchical Solvers (Final Technical Report)

This report documents research activities conducted at CU Boulder as part of Extending PETSc’s Composable Hierarchical Solvers, which has been part of a collaboration with Argonne National Laboratory (separate award). Our work has focused on performance-portable end-to-end GPU solvers demonstrated via exemplary applications in nonlinear fluid and structural mechanics. We describe advances in algorithmic composition and analysis in the context of these applications, but the implementations are fully documented and decoupled, and in use by other projects. We believe the vertical integration achieved through collaboration with ECP’s CEED and the PSAAP center at CU was necessary to take risks with data structures and algorithms.

42 ENGINEERING↗

DOE OSTI2024

Development of Lightweight Structural Materials with Improved Properties for Fission Batteries

The notion of a “fission battery” conveys a vision focused on realizing very simple “plug-and-play” nuclear systems that can be integrated into a variety of applications requiring affordable, reliable energy in the form of electricity and/or heat and function without operations and maintenance staff. Fission batteries require lightweight structural materials to increase their mobility, and the lightweight materials must demonstrate structural resilience under various conditions. The objective of this work is to develop lattice structured lightweight structural material featuring a good combination of mechanical properties using advanced modeling and simulation together with an advanced additive manufacturing technique such as laser powder bed fusion. The preliminary results show that different lattice structures and types can be successfully meshed using nTopology software, and the lattice structure data can be successfully transformed to Multiphysics Object-Oriented Simulation (MOOSE) Environment input. Finite Element Analysis (FEA) displays that, at macro/engineering scale simulation, the weight saving design has an obvious effect on tensile behavior such as effective elastic modulus and yield stress. The novel approaches of this work are (1) development of lattice structures for improved mechanical properties using advanced simulation and modeling techniques; and (2) model predictions of the mechanical properties (e.g., strength and stress distribution) of macroscopic materials in order to preliminarily select a lattice structure for additive manufacturing.

36 MATERIALS SCIENCE↗

DOE OSTI2024

COMPUTER-AIDED LATTICE DESIGN AND ADVANCED MODELING FOR THE DEVELOPMENT OF LIGHTWEIGHT STRUCTURAL MATERIALS

36 MATERIALS SCIENCE↗

DOE OSTI2024

Development of Lightweight Structural Materials with Improved Properties for Fission Batteries

The notion of a “fission battery” conveys a vision focused on realizing very simple “plug-and-play” nuclear systems that can be integrated into a variety of applications requiring affordable, reliable energy in the form of electricity and/or heat and function without operations and maintenance staff. Fission batteries require lightweight structural materials to increase their mobility, and the lightweight materials must demonstrate structural resilience under various conditions. The objective of this work is to develop lightweight structural material featuring a good combination of mechanical properties using advanced modeling and simulation together with an advanced additive manufacturing technique such as laser powder bed fusion. The preliminary results show that different lattice structures and types can be successfully meshed using nTopology software, and the lattice structure data can be successfully transformed to Multiphysics Object-Oriented Simulation Environment (MOOSE) input. Finite Element Analysis (FEA) displays that, at macro/engineering scale simulation, the weight saving design has an obvious effect on tensile behavior such as effective elastic modulus and yield stress. The novel approaches of this work are (1) development of optimized lattice structures for improved mechanical properties using advanced simulation and modeling techniques; and (2) model predictions of the mechanical properties (e.g., strength and stress distribution) of macroscopic materials in order to preliminarily select a lattice structure for additive manufacturing.

36 MATERIALS SCIENCE↗

DOE OSTI2017

Improved treatment of exact exchange in Quantum ESPRESSO

Here, we present an algorithm and implementation for the parallel computation of exact exchange in Quantum ESPRESSO (QE) that exhibits greatly improved strong scaling. QE is an open-source software package for electronic structure calculations using plane wave density functional theory, and supports the use of local, semi-local, and hybrid DFT functionals. Wider application of hybrid functionals is desirable for the improved simulation of electronic band energy alignments and thermodynamic properties, but the computational complexity of evaluating the exact exchange potential limits the practical application of hybrid functionals to large systems and requires efficient implementations. We demonstrate that existing implementations of hybrid DFT that utilize a single data structure for both the local and exact exchange regions of the code are significantly limited in the degree of parallelization achievable. We present a band-pair parallelization approach, in which the calculation of exact exchange is parallelized and evaluated independently from the parallelization of the remainder of the calculation, with the wavefunction data being efficiently transformed on-the-fly into a form that is optimal for each part of the calculation. For a 64 water molecule supercell, our new algorithm reduces the overall time to solution by nearly an order of magnitude.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1996

