Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Cluster computing”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Variability in NGC 3201 Giant Stars and Its Impact on Their Spectroscopic [Fe/H] Determination

We present the analysis of 34 light curves in V and I of 17 giant stars in the globular cluster NGC 3201 to check if such stars are variable and if their variability has some kind of impact on the iron abundance as obtained from spectroscopic measurements. First, we computed the generalized Lomb–Scargle and phase dispersion minimization periodograms of the sample to check if the stars were variables. In this way, seven stars of the sample were found to be nonvariable, two stars are considered as possible variables, and eight stars were found to be variable, with periods ranging from 0.0881 ± 0.0001 to 0.5418 ± 0.0027 days. According to the literature, the variables have distinct values of [Fe I/H]: the three most metal-rich stars are in the red giant branch (RGB) stage, one has [Fe I/H] = −1.37 dex, while the other two have [Fe I/H] = −1.31 dex. The two most metal-poor variables have [Fe I/H] = −1.61 dex and [Fe I/H] = −1.62 dex, and are AGB stars; the remaining variables have [Fe I/H] = −1.44, −1.48, and −1.50 dex, the first two being RGB stars while the last is an AGB star. On the other hand, stars that appear to be nonvariable have −1.56 ≤ [Fe I/H] ≤ −1.40. We conclude that variability somehow affects the spectroscopic determination of the iron content of giant stars in NGC 3201, increasing the iron spread of the cluster. If variability is not taken into account, this spread could be incorrectly interpreted as due to an intrinsic iron spread affecting the stars of the cluster.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Unified Communication Optimization Strategies for Sparse Triangular Solver on CPU and GPU Clusters

This paper presents a unified communication optimization framework for sparse triangular solve (SpTRSV) algorithms on CPU and GPU clusters. The framework builds upon a 3D communication-avoiding (CA) layout of Px × Py × Pz processes that divides a sparse matrix into Pz submatrices, each handled by a Px × Py 2D grid with block-cyclic distribution. We propose three communication optimization strategies: First, a new 3D SpTRSV algorithm is developed, which trades the inter-grid communication and synchronization with replicated computation. This design requires only one inter-grid synchronization, and the inter-grid communication is efficiently implemented with sparse allreduce operations. Second, broadcast and reduction communication trees are used to reduce message latency of the intra-grid 2D communication on CPU clusters. Finally, we leverage GPU-initiated one-sided communication to implement the communication trees on GPU clusters. With these nested inter- and intra-grid communication optimization strategies, the proposed 3D SpTRSV algorithm can attain up to 3.45x speedups compared to the baseline 3D SpTRSV algorithm using up to 2048 Cori Haswell CPU cores. In addition, the proposed GPU 3D SpTRSV algorithm can achieve up to 6.5x speedups compared to the proposed CPU 3D SpTRSV algorithm with Pz up to 64. Finally it is remarkable that the proposed GPU 3D SpTRSV can scale to 256 GPUs using the Perlmutter system while the existing 2D SpTRSV algorithm can only scale up to 4 GPUs.

Sao, Piyush↗
DOE OSTI2024

Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

Premise: The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics. Methods: Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized. Results: Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method. Discussion: The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Physics-based reward driven image analysis in microscopy

The rise of electron microscopy has expanded our ability to acquire nanometer and atomically resolved images of complex materials. The resulting vast datasets are typically analyzed by human operators, an intrinsically challenging process due to the multiple possible analysis steps and the corresponding need to build and optimize complex analysis workflows. We present a methodology based on the concept of a Reward Function coupled with Bayesian Optimization, to optimize image analysis workflows dynamically. The Reward Function is engineered to closely align with the experimental objectives and broader context and is quantifiable upon completion of the analysis. Here, cross-section, high-angle annular dark field (HAADF) images of ion-irradiated (Y, Dy)Ba 2 Cu 3 O 7–δ thin-films were used as a model system. The reward functions were formed based on the expected materials density and atomic spacings and used to drive multi-objective optimization of the classical Laplacian-of-Gaussian (LoG) method. These results can be benchmarked against the DCNN segmentation. This optimized LoG* compares favorably against DCNN in the presence of the additional noise. We further extend the reward function approach towards the identification of partially-disordered regions, creating a physics-driven reward function and action space of high-dimensional clustering. We pose that with correct definition, the reward function approach allows real-time optimization of complex analysis workflows at much higher speeds and lower computational costs than classical DCNN-based inference, ensuring the attainment of results that are both precise and aligned with the human-defined objectives.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

