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At least 91 records · Page 5

An extensive assessment of the performance of pairwise and many-body interaction potentials in reproducing ab initio benchmark binding energies for water clusters n = 2–25

We assess the performance of 7 pairwise additive (TIP3P, TIP4P, TIP4P-ice, TIP5P, OPC, SPC, SPC/E) and 8 families of many-body potentials (q-AQUA, HIPPO, AMOEBA, EFP, TTM, WHBB, MB-pol, MB-UCB) in reproducing high-level ab initio benchmark values, CCSD(T) or MP2 at the complete basis set (CBS) limit for the binding energy and the many-body expansion (MBE) of water clusters n = 2–11, 16–17, 20, 25. By including a large range of cluster sizes having dissimilar hydrogen bonding networks, we obtain an understanding of how these potentials perform for different hydrogen bonding arrangements that are mostly outside of their parameterization range. While it is appropriate to compare the results of ab initio based many-body potentials directly to the electronic binding energies (D e 's), the pairwise additive ones are compared to the enthalpies at T = 298 K, ΔH(298 K), as the latter class of force fields are parametrized to reproduce enthalpies (implicitly accounting for zero-point energy corrections) rather than binding energies. We find that all pairwise additive potentials considered overestimate the reference ΔH values for the n = 2–25 clusters by >13%. For the water dimer (n = 2) in particular, the errors are in the range 83–119% for the pairwise additive potentials studied since these are based on an effective rather than the true 2-body interaction specifically designed as a means of partially accounting for the missing many-body terms. This stronger 2-body interaction is achieved by an enhanced monomer dipole moment that mimics its increase from the gas phase monomer to the condensed phase value. Indeed, for cluster sizes n ≥ 4 the percent deviations become slightly smaller (albeit all exceeding 13%). In contrast, we find that the many-body potentials perform more accurately in reproducing the electronic binding energies (D e 's) throughout the entire cluster range (n = 2–25), all reproducing the ab initio benchmark binding energies within ±7% of the respective CBS values. We further assess the ability of a subset of the many-body potentials (MB-UCB, q-AQUA, MB-pol, and TTM2.1-F) to also reproduce the magnitude of the ab initio many-body energy terms for water cluster sizes n = 7, 10, 16 and 17. The potentials show an overall good agreement with the available benchmark values. However, we identify characteristic differences upon comparing the many-body terms at both the ab initio-optimized geometries and the respective potential-optimized geometries to the reference ab initio values. Additionally, by applying this analysis to a wide range of cluster sizes, trends in the MBE of the potentials with increasing cluster size can be identified. Finally, in an attempt to draw a parallel between the pairwise additive and many-body potentials, we report the analysis of the individual molecular dipole moments for water clusters with 1 to ~4 solvation shells with the TTM2.1-F potential. We find that the internally solvated water molecules have in general a larger molecular dipole moment ranging from 2.6–3.0 D. This justifies the use of an enhanced, with respect to the gas-phase value, molecular dipole moment for the pairwise additive potentials, which is intended to fold in the many body terms into an effective (enhanced) pairwise interaction through the choice of the charges. These results have important implications for the development of future generations of efficient, transferable, and highly accurate classical interaction potentials in both the pairwise additive and many-body categories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

lustre_fssync

lustre_fssync is a tool used to sync an entire Lustre file system from one cluster to another. It uses Lustre user quotas, parallel I/O utilities and the SLURM resource manager to balance and synchronize all contents between systems.

