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At least 361 records · Page 20

Convergent Concordant Mode Approach for Molecular Vibrations: CMA-2

The concordant mode approach (CMA) is a promising new scheme for dramatically increasing the system size and level of theory achievable in quantum chemical computations of molecular vibrational frequencies. Here, we achieve advances in the CMA hierarchy by computations targeting CCSD(T)/cc-pVTZ (coupled cluster singles and doubles with perturbative triples using a correlation-consistent polarized-valence triple-ζ basis set) benchmarks within the G2 molecular test set, executing a statistical analysis for 1501 frequencies from 111 compounds and then separately solving the refractory case of pyridine. First, MP2/cc-pVTZ (second-order Møller–Plesset perturbation theory with the same basis set) proves to be an excellent and preferred choice for generating the underlying (Level B) normal modes of the CMA scheme. Utilizing this Level B within the CMA-0A method reproduces the 1501 benchmark frequencies with a mean absolute error (MAE) of only 0.11 cm –1 and an attendant standard deviation of 0.49 cm –1 . Second, a convergent CMA-2 method is constituted that allows efficient computation of higher level (Level A) frequencies to any reasonable accuracy threshold by using only Hartree–Fock (HF) and MP2 or density functional theory (DFT) data to generate ξ parameters, which select the sparse off-diagonal force field elements for explicit evaluation at Level A. When Level B = MP2/cc-pVTZ, a cutoff of ξ = 0.02 provides an average maximum absolute error per molecule of only 0.17 cm –1 by incurring merely a 33% increase in average cost over CMA-0A. This CMA-2 method also eradicates the 4 problematic CMA-0A outliers of pyridine with even less effort (ξ = 0.04, 22% increase). Finally, the newly developed CMA procedures are shown to be highly successful when applied to 1-(1H-pyrrol-3-yl)ethanol, a new test molecule with diverse types of vibration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An analytical transformation technique for generating uniformly spaced computational mesh

An analytical transformation method which can map arbitrary physical coordinate grid distribution into desired computational coordinate with uniform grid distribution is derived. The transformation function and its higher derivatives are differentiable. Salient features include; (1) precise control of grid sizes; (2) more than one location of clustered grids; (3) exact positioning of particular computational nodes in the physical plane; and (4) ensuring several patches of uniformly spaced grids in the physical plane for the higher accuracies (such as at the boundaries), etc., while keeping the variation of grid spacing continuous to avoid numerical instability.

Oh, Y. H.↗

The evolution of X-ray clusters in a cold plus hot dark matter universe

We present the first self-consistently computed results on the evolution of X-ray properties of galaxy clusters in a cold + hot dark matter (CHDM) model. We have performed a hydrodynamic plus N-body simulation for the COBE-compatible CHDM model with standard mass components: Omega(sub hot) = 0.3, Omega (sub cold) = 0.6 and Omega(sub baryon) = 0.1 (h = 0.5). In contrast with the CDM model, which fails to reproduce the observed temperature distribution function dN/dT (Bryan et al. 1994b), the CHDM model fits the observational dN/dT quite well. Our results on X-ray luminosity are less firm but even more intriguing. We find that the resulting X-ray luminosity functions at redshifts z = 0.0, 0.2, 0.4, 0.7 are well fit by observations, where they overlap. The fact that both temperatures and luminosities provide a reasonable fit to the available observational data indicates that, unless we are missing some essential physics, there is neither room nor need for a large fraction of gas in rich clusters: 10% (or less) in baryons is sufficient to explain their X-ray properties. We also see a tight correlation between X-ray luminosity and gas temperature.