MB-Fit: Software infrastructure for data-driven many-body potential energy functions

Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Sub-system self-consistency in coupled cluster theory

Here, in this article, we provide numerical evidence indicating that the single-reference coupled-cluster (CC) energies can be calculated alternatively to their copybook definition. We demonstrate that the CC energy can be reconstructed by diagonalizing the effective Hamiltonians describing correlated sub-systems of the many-body system. In the extreme case, we provide numerical evidence that the CC energy can be reproduced through the diagonalization of the effective Hamiltonian describing sub-system composed of a single electron. These properties of the CC formalism can be exploited to design protocols to define effective interactions in sub-systems used as probes to calculate the energy of the entire system and introduce a new type of self-consistency for approximate CC approaches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Understanding Solid Electrolyte Interphase Nucleation and Growth on Lithium Metal Surfaces

Experiments and theory are needed to decode the exact structure and distribution of components of a passivation layer formed at the anode surface of Li metal batteries, known as the Solid Electrolyte Interphase (SEI). Due to the inherent dynamic behavior as well as the lithium reactivity, the SEI structure and its growth mechanisms are still unclear. This study uses molecular simulation and computational chemistry tools to investigate the initial nucleation and growth dynamics of LiOH and Li2O that provide us with thermodynamics and structural information about the nucleating clusters of each species. Following the most favorable pathways for the addition of each of the components to a given nascent SEI cluster reveals their preferential nucleation mechanisms and illustrates different degrees of crystallinity and electron density distribution that are useful to understand ionic transport through SEI blocks.

25 ENERGY STORAGE↗
DOE OSTI2024

How Aqueous Solvation Impacts the Frequencies and Intensities of Infrared Absorption Bands in Flavin: The Quest for a Suitable Solvent Model

FTIR spectroscopy accompanied by quantum chemical simulations can reveal important information about molecular structure and intermolecular interactions in the condensed phase. Simulations typically account for the solvent either through cluster quantum mechanical (QM) models, polarizable continuum models (PCM), or hybrid quantum mechanical/molecular mechanical (QM/MM) models. Recently, we studied the effect of aqueous solvent interactions on the vibrational frequencies of lumiflavin, a minimal flavin model, using cluster QM and PCM models. Those models successfully reproduced the relative frequencies of four prominent stretching modes of flavin’s isoalloxazine ring in the diagnostic 1450–1750 cm−1 range but poorly reproduced the relative band intensities. Here, we extend our studies on this system and account for solvation through a series of increasingly sophisticated models. Only by combining elements of QM clusters, QM/MM, and PCM approaches do we obtain an improved agreement with the experiment. The study sheds light more generally on factors that can impact the computed frequencies and intensities of IR bands in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Extension of frozen natural orbital approximation to open-shell references: Theory, implementation, and application to single-molecule magnets