Harr, CameronM↗

ELECTRONIC STRUCTURE METHODS AND PROTOCOLS WITH APPLICATION TO DYNAMICS, KINETICS AND THERMOCHEMISTRY

Hydrocarbon combustion involves the reaction dynamics of a tremendous number of species beginning with many-component fuel mixtures and proceeding via a complex system of intermediates to form primary and secondary products. Combustion conditions corresponding to new advanced engines and/or alternative fuels rely increasingly on autoignition and low-temperature-combustion chemistry. In these regimes various transient radical species such as HO2, ROO·, ·QOOH, HCO, NO2, HOCO, and Criegee intermediates play important roles in determining the detailed as well as more general dynamics. A clear understanding and accurate representation of these processes is needed for effective modeling. Given the difficulties associated with making reliable experimental measurements of these systems, computation can play an important role in developing these energy technologies. Accurate calculations have their own challenges since even within the simplest dynamical approximations such as transition state theory, the rates depend exponentially on critical barrier heights and these may be sensitive to the level of quantum chemistry. Moreover, it is well-known that in many cases it is necessary to go beyond statistical theories and consider the dynamics. Quantum tunneling, resonances, radiative transitions, and non-adiabatic effects governed by spin-orbit or derivative coupling can be determining factors in those dynamics. Building upon progress made during a period of prior support through the DOE Early Career Program, this project combines developments in the areas of potential energy surface (PES) fitting and multistate multireference quantum chemistry to allow spectroscopically and dynamically/kinetically accurate investigations of key molecular systems (such as those mentioned above), many of which are radicals with strong multireference character and have the possibility of multiple electronic states contributing to the observed dynamics. An ongoing area of investigation is to develop general strategies for robustly convergent electronic structure theory for global multichannel reactive surfaces including diabatization of energy and other relevant surfaces such as dipole transition. Combining advances in ab initio methods with automated interpolative PES fitting allows the construction of high-quality PESs (incorporating thousands of high-level data) to be done rapidly through parallel processing on high-performance computing (HPC) clusters. In addition, new methods and approaches to electronic structure theory will be developed and tested through applications. This project will explore limitations in traditional multireference calculations (e.g., MRCI) such as those imposed by internal contraction, lack of high-order correlation treatment and poor scaling. Methods such as DMRG-based extended active-space CASSCF and various Quantum Monte Carlo (QMC) methods will be applied (including VMC/DMC and FCIQMC). Insight into the relative significance of different orbital spaces and the robustness of application of these approaches on leadership class computing architectures will be gained. Synergy with other components of this research program such as automated PES fitting and multireference quantum chemistry will be used to address challenges encountered by the standard approaches to computational thermochemistry (those being single-reference quantum chemistry and perturbative treatments of the anharmonic vibrational energy, which break down for some cases of electronic structure or floppy strongly coupled vibrational modes).

74 ATOMIC AND MOLECULAR PHYSICS↗

Flow Redirection and Induction in Steady State (FLORIS) Wind Plant Power Production Data Sets

This dataset contains turbine- and plant-level power outputs for 252,500 cases of diverse wind plant layouts operating under a wide range of yawing and atmospheric conditions. The power outputs were computed using the Gaussian wake model in NREL's FLOw Redirection and Induction in Steady State (FLORIS) model, version 2.3.0. The 252,500 cases include 500 unique wind plants generated randomly by a specialized Plant Layout Generator (PLayGen) that samples randomized realizations of wind plant layouts from one of four canonical configurations: (i) cluster, (ii) single string, (iii) multiple string, (iv) parallel string. Other wind plant layout parameters were also randomly sampled, including the number of turbines (25-200) and the mean turbine spacing (3D-10D, where D denotes the turbine rotor diameter). For each layout, 500 different sets of atmospheric conditions were randomly sampled. These include wind speed in 0-25 m/s, wind direction in 0 deg.-360 deg., and turbulence intensity chosen from low (6%), medium (8%), and high (10%). For each atmospheric inflow scenario, the individual turbine yaw angles were randomly sampled from a one-sided truncated Gaussian on the interval 0 deg.-30 deg. oriented relative to wind inflow direction. This random data is supplemented with a collection of yaw-optimized samples where FLORIS was used to determine turbine yaw angles that maximize power production for the entire plant. To generate this data, a subset of cases were selected (50 atmospheric conditions from 50 layouts each for a total of additional 2,500 cases) for which FLORIS was re-run with wake steering control optimization. The IEA onshore reference turbine, which has a 130 m rotor diameter, a 110 m hub height, and a rated power capacity of 3.4 MW was used as the turbine for all simulations. The simulations were performed using NREL's Eagle high performance computing system in February 2021 as part of the Spatial Analysis for Wind Technology Development project funded by the U.S. Department of Energy Wind Energy Technologies Office. The data was collected, reformatted, and preprocessed for this OEDI submission in May 2023 under the Foundational AI for Wind Energy project funded by the U.S. Department of Energy Wind Energy Technologies Office. This dataset is intended to serve as a benchmark against which new artificial intelligence (AI) or machine learning (ML) tools may be tested. Baseline AI/ML methods for analyzing this dataset have been implemented, and a link to their repository containing those models has been provided. The .h5 data file structure can be found in the GitHub repository under explore_wind_plant_data_h5.ipynb.