Bryan, Greg L.↗

Accessing and Visualizing scientific spatiotemporal data

This paper discusses work done by JPL 's Parallel Applications Technologies Group in helping scientists access and visualize very large data sets through the use of multiple computing resources, such as parallel supercomputers, clusters, and grids These tools do one or more of the following tasks visualize local data sets for local users, visualize local data sets for remote users, and access and visualize remote data sets The tools are used for various types of data, including remotely sensed image data, digital elevation models, astronomical surveys, etc The paper attempts to pull some common elements out of these tools that may be useful for others who have to work with similarly large data sets.

data sets↗

Reducing the Volume of NASA Earth-Science Data

A computer program reduces data generated by NASA Earth-science missions into representative clusters characterized by centroids and membership information, thereby reducing the large volume of data to a level more amenable to analysis. The program effects an autonomous data-reduction/clustering process to produce a representative distribution and joint relationships of the data, without assuming a specific type of distribution and relationship and without resorting to domain-specific knowledge about the data. The program implements a combination of a data-reduction algorithm known as the entropy-constrained vector quantization (ECVQ) and an optimization algorithm known as the differential evolution (DE). The combination of algorithms generates the Pareto front of clustering solutions that presents the compromise between the quality of the reduced data and the degree of reduction. Similar prior data-reduction computer programs utilize only a clustering algorithm, the parameters of which are tuned manually by users. In the present program, autonomous optimization of the parameters by means of the DE supplants the manual tuning of the parameters. Thus, the program determines the best set of clustering solutions without human intervention.

Lee, Seungwon↗

Tuning Catalytic Reactivity via Wetting Control through Oxygen Vacancies: Ru Clusters on Anatase TiO 2 and CeO 2 Supports

The shape of supported metal particles regulates their catalytic reactivity and is determined by the degree of wetting between the metal particle and the support surface. Flattened particles that wet support surfaces were reported in various catalytic systems, particularly in the subnanometer size regime. Such consequential metal–support wetting phenomena are poorly understood, and methods to study them on powder catalysts under realistic conditions are lacking. Here, we investigate the size-dependent wetting behaviors of Ru particles on two reducible-oxide supports, anatase TiO 2 (TiO 2 -A) and CeO 2 , under reducing catalytic conditions. X-ray absorption spectroscopy (XAS), low-energy ion scattering (LEIS), and density functional theory (DFT) are combined to determine the shape of Ru particles. Ru particles remain three-dimensional without wetting the TiO 2 -A support within the coverage range studied (0.06–0.98 Ru nm –2 ). In contrast, at low coverages (<0.25 Ru nm –2 ), Ru wets the CeO 2 support to form flat, disordered structures. The higher wettability of CeO 2 than TiO 2 -A is attributed to oxygen vacancies in the near-surface region. The shape difference between small Ru particles or clusters on the two supports leads to drastically contrasting catalytic reactivities in polyolefin hydrogenolysis, despite similar diameters. As a result, this work highlights the implications of metal–support wetting, or cluster shape, on catalytic behaviors of small metal clusters, while establishing the foundation for future systematic studies of such a phenomenon in realistic systems, by delivering a multitechnique methodology and revealing governing fundamental principles.

42 ENGINEERING↗

MEDUSA - An overset grid flow solver for network-based parallel computer systems

Continuing improvement in processing speed has made it feasible to solve the Reynolds-Averaged Navier-Stokes equations for simple three-dimensional flows on advanced workstations. Combining multiple workstations into a network-based heterogeneous parallel computer allows the application of programming principles learned on MIMD (Multiple Instruction Multiple Data) distributed memory parallel computers to the solution of larger problems. An overset-grid flow solution code has been developed which uses a cluster of workstations as a network-based parallel computer. Inter-process communication is provided by the Parallel Virtual Machine (PVM) software. Solution speed equivalent to one-third of a Cray-YMP processor has been achieved from a cluster of nine commonly used engineering workstation processors. Load imbalance and communication overhead are the principal impediments to parallel efficiency in this application.

Smith, Merritt H.↗

Parallel Navier-Stokes computations on shared and distributed memory architectures

We study a high order finite difference scheme to solve the time accurate flow field of a jet using the compressible Navier-Stokes equations. As part of our ongoing efforts, we have implemented our numerical model on three parallel computing platforms to study the computational, communication, and scalability characteristics. The platforms chosen for this study are a cluster of workstations connected through fast networks (the LACE experimental testbed at NASA Lewis), a shared memory multiprocessor (the Cray YMP), and a distributed memory multiprocessor (the IBM SPI). Our focus in this study is on the LACE testbed. We present some results for the Cray YMP and the IBM SP1 mainly for comparison purposes. On the LACE testbed, we study: (1) the communication characteristics of Ethernet, FDDI, and the ALLNODE networks and (2) the overheads induced by the PVM message passing library used for parallelizing the application. We demonstrate that clustering of workstations is effective and has the potential to be computationally competitive with supercomputers at a fraction of the cost.