A mixed volume grid approach for the Euler and Navier-Stokes equations

An approach for solving the compressible Euler and Navier-Stokes equations upon meshes composed of nearly arbitrary polyhedra is described. Each polyhedron is constructed from an arbitrary number of triangular and quadrilateral face elements, allowing the unified treatment of tetrahedral, prismatic, pyramidal, and hexahedral cells, as well the general cut cells produced by Cartesian mesh approaches. The basics behind the numerical approach and the resulting data structures are described. The accuracy of the mixed volume grid approach is assessed by performing a grid refinement study upon a series of hexahedral, tetrahedral, prismatic, and Cartesian meshes for an analytic inviscid problem. A series of laminar validation cases are made, comparing the results upon differing grid topologies to each other, to theory, and experimental data. A computation upon a prismatic/tetrahedral mesh is made simulating the laminar flow over a wall/cylinder combination.

Coirier, William J.↗

NASA NTRS2003

Direct Manipulation in Virtual Reality

Virtual Reality interfaces offer several advantages for scientific visualization such as the ability to perceive three-dimensional data structures in a natural way. The focus of this chapter is direct manipulation, the ability for a user in virtual reality to control objects in the virtual environment in a direct and natural way, much as objects are manipulated in the real world. Direct manipulation provides many advantages for the exploration of complex, multi-dimensional data sets, by allowing the investigator the ability to intuitively explore the data environment. Because direct manipulation is essentially a control interface, it is better suited for the exploration and analysis of a data set than for the publishing or communication of features found in that data set. Thus direct manipulation is most relevant to the analysis of complex data that fills a volume of three-dimensional space, such as a fluid flow data set. Direct manipulation allows the intuitive exploration of that data, which facilitates the discovery of data features that would be difficult to find using more conventional visualization methods. Using a direct manipulation interface in virtual reality, an investigator can, for example, move a data probe about in space, watching the results and getting a sense of how the data varies within its spatial volume.

Bryson, Steve↗

DOE OSTI2018

Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase

The PLP-dependent l-arginine hydroxylase/deaminase MppP from Streptomyces wadayamensis (SwMppP) is involved in the biosynthesis of l-enduracididine, a nonproteinogenic amino acid found in several nonribosomally produced peptide antibiotics. SwMppP uses only PLP and molecular oxygen to catalyze a 4-electron oxidation of l-arginine to form a mixture of 2-oxo-4(S)-hydroxy-5-guanidinovaleric acid and 2-oxo-5-guanidinovaleric acid. Steady-state kinetics analysis in the presence and absence of catalase shows that one molecule of peroxide is formed for every molecule of dioxygen consumed in the reaction. Moreover, for each molecule of 2-oxo-4(S)-hydroxy-5-guanidinovaleric acid produced, two molecules of dioxygen are consumed, suggesting that both the 4-hydroxy and 2-keto groups are derived from water. This was confirmed by running the reactions using either [18] O 2 or H 2 [18] O and analyzing the products by ESI-MS. Incorporation of [18] O was only observed when the reaction was performed in H 2 [18] O. Crystal structures of SwMppP with l-arginine, 2-oxo-4(S)-hydroxy-5-guanidinovaleric acid, or 2-oxo-5-guanidinovaleric acid bound were determined at resolutions of 2.2, 1.9. and 1.8 Å, respectively. The structural data show that the N-terminal portion of the protein is disordered unless substrate or product is bound in the active site, in which case it forms a well-ordered helix that covers the catalytic center. This observation suggested that the N-terminal helix may have a role in substrate binding and/or catalysis. Our structural and kinetic characterizations of N-terminal variants show that the N-terminus is critical for catalysis. Here, in light of this new information, we have refined our previously proposed mechanism of the SwMppP-catalyzed oxidation of l-arginine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Mitigating the optical depth degeneracy using the kinematic Sunyaev-Zel’dovich effect with CMB-S4 data