AI↗

Distributed non-negative matrix factorization with determination of the number of latent features

The holistic analysis and understanding of the latent (that is, not directly observable) variables and patterns buried in large datasets is crucial for data-driven science, decision making and emergency response. Such exploratory analyses require devising unsupervised learning methods for data mining and extraction of the latent features, and non-negative matrix factorization (NMF) is one of the prominent such methods. NMF is based on compute-intense non-convex constrained minimization, which, for large datasets requires fast and distributed algorithms. However, current parallel implementations of NMF fail to estimate the number of latent features. In practice, identifying these features is both difficult and significant for pattern recognition and latent feature analysis, especially for large dense matrices. Here, we introduce a distributed NMF algorithm coupled with distributed custom clustering followed by a stability analysis on dense data, which we call DnMFk, to determine the number of latent variables. The results on synthetic data and the classical Swimmer data set demonstrate the accuracy of model determination while scaling nearly linearly across multiple processors for large data. Further, we employ DnMFk to determine the number of hidden features from a terabyte matrix.

97 MATHEMATICS AND COMPUTING↗

Parallel Programming in MCNP6

Monte Carlo N-Particle (MCNP)1 is a general-purpose Monte Carlo particle transport code developed by Los Alamos National Laboratory (LANL). To efficiently handle long simulations, MCNP version 6 (MCNP6) supports parallel execution using two primary programming models: • Shared-memory task-based threading using OpenMP (Open Multi-Processing), and • Distributed-memory calculations using MPI (Message Passing Interface). The OpenMP and MPI programming models enable MCNP6 to scale from desktop systems to high-performance computing (HPC) clusters, allowing users to run MCNP in one of three parallel modes: • OpenMP-only, • MPI-only, and • Hybrid (MPI + OpenMP). The choice of parallelization mode depends on the underlying computer architecture and the characteristics of the simulation problem.

97 MATHEMATICS AND COMPUTING↗

Serial2Parallel

In the era of machine learning, we often need to run the same code/script many times with little or no variations (e.g., performance evaluation, data preprocessing, data generation, hyperparameter tuning, etc.). It is not a problem when you just need to do that a few times, but when the number of repetitions becomes very large, it can be a daunting task. The code “Serial2Parallel” provides an easy way for users to be able to run many numbers of any serial code/scripts in a parallel manner across multiple nodes in an message passing interface (MPI) cluster. The code includes the server program that deals with task pool management and client program that processes task. The server gets the tasks ready and waits for clients' connections. The client code pulls tasks from the server and processes them. The client code will run in parallel.

Sangkeun, MattLee↗

Early Results from GLASS-JWST. II. NIRCam Extragalactic Imaging and Photometric Catalog

We present the reduced images and multiwavelength catalog of the first JWST NIRCam extragalactic observations from the GLASS Early Release Science Program, obtained as coordinated parallels of the NIRISS observations of the Abell 2744 cluster. Images in seven bands (F090W, F115W, F150W, F200W, F277W, F356W, and F444W) have been reduced using an augmented version of the official JWST pipeline; we discuss the procedures adopted to remove or mitigate defects in the raw images. We obtain a multiband catalog by means of forced aperture photometry on point-spread function (PSF)-matched images at the position of F444W-detected sources. The catalog is intended to enable early scientific investigations, and it is optimized for faint galaxies; it contains 6368 sources, with limiting magnitude 29.7 at 5 σ in F444W. We release both images and catalog in order to allow the community to become familiar with the JWST NIRCam data and evaluate their merit and limitations given the current level of knowledge of the instrument.

79 ASTRONOMY AND ASTROPHYSICS↗

Virtual Log-Structured Storage for High-Performance Streaming

Over the past decade, given the higher number of data sources (e.g., Cloud applications, Internet of things) and critical business demands, Big Data transitioned from batch-oriented to real-time analytics. Stream storage systems, such as Apache Kafka, are well known for their increasing role in real-time Big Data analytics. For scalable stream data ingestion and processing, they logically split a data stream topic into multiple partitions. Stream storage systems keep multiple data stream copies to protect against data loss while implementing a stream partition as a replicated log. This architectural choice enables simplified development while trading cluster size with performance and the number of streams optimally managed. This paper introduces a shared virtual log-structured storage approach for improving the cluster throughput when multiple producers and consumers write and consume in parallel data streams. Stream partitions are associated with shared replicated virtual logs transparently to the user, effectively separating the implementation of stream partitioning (and data ordering) from data replication (and durability). We implement the virtual log technique in the KerA stream storage system. When comparing with Apache Kafka, KerA improves the cluster ingestion throughput by up to 4x when multiple producers write over hundreds of data streams.

consistent stream ordering↗

Symbol alphabets in QCD and flag cluster algebras

The full 245-letter symbol alphabet for all planar massless two-loop six-point Feynman integrals was recently determined in arXiv:2412.19884 and arXiv:2501.01847. In a parallel mathematical development, it was shown in arXiv:2408.14956 that there is an embedding of the cluster algebra associated to the partial flag variety $\mathcal{Fl}$ $2,n-2;n$ , which describes the kinematics of n massless particles, into that of the Grassmannian Gr(n–2, 2n–4). In this paper we connect these developments by showing that most of the rational symbol letters can be expressed in terms of flag cluster variables, and that all of the algebraic symbol letters arise from infinite mutation sequences.