Hayder, M. Ehtesham↗

MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes

While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.

59 BASIC BIOLOGICAL SCIENCES↗

Classical Preoptimization Approach for ADAPT-VQE: Maximizing the Potential of High-Performance Computing Resources to Improve Quantum Simulation of Chemical Applications

The ADAPT-VQE algorithm is a promising method for generating a compact ansatz based on derivatives of the underlying cost function, and it yields accurate predictions of electronic energies for molecules. In this work, we report the implementation and performance of ADAPT-VQE with our recently developed sparse wave function circuit solver (SWCS) in terms of accuracy and efficiency for molecular systems with up to 52 spin orbitals. The SWCS can be tuned to balance computational cost and accuracy, which extends the application of ADAPT-VQE for molecular electronic structure calculations to larger basis sets and a larger number of qubits. Using this tunable feature of the SWCS, we propose an alternative optimization procedure for ADAPT-VQE to reduce the computational cost of the optimization. Furthermore, by preoptimizing a quantum simulation with a parametrized ansatz generated with ADAPT-VQE/SWCS, we aim to utilize the power of classical high-performance computing in order to minimize the work required on noisy intermediate-scale quantum hardware, which offers a promising path toward demonstrating quantum advantage for chemical applications.

ADAPT-VQE↗

Capturing Surface Coverage Effects in Heterogeneous Catalysis

Adsorbate–adsorbate lateral interactions at relevant surface coverages have a significant effect on chemical kinetics, thereby influencing the activity of a heterogeneous catalyst. Coverage-dependent kinetic and thermodynamic parameters therefore must be included in studies of such complex systems to properly predict the turnover frequencies and kinetic trends. Thus, it becomes extremely important to accurately capture the strength of lateral interactions between neighboring species under realistic reaction conditions. In this Perspective, we discuss the various existing computational and experimental methods for determining adspecies coverage and configurational effects. The choice of the tools and methods employed in such studies depends on factors such as time, length scales, computational cost, the presence of solvents, and reaction conditions. The applications of each method and the respective challenges are also discussed here. As a result, we discuss the recent developments and future of the state-of-the-art for inclusion of surface coverage and configuration into a holistic picture for accurate predictions of catalytic behavior.

09 BIOMASS FUELS↗

COSMIC DAWN: Distributed Analysis of Wireless at Nextscale

Distributed Analysis of Wireless at Nextscale (DAWN) is a novel simulation framework for large-scale design-space exploration (DSE) of unmodified software-defined radio (SDR) applications interacting in a scalable, high-fidelity, virtual physics environment. The software-defined nature of the coupled software-physics simulation leverages hardware emulation to permit in-depth examination and modification of not only the electromagnetic environment, including each signal in flight, but also the precise state of system software and components. DAWN supports modular, customizable physics environments allowing realistic propagation effects so that computationally efficient empirical models, reduced order/surrogate models, or large-scale, high-fidelity, site-specific simulations can be used as a propagation medium based on scenario requirements. This paper introduces DAWN’s design and initial implementation, detailing key architectural components, including the Physics Realization Engine (PhyRE), Runtime Infrastructure for Simulation Environments (RISE), and the design space exploration (DSE) suite. It concludes with demonstrations using unmodified 4G/LTE software available from srsRAN on computing resources ranging from a small cluster to ORNL’s Frontier Exascale system.

