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At least 829 records · Page 46

Collaborative research: Dynamics of electrostatic solitary waves and their effects on current layers

The project has accomplished the following achievements including the goals outlined in the original proposal. Generation and measurements of Debye-scale electron holes in laboratory: We have generated by beam injections electron solitary waves in the LAPD experiments. The measurements were made possible by the fabrication of the state-of-the-art microprobes at UCLA to measure Debye-scale electric fields [Chiang et al., 2011]. We obtained a result that challenged the state of knowledge about electron hole generation. We found that the electron holes were not due to two-stream instability, but generated by a current-driven instability that also generated whistler-mode waves [Lefebvre et al., 2011, 2010b]. Most of the grant supported a young research scientist Bertrand Lefebvre who led the dissemination of the laboratory experimental results. In addition to two publications, our work relevant to the laboratory experiments on electron holes has resulted in 7 invited talks [Chen, 2007, 2009; Pickett et al., 2009a; Lefebvre et al., 2010a; Pickett et al., 2010; Chen et al., 2011c, b] (including those given by the co-I Jolene Pickett) and 2 contributed talks [Lefebvre et al., 2009b, a]. Discovery of elecctron phase-space-hole structure in the reconnection electron layer: Our theoretical analyses and simulations under this project led to the discovery of an inversion electric field layer whose phase-space signature is an electron hole within the electron diffusion layer in 2D anti-parallel reconnection [Chen et al., 2011a]. We carried out particle tracing studies to understand the electron orbits that result in the phase-space hole structure. Most importantly, we showed that the current density in the electron layer is limited in collisionless reconnection with negligible guide field by the cyclotron turning of meandering electrons. Comparison of electrostatic solitary waves in current layers observed by Cluster and in LAPD: We compared the ESWs observed in a supersubstorm by the Cluster spacecraft and those measured in LAPD. One of the similarities in the characteristics of ESWs observed in space and in LAPD is that the time duration tends to be approximately the inverse of the electron plasma frequency [Pickett et al., 2009b]. Discovery of suprathermal electron bursts inside a series of magnetic islands: Our effort in examining the roles of ESWs in reconnection current layers resulted in the serendipitous discovery that was published in Nature Physics. In earth’s magnetosphere, we observed through the measurements from the four Cluster spacecraft, a series of magnetic islands and suprathermal electron bursts within the islands. The islands were identified to be effectively acceleration sites for electrons [Chen et al., 2008, 2009].

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Laboratory Astrophysics using a Microcalorimeter and Bragg Crystal Spectrometer on an Electron Beam Ion Trap

During the past year we have been preparing our new microcalorimeter system for permanent delivery to the NIST EBIT. Unfortunately, there have been delays due to technical difficulties in the fabrication of the two-stage adiabatic demagnetization refrigerator and in the life expectancy of the thin windows used for internal thermal baffling of the infrared radiation. These problems have been solved and we are completing tests of the entire system and it will be set up at NIST during the first week of May. Several photos of the new system are shown in Figures 1A and 1B. This microcalorimeter spectrometer only requires helium refills every three days (as opposed to every 24 hours) and it will hold a temperature! of 65 mK for up to 48 hours (as opposed to 8 hours). Consequently, the efficiency of data acquisition will improve dramatically. In parallel we have published a paper that reviews our previous work (Takacs et al. 2003), especially on Fe XVII, in the context of recent measurements by other groups. This paper is included. We highlight a recent measurement of a broad band spectrum of Fe in Figure 2 that simultaneously includes L and K radiation. It is compared with the simulated spectrum of the Perseus Cluster that one could expect to obtain with a microcalorimeter in the focus of a grazing incidence telescope such as the one being designed for Constellation X. Both the charge state distributions and the relative intensity ratios of the emission lines within the particular charge state are very similar in the two spectra. This further demonstrates the importance and relevance of the laboratory measurements in predicting the components of cosmic spectra.