Natural orbitals are often used to achieve a more compact representation of correlated wave-functions. Using natural orbitals computed as eigenstates of the virtual–virtual block of the state density matrix instead of the canonical Hartree–Fock orbitals results in smaller errors when the same fraction of virtual space is frozen. This strategy, termed frozen natural orbital (FNO) approach, is effective in reducing the cost of regular coupled-cluster (CC) calculations and some multistate methods, such as EOM-IP-CC (equation-of-motion CC for ionization potentials). This contribution extends the FNO approach to the EOM-SF-CC ansatz (EOM-CC with spin-flip). In contrast to EOM-IP-CCSD, EOM-SF-CCSD relies on high-spin open-shell references. Using FNOs computed for an open-shell reference leads to an erratic behavior of the EOM-SF-CC energies and properties due to an inconsistent truncation of the α and β orbital spaces. A general solution to problems arising in the EOM-CC calculations utilizing open-shell references, termed OSFNO (open-shell FNO), is proposed. Furthermore, by means of singular value decomposition (SVD) of the overlap matrix of the α and β orbitals, the OSFNO algorithm identifies the corresponding orbitals and determines virtual orbitals corresponding to the singly occupied space. This is followed by SVD of the singlet part of the state density matrix in the remaining virtual orbital subspace. The so-computed FNOs preserve the spin purity of the open-shell orbital subspace to the extent allowed by the original reference, thus facilitating a safe truncation of the virtual space. The performance of OSFNO is benchmarked for selected diradicals and triradicals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Giant Wilson loops and AdS 2 /dCFT 1

The 1/2-BPS Wilson loop in N = 4 supersymmetric Yang-Mills theory is an important and well-studied example of conformal defect. In particular, much work has been done for the correlation functions of operator insertions on the Wilson loop in the fundamental representation. In this paper, we extend such analyses to Wilson loops in the large-rank symmetric and antisymmetric representations, which correspond to probe D3 and D5 branes with AdS 2 × S 2 and AdS 2 × S 4 worldvolume geometries, ending at the AdS 5 boundary along a one-dimensional contour. We first compute the correlation functions of protected scalar insertions from supersymmetric localization, and obtain a representation in terms of multiple integrals that are similar to the eigenvalue integrals of the random matrix, but with important differences. Using ideas from the Fermi Gas formalism and the Clustering method, we evaluate their large N limit exactly as a function of the ’t Hooft coupling. The results are given by simple integrals of polynomials that resemble the Q-functions of the Quantum Spectral Curve, with integration measures depending on the number of insertions. Next, we study the correlation functions of fluctuations on the probe D3 and D5 branes in AdS. We compute a selection of three- and four-point functions from perturbation theory on the D-branes, and show that they agree with the results of localization when restricted to supersymmetric kinematics. We also explain how the difference of the internal geometries of the D3 and D5 branes manifests itself in the localization computation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

The Effect of Geometry, Spin, and Orbital Optimization in Achieving Accurate, Correlated Results for Iron–Sulfur Cubanes

Iron–sulfur clusters comprise an important functional motif in the catalytic centers of biological systems, capable of enabling important chemical transformations at ambient conditions. This remarkable capability derives from a notoriously complex electronic structure that is characterized by a high density of states that is sensitive to geometric changes. The spectral sensitivity to subtle geometric changes has received little attention from correlated, large active space calculations, owing partly to the exceptional computational complexity for treating these large and correlated systems accurately. Here, to provide insight into this aspect, we report the first Complete Active Space Self Consistent Field (CASSCF) calculations for different geometries of the [Fe(II/III) 4 S 4 (SMe) 4 ] -2 clusters using two complementary, correlated solvers: spin-pure Adaptive Sampling Configuration Interaction (ASCI) and Density Matrix Renormalization Group (DMRG). We find that the previously established picture of a double-exchange driven magnetic structure, with minute energy gaps (<1 mHa) between consecutive spin states, has a weak dependence on the underlying geometry. However, the spin gap between the singlet and the spin state 2S + 1 = 19, corresponding to a maximal number of Fe-d electrons being unpaired and of parallel spin, is strongly geometry dependent, changing by a factor of 3 upon slight deformations that are still within biologically relevant parameters. The CASSCF orbital optimization procedure, using active spaces as large as 86 electrons in 52 orbitals, was found to reduce this gap compared to typical mean-field orbital approaches. Our results show the need for performing large active space calculations to unveil the challenging electronic structure of these complex catalytic centers and should serve as accurate starting points for fully correlated treatments upon inclusion of dynamical correlation outside the active space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Solute-vacancy clustering in aluminum

