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At least 1,405 records · Page 78

Combining artificial intelligence and physics-based modeling to directly assess atomic site stabilities: from sub-nanometer clusters to extended surfaces

The performance of functional materials is dictated by chemical and structural properties of individual atomic sites. In catalysts, for instance, the thermodynamic stability of constituting atomic sites is a key descriptor from which more complex properties, such as molecular adsorption energies and reaction rates, can be derived. In this study, we present a widely applicable machine learning (ML) approach to instantaneously compute the stability of individual atomic sites in structurally and electronically complex nano-materials. Conventionally, we determine such site stabilities using computationally intensive first-principles calculations. With our approach, we predict the stability of atomic sites in sub-nanometer metal clusters of 3–55 atoms with mean absolute errors in the range of 0.11–0.14 eV. To extract physical insights from the ML model, we introduce a genetic algorithm (GA) for feature selection. This algorithm distills the key structural and chemical properties governing the stability of atomic sites in size-selected nanoparticles, allowing for physical interpretability of the models and revealing structure–property relationships. The results of the GA are generally model and materials specific. In the limit of large nanoparticles, the GA identifies features consistent with physics-based models for metal–metal interactions. By combining the ML model with the physics-based model, we predict atomic site stabilities in real time for structures ranging from sub-nanometer metal clusters (3–55 atom) to larger nanoparticles (147 to 309 atoms) to extended surfaces using a physically interpretable framework. Finally, we present a proof of principle showcasing how our approach can determine stable and active nanocatalysts across a generic materials space of structure and composition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Power System Decomposition for Practical Implementation of Bulk-Grid Voltage Control Methods

Power system algorithms such as AC optimal power flow and coordinated volt/var control of the bulk power system are computationally intensive and become difficult to solve in operational time frames. The computational time required to run these algorithms increases exponentially as the size of the power system increases. The solution time for multiple subsystems is less than that for solving the entire system simultaneously, and the local nature of the voltage problem lends itself to such decomposition. This paper describes an algorithm that can be used to perform power system decomposition from the point of view of the voltage control problem. Our approach takes advantage of the dominant localized effect of voltage control and is based on clustering buses according to the electrical distances between them. One of the contributions of the paper is to use multidimensional scaling to compute n-dimensional Euclidean coordinates for each bus based on electrical distance to perform algorithms like K-means clustering. A simple coordinated reactive power control of photovoltaic inverters for voltage regulation is used to demonstrate the effectiveness of the proposed decomposition algorithm and its components. The proposed decomposition method is demonstrated on the IEEE 118-bus system.

multidimensional scaling↗

Solid state {sup 1}H spin-lattice relaxation and isolated-molecule and cluster electronic structure calculations in organic molecular solids: The relationship between structure and methyl group and t-butyl group rotation

We report ab initio density functional theory electronic structure calculations of rotational barriers for t-butyl groups and their constituent methyl groups both in the isolated molecules and in central molecules in clusters built from the X-ray structure in four t-butyl aromatic compounds. The X-ray structures have been reported previously. We also report and interpret the temperature dependence of the solid state {sup 1}H nuclear magnetic resonance spin-lattice relaxation rate at 8.50, 22.5, and 53.0 MHz in one of the four compounds. Such experiments for the other three have been reported previously. We compare the computed barriers for methyl group and t-butyl group rotation in a central target molecule in the cluster with the activation energies determined from fitting the {sup 1}H NMR spin-lattice relaxation data. We formulate a dynamical model for the superposition of t-butyl group rotation and the rotation of the t-butyl group's constituent methyl groups. The four compounds are 2,7-di-t-butylpyrene, 1,4-di-t-butylbenzene, 2,6-di-t-butylnaphthalene, and 3-t-butylchrysene. We comment on the unusual ground state orientation of the t-butyl groups in the crystal of the pyrene and we comment on the unusually high rotational barrier of these t-butyl groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fragment-based {sup 13}C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods

We assess the quality of fragment-based ab initio isotropic {sup 13}C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic {sup 13}C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A case study of tuning MapReduce for efficient Bioinformatics in the cloud

The combination of the Hadoop MapReduce programming model and cloud computing allows biological scientists to analyze next-generation sequencing (NGS) data in a timely and cost-effective manner. Cloud computing platforms remove the burden of IT facility procurement and management from end users and provide ease of access to Hadoop clusters. However, biological scientists are still expected to choose appropriate Hadoop parameters for running their jobs. More importantly, the available Hadoop tuning guidelines are either obsolete or too general to capture the particular characteristics of bioinformatics applications. In this paper, we aim to minimize the cloud computing cost spent on bioinformatics data analysis by optimizing the extracted significant Hadoop parameters. When using MapReduce-based bioinformatics tools in the cloud, the default settings often lead to resource underutilization and wasteful expenses. We choose k-mer counting, a representative application used in a large number of NGS data analysis tools, as our study case. Experimental results show that, with the fine-tuned parameters, we achieve a total of 4× speedup compared with the original performance (using the default settings). Finally, this paper presents an exemplary case for tuning MapReduce-based bioinformatics applications in the cloud, and documents the key parameters that could lead to significant performance benefits.