Brinton, John C.↗

Genarris 2.0: A Random Structure Generator for Molecular Crystals

Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine. Program summary Program Title: Genarris 2.0 Program Files doi: http://dx.doi.org/10.17632/grx6mz4pjn.1 Licensing provisions: BSD-3 Clause Programming language: Python, C External routines/libraries: Spglib, ASE, pymatgen, SciPy, mpi4py, scikit-learn, PyTorch, FHI-aims. Nature of problem: Molecular crystal structure prediction. Solution method: Genarris 2.0 generates molecular crystal structures over the 230 space groups, on general and special Wyckoff positions, using physical constraints. Down-sampling of the generated structures may be performed subsequently, based on molecular crystal packing descriptors and an unsupervised machine learning algorithm. Lastly, ab initio structure relaxation may be performed for the final pool. Depending on the user-defined workflow implemented, Genarris may be used to generate diverse molecular crystal datasets to seed evolutionary algorithms or to train machine learning algorithms or as a standalone crystal structure prediction method. Restrictions: For crystal structure generation, the molecule of interest must be semi-rigid with no bond rotational degrees of freedom. Unusual features: Genarris 2.0 is a highly distributed program, making use of MPI for Python parallelization. The user has the ability to design and implement workflows by executing a user-defined list of procedures. Genarris 2.0 offers new features including a machine learning model for estimating the molecular volume in the solid state from the single molecule structure, structure generation in special Wyckoff positions of space groups, hierarchical structure checks including rigorous treatment of non-orthogonal structures, and clustering and down-selection workflows combining first principles simulations with machine learning. (C) 2020 Elsevier B.V. All rights reserved.

Crystal structure prediction↗

Cluster synthesis of monodisperse rutile-TiO2 nanoparticles and dielectric TiO2-vinylidene fluoride oligomer nanocomposites

The embedding of oxide nanoparticles in polymer matrices produces a greatly enhanced dielectric response by combining the high dielectric strength and low loss of suitable host polymers with the high electric polarizability of nanoparticles. The fabrication of oxide-polymer nanocomposites with well-controlled distributions of nanoparticles is, however, challenging due to the thermodynamic and kinetic barriers between the polymer matrix and nanoparticle fillers. In the present study, monodisperse TiO2 nanoparticles having an average particle size of 14.4 nm and predominant rutile phase were produced using a cluster-deposition technique without high-temperature thermal annealing and subsequently coated with uniform vinylidene fluoride oligomer (VDFO) molecules using a thermal evaporation source, prior to deposition as TiO2-VDFO nanocomposite films on suitable substrates. The molecular coatings on TiO2 nanoparticles serve two purposes, namely to prevent the TiO2 nanoparticles from contacting each other and to couple the nanoparticle polarization to the matrix. Parallel-plate capacitors made of TiO2-VDFO nanocomposite film as the dielectric exhibit minimum dielectric dispersion and low dielectric loss. Dielectric measurements also show an enhanced effective dielectric constant in TiO2-VDFO nanocomposites as compared to that of pure VDFO. This study demonstrates for the first time a unique electroactive particle coating in the form of a ferroelectric VDFO that has high-temperature stability as compared to conventionally used polymers for fabricating dielectric oxide-polymer nanocomposites.

Balasubramanian, B↗

Oxygen tracer diffusion in single-crystal alumina

Oxygen tracer diffusion coefficients are determined in single-crystal alumina samples with differing dopant levels using the gas-exchange technique. The diffusion direction is parallel to the c-axis and the ambient PO2 is 1 atm (100,000 Pa) for all experiments except a single run with a low PO2, approximately 10 to the -15th atm (10 to the -10th Pa) produced by a CO/CO2 mixture. The diffusion is insensitive to both impurities and ambient PO2. The insensitivities are discussed in terms of point-defect clustering. Prior tracer studies are compared and discussed.