In this study, we present an extensive first-principles database of solute-vacancy, homoatomic, heteroatomic solute-solute, and solute-solute-vacancy binding energies of relevant alloying elements in aluminum. We particularly focus on the systems with major alloying elements in aluminum, i.e., Cu, Mg, and Si. The computed binding energies of solute-vacancy, solute-solute pairs, and solute-solute-vacancy triplets agree with available experiments and theoretical results in literature. We consider physical factors such as solute size and formation energies of intermetallic compounds to correlate with binding energies. Systematic studies of the homoatomic solute-solute-vacancy and heteroatomic (Cu, Mg, or Si)-solute-vacancy complexes reveal the overarching effect of the vacancy in stabilizing solute-solute pairs. The binding energy database presented here elucidates the interaction between solute cluster and vacancy in aluminum, and it is expected to provide insight into the design of advanced Al alloys with tailored properties.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Methods to Calculate Electronic Excited-State Dynamics for Molecules on Large Metal Clusters with Many States: Ensuring Fast Overlap Calculations and a Robust Choice of Phase

Here, we present an efficient set of methods for propagating excited-state dynamics involving a large number of configuration interaction singles (CIS) or Tamm-Dancoff approximation (TDA) single-reference excited states. Specifically, (i) following Head-Gordon et al., we implement an exact evaluation of the overlap of singly-excited CIS/TDA electronic states at different nuclear geometries using a biorthogonal basis and (ii) we employ a unified protocol for choosing the correct phase for each adiabat at each geometry. For many-electron systems, the combination of these techniques significantly reduces the computational cost of integrating the electronic Schrodinger equation and imposes minimal overhead on top of the underlying electronic structure calculation. As a demonstration, we calculate the electronic excited-state dynamics for a hydrogen molecule scattering off a silver metal cluster, focusing on high-lying excited states, where many electrons can be excited collectively and crossings are plentiful. Interestingly, we find that the high-lying, plasmon-like collective excitation spectrum changes with nuclear dynamics, highlighting the need to simulate non-adiabatic nuclear dynamics and plasmonic excitations simultaneously. In the future, the combination of methods presented here should help theorists build a mechanistic understanding of plasmon-assisted charge transfer and excitation energy relaxation processes near a nanoparticle or metal surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The General Atomic and Molecular Electronic Structure System (GAMESS): Novel Methods on Novel Architectures

The primary focus of GAMESS over the last 5 years has been the development of new high-performance codes that are able to take effective and efficient advantage of the most advanced computer architectures, both CPU and accelerators. These efforts include employing density fitting and fragmentation methods to reduce the high scaling of well-correlated (e.g., coupled-cluster) methods as well as developing novel codes that can take optimal advantage of graphical processing units and other modern accelerators. Because accurate wave functions can be very complex, an important new functionality in GAMESS is the quasi-atomic orbital analysis, an unbiased approach to the understanding of covalent bonds embedded in the wave function. Finally, best practices for the maintenance and distribution of GAMESS are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Comparing the structures and photophysical properties of two charge transfer co-crystals

Organic co-crystals have emerged as a promising class of semiconductors for next-generation optoelectronic devices due to their unique photophysical properties. This paper presents a joint experimental-theoretical study comparing the crystal structure, spectroscopy, and electronic structure of two charge transfer co-crystals. Reported herein is a novel co-crystal Npe:TCNQ, formed from 4-(1-naphthylvinyl)pyridine (Npe) and 7,7,8,8-tetracyanoquinodimethane (TCNQ) via molecular self-assembly. This work also presents a revised study of the co-crystal composed of Npe and 1,2,4,5-tetracyanobenzene (TCNB) molecules, Npe:TCNB, herein reported with a higher-symmetry (monoclinic) crystal structure than previously published. Npe:TCNB and Npe:TCNQ dimer clusters are used as theoretical model systems for the co-crystals; the geometries of the dimers are compared to geometries of the extended solids, which are computed with periodic boundary conditions density functional theory. UV-Vis absorption spectra of the dimers are computed with time-dependent density functional theory and compared to experimental UV-Vis diffuse reflectance spectra. Both Npe:TCNB and Npe:TCNQ are found to exhibit neutral character in the S 0 state and ionic character in the S 1 state. In conclusion, the high degree of charge transfer in the S 1 state of both Npe:TCNB and Npe:TCNQ is rationalized by analyzing the changes in orbital localization associated with the S 1 transitions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Magnetic structure, excitations and short-range order in honeycomb Na 2 Ni 2 TeO 6