Wise, Mike [ORNL] (ORCID:0000000266120641)↗

Ab Initio Many Body Quantum Embedding and Local Correlation in Crystalline Materials using Interpolative Separable Density Fitting

We present an efficient implementation of ab initio many-body quantum embedding and local correlation methods for infinite periodic systems through translational symmetry adapted interpolative separable density fitting, an approach which reduces the scaling of the calculations to only linear with the number of k-points. Employing this methodology, we compute correlated ground-state coupled cluster energies within density matrix embedding and local natural orbital correlation frameworks for both weakly and strongly correlated solids, using up to 1000 k-points. By extrapolating the local correlation domains and k-point sampling we further obtain estimates of the full coupled cluster with singles, doubles, and perturbative triples ground-state energies in the thermodynamic limit.

Chemical Physics (physics.chem-ph)↗

Time-shared Cathode Ray Tube

Time-shared cathode tube provides high quality display at low cost display stations which utilize television moniters. It updates a cluster of graphic displays from a computer and is useful in systems not equipped for graphics time-sharing.

Herndon, E. S.↗

Mars: Definition and characterization of global surface units with emphasis on composition

Viking 2 approach maps of red and violet normal albedo are used to define units of similar optical properties for a large area of the Martian surface. Computer processing of these data reveals clusters of albedo values relating to specific, contiguous regions of the planet, with some unit boundaries being of a gradational nature while others are more discrete. A study of the albedo properties of analog materials measured in the laboratory, and of telescopic spectrophotometry of Mars, indicates that both hydroxylated and hematitic oxidized materials exist on the surface. The most probable surface expression of global dust and/or high albedo soils is in the classical bright region, Arabia. Most low albedo features in the region studied have red and violet albedos that are consistent with a dark substrate, such as basalt, coated by, or mixed with, a fine grained alteration product.

Mccord, T. B.↗

Hot gas in evolving galaxy clusters and groups - Implications for the microwave and X-ray backgrounds

A phenomenological model for the luminosity function of galaxy groups and clusters allows its evolution to be described in terms of the two-point galaxy correlation function. The observable properties of hot gas in virialized groups and clusters at high redshift have been computed. These include the spectral distortion by Comptonization of the cosmic blackbody spectrum, fluctuations in the cosmic microwave background arising by this same process, and the diffuse X-ray background and fluctuations therein arising from thermal emission by the intracluster gas.

Schaeffer, Richard↗

Numerical analysis of base flowfield at high altitude for a four-engine clustered nozzle configuration

The objective of this study is to benchmark a four-engine clustered nozzle base flowfield with a computational fluid dynamics (CFD) model. The CFD model is a pressure based, viscous flow formulation. An adaptive upwind scheme is employed for the spatial discretization. The upwind scheme is based on second and fourth order central differencing with adaptive artificial dissipation. Qualitative base flow features such as the reverse jet, wall jet, recompression shock, and plume-plume impingement have been captured. The computed quantitative flow properties such as the radial base pressure distribution, model centerline Mach number and static pressure variation, and base pressure characteristic curve agreed reasonably well with those of the measurement. Parametric study on the effect of grid resolution, turbulence model, inlet boundary condition and difference scheme on convective terms has been performed. The results showed that grid resolution and turbulence model are two primary factors that influence the accuracy of the base flowfield prediction.

Wang, Ten-See↗

Numerical study of base pressure characteristic curve for a four-engine clustered nozzle configuration

The objective of this study is to benchmark a four-engine clustered nozzle base flowfield with a computational fluid dynamics (CFD) model. The CFD model is a three-dimensional pressure-based, viscous flow formulation. An adaptive upwind scheme is employed for the spatial discretization. The upwind scheme is based on second and fourth order central differencing with adaptive artificial dissipation. Qualitative base flow features such as the reverse jet, wall jet, recompression shock, and plume-plume impingement have been captured. The computed quantitative flow properties such as the radial base pressure distribution, model centerline Mach number and static pressure variation, and base pressure characteristic curve agreed reasonably well with those of the measurement. Parametric study on the effect of grid resolution, turbulence model, inlet boundary condition and difference scheme on convective terms has been performed. The results showed that grid resolution had a strong influence on the accuracy of the base flowfield prediction.

Wang, Ten-See↗