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At least 1,279 records · Page 71
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Implementation of Relativistic Coupled Cluster Theory for Massively Parallel GPU-Accelerated Computing Architectures

In this paper, we report reimplementation of the core algorithms of relativistic coupled cluster theory aimed at modern heterogeneous high-performance computational infrastructures. The code is designed for parallel execution on many compute nodes with optional GPU coprocessing, accomplished via the new ExaTENSOR back end. The resulting ExaCorr module is primarily intended for calculations of molecules with one or more heavy elements, as relativistic effects on the electronic structure are included from the outset. In the current work, we thereby focus on exact two-component methods and demonstrate the accuracy and performance of the software. The module can be used as a stand-alone program requiring a set of molecular orbital coefficients as the starting point, but it is also interfaced to the DIRAC program that can be used to generate these. We therefore also briefly discuss an improvement of the parallel computing aspects of the relativistic self-consistent field algorithm of the DIRAC program.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Long-time dynamics through parallel trajectory splicing

Simulating the atomistic evolution of materials over long time scales is a longstanding challenge, especially for complex systems where the distribution of barrier heights is very heterogeneous. Such systems are difficult to investigate using conventional long-time scale techniques, and the fact that they tend to remain trapped in small regions of configuration space for extended periods of time strongly limits the physical insights gained from short simulations. We introduce a novel simulation technique, Parallel Trajectory Splicing (ParSplice), that aims at addressing this problem through the timewise parallelization of long trajectories. The computational efficiency of ParSplice stems from a speculation strategy whereby predictions of the future evolution of the system are leveraged to increase the amount of work that can be concurrently performed at any one time, hence improving the scalability of the method. ParSplice is also able to accurately account for, and potentially reuse, a substantial fraction of the computational work invested in the simulation. We validate the method on a simple Ag surface system and demonstrate substantial increases in efficiency compared to previous methods. As a result, we then demonstrate the power of ParSplice through the study of topology changes in Ag 42 Cu 13 core–shell nanoparticles.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics

Molecular simulations of systems with multiple copies of identical atoms or molecules may require the biasing of numerous, degenerate collective variables (CVs) to accelerate sampling. Recently, a variation of metadynamics (MetaD) named parallel bias metadynamics (PBMetaD) has been shown to make biasing of many CVs more tractable. We extended the PBMetaD scheme so that it partitions degenerate CVs into families that share the same bias potential, consequently expediting convergence of the free-energy landscape. We tested our method, named parallel bias metadynamics with partitioned families, on 3, 21, and 78 CV systems and obtained an approximately proportional increase in convergence speed compared to standard PBMetaD.

Prakash, Arushi↗
DOE OSTI2018

Fast Real-Time Time-Dependent Density Functional Theory Calculations with the Parallel Transport Gauge

Real-time time-dependent density functional theory (RT-TDDFT) is known to be hindered by the very small time step (attosecond or smaller) needed in the numerical simulation, because of the fast oscillation of electron wave functions, which significantly limits its range of applicability for the study of ultrafast dynamics. In this paper, we demonstrate that such oscillation can be considerably reduced by optimizing the gauge choice