Na 2 Ni 2 TeO 6 has a layered hexagonal structure with a honeycomb lattice constituted by Ni 2+ and a chiral charge distribution of Na + that resides between the Ni layers. In the present work, the antiferromagnetic transition temperature of Na 2 Ni 2 TeO 6 is confirmed at TN˜ 27 K, and further, it is found to be robust up to 8 T magnetic field and 1.2 GPa external pressure; and, without any frequency-dependence. Slight deviations from nominal Na-content (up to 5%) does not seem to influence the magnetic transition temperature, TN. Isothermal magnetization curves remain almost linear up to 13 T. Our analysis of neutron diffraction data shows that the magnetic structure of Na 2 Ni 2 TeO 6 is faithfully described by a model consisting of two phases described by the commensurate wave vectors vec kc, (0.5 0 0) and (0.5 0 0.5), with an additional short-range order component incorporated in to the latter phase. Consequently, a zig-zag long-range ordered magnetic phase of Ni 2+ results in the compound, mixed with a short-range ordered phase, which is supported by our specific heat data. Theoretical computations based on density functional theory (DFT) predict predominantly in-plane magnetic exchange interactions that conform to a J1-J2-J3 model with a strong J3 term. The computationally predicted parameters lead to a reliable estimate for TN and the experimentally observed zig-zag magnetic structure. A spin wave excitation in Na 2 Ni 2 TeO 6 at E ˜ 5 meV at T = 5 K is mapped out through inelastic neutron scattering experiments, which is reproduced by linear spin wave theory calculations using the J values from our computations. Our specific heat data and inelastic neutron scattering data strongly indicate the presence of short-range spin correlations, at T > TN, stemming from incipient antiferromagnetic clusters.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Lieb-Robinson Bounds with Exponential-in-Volume Tails

Lieb-Robinson bounds demonstrate the emergence of locality in many-body quantum systems. Intuitively, Lieb-Robinson bounds state that, with local or exponentially decaying interactions, the correlation that can be built up between two sites separated by distance 𝑟 after a time 𝑡 decays as exp (𝑣⁢𝑡 −𝑟), where 𝑣 is the emergent Lieb-Robinson velocity. In many problems, it is important to also capture how much of an operator grows to act on 𝑟 𝑑 sites in 𝑑 spatial dimensions. Perturbation theory and cluster expansion methods suggest that, at short times, these volume-filling operators are suppressed as exp (−𝑟 𝑑 ). We confirm this intuition, showing that, for 𝑟 >𝑣⁢𝑡, the volume-filling operator is suppressed by exp (−(𝑟−𝑣⁢𝑡) 𝑑 /(𝑣⁢𝑡) 𝑑−1 ). This closes a conceptual and practical gap between the cluster expansion and the Lieb-Robinson bound. We then present two very different applications of this new bound. Firstly, we obtain improved bounds on the classical computational resources necessary to simulate many-body dynamics with error tolerance 𝜀 for any finite time 𝑡: as 𝜀 becomes sufficiently small, only 𝜀 −O⁡(𝑡 𝑑−1 ) resources are needed. A protocol that likely saturates this bound is given. Secondly, we prove that disorder operators have volume-law suppression near the “solvable (Ising) point” in quantum phases with spontaneous symmetry breaking, which implies a new diagnostic for distinguishing many-body phases of quantum matter.

computational complexity↗