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DOE OSTI2016

Coupling LAMMPS and the vl3 Framework for Co-Visualization of Atomistic Simulations

In this work we perform in-situ visualization of molecular dynamics simulations, which can help scientists to visualize simulation output on-the-fly, without incurring storage overheads. We present a case study to couple LAMMPS, the large-scale molecular dynamics simulation code with vl3, our parallel framework for large-scale visualization and analysis. Our motivation is to identify effective approaches for covisualization and exploration of large-scale atomistic simulations at interactive frame rates.We propose a system of coupled libraries and describe its architecture, with an implementation that runs on GPU-based clusters. We present the results of strong and weak scalability experiments, as well as future research avenues based on our results.

co-visualization↗

DOE OSTI2018

Self-optimized construction of transition rate matrices from accelerated atomistic simulations with Bayesian uncertainty quantification

Here, a massively parallel method to build large transition rate matrices from temperature-accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is used to estimate the expected residence time in the known state space, providing crucial uncertainty quantification for higher-scale simulation schemes such as kinetic Monte Carlo or cluster dynamics. The estimators are additionally used to optimize where exploration is performed and the degree of temperature acceleration on the fly, giving an autonomous, optimal procedure to explore the state space of complex systems. The method is tested against exactly solvable models and used to explore the dynamics of C15 interstitial defects in iron. Our uncertainty quantification scheme allows for accurate modeling of the evolution of these defects over timescales of several seconds.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Structural evidence for intermediates during O 2 formation in photosystem II

In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn 4 CaO 5 cluster first stores four oxidizing equivalents, the S 0 to S 4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O–O bond formation chemistry. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok’s photosynthetic water oxidation cycle, the S 3 →[S 4 ]→S 0 transition where O 2 is formed and Kok’s water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn 4 CaO 5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom O x , which was introduced as a bridging ligand between Ca and Mn1 during the S 2 →S 3 transition disappears or relocates in parallel with Y z reduction starting at approximately 700 μs after the third flash. The onset of O 2 evolution, as indicated by the shortening of the Mn1–Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Evidence of the ion cyclotron resonance at proton kinetic scales in the solar wind

The k-filtering and wave polarization techniques are applied to Cluster magnetic field data at four intervals of fast free (not connected to Earth's foreshock) solar wind. In addition to the commonly observed population of magnetic field fluctuations propagating at quasi-perpendicular angles to the global mean field B{sub 0}, a population of fluctuations propagating at quasi-parallel angles are also observed when no local plasma instability can be identified. At low wavenumbers (kv{sub A}/Ω{sub p} ≤ 0.6) both components are present, and have powers of similar strength, while at higher wavenumbers (kv{sub A}Ω{sub p} > 0.6) only the perpendicular component can be identified. Here v{sub A} and Ω{sub p} are the Alfvén speed and the proton (angular) gyration frequency, k denotes the wavenumber. The dispersion curve obtained (and the ratio of the magnitudes of left and right hand polarized fluctuations) shows a sharp transition (and decrease) at (kv{sub A}/Ω{sub p}) ∼ 0.6, which corresponds to a spacecraft frequency f {sub sc} = 0.32 Hz. At higher wavenumbers the measurements agree with previous studies indicating the presence of kinetic Alfvén wave (KAW) turbulence or a mixture of KAW turbulence and convected structures. The parallel component displays a scaling of k{sub ∥}{sup −δ} where the spectral index δ ranges between about 5/3 and 2 although the number of data points does not warrant an accurate determination. The origins of the observed parallel component are unclear. The presence of a parallel component is consistent with ion cyclotron waves, and we interpret the sharp drop of this component at higher wavenumbers as evidence that the ion cyclotron resonance is occurring in the solar wind intervals studied.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

A Case Study of LLVM-Based Analysis for Optimizing SIMD Code Generation

This paper presents a methodology for using LLVM-based tools to tune the DCA++ (dynamical cluster approximation) application that targets the new ARM A64FX processor. The goal is to describe the changes required for the new architecture and generate efficient single instruction/multiple data (SIMD) instructions that target the new Scalable Vector Extension instruction set. During manual tuning, the authors used the LLVM tools to improve code parallelization by using OpenMP SIMD, refactored the code and applied transformation that enabled SIMD optimizations, and ensured that the correct libraries were used to achieve optimal performance. By applying these code changes, code speed was increased by 1.98× and 78 GFlops were achieved on the A64FX processor. The authors aim to automatize parts of the efforts in the OpenMP Advisor tool, which is built on top of existing and newly introduced LLVM tooling.

Huber, Joseph↗

DOE OSTI2016

Structural modulation and luminescent properties of four Cd{sup II} coordination architectures based on 3-(pyridin-4-yl)-5-(pyrazin-2-yl)-1H-1,2,4-triazole and flexible/rigid dicarboxylate ligands

To systematically investigate the influence of the flexible or rigid auxiliary ligands on the structures and properties of transition metal compounds, we synthesized four new d{sup 10} coordination polymers (CPs) from 3-(pyridin-4-yl)-5-(pyrazin-2-yl)-1H-1,2,4-triazole (4-Hpzpt) and flexible/rigid dicarboxylate ligands, [Cd(4-pzpt){sub 2}]{sub n} (1), [Cd{sub 3}(4-pzpt){sub 2}(suc){sub 2}]{sub n} (2), [Cd{sub 2}(4-Hpzpt)(nbc){sub 2}(H{sub 2}O)]{sub n} (3) and ([Cd{sub 2}(4-pzpt){sub 2}(tfbdc)(H{sub 2}O){sub 4}]·H{sub 2}O){sub n} (4) (H{sub 2}suc=1,2-ethanedicarboxylic acid, H{sub 2}nbc=hthalene-1,4-dicarboxylic acid, H{sub 2}tfbdc =2,3,5,6-tetrafluoroterephthalic acid). Single crystal X-ray analysis indicates that compound 1 shows a 4{sup 4}-sql layer, which is extended to a 3D network via nonclassical C–H{sup …}N hydrogen bonds. Compound 2 possesses a 6-connected pcu-4{sup 12}0.6{sup 3} net composed of trinuclear Cd{sup II}-clusters. Compound 3 represents a rare 3D (3,4,4,5)-connected topology with a Schläfli symbol of (4·6·7)(4·5{sup 3}·7{sup 2})(5{sup 3}·6·7·9)(4{sup 2}·5{sup 5}·6·7{sup 2}). Compound 4 exhibits a 2D+2D→2D parallel interpenetrated 6{sup 3}-hcb network. The adjacent 2D networks are interdigitated with each other to form the resulting 3D supramolecular architecture through classical O–H{sup …}N and O–H{sup …}O hydrogen bonds. Structural diversities indicate that the nature of flexible/rigid-dicarboxlates plays crucial roles in modulating structures of these compounds. Moreover, the luminescent properties of them have been briefly investigated. - Graphical abstract: Four new Cd{sup II} coordination architectures constructed from the primary ligand 4-Hpzpt and flexible/rigid dicarboxylate coligands. Structural diversities indicate that the nature of flexible/rigid-dicarboxlates plays crucial roles in modulating structures of these compounds. And more, the thermal stability and luminescence are discussed. - Highlights: • Four new Cd{sup II} compounds with 4-Hpzpt and flexible/rigid dicarboxylate coligands. • Structural analysis of all compounds. • luminescent property of all compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Direct conversion of methane to aromatics and hydrogen via a heterogeneous trimetallic synergistic catalyst

Abstract Non-oxidative methane dehydro-aromatization reaction can co-produce hydrogen and benzene effectively on a molybdenum-zeolite based thermochemical catalyst, which is a very promising approach for natural-gas upgrading. However, the low methane conversion and aromatics selectivity and weak durability restrain the realistic application for industry. Here, a mechanism for enhancing catalysis activity on methane activation and carbon-carbon bond coupling has been found to promote conversion and selectivity simultaneously by adding platinum–bismuth alloy cluster to form a trimetallic catalyst on zeolite (Pt-Bi/Mo/ZSM-5). This bimetallic alloy cluster has synergistic interaction with molybdenum: the formed CH 3 * from Mo 2 C on the external surface of zeolite can efficiently move on for C-C coupling on the surface of Pt-Bi particle to produce C 2 compounds, which are the key intermediates of oligomerization. This pathway is parallel with the catalysis on Mo inside the cage. This catalyst demonstrated 18.7% methane conversion and 69.4% benzene selectivity at 710 °C. With 95% methane/5% nitrogen feedstock, it exhibited robust stability with slow deactivation rate of 9.3% after 2 h and instant recovery of 98.6% activity after regeneration in hydrogen. The enhanced catalytic activity is strongly associated with synergistic interaction with Mo and ligand effects of alloys by extensive mechanism studies and DFT calculation.

03 NATURAL GAS↗

DOE OSTI2019

CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria

Advances in the prediction of biosynthetic gene clusters (BGCs) from genomic and metagenomic data have made the large-scale identification of candidate secondary metabolite biosynthesis pathways routine. However, most predicted BGCs cannot be successfully expressed in the limited range of expression hosts currently available, which prevents the identification and characterization of their respective products. Here we show that parallelized use of a phylogenetically and physiologically diverse panel of purpose-engineered chassis strains offers a versatile strategy for the rapid activation of BGCs. We domesticated an ensemble of 25 diverse ?-proteobacteria from 11 different genera by integrating a unified landing pad that enables efficient introduction of large BGCs into their genome. We deployed this chassis-independent recombinase-assisted genome engineering (CRAGE) strategy to express several previously posited but experimentally elusive non-ribosomal peptide synthase (NRPS) and NRPSpolyketide synthase (PKS) hybrid BGCs from Photorhabdus luminescens. Successful activation of 6 BGCs identified 21 products, including several with likely roles in host-microbe interactions. Taken together, we illustrate how the regulatory and physiological diversity naturally present across bacteria can be harnessed for the exploration of novel bioproducts and provide a sizable panel of domesticated chassis strains to enable this strategy.

applied microbiology, genetic engineering, industr↗

DOE OSTI2012

pGraph: Efficient Parallel Construction of Large-Scale Protein Sequence Homology Graphs

Detecting sequence homology between protein sequences is a fundamental problem in computational molecular biology, with a pervasive application in nearly all analyses that aim to structurally and functionally characterize protein molecules. While detecting the homology between two protein sequences is relatively inexpensive, detecting pairwise homology for a large number of protein sequences can become computationally prohibitive for modern inputs, often requiring millions of CPU hours. Yet, there is currently no robust support to parallelize this kernel. In this paper, we identify the key characteristics that make this problemparticularly hard to parallelize, and then propose a new parallel algorithm that is suited for detecting homology on large data sets using distributed memory parallel computers. Our method, called pGraph, is a novel hybrid between the hierarchical multiple-master/worker model and producer-consumer model, and is designed to break the irregularities imposed by alignment computation and work generation. Experimental results show that pGraph achieves linear scaling on a 2,048 processor distributed memory cluster for a wide range of inputs ranging from as small as 20,000 sequences to 2,560,000 sequences. In addition to demonstrating strong scaling, we present an extensive report on the performance of the various system components and related parametric studies.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2016

Solar wind compressible turbulence near proton scales: Cluster observations

The solar wind compressible turbulence attracts more attention recently due to its possible role in plasma heating. Using the plasma density and magnetic field measured simultaneously by the Cluster C1 probe, we statistically investigate the wave characteristics of the proton-scale compressible turbulence. In most cases, the density and magnetic field strength fluctuations almost show no positive correlation, suggesting the absence of fast mode waves. Moreover, the magnetic compressibility C{sub b} as measured by the level of magnetic fluctuations parallel to the background field, is enhanced continuously around proton scales and is consistent with kinetic Alfvén wave (KAW) prediction. Interestingly, kinetic slow mode waves (KSW) are identified in a few cases through large values of C{sub b} and plasma compressibility C{sub p}, together with the the anti-correlation between n and B. We suggest that both KAW and KSW can account for the compressible fluctuations energy, while their relative proportions under certain plasma condition require further studies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2019

Approximate Green’s Function Coupled Cluster A Method Employing Effective Dimension Reduction

The Green’s function coupled cluster (GFCC) method, originally proposed in the early 1990s, is a powerful many-body tool for computing and analyzing the electronic structures of molecular structures and periodic systems, especially when electrons are strongly correlated. However, in order for the GFCC method to become an approach that can be routinely used in the electronic structure calculations, more robust linear algebraic techniques and approximations need to be employed to reduce its extremely high computational overhead. In our recent studies, we showed that the GFCC equation can be numerically solved by seeking solutions of multiple linear systems in the frequency regime of interest, which can be easily distributed in a massively parallel environment, and broaden the avenue for more state-of-the-art numerical linear algebraic tools associated with multiple linear systems to be kicked in to this field. In the present pursuit of this practice, we show a successful application of model order reduction (MOR) techniques in the GFCC framework. Briefly speaking, for a frequency regime of interest that requires a high resolution of spectral function, instead of solving GFCC linear equation in the original dimension for every single frequency point, an easily-solvable linear system model with reduced dimension can be built upon projecting the original GFCC linear system into a subspace, from which the interpolation and extrapolation can give a reasonable approximation to the results of the original GFCC linear equations. Here, we show that the subspace can be properly constructed in an iterative manner from the auxiliary vectors of the GFCC linear equations at some select frequencies inside the frequency regime. During the iterations, the quality of the subspace, as well as the linear system model, can be systematically improved. The approach is tested in this work in terms of the efficiency and accuracy of computing spectral functions for some typical molecular systems including carbon monoxide, 1,3-butadiene, benzene, and adenine molecules. As a byproduct, the high quality linear system model is also found to be able to provide high quality initial guess for the existing linear solver to improve the convergence performance.

Peng, Bo↗

DOE OSTI2025

MBX V1.2: Accelerating Data-Driven Many-Body Molecular Dynamics Simulations

The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these potential energy functions integrate physics-based and machine-learned many-body terms trained on electronic structure data calculated at the "gold standard" coupled-cluster level of theory. Recent advancements in MBX have focused on optimizing its performance, resulting in the release of MBX v1.2. While the inherently many-body nature of MB-pol and MB-nrg ensures high accuracy, it poses computational challenges. MBX v1.2 addresses these challenges with significant performance improvements, including enhanced parallelism that fully harnesses the power of modern multicore CPUs. In conclusion, these advancements enable simulations on nanosecond time scales for condensed-phase systems, significantly expanding the scope of high-accuracy, predictive simulations of complex molecular systems powered by data-driven many-body potential energy functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Real-space pseudopotential method for computing the vibrational Stark effect

The vibrational Stark shift is an important effect in determining the electrostatic environment for molecular or condensed matter systems. However, accurate ab initio calculations of the vibrational Stark effect are a technically demanding challenge. In this paper, we make use of density functional theory constructed on a real-space grid to expedite the computation of this effect. Our format is especially advantageous for the investigation of small molecules in finite fields as cluster boundary conditions eliminate spurious supercell interactions and allow for charged systems, while convergence is controlled by a single parameter, the grid spacing. The Stark tuning rate is highly sensitive to the interaction between anharmonicity in a vibrational mode and the applied field. To ensure this subtle interaction is fully captured, we apply three parallel approaches: a direct finite field, a perturbative method, and a molecular dynamics method. Finally, we illustrate this method by applying it to several small molecules containing C–O and C–N bonds and show that a consistent result can be obtained.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2019

Roadmap on photonic, electronic and atomic collision physics: I. Light–matter interaction

We publish three Roadmaps on photonic, electronic and atomic collision physics in order to celebrate the 60th anniversary of the ICPEAC conference. In Roadmap I, we focus on the light–matter interaction. In this area, studies of ultrafast electronic and molecular dynamics have been rapidly growing, with the advent of new light sources such as attosecond lasers and x-ray free electron lasers. In parallel, experiments with established synchrotron radiation sources and femtosecond lasers using cutting-edge detection schemes are revealing new scientific insights that have never been exploited. Relevant theories are also being rapidly developed. Target samples for photon-impact experiments are expanding from atoms and small molecules to complex systems such as biomolecules, fullerene, clusters and solids. This Roadmap aims to look back along the road, explaining the development of these fields, and look forward, collecting contributions from twenty leading groups from the field.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2011

Using the Global Arrays Toolkit to Reimplement NumPy for Distributed Computation

Global Arrays (GA) is a software system from Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared memory programming interface to manipulate distributed defense arrays. Using a combination of GA and NumPy, we have reimplemented NumPy as a distributed drop-in replacement called Global Arrays in NumPy (GAiN). Scalability studies will be presented showing the utility of developing serial NumPy codes which can later run on more capable clusters or supercomputers.

Global Arrays↗

DOE OSTI2019

High resolution ENDOR spectroscopy combined with quantum chemical calculations reveals the structure of the nitrogenase Janus intermediate E4(4H)

We have shown that the key state in N2 reduction to two NH3 by the enzyme nitrogenase is the E4(4H), ‘Janus’ intermediate, which has accumulated four [e-/H+] and is poised to undergo reductive elimination of H2 coupled to N2 binding and activation. Initial 1H and 95Mo ENDOR studies of freeze-trapped E4(4H) revealed the catalytic multi-metallic cluster (FeMo-co) binds two Fe-bridging hydrides, [Fe-H-Fe]. However, the analysis failed to provide a satisfactory picture of structure - the relative spatial relationships of the two [Fe-H-Fe]. Our recent density functional theory (DFT) study yielded a lowest-energy form, denoted E4(4H)(a), with two parallel Fe-H-Fe planes bridging pairs of ‘anchor’ Fe on the Fe2,3,6,7 face of FeMo-co. However, the relative energies of structures E4(4H)(b), with one bridging and one terminal hydride, and E4(4H)(c), with one pair of anchor Fe supporting two bridging hydrides, were not beyond the uncertainties of the calculation. Moreover, a structure of V-dependent nitrogenase resulted in a proposed structure analogous to E4(4H)(c), and additional structures have been proposed by DFT studies of others. To resolve the nature of hydride binding to the Janus intermediate, we performed exhaustive, high-resolution CW-stochastic 1H-ENDOR experiments using improved instrumentation, Mims 2H ENDOR, and a pulsed-ENDOR protocol (‘PESTRE’) to obtain absolute hyperfine-interaction signs. These measurements are coupled to DFT structural models through an analytical point-dipole Hamiltonian for the hydride electron-nuclear dipolar coupling to its ‘anchoring’ Fe ions, an approach that overcomes limitations inherent in both experimental interpretation and computational accuracy. The result: the freeze-trapped, lowest-energy Janus intermediate structure is E4(4H)(a).

Hoeke, Veronica↗

DOE OSTI2015

Chemical accuracy from quantum Monte Carlo for the benzene dimer

We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of −2.3(4) and −2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is −2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2012

PWR internal flow modeling with fuel assemblies details

This study is an example of a massive parallel computing of the coolant flow in a nuclear reactor. It resolves the flow velocities in each assembly on pin level and predicts the flow distribution in complex geometries such as the lower and upper reactor plenums. The size of the developed model (1.035 billion cells) required the runs to be executed on the NCCS clusters (www.nccs.gov). STAR-CCM+ code (www.ed-adapco.com) was installed on two clusters: JAGUARXT5 and FROST, both of which were capable of executing this model. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