97 MATHEMATICS AND COMPUTING↗

Scaling and Quality of Modularity Optimization Methods for Graph Clustering

Real-world graphs exhibit structures known as “communities” or “clusters” consisting of a group of vertices with relatively high connectivity between them, as compared to the rest of the vertices in the network. Graph clustering or community detection is a fundamental graph operation used to analyze real-world graphs occurring in the areas of computational biology, cybersecurity, electrical grids, etc. Similar to other graph algorithms, owing to irregular memory accesses and inherently sequential nature, current algorithms for community detection are challenging to parallelize. However, in order to analyze large networks, it is important to develop scalable parallel implementations of graph clustering that are capable of exploiting the architectural features of modern supercomputers. In response to the 2019 Streaming Graph Challenge, we present quality and performance analysis of our distributed- memory community detection using Vite, which is our distributed memory implementation of the popular Louvain method, on the ALCF Theta supercomputer. Clustering methods such as Louvain that rely on modularity maximization are known to suffer from the resolution limit problem, preventing identification of clusters of certain sizes. Hence, we also include quality analysis of our shared-memory implementation of the Fast-tracking Resistance method, in comparison with Louvain on the challenge datasets. Furthermore, we introduce an edge-balanced graph distribution for our distributed memory implementation, that significantly reduces communication, offering up to 80% improvement in the overall execution time. In addition to performance/quality analysis, we also include details on the power/energy consumption, and memory traffic of the distributed-memory clustering implementation using real-world graphs with over a billion edges.

Ghosh, Sayan↗

Bead–Spring Simulation of Ionomer Melts—Studying the Effects of Chain-Length and Associating Group Fraction on Equilibrium Structure and Extensional Flow Behavior

Ionomers are associative polymers with diverse applications ranging from selective membranes and high-performance adhesives to abrasion- and chemical-resistant coatings, insulation layers, vacuum packaging, and foamed sheets. Within equilibrium melt, the ionic or associating groups are known to form thermally reversible, associative clusters whose presence can significantly affect the system’s mechanical, viscoelastic, and transport properties. It is, thus, of great interest to understand how to control such clusters’ size distribution, shape, and stability through the designed choice of polymer architecture and the ionic groups’ fraction, arrangement, and interaction strength. In this work, we represent linear associating polymers using a Kremer–Grest type bead–spring model and perform large-scale MD simulations to explore the effect of polymer chain-length (l) and fraction (f s ) of randomly placed associating groups on the size distribution and stability of formed clusters. We consider different chain-lengths (below and above entanglement), varying fractions of associating groups (represented by ‘sticky’ beads) between 5 and 20%, and a fixed sticky–sticky nonbond interaction strength of four times that between regular non-associating beads. For all melts containing associating groups the equilibrium structure factor S(q) displays a signature ionomer peak at low wave vector q whose intensity increases with increasing f s and l. The average cluster size Nc increases with f s . However, the effect of chain-length on Nc appears to be pronounced only at higher values of f s . Under extensional flows, the computed stress (and viscosity) is higher at higher f s and l regardless of strain rate. Beyond a critical strain rate, we observe fragmentation of the associative clusters, which has interesting effects on the stress/viscous response.

36 MATERIALS SCIENCE↗

Fluorescence of PRODAN in Water: a Computational QM/MM MD Study

Fluorescent properties of PRODAN (6-propionyl-2-dimethylaminonaphthalene) in water were studied by means of excited state molecular dynamics simulations employing a combined quantum mechanical and molecular mechanical approach with the time-dependent density functional theory (TD-DFT QM/MM MD). The state of the art coupled cluster method was used to benchmark density functional theory calculations. The influence of the water environment on PRODAN emission was investigated by employing several computational schemes with varying description of the solvent. The issue of the molecular geometry of the excited state PRODAN molecule in water was addressed. The experimental emission spectrum was reproduced for the planar excited state conformer of PRODAN in the extended environment of 300 explicit water molecules. The planar conformer was shown to be predominantly responsible for fluorescence. The twisted isomer is strongly stabilized in water, but rapidly evolve towards a conical intersection, and hence the twisted conformer is fluorescently inactive.

calculations↗

Numerically exact generalized Green's function cluster expansions for electron-phonon problems