The epoch of reionization is one of the major phase transitions in the history of the universe, and is a focus of ongoing and upcoming cosmic microwave background (CMB) experiments with improved sensitivity to small-scale fluctuations. Reionization also represents a significant contaminant to CMB-derived cosmological parameter constraints, due to the degeneracy between the Thomson-scattering optical depth, $\tau$, and the amplitude of scalar perturbations, $A_s$. This degeneracy subsequently hinders the ability of large-scale structure data to constrain the sum of the neutrino masses, a major target for cosmology in the 2020s. In this work, we explore the kinematic Sunyaev-Zel'dovich (kSZ) effect as a probe of reionization, and show that it can be used to mitigate the optical depth degeneracy with high-sensitivity, high-resolution data from the upcoming CMB-S4 experiment. We discuss the dependence of the kSZ power spectrum on physical reionization model parameters, as well as on empirical reionization parameters, namely $\tau$ and the duration of reionization, $\Delta z$. We show that by combining the kSZ two-point function and the reconstructed kSZ four-point function, degeneracies between $\tau$ and $\Delta z$ can be strongly broken, yielding tight constraints on both parameters. We forecast $\sigma(\tau) = 0.003$ and $\sigma(\Delta z) = 0.25$ for a combination of CMB-S4 and Planck data, including detailed treatment of foregrounds and atmospheric noise. The constraint on $\tau$ is nearly identical to the cosmic-variance limit that can be achieved from large-angle CMB polarization data. The kSZ effect thus promises to yield not only detailed information about the reionization epoch, but also to enable high-precision cosmological constraints on the neutrino mass.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1990

Development of multiple source data processing for structural analysis at a regional scale

Various image processing techniques developed for enhancement and extraction of linear features, of interest to the structural geologist, from digital remote sensing, geologic, and gravity data, are presented. These techniques include: (1) automatic detection of linear features and construction of rose diagrams from Landsat MSS data; (2) enhancement of principal structural directions using selective filters on Landsat MSS, Spacelab panchromatic, and HCMM NIR data; (3) directional filtering of Spacelab panchromatic data using Fast Fourier Transform; (4) detection of linear/elongated zones of high thermal gradient from thermal infrared data; and (5) extraction of strong gravimetric gradients from digitized Bouguer anomaly maps. Processing results can be compared to each other through the use of a geocoded database to evaluate the structural importance of each lineament according to its depth: superficial structures in the sedimentary cover, or deeper ones affecting the basement. These image processing techniques were successfully applied to achieve a better understanding of the transition between Provence and the Pyrenees structural blocks, in southeastern France, for an improved structural interpretation of the Mediterranean region.

Carrere, Veronique↗

DOE OSTI2018

Multiplexed characterization of complex gas-phase mixtures combining chirped-pulse Fourier transform microwave spectroscopy and VUV photoionization time-of-flight mass spectrometry

We examine details of the design and operation of a single apparatus that combines Chirped-Pulse Fourier Transform Microwave (CP-FTMW) spectroscopy with vacuum ultraviolet (VUV) photoionization Time-of-Flight Mass Spectrometry (TOFMS). The supersonic expansion used for cooling samples is interrogated first by passing through the region between two microwave horns capable of broadband excitation and detection in the 2-18 GHz frequency region of the microwave. After passing through this region, the expansion is skimmed to form a molecular beam, before being probed with 118 nm (10.5 eV) single-photon VUV photoionization in a linear time-of-flight mass spectrometer. The two detection schemes are powerfully complementary to one another. CP-FTMW detects all components with significant permanent dipole moments. Rotational transitions provide high-resolution structural data. VUV TOFMS provides a gentle and general method for ionizing all components of a gas phase mixture with ionization thresholds below 10.5 eV, providing their molecular formulae. The advantages, complementarity, and limitations of the combined methods are highlighted through findings on two gas-phase mixtures made up of (i) three furanic compounds, two of which are structural isomers of one another, and (ii) the effluent from a flash pyrolysis source with o-guaiacol as the precursor.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Common Electric Power Transmission System Model JSON Schema Specification

The Common Electric Power Transmission System Model (CTM) is an intuitive, extensible, language-agnostic, and error-resistant specification of electric power network components parameter names and units, and relation between components, intended for use by the research community developing new computational methods for power systems operations and simulation. Power system datasets following the CTM specification can be read as dictionaries and manipulated in that form in most programming languages (e.g., Python, Julia, C++). This standard data structure in CTM makes it easy to work in multiple power systems domains (e.g., economic operation, reliability assessment, electricity markets, stability assessment, etc.) without requiring conversions between use-case-specific file formats with information loss in the process. This repository specifies CTM as a JSON Schema, provides documentation, derivate (code-generated) implementations of CTM, and example data and usage of the schema for important use cases.

Aravena Solis, Ignacio↗

DOE OSTI2016

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra

Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a “bird’s eye view” of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem. Results: We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry data sets showed that TopMG outperformed existing methods in identifying complex proteoforms.