97 MATHEMATICS AND COMPUTING↗

Distributed-Memory Parallel Symmetric Nonnegative Matrix Factorization

We develop the first distributed-memory parallel implementation of Symmetric Nonnegative Matrix Factorization (SymNMF), a key data analytics kernel for clustering and dimensionality reduction. Our implementation includes two different algorithms for SymNMF, which give comparable results in terms of time and accuracy. The first algorithm is a parallelization of an existing sequential approach that uses solvers for non symmetric NMF. The second algorithm is a novel approach based on the Gauss-Newton method. It exploits second-order information without incurring large computational and memory costs. We evaluate the scalability of our algorithms on the Summit system at Oak Ridge National Laboratory, scaling up to 128 nodes (4,096 cores) with 70% efficiency. Additionally, we demonstrate our software on an image segmentation task.

Eswar, Srinivas↗

Fast tree-based algorithms for DBSCAN for low-dimensional data on GPUs

DBSCAN is a well-known density-based clustering algorithm to discover arbitrary shape clusters. While conceptually simple in serial, the algorithm is challenging to efficiently parallelize on manycore GPU architectures. Common pitfalls, such as asynchronous range query calls, result in high thread execution divergence in many implementations. In this paper, we propose a new framework for GPU-accelerated DBSCAN, and describe two tree-based algorithms within that framework. Both algorithms fuse the search for neighbors with updating cluster information, but differ in their treatment of dense regions of the data. We show that the time taken to compute clusters is at most twice that of determination of the neighbors. We compare the proposed algorithms with existing CPU and GPU implementations, and demonstrate their competitiveness and performance using a fast traversal structure (bounding volume hierarchy) for low dimensional data. We also show that the memory usage can be reduced by processing object neighbors dynamically without storing them.

Prokopenko, Andrey↗

GUNDAM: a toolkit for fast spatial correlation functions in galaxy surveys

ABSTRACT We describe the capabilities of a new software package to calculate two-point correlation functions (2PCFs) of large galaxy samples. The code can efficiently estimate 3D/projected/angular 2PCFs with a variety of statistical estimators and bootstrap errors, and is intended to provide a complete framework (including calculation, storage, manipulation, and plotting) to perform this type of spatial analysis with large redshift surveys. Gundam implements a very fast skip list/linked list algorithm that efficiently counts galaxy pairs and avoids the computation of unnecessary distances. It is several orders of magnitude faster than a naive pair counter, and matches or even surpass other advanced algorithms. The implementation is also embarrassingly parallel, making full use of multicore processors or large computational clusters when available. The software is designed to be flexible, user friendly and easily extensible, integrating optimized, well-tested packages already available in the astronomy community. Out of the box, it already provides advanced features such as custom weighting schemes, fibre collision corrections and 2D correlations. Gundam will ultimately provide an efficient toolkit to analyse the large-scale structure ‘buried’ in upcoming extremely large data sets generated by future surveys.

Donoso, E.↗

The global star formation law by supernova feedback

ABSTRACT We address a simple model where the Kennicutt–Schmidt (KS) relation between the macroscopic densities of star formation rate (SFR, ρsfr) and gas (n) in galactic discs emerges from self-regulation of the SFR via supernova feedback. It arises from the physics of supernova bubbles, insensitive to the microscopic SFR recipe and not explicitly dependent on gravity. The key is that the filling factor of SFR-suppressed supernova bubbles self-regulates to a constant, f ∼ 0.5. Expressing the bubble fading radius and time in terms of n, the filling factor is $f\propto S\, n^{-s}$ with s ≃ 1.5, where S is the supernova rate density. A constant f thus refers to ρsfr ∝ n1.5, with a density-independent SFR efficiency per free-fall time ∼0.01. The self-regulation to f ∼ 0.5 and the convergence to a KS relation independent of the local SFR recipe are demonstrated in cosmological and isolated-galaxy simulations using different codes and recipes. In parallel, the spherical analysis of bubble evolution is generalized to clustered supernovae, analytically and via simulations, yielding s ≃ 1.5 ± 0.5. An analysis of photoionized bubbles about pre-supernova stars yields a range of KS slopes but the KS relation is dominated by the supernova bubbles. Superbubble blowouts may lead to an alternative self-regulation by outflows and recycling. While the model is oversimplified, its simplicity and validity in the simulations may argue that it captures the origin of the KS relation.