We generalize the family of approximate momentum average methods to formulate a numerically exact, convergent hierarchy of equations whose solution provides an efficient algorithm to compute the Green's function of a particle dressed by bosons suitable in the entire parameter regime. We use this approach to extract ground-state properties and spectral functions. Our approximation-free framework, dubbed the generalized Green's function cluster expansion (GGCE), allows access to exact numerical results in the extreme adiabatic limit, where many standard methods struggle or completely fail. We showcase the performance of the method, specializing three important models of charge-boson coupling in solids and molecular complexes: the molecular Holstein model, which describes coupling between charge density and local distortions, the Peierls model, which describes modulation of charge hopping due to intersite distortions, and a more complex Holstein + Peierls system with couplings to two different phonon modes, paradigmatic of charge-lattice interactions in organic crystals. Furthermore, the GGCE serves as an efficient approach that can be systematically extended to different physical scenarios, thus providing a tool to model the frequency dependence of dressed particles in realistic settings.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Comparing Dark Energy Survey and HST –CLASH observations of the galaxy cluster RXC J2248.7-4431: implications for stellar mass versus dark matter

We derive the stellar mass fraction in the galaxy cluster RXC J2248.7-4431 observed with the Dark Energy Survey (DES) during the Science Verification period. We compare the stellar mass results from DES (five filters) with those from the Hubble Space Telescope Cluster Lensing And Supernova Survey (CLASH; 17 filters). When the cluster spectroscopic redshift is assumed, we show that stellar masses from DES can be estimated within 25 per cent of CLASH values. We compute the stellar mass contribution coming from red and blue galaxies, and study the relation between stellar mass and the underlying dark matter using weak lensing studies with DES and CLASH. An analysis of the radial profiles of the DES total and stellar mass yields a stellar-to-total fraction of f(star) = (6.8 +/- 1.7) x 10(-3) within a radius of r(200c) similar or equal to 2 Mpc. Our analysis also includes a comparison of photometric redshifts and star/galaxy separation efficiency for both data sets. We conclude that space-based small field imaging can be used to calibrate the galaxy properties in DES for the much wider field of view. The technique developed to derive the stellar mass fraction in galaxy clusters can be applied to the similar to 100 000 clusters that will be observed within this survey and yield important information about galaxy evolution.

Palmese, A.↗

The integration of heterogeneous resources in the CMS Submission Infrastructure for the LHC Run 3 and beyond

While the computing landscape supporting LHC experiments is currently dominated by x86 processors at WLCG sites, this configuration will evolve in the coming years. LHC collaborations will be increasingly employing HPC and Cloud facilities to process the vast amounts of data expected during the LHC Run 3 and the future HL-LHC phase. These facilities often feature diverse compute resources, including alternative CPU architectures like ARM and IBM Power, as well as a variety of GPU specifications. Using these heterogeneous resources efficiently is thus essential for the LHC collaborations reaching their future scientific goals. The Submission Infrastructure (SI) is a central element in CMS Computing, enabling resource acquisition and exploitation by CMS data processing, simulation and analysis tasks. The SI must therefore be adapted to ensure access and optimal utilization of this heterogeneous compute capacity. Some steps in this evolution have been already taken, as CMS is currently using opportunistically a small pool of GPU slots provided mainly at the CMS WLCG sites. Additionally, Power9 processors have been validated for CMS production at the Marconi-100 cluster at CINECA. This note will describe the updated capabilities of the SI to continue ensuring the efficient allocation and use of computing resources by CMS, despite their increasing diversity. The next steps towards a full integration and support of heterogeneous resources according to CMS needs will also be reported.

Pérez-Calero Yzquierdo, Antonio↗

Magnetic field induced phase transitions of the triangular spin model

In this work, motivated by a recent inelastic neutron scattering experiment on YbMgGaO 4 , I study the homogeneous spin model on the triangular lattice using the cluster mean-field theory and exact diagonalization. Phase diagrams with and without magnetic field are computed. The results show that the magnetic field can induce the phase transition from the spin liquid state (or the stripe state) to the 120 ° antiferromagnetic state. These phase transitions are suppressed by the next-nearest-neighbor exchange interaction J 2 / J 1 and vanish as J 2 / J 1 > 0.11 . I analyze a parameter space at J 2 / J 1 = 0.1 , where a field induced phase transition can occur, and find that the deviation of the theoretical spin excitation energy from the experimental data is only about 0.054. These results imply that an effective homogeneous spin model still applies to YbMgGaO 4 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