Dynamic Programming↗

NASA NTRS1989

Fractal image compression

Fractals are geometric or data structures which do not simplify under magnification. Fractal Image Compression is a technique which associates a fractal to an image. On the one hand, the fractal can be described in terms of a few succinct rules, while on the other, the fractal contains much or all of the image information. Since the rules are described with less bits of data than the image, compression results. Data compression with fractals is an approach to reach high compression ratios for large data streams related to images. The high compression ratios are attained at a cost of large amounts of computation. Both lossless and lossy modes are supported by the technique. The technique is stable in that small errors in codes lead to small errors in image data. Applications to the NASA mission are discussed.

Barnsley, Michael F.↗

DOE OSTI2017

The exploration of nonlinear elasticity and its efficient parameterization for crystalline materials

Conventional approaches to analyzing the very large coherency strains that can occur during solid-state phase transformations are founded in linear elasticity and rely on infinitesimal strain metrics. Despite this, there are many technologically important examples where misfit strains of multi-phase mixtures are very large during their synthesis and/or application. Here in this paper, we present a framework for constructing strain-energy expressions and stress-strain relationships beyond the linear-elastic limit for crystalline solids. This approach utilizes group theoretical concepts to minimize both the number of free parameters in the strain-energy expression and amount of first-principles training data required to parameterize strain-energy models that are invariant to all crystal symmetries. Within this framework, the strain-energy and elastic stiffness can be described to high accuracy in terms of a set of conventional symmetry-adapted finite strain metrics that we define independent of crystal symmetry. As an illustration, we use first-principles electronic structure data to parameterize strain energy polynomials and employ them to explore the strain- energy surfaces of HCP Zr and Mg, as well as several important Zr-H and Mg-Nd phases that are known to precipitate coherently within the HCP matrices of Zr and Mg.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Experimental and Theoretical Study of the Electronic Structures of Lanthanide Indium Perovskites LnInO 3

Ternary lanthanide indium oxides LnInO 3 (Ln = La, Pr, Nd, Sm) were synthesized by high-temperature solid-state reaction and characterized by Xray powder diffraction. Rietveld refinement of the powder patterns showed the LnInO 3 materials to be orthorhombic perovskites belonging to the space group Pnma, based on almost-regular InO 6 octahedra and highly distorted LnO 12 polyhedra. Experimental structural data were compared with results from density functional theory (DFT) calculations employing a hybrid Hamiltonian. Valence region X-ray photoelectron and K-shell X-ray emission and absorption spectra of the LnInO 3 compounds were simulated with the aid of the DFT calculations. Photoionization of lanthanide 4f orbitals gives rise to a complex final-state multiplet structure in the valence region for the 4f n compounds PrInO 3 , NdInO 3 , and SmInO 3 , and the overall photoemission spectral profiles were shown to be a superposition of final-state 4f n-1 terms onto the cross-section weighted partial densities of states from the other orbitals. The occupied 4f states are stabilized in moving across the series Pr-Nd-Sm. Band gaps were measured using diffuse reflectance spectroscopy. These results demonstrated that the band gap of LaInO 3 is 4.32 eV, in agreement with DFT calculations. This is significantly larger than a band gap of 2.2 eV first proposed in 1967 and based on the idea that In 4d states lie above the top of the O 2p valence band. However, both DFT and X-ray spectroscopy show that In 4d is a shallow core level located well below the bottom of the valence band. Band gaps greater than 4 eV were observed for NdInO 3 and SmInO 3 , but a lower gap of 3.6 eV for PrInO 3 was shown to arise from the occupied Pr 4f states lying above the main O 2p valence band.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Designing Mixed Detergent Micelles for Uniform Neutron Contrast

Micelle-forming detergents provide an amphipathic environment that mimics lipid bilayers and are important tools used to solubilize and stabilize membrane proteins in solution for in vitro structural investigations. Small-angle neutron scattering (SANS) performed at the neutron contrast match point of detergent molecules allows observing the scattering signal from membrane proteins unobstructed by contributions from the detergent. However, we show here that even for a perfectly average-contrast matched detergent there arises significant core-shell scattering from the contrast difference between aliphatic detergent tails and hydrophilic head groups. This residual signal at the average detergent contrast match point interferes with interpreting structural data of membrane proteins. This complication is often made worse by the presence of excess empty (protein-free) micelles. Here, we present an approach for the rational design of mixed micelles containing a deuterated detergent analog, which eliminates neutron contrast between core and shell, and allows the micelle scattering to be fully contrast matched to unambiguously resolve membrane protein structure using solution SANS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