79 ASTRONOMY AND ASTROPHYSICS↗

CSRI Summer Proceedings 2020

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researchers to learn about problems in computer and computational science at DOE laboratories. Participants conduct leading-edge research, interact with scientists and engineers at the laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, adaptivity and mesh refinement, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, data-intensive computing, environments for scalable computing, parallel input/output, advanced architectures, and theoretical computer science. The CSRI Summer Program is organized by CSRI and typically includes the organization of a weekly seminar series and the publication of a summer proceedings. In 2020, the CSRI summer program was executed completely virtually; all student interns worked from home, due to the COVID-19 pandemic.

97 MATHEMATICS AND COMPUTING↗

Discovery of Extended Tidal Tails around the Globular Cluster Palomar 13

We use photometry from the DECam Legacy Survey to detect candidate tidal tails extending ~5° on either side of the Palomar 13 globular cluster. The tails are aligned with the proper motion of Palomar 13 and are consistent with its old, metal-poor stellar population. We identify three RR Lyrae stars (RRLs) that are plausibly associated with the tails, in addition to four previously known in the cluster. From these RRLs, we find that the mean distance to the cluster and tails is 23.6 ± 0.2 kpc and estimate the total (initial) luminosity of the cluster to be , consistent with previous claims that its initial luminosity was higher than its current luminosity. Combined with previously determined proper motion and radial velocity measurements of the cluster, we find that Palomar 13 is on a highly eccentric orbit (e ~ 0.8) with a pericenter of ~9 kpc and an apocenter of ~69 kpc, and a recent pericentric passage of the cluster ~75 Myr ago. We note a prominent linear structure in the interstellar dust map that runs parallel to the candidate tidal features, but conclude that reddening due to dust is unlikely to account for the structure that we observe. If confirmed, the Palomar 13 stellar stream would be one of very few streams with a known progenitor system, making it uniquely powerful for studying the disruption of globular clusters, the formation of the stellar halo, and the distribution of matter within our Galaxy.

79 ASTRONOMY AND ASTROPHYSICS↗

Chandra Follow-up of the SDSS DR8 Redmapper Catalog Using the MATCha Pipeline

In order to place constraints on cosmology through optical surveys of galaxy clusters, one must first understand the properties of those clusters. To this end, we introduce the Mass Analysis Tool for Chandra (MATCha), a pipeline that uses a parallellized algorithm to analyze archival Chandra data. MATCha simultaneously calculates X-ray temperatures and luminosities and performs centering measurements for hundreds of potential galaxy clusters using archival X-ray exposures. We run MATCha on the redMaPPer SDSS DR8 cluster catalog and use MATCha's output X-ray temperatures and luminosities to analyze the galaxy cluster temperature–richness, luminosity–richness, luminosity–temperature, and temperature–luminosity scaling relations. We detect 447 clusters and determine 246 r 2500 temperatures across all redshifts. Within 0.1 < z < 0.35, we find that r 2500 T X scales with optical richness (λ) as $\mathrm{ln}\left(\tfrac{{k}_{B}{T}_{{\rm{X}}}}{1.0\,\mathrm{keV}}\right)=(0.52\pm 0.05)\mathrm{ln}\left(\tfrac{\lambda }{70}\right)+(1.85\pm 0.03)$ with an intrinsic scatter of $0.27\pm 0.02$ ($1\sigma $). We investigate the distribution of offsets between the X-ray center and redMaPPer center within 0.1 < z < 0.35, finding that 68%.3 ± 6.5% of clusters are well-centered. However, we find a broad tail of large offsets in this distribution, and we explore some of the causes of redMaPPer miscentering.

79 ASTRONOMY AND ASTROPHYSICS↗

Measuring the homogeneity of the universe using polarization drift

We propose a method to probe the homogeneity of a general universe, without assuming symmetry. We show that isotropy can be tested at remote locations on the past lightcone by comparing the line-of-sight and transverse expansion rates, using the time dependence of the polarization of Cosmic Microwave Background photons that have been inverse-Compton scattered by the hot gas in massive clusters of galaxies. This probes a combination of remote transverse and parallel components of the expansion rate of the metric, and we may use radial baryon acoustic oscillations or cosmic clocks to measure the parallel expansion rate. Thus we can test remote isotropy, which is a key requirement of a homogeneous universe. We provide explicit formulas that connect observables and properties of the metric.

79 ASTRONOMY AND ASTROPHYSICS↗