Cawley, James D.↗

Stochastic GW -GPU: Rapid Quasi-Particle Energies for Molecules beyond 10,000 Atoms

StochasticGW is a code for computing accurate quasi-particle (QP) energies of molecules and material systems in the GW approximation. StochasticGW utilizes the stochastic Resolution of the Identity (sROI) technique to enable a massively parallel implementation with computational costs that scale semilinearly with system size, allowing the method to access systems with tens of thousands of electrons. Here, we introduce a new implementation, StochasticGW-GPU, for which the main bottleneck steps have been ported to GPUs and give substantial performance improvements over previous versions of the code. We showcase the new code by computing band gaps of hydrogenated silicon clusters (Si x H y ) containing up to 10,001 atoms and 35,144 electrons, and we obtain individual QP energies with a statistical precision of better than ±0.03 eV with times-to-solution of less than 1 h.

Thomas, Phillip S. [Lawrence Berkeley National Lab↗

How good are polarizable and flexible models for water: Insights from a many-body perspective

We present a systematic analysis of state-of-the-art polarizable and flexible water models from a many-body perspective, with a specific focus on their ability to represent the Born–Oppenheimer potential energy surface of water from the gas to the liquid phase. Using coupled cluster data in the completed basis set limit as a reference, we examine the accuracy of the polarizable models in reproducing individual many-body contributions to interaction energies and harmonic frequencies of water clusters and compare their performance with that of MB-pol, an explicit many-body model that has been shown to correctly predict the properties of water across the entire phase diagram. Based on these comparisons, we use MB-pol as a reference to analyze the ability of the polarizable models to reproduce the energy landscape of liquid water under ambient conditions. We find that, while correctly reproducing the energetics of minimum-energy structures, the polarizable models examined in this study suffer from inadequate representations of many-body effects for distorted configurations. To investigate the role played by geometry-dependent representations of 1-body charge distributions in reproducing coupled cluster data for both interaction and many-body energies, we introduce a simplified version of MB-pol that adopts fixed atomic charges and demonstrate that the new model retains the same accuracy as the original MB-pol model. Based on the analyses presented in this study, we believe that future developments of both polarizable and explicit many-body models should continue in parallel and would benefit from synergistic efforts aimed at integrating the best aspects of the two theoretical/computational frameworks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Dynamical and Statistical Characterization of U.S. Extreme Precipitation Events and Their Associated Large-Scale Meteorological Patterns

Abstract Regional patterns of extreme precipitation events occurring over the continental United States are identified via hierarchical cluster analysis of observed daily precipitation for the period 1950–2005. Six canonical extreme precipitation patterns (EPPs) are isolated for the boreal warm season and five for the cool season. The large-scale meteorological pattern (LMP) inducing each EPP is identified and used to create a “base function” for evaluating a climate model’s potential for accurately representing the different patterns of precipitation extremes. A parallel analysis of the Community Climate System Model, version 4 (CCSM4), reveals that the CCSM4 successfully captures the main U.S. EPPs for both the warm and cool seasons, albeit with varying degrees of accuracy. The model’s skill in simulating each EPP tends to be positively correlated with its capability in representing the associated LMP. Model bias in the occurrence frequency of a governing LMP is directly related to the frequency bias in the corresponding EPP. In addition, however, discrepancies are found between the CCSM4’s representation of LMPs and EPPs over regions such as the western United States and Midwest, where topographic precipitation influences and organized convection are prominent, respectively. In these cases, the model representation of finer-scale physical processes appears to be at least equally important compared to the LMPs in driving the occurrence of extreme precipitation.

54 ENVIRONMENTAL SCIENCES↗

A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes

During microbial evolution, genome rearrangement increases with increasing sequence divergence. If the relationship between synteny and sequence divergence can be modeled, gene clusters in genomes of distantly related organisms exhibiting anomalous synteny can be identified and used to infer functional conservation. We applied the phylogenetic pairwise comparison method to establish and model a strong correlation between synteny and sequence divergence in all 634 available Archaeal and Bacterial genomes from the NCBI database and four newly assembled genomes of uncultivated Archaea from an acid mine drainage (AMD) community. In parallel, we established and modeled the trend between synteny and functional relatedness in the 118 genomes available in the STRING database. By combining these models, we developed a gene functional annotation method that weights evolutionary distance to estimate the probability of functional associations of syntenous proteins between genome pairs. The method was applied to the hypothetical proteins and poorly annotated genes in newly assembled acid mine drainage Archaeal genomes to add or improve gene annotations. This is the first method to assign possible functions to poorly annotated genes through quantification of the probability of gene functional relationships based on synteny at a significant evolutionary distance, and has the potential for broad application.

59 BASIC BIOLOGICAL SCIENCES↗

Oxygen diffusion in alpha-Al2O3

Oxygen self diffusion coefficients were determined in single crystal alpha-Al2O3 using the gas exchange technique. The samples were semi-infinite slabs cut from five different boules with varying background impurities. The diffusion direction was parallel to the c-axis. The tracer profiles were determined by two techniques, single spectrum proton activation and secondary ion mass spectrometry. The SIMS proved to be a more useful tool. The determined diffusion coefficients, which were insensitive to impurity levels and oxygen partial pressure, could be described by D = .00151 exp (-572kJ/RT) sq m/s. The insensitivities are discussed in terms of point defect clustering. Two independent models are consistent with the findings, the first considers the clusters as immobile point defect traps which buffer changes in the defect chemistry. The second considers clusters to be mobile and oxygen diffusion to be intrinsic behavior, the mechanism for oxygen transport involving neutral clusters of Schottky quintuplets.

Cawley, J. D.↗

Applied Parallel Metadata Indexing

The GPFS Archive is parallel archive is a parallel archive used by hundreds of users in the Turquoise collaboration network. It houses 4+ petabytes of data in more than 170 million files. Currently, users must navigate the file system to retrieve their data, requiring them to remember file paths and names. A better solution might allow users to tag data with meaningful labels and searach the archive using standard and user-defined metadata, while maintaining security. last summer, I developed the backend to a tool that adheres to these design goals. The backend works by importing GPFS metadata into a MongoDB cluster, which is then indexed on each attribute. This summer, the author implemented security and developed the user interfae for the search tool. To meet security requirements, each database table is associated with a single user, which only stores records that the user may read, and requires a set of credentials to access. The interface to the search tool is implemented using FUSE (Filesystem in USErspace). FUSE is an intermediate layer that intercepts file system calls and allows the developer to redefine how those calls behave. In the case of this tool, FUSE interfaces with MongoDB to issue queries and populate output. A FUSE implementation is desirable because it allows users to interact with the search tool using commands they are already familiar with. These security and interface additions are essential for a usable product.

97 MATHEMATICS AND COMPUTING↗

A quantitative model of application slow-down in multi-resource shared systems

Scheduling multiple jobs onto a platform enhances system utilization by sharing resources. The benefits from higher resource utilization include reduced cost to construct, operate, and maintain a system, which often include energy consumption. Maximizing these benefits comes at a price-resource contention among jobs increases job completion time. In this study, we analyze slow-downs of jobs due to contention for multiple resources in a system; referred to as dilation factor. We observe that multiple-resource contention creates non-linear dilation factors of jobs. From this observation, we establish a general quantitative model for dilation factors of jobs in multi-resource systems. A job is characterized by a vector-valued loading statistics and dilation factors of a job set are given by a quadratic function of their loading vectors. We demonstrate how to systematically characterize a job, maintain the data structure to calculate the dilation factor (loading matrix), and calculate the dilation factor of each job. We validate the accuracy of the model with multiple processes running on a native Linux server, virtualized servers, and with multiple MapReduce workloads co-scheduled in a cluster. Evaluation with measured data shows that the D-factor model has an error margin of less than 16%. We extended the D-factor model to capture the slow-down of applications when multiple identical resources exist such as multi-core environments and multi-disks environments. Finally, validation results of the extended D-factor model with HPC checkpoint applications on the parallel file systems show that D-factor accurately captures the slow down of concurrent applications in such environments.

97 MATHEMATICS AND COMPUTING↗

Porting fragmentation methods to GPUs using an OpenMP API: Offloading the resolution-of-the-identity second-order Møller–Plesset perturbation method

Here, using an OpenMP Application Programming Interface, the resolution-of-the-identity second-order Møller–Plesset perturbation (RI-MP2) method has been off-loaded onto graphical processing units (GPUs), both as a standalone method in the GAMESS electronic structure program and as an electron correlation energy component in the effective fragment molecular orbital (EFMO) framework. First, a new scheme has been proposed to maximize data digestion on GPUs that subsequently linearizes data transfer from central processing units (CPUs) to GPUs. Second, the GAMESS Fortran code has been interfaced with GPU numerical libraries (e.g., NVIDIA cuBLAS and cuSOLVER) for efficient matrix operations (e.g., matrix multiplication, matrix decomposition, and matrix inversion). The standalone GPU RI-MP2 code shows an increasing speedup of up to 7.5× using one NVIDIA V100 GPU with one IBM 42-core P9 CPU for calculations on fullerenes of increasing size from 40 to 260 carbon atoms using the 6-31G(d)/cc-pVDZ-RI basis sets. A single Summit node with six V100s can compute the RI-MP2 correlation energy of a cluster of 175 water molecules using the correlation consistent basis sets cc-pVDZ/cc-pVDZ-RI containing 4375 atomic orbitals and 14 700 auxiliary basis functions in ~0.85 h. In the EFMO framework, the GPU RI-MP2 component shows near linear scaling for a large number of V100s when computing the energy of an 1800-atom mesoporous silica nanoparticle in a bath of 4000 water molecules. The parallel efficiencies of the GPU RI-MP2 component with 2304 and 4608 V100s are 98.0% and 96.1%, respectively.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The PAndAS field of streams: Stellar structures in the milky way halo toward Andromeda and Triangulum

We reveal the highly structured nature of the Milky Way (MW) stellar halo within the footprint of the Pan-Andromeda Archaeological Survey (PAndAS) photometric survey from blue main sequence (MS) and MS turn-off stars. We map no fewer than five stellar structures within a heliocentric range of ∼5-30 kpc. Some of these are known (the Monoceros Ring, the Pisces/Triangulum globular cluster stream), but we also uncover three well-defined stellar structures that could be, at least partly, responsible for the so-called Triangulum/Andromeda and Triangulum/Andromeda 2 features. In particular, we trace a new faint stellar stream located at a heliocentric distance of ∼17 kpc. With a surface brightness of Σ {sub V} ∼ 32-32.5 mag arcsec{sup –2}, it follows an orbit that is almost parallel to the Galactic plane north of M31 and has so far eluded surveys of the MW halo as these tend to steer away from regions dominated by the Galactic disk. Investigating our follow-up spectroscopic observations of PAndAS, we serendipitously uncover a radial velocity signature from stars that have colors and magnitudes compatible with the stream. From the velocity of eight likely member stars, we show that this stellar structure is dynamically cold, with an unresolved velocity dispersion that is lower than 7.1 km s{sup –1} at the 90% confidence level. Along with the width of the stream (300-650 pc), its dynamics point to a dwarf-galaxy-accretion origin. The numerous stellar structures we can map in the MW stellar halo between 5 and 30 kpc and their varying morphology is a testament to the complex nature of the stellar halo at these intermediate distances.

79 ASTRONOMY AND ASTROPHYSICS↗

Asynchronous domain decomposition methods for nonlinear PDEs

One- and two-level parallel asynchronous methods for the numerical solution of nonlinear systems of equations, especially those arising from (nonlinear) partial differential equations, are studied. The proposed methods are based on domain decomposition techniques. Local convergence theorems are presented in several cases, with appropriate hypotheses. Computational results on a shared memory multiprocessor machine for various problems exhibiting nonlinearities are reported, illustrating the potential of these asynchronous methods, especially for heterogeneous clusters.

97 MATHEMATICS AND COMPUTING↗

OpenSHMEM Implementation of IOR Benchmark

The benchmarking effort within the Computational Research & Development Programs at the Oak Ridge National Laboratory (ORNL) seeks to design and enable High Performance Computing (HPC) benchmarks and test suites. The work described in this report is a part of the effort focusing on the comparison and analysis of OpenSHMEM implementations using the Interleave Or Random (IOR) software for benchmarking parallel file system using POSIX, MPIIO, or HDF5 interfaces. We describe the effort to emulate the MPIIO parallel collective capabilities in the IOR benchmark using OpenSHMEM communication. One development effort was in emulating the MPI derived datatype used in the read/write operations and in setting the file view. Another effort was in implementing an internal cache in OpenSHMEM distributed shared memory to facilitate global collective I/O operations. Experiments comparing collective I/O in MPIIO implementations with the OpenSHMEM implementations were performed on the SGI Turing Cluster and the Cray XK7 Titan supercomputer at the Oak Ridge Leadership Computing Facility (OLCF). The preliminary results suggest that on the Cray XK7 Titan, the MPIIO implementations obtained higher write performance and the OpenSHMEM version obtained slightly higher read performance. On the SGI Turing Cluster, the MPIIO implementations obtained slightly higher performance over the OpenSHMEM implementations on large files.

97 MATHEMATICS AND COMPUTING↗

Transverse Dimensions of Chorus in the Source Region

We report measurement of whistler-mode chorus by the four Cluster spacecraft at close separations. We focus our analysis on the generation region close to the magnetic equatorial plane at a radial distance of 4.4 Earth's radii. We use both linear and rank correlation analysis to define perpendicular dimensions of the sources of chorus elements below one half of the electron cyclotron frequency. Correlation is significant throughout the range of separation distances of 60-260 km parallel to the field line and 7-100 km in the perpendicular plane. At these scales, the correlation coefficient is independent for parallel separations, and decreases with perpendicular separation. The observations are consistent with a statistical model of the source region assuming individual sources as gaussian peaks of radiated power with a common half-width of 35 km perpendicular to the magnetic field. This characteristic scale is comparable to the wavelength of observed waves.

Santolik, O.↗

Modeling Large-Scale Slim Fly Networks Using Parallel Discrete-Event Simulation

As supercomputers approach exascale performance, the increased number of processors translates to an increased demand on the underlying network interconnect. We present that the slim fly network topology, a new low-diameter, low-latency, and low-cost interconnection network, is gaining interest as one possible solution for next-generation supercomputing interconnect systems. In this article, we present a high-fidelity slim fly packet-level model leveraging the Rensselaer Optimistic Simulation System (ROSS) and Co-Design of Exascale Storage (CODES) frameworks. We validate the model with published work before scaling the network size up to an unprecedented 1 million compute nodes and confirming that the slim fly observes peak network throughput at extreme scale. In addition to synthetic workloads, we evaluate large-scale slim fly models with real communication workloads from applications in the Design Forward program with over 110,000 MPI processes. We show strong scaling of the slim fly model on an Intel cluster achieving a peak network packet transfer rate of 2.3 million packets per second and processing over 7 billion discrete events using 128 MPI tasks. Enabled by the strong performance capabilities of the model, we perform a detailed application trace and routing protocol performance study. Lastly, through analysis of metrics such as packet latency, hop count, and congestion, we find that the slim fly network is able to leverage simple minimal routing and achieve the same performance as more complex adaptive routing for tested DOE benchmark applications.

97 MATHEMATICS AND COMPUTING↗