LACEwING: A New Moving Group Analysis Code

We present a new nearby young moving group (NYMG) kinematic membership analysis code, LocAting Constituent mEmbers In Nearby Groups (LACEwING), a new Catalog of Suspected Nearby Young Stars, a new list of bona fide members of moving groups, and a kinematic traceback code. LACEwING is a convergence-style algorithm with carefully vetted membership statistics based on a large numerical simulation of the Solar Neighborhood. Given spatial and kinematic information on stars, LACEwING calculates membership probabilities in 13 NYMGs and three open clusters within 100 pc. In addition to describing the inputs, methods, and products of the code, we provide comparisons of LACEwING to other popular kinematic moving group membership identification codes. As a proof of concept, we use LACEwING to reconsider the membership of 930 stellar systems in the Solar Neighborhood (within 100 pc) that have reported measurable lithium equivalent widths. We quantify the evidence in support of a population of young stars not attached to any NYMGs, which is a possible sign of new as-yet-undiscovered groups or of a field population of young stars.

79 ASTRONOMY AND ASTROPHYSICS↗

On the geometric dependence of the molecular dipole polarizability in water: A benchmark study of higher-order electron correlation, basis set incompleteness error, core electron effects, and zero-point vibrational contributions

In this work, we investigate how geometric changes influence the static dipole polarizability ($α$) of a water molecule by explicitly computing the corresponding dipole polarizability surface (DPS) across 3125 total (1625 symmetry-unique) geometries using linear response coupled cluster theory including single, double, and triple excitations (LR-CCSDT) and the doubly augmented triple-$ζ$ basis set (d-aug-cc-pVTZ). Analytical formulae based on power series expansions of this $ab initio$ surface are generated using linear least-squares analysis and provide highly accurate estimates of this quantity as a function of molecular geometry (i.e., bond and angle variations) in a computationally tractable manner. An additional database, which consists of 25 representative molecular geometries and incorporates a more thorough treatment of both basis sets and core electron effects, is provided as a current benchmark for this quantity and the corresponding leading-order $C_6$ dispersion coefficient. This database has been utilized to assess the importance of these effects as well as the relative accuracy that can be obtained using several quantum chemical methods and a library of density functional approximations. In addition to high-level electron correlation methods (like CCSD) and our analytical least-squares formulae, we find that the SCAN0, PBE0, MN15, and B97-2 hybrid functionals yield the most accurate descriptions of the molecular polarizability tensor in H 2 O. Using first-order perturbation theory, we compute the zero-point vibrational correction to $α$ at the CCSDT/d-aug-cc-pVTZ level and find that this correction contributes approximately 3% to the isotropic ($α$ iso ) and nearly 50% to the anisotropic ($α$ aniso ) polarizability values. In doing so, we find that $α$ iso = 9.8307 bohr 3 , which is in excellent agreement with the experimental value of 9.83 ± 0.02 bohr 3 provided by Russell and Spackman. The DPS reported herein provides a benchmark-quality quantum mechanical estimate of this fundamental quantity of interest and should find extensive use in the development (and assessment) of next-generation force fields and machine-learning based approaches for modeling water in complex condensed-phase environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High Performance Network Monitoring [Slides]

Network Monitoring requires a substantial use of data and error analysis to overcome issues with clusters. Zenoss and Splunk help to monitor system log messages that are reporting issues about the clusters to monitoring services. Infiniband infrastructure on a number of clusters upgraded to ibmon2. ibmon2 requires different filters to report errors to system administrators. Focus for this summer is to: (1) Implement ibmon2 filters on monitoring boxes to report system errors to system administrators using Zenoss and Splunk; (2) Modify and improve scripts for monitoring and administrative usage; (3) Learn more about networks including services and maintenance for high performance computing systems; and (4) Gain a life experience working with professionals under real world situations. Filters were created to account for clusters running ibmon2 v1.0.0-1 10 Filters currently implemented for ibmon2 using Python. Filters look for threshold of port counters. Over certain counts, filters report errors to on-call system administrators and modifies grid to show local host with issue.

97 MATHEMATICS AND COMPUTING↗

Pairing correlations in the cuprates: A numerical study of the three-band Hubbard model

We study the three-band Hubbard model for the copper oxide plane of the high-temperature superconducting cuprates using determinant quantum Monte Carlo and the dynamical cluster approximation (DCA) and provide a comprehensive view of the pairing correlations in this model using these methods. Specifically, we compute the pair-field susceptibility and study its dependence on temperature, doping, interaction strength, and charge-transfer energy. Using the DCA, we also solve the Bethe-Salpeter equation for the two-particle Green's function in the particle-particle channel to determine the transition temperature to the superconducting phase on smaller clusters. Our calculations reproduce many aspects of the cuprate phase diagram and indicate that there is an “optimal” value of the charge-transfer energy for the model where T c is largest. Finally, these results have implications for our understanding of superconductivity in both the cuprates and other doped charge-transfer insulators.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