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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.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
NASA NTRS1989

Data traffic reduction schemes for Cholesky factorization on asynchronous multiprocessor systems

Communication requirements of Cholesky factorization of dense and sparse symmetric, positive definite matrices are analyzed. The communication requirement is characterized by the data traffic generated on multiprocessor systems with local and shared memory. Lower bound proofs are given to show that when the load is uniformly distributed the data traffic associated with factoring an n x n dense matrix using n to the alpha power (alpha less than or equal 2) processors is omega(n to the 2 + alpha/2 power). For n x n sparse matrices representing a square root of n x square root of n regular grid graph the data traffic is shown to be omega(n to the 1 + alpha/2 power), alpha less than or equal 1. Partitioning schemes that are variations of block assignment scheme are described and it is shown that the data traffic generated by these schemes are asymptotically optimal. The schemes allow efficient use of up to O(n to the 2nd power) processors in the dense case and up to O(n) processors in the sparse case before the total data traffic reaches the maximum value of O(n to the 3rd power) and O(n to the 3/2 power), respectively. It is shown that the block based partitioning schemes allow a better utilization of the data accessed from shared memory and thus reduce the data traffic than those based on column-wise wrap around assignment schemes.

Naik, Vijay K.↗
DOE OSTI2021

A multi-center quadrature scheme for the molecular continuum

We report a common way to evaluate electronic integrals for polyatomic molecules is to use Becke’s partitioning scheme (Becke and Chem, 1988) in conjunction with overlapping grids centered at each atomic site. The Becke scheme was designed for integrands that fall off rapidly at large distances, such as those approximating bound electronic states. When applied to states in the electronic continuum, however, Becke scheme exhibits slow convergence and it is highly redundant. Here, we present a modified version of Becke scheme that is applicable to functions of the electronic continuum, such as those involved in molecular photoionization and electron–molecule scattering, and which ensures convergence and efficiency comparable to those realized in the calculation of bound states. In this modified scheme, the atomic weights already present in Becke’s partition are smoothly switched off within a range of few bond lengths from their respective nuclei, and complemented by an asymptotically unitary weight. The atomic integrals are evaluated on small spherical grids, centered on each atom, with size commensurate to the support of the corresponding atomic weight. The residual integral of the interstitial and long-range region is evaluated with a central master grid. The accuracy of the method is demonstrated by evaluating integrals involving integrands containing Gaussian Type Orbitals and Yukawa potentials, on the atomic sites, as well as spherical Bessel functions centered on the master grid. These functions are representative of those encountered in realistic electron-scattering and photoionization calculations in polyatomic molecules.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS1992

A performance study of sparse Cholesky factorization on INTEL iPSC/860

The problem of Cholesky factorization of a sparse matrix has been very well investigated on sequential machines. A number of efficient codes exist for factorizing large unstructured sparse matrices. However, there is a lack of such efficient codes on parallel machines in general, and distributed machines in particular. Some of the issues that are critical to the implementation of sparse Cholesky factorization on a distributed memory parallel machine are ordering, partitioning and mapping, load balancing, and ordering of various tasks within a processor. Here, we focus on the effect of various partitioning schemes on the performance of sparse Cholesky factorization on the Intel iPSC/860. Also, a new partitioning heuristic for structured as well as unstructured sparse matrices is proposed, and its performance is compared with other schemes.

Zubair, M.↗
DOE OSTI2019

A robust hierarchical solver for ill-conditioned systems with applications to ice sheet modeling

A hierarchical solver is proposed for solving sparse ill-conditioned linear systems in parallel. The solver is based on a modification of the LoRaSp method, but employs a deferred-compression technique, which provably reduces the approximation error and significantly improves efficiency. Moreover, the deferred-compression technique introduces minimal overhead and does not affect parallelism. As a result, the new solver achieves linear computational complexity under mild assumptions and excellent parallel scalability. To demonstrate the performance of the new solver, we focus on applying it to solve sparse linear systems arising from ice sheet modeling. The strong anisotropic phenomena associated with the thin structure of ice sheets creates serious challenges for existing solvers. To address the anisotropy, we additionally developed a customized partitioning scheme for the solver, which captures the strong-coupling direction accurately. In general, the partitioning can be computed algebraically with existing software packages, and thus the new solver is generalizable for solving other sparse linear systems. Our results show that ice sheet problems of about 300 million degrees of freedom have been solved in just a few minutes using a thousand processors.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

pyEF: A Python Framework for QM and QM/MM Atom-Wise Electric Field Analysis

We introduce pyEF, a software package for computing molecular electric fields, electrostatic interaction energies, and electrostatic potentials from quantum mechanical (QM) atom-centered multipole expansions with atom-wise decomposable contributions. We demonstrate the computational efficiency and accuracy of this QM-derived electric field evaluation tool through several tests. To assess the influence of the underlying QM method and charge partitioning scheme on these electrostatic quantities, we analyze over 250 configurations of an acetone solute molecule in five solvents of variable polarity. We find that electric field calculations are highly sensitive to the choice of charge partitioning method. Even among real-space charge schemes, acetone Stark tuning rates differ by up to a factor of 2. Benchmarking computed solvent dipole moments against experimental bulk values, we conclude that the CM5, ADCH, and Hirshfeld-I charge schemes most reliably capture solvent electrostatics and therefore provide a more faithful foundation for computing electric fields. When constructed from these real-space charges, electric fields are nearly insensitive to basis set size and monotonically increase in magnitude with higher Fock exchange. We also demonstrate efficient convergence of QM electrostatics when more distant molecules are represented solely by MM point charges, reducing computational overhead. Leveraging these findings, we demonstrate the use of pyEF to deduce environmental effects on a transition metal complex from a Ga 4 L 6 12– nanocage and quantify the dominant role of organic linkers in orchestrating electrostatic preorganization.

electric fields↗
DOE OSTI2023

Interface flux recovery framework for constructing partitioned heterogeneous time-integration methods

A common approach for the development of partitioned schemes employing different time integrators on different subdomains is to lag the coupling terms in time. This can lead to accuracy issues, especially in multistage methods. Here, in this article, we present a novel framework for partitioned heterogeneous time-integration methods, which allows the coupling of arbitrary multistage and multistep methods without reducing their order of accuracy. At the core of our approach are accurate estimates of the interface flux obtained from the Schur complement of an auxiliary monolithic system. We use these estimates to construct a polynomial-in-time approximation of the interface flux over the current time coupling window. This approximation provides the interface boundary conditions necessary to decouple the subdomain problems at any point within the coupling window. In so doing our framework enables a flexible choice of time-integrators for the individual subproblems without compromising the time-accuracy at the coupled problem level. This feature is the main distinction between our framework and other approaches. To demonstrate the framework, we construct a family of partitioned heterogeneous time-integration methods, combining multistage and multistep methods, for a simplified tracer transport component of the coupled air-sea system in Earth system models. We report numerical tests evaluating accuracy and flux conservation for different pairs of time-integrators from the explicit Runge-Kutta and Adams-Moulton families.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Implications of reduced-complexity aerosol thermodynamics on organic aerosol mass concentration and composition over North America

Atmospheric organic aerosol (OA) mass concentrations can be affected by water uptake through its impact on the gas–particle partitioning of semi-volatile compounds. Current chemical transport models (CTMs) neglect this process. We have implemented the Binary Activity Thermodynamics model coupled to a volatility basis set partitioning scheme in the GEOS-Chem CTM, providing an efficient reduced-complexity OA model that predicts relative-humidity-dependent mixing and partitioning thermodynamics, while limiting the impact on computational efficiency. We provide a quantitative assessment of this water-sensitive OA treatment, focusing on a subdomain over North America. The updated OA scheme predicts a spatiotemporal mean enhancement in surface-level OA mass concentration of 145 % for January 2019 and 76 % for July 2019 compared to GEOS-Chem's most advanced OA scheme. The temporal mean surface-level OA organic mass concentration can increase by up to ∼590 % for January 2019 and ∼280 % for July 2019, with the greatest enhancements occurring over the ocean. The updated OA scheme also quantifies the OA-associated water content. The simulations show how different OA precursors and related OA surrogates contribute and respond to water uptake, including that due to changes in temperature and relative humidity over the diurnal cycle in selected winter and summer months. These results are independent of future CTM improvements involving updates to chemical reaction schemes and emission inventories. Our water-sensitive OA scheme allows for a better representation of the seasonal and regional variations in OA mass concentration in CTMs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

High Performance Computing Based Parallel HIearchical Modal Association Clustering (HPAR HMAC)

For many applications, clustering is a crucial step in order to gain insight into the makeup of a dataset. The best approach to a given problem often depends on a variety of factors, such as the size of the dataset, time restrictions, and soft clustering requirements. The HMAC algorithm seeks to combine the strengths of 2 particular clustering approaches: model-based and linkage-based clustering. One particular weakness of HMAC is its computational complexity. HMAC is not practical for mega-scale data clustering. For high-definition imagery, a user would have to wait months or years for a result; for a 16-megapixel image, the estimated runtime skyrockets to over a decade! To improve the execution time of HMAC, it is reasonable to consider an multi-core implementation that utilizes available system resources. An existing imple-mentation (Ray and Cheng 2014) divides the dataset into N partitions - one for each thread prior to executing the HMAC algorithm. This implementation benefits from 2 types of optimization: parallelization and divide-and-conquer. By running each partition in parallel, the program is able to accelerate computation by utilizing more system resources. Although the parallel implementation provides considerable improvement over the serial HMAC, it still suffers from poor computational complexity, O(N2). Once the maximum number of cores on a system is exhausted, the program exhibits slower behavior. We now consider a modification to HMAC that involves a recursive partitioning scheme. Our modification aims to exploit divide-and-conquer benefits seen by the parallel HMAC implementation. At each level in the recursion tree, partitions are divided into 2 sub-partitions until a threshold size is reached. When the partition can no longer be divided without falling below threshold size, the base HMAC algorithm is applied. This results in a significant speedup over the parallel HMAC.

Patlolla, Dilip R↗
DOE OSTI2018

Partitioning and Communication Strategies for Sparse Non-negative Matrix Factorization

Non-negative matrix factorization (NMF), the problem of finding two non-negative low-rank factors whose product approximates an input matrix, is a useful tool for many data mining and scientific applications such as topic modeling in text mining and unmixing in microscopy. In this paper, we focus on scaling algorithms for NMF to very large sparse datasets and massively parallel machines by employing effective algorithms, communication patterns, and partitioning schemes that leverage the sparsity of the input matrix. We consider two previous works developed for related problems, one that uses a fine-grained partitioning strategy using a point-to-point communication pattern and one that uses a Cartesian, or checkerboard, partitioning strategy using a collective-based communication pattern. We show that a combination of the previous approaches balances the demands of the various computations within NMF algorithms and achieves high efficiency and scalability. From the experiments, we see that our proposed strategy runs up to 10x faster than the state of the art on real-world datasets.

Kaya, Oguz↗
NASA NTRS1990

Constraint treatment techniques and parallel algorithms for multibody dynamic analysis

Computational procedures for kinematic and dynamic analysis of three-dimensional multibody dynamic (MBD) systems are developed from the differential-algebraic equations (DAE's) viewpoint. Constraint violations during the time integration process are minimized and penalty constraint stabilization techniques and partitioning schemes are developed. The governing equations of motion, a two-stage staggered explicit-implicit numerical algorithm, are treated which takes advantage of a partitioned solution procedure. A robust and parallelizable integration algorithm is developed. This algorithm uses a two-stage staggered central difference algorithm to integrate the translational coordinates and the angular velocities. The angular orientations of bodies in MBD systems are then obtained by using an implicit algorithm via the kinematic relationship between Euler parameters and angular velocities. It is shown that the combination of the present solution procedures yields a computationally more accurate solution. To speed up the computational procedures, parallel implementation of the present constraint treatment techniques, the two-stage staggered explicit-implicit numerical algorithm was efficiently carried out. The DAE's and the constraint treatment techniques were transformed into arrowhead matrices to which Schur complement form was derived. By fully exploiting the sparse matrix structural analysis techniques, a parallel preconditioned conjugate gradient numerical algorithm is used to solve the systems equations written in Schur complement form. A software testbed was designed and implemented in both sequential and parallel computers. This testbed was used to demonstrate the robustness and efficiency of the constraint treatment techniques, the accuracy of the two-stage staggered explicit-implicit numerical algorithm, and the speed up of the Schur-complement-based parallel preconditioned conjugate gradient algorithm on a parallel computer.

Chiou, Jin-Chern↗
DOE OSTI2021

Projector-Based Quantum Embedding for Molecular Systems: An Investigation of Three Partitioning Approaches

Projector-based embedding is a relatively recent addition to the collection of methods that seek to utilize chemical locality to provide improved computational efficiency. This work considers the interactions between the different proposed procedures for this method and their effects on the accuracy of the results. The interplay between the embedded background, projector type, partitioning scheme, and level of atomic orbital (AO) truncation are investigated on a selection of reactions from the literature. The Huzinaga projection approach proves to be more reliable than the level-shift projection when paired with other procedural options. Active subsystem partitioning from the subsystem projected AO decomposition (SPADE) procedure proves slightly better than the combination of Pipek-Mezey localization and Mulliken population screening (PMM). Along with these two options, a new partitioning criteria is proposed based on subsystem von Neumann entropy and the related subsystem orbital occupancy. This new method overlaps with the previous PMM method, but the screening process is computationally simpler. Finally, AO truncation proves to be a robust option for the tested systems when paired with the Huzinaga projection, with satisfactory results being acquired at even the most severe truncation level.

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

A Novel Partitioned Approach for Reduced Order Model—Finite Element Model (ROM-FEM) and ROM-ROM Coupling

Partitioned methods allow one to build a simulation capability for coupled problems by reusing existing single-component codes. In so doing, partitioned methods can shorten code development and validation times for multiphysics and multiscale applications. In this work, we consider a scenario in which one or more of the “codes” being coupled are projection-based reduced order models (ROMs), introduced to lower the computational cost associated with a particular component. We simulate this scenario by considering a model interface problem that is discretized independently on two non-overlapping subdomains. Here we then formulate a partitioned scheme for this problem that allows the coupling between a ROM “code” for one of the subdomains with a finite element model (FEM) or ROM “code” for the other subdomain. The ROM “codes” are constructed by performing proper orthogonal decomposition (POD) on a snapshot ensemble to obtain a low-dimensional reduced order basis, followed by a Galerkin projection onto this basis. The ROM and/or FEM “codes” on each subdomain are then coupled using a Lagrange multiplier representing the interface flux. To partition the resulting monolithic problem, we first eliminate the flux through a dual Schur complement. Application of an explicit time integration scheme to the transformed monolithic problem decouples the subdomain equations, allowing their independent solution for the next time step. We show numerical results that demonstrate the proposed method’s efficacy in achieving both ROM-FEM and ROM-ROM coupling.

de Castro, Amy↗
DOE OSTI2022

The role of surface forces in environment-enhanced cracking of brittle solids

Fracture initiation and propagation in brittle materials is promoted in surface-reactive (sorptive) environments, a phenomenon known as subcritical crack growth (SCG). Laboratory measured crack-propagation velocity vs. stress intensity factor relationships typically exhibit highly nonlinear, multi-stage characteristics that are sensitive to environmental factors such as adsorbate concentration and temperature. For practical purposes, empirical relationships (e.g., a power law) have been used to describe this complex phenomenon. However, how the overall SCG behavior emerges from the underlying fundamental processes near the crack tip, such as the interaction of the crack surfaces separated by only a few nanometers and mass transport within the nano-confined space, is still not well understood. This paper develops a mechanistic, surface-force-based fracture theory (SFFT) which integrates surface force models, fluid transport models, and linear elastic fracture mechanics to quantitatively explain the multi-stage characteristics of SCG in brittle solids. A numerical model is developed based on SFFT and solved through an implicit partitioned scheme for efficiency and modularity. The results are validated by Wiederhorn's data on crack propagation in soda-lime glasses at a wide range of relative humidity levels. We show that, for the first time, the entire range of an SCG curve can be captured by a single physics-based model. The predicted SCG curves reveal that the development of repulsive disjoining pressure behind the crack tip can be responsible for the reduced apparent fracture toughness in a sorptive environment. In conclusion, the shape of the SCG curve, and its changes with respect to the environment, is found to critically depend on the assumed transport models.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Implementation and Validation of Constrained Density Functional Theory Forces in the CP2K Package

Constrained density functional theory (CDFT) is a powerful tool for the prediction of electron transfer parameters in condensed phase simulations at a reasonable computational cost. In this work we present an extension to CDFT in the popular mixed Gaussian/plane wave electronic structure package CP2K, implementing the additional force terms arising from a constraint based on Hirshfeld charge partitioning. This improves upon the existing Becke partitioning scheme, which is prone to give unphysical atomic charges. We verify this implementation for a variety of systems: electron transfer in (H 2 O) 2 + in vacuum, electron tunnelling between oxygen vacancy centers in solid MgO, and electron self-exchange in aqueous Ru 2+ -Ru 3+ . We find good agreement with previous plane-wave CDFT results for the same systems, but at a significantly lower computational cost, and we discuss the general reliability of condensed phase CDFT calculations.

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

Efficient Calculation of NMR Shielding Constants Using Composite Method Approximations and Locally Dense Basis Sets

This paper presents a systematic study of applying composite method approximations with locally dense basis sets (LDBS) to efficiently calculate NMR shielding constants in small and medium-sized molecules. The pcSseg-n series of basis sets are shown to have similar accuracy to the pcS-n series when n ≥ 1 and can slightly reduce computational costs. We identify two different LDBS partition schemes that perform very effectively for density functional calculations. Here, we select a large subset of the recent NS372 database containing 290 H, C, N, and O shielding values evaluated by reference methods on 106 molecules to carefully assess methods of the high, medium, and low computational costs to make practical recommendations. Our assessment covers conventional electronic structure methods (density functional theory and wave function) with global basis calculations, as well as their use in one of the satisfactory LDBS approaches, and a range of composite approaches, also with and without LDBS. Altogether 99 methods are evaluated. On this basis, we recommend different methods to reach three different levels of accuracy and time requirements across the four nuclei considered.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Many-Body Benchmark of Electronic Charge and Spin Densities for Li 1–x NiO 2

Accurate benchmarks are particularly important for highly correlated oxides as mean-field approximations often fail to describe the subtle balance of charge transfer and magnetism in these materials with an accuracy comparable to experimental needs. Here we present accurate diffusion Monte Carlo (DMC) results of the electronic charge and spin densities for the tunable highly correlated oxide Li 1–x NiO 2 for x = 0, 1/2, and 1. To enable quantitative comparisons, we introduce a robust density-partitioning scheme, extending Voronoi analysis to assign atomic charges from spatially noisy DMC densities. We then benchmark common approximations used in density functional theory (DFT). Comparison against DMC shows that r 2 SCAN delivers the most balanced performance across charge, spin, and radial density descriptors, nearly reproducing DMC results for LiNiO 2 and apical Ni sites in Li 0.5 NiO 2 . Hybrid functionals (PBE0, SCAN0) perform unexpectedly poorly, and PBE + U + V yields inconsistent trends between charge and spin densities. Therefore, the r 2 SCAN functional minimizes errors relative to DMC while capturing the variable valence of the Ni ion and also retaining the computational efficiency of DFT for large-scale simulations of the tunable structural and electronic phases of Li1−xNiO2. Our study highlights the importance of accurate benchmarking of the fundamental quantities involved in DFT to select appropriate DFT approximations in order to advance the predictive modeling of charge-transfer-driven phenomena in correlated electron systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Transferable Dynamic Molecular Charge Assignment Using Deep Neural Networks

We report that the ability to accurately and efficiently compute quantum-mechanical partial atomistic charges has many practical applications, such as calculations of IR spectra, analysis of chemical bonding, and classical force field parametrization. Machine learning (ML) techniques provide a possible avenue for the efficient prediction of atomic partial charges. Modern ML advances in the prediction of molecular energies [i.e., the hierarchical interacting particle neural network (HIP-NN)] has provided the necessary model framework and architecture to predict transferable, extensible, and conformationally dynamic atomic partial charges based on reference density functional theory (DFT) simulations. Utilizing HIP-NN, we show that ML charge prediction can be highly accurate over a wide range of molecules (both small and large) across a variety of charge partitioning schemes such as the Hirshfeld, CM5, MSK, and NBO methods. To demonstrate transferability and size extensibility, we compare ML results with reference DFT calculations on the COMP6 benchmark, achieving errors of 0.004e – (elementary charge). This is remarkable since this benchmark contains two proteins that are multiple times larger than the largest molecules in the training set. An application of our atomic charge predictions on nonequilibrium geometries is the generation of IR spectra for organic molecules from dynamical trajectories on a variety of organic molecules, which show good agreement with calculated IR spectra with reference method. Critically, HIP-NN charge predictions are many orders of magnitude faster than direct DFT calculations. Lastly, these combined results provide further evidence that ML (specifically HIP-NN) provides a pathway to greatly increase the range of feasible simulations while retaining quantum-level accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

High-throughput predictions of metal–organic framework electronic properties: theoretical challenges, graph neural networks, and data exploration

Abstract With the goal of accelerating the design and discovery of metal–organic frameworks (MOFs) for electronic, optoelectronic, and energy storage applications, we present a dataset of predicted electronic structure properties for thousands of MOFs carried out using multiple density functional approximations. Compared to more accurate hybrid functionals, we find that the widely used PBE generalized gradient approximation (GGA) functional severely underpredicts MOF band gaps in a largely systematic manner for semi-conductors and insulators without magnetic character. However, an even larger and less predictable disparity in the band gap prediction is present for MOFs with open-shell 3 d transition metal cations. With regards to partial atomic charges, we find that different density functional approximations predict similar charges overall, although hybrid functionals tend to shift electron density away from the metal centers and onto the ligand environments compared to the GGA point of reference. Much more significant differences in partial atomic charges are observed when comparing different charge partitioning schemes. We conclude by using the dataset of computed MOF properties to train machine-learning models that can rapidly predict MOF band gaps for all four density functional approximations considered in this work, paving the way for future high-throughput screening studies. To encourage exploration and reuse of the theoretical calculations presented in this work, the curated data is made publicly available via an interactive and user-friendly web application on the Materials Project.

36 MATERIALS SCIENCE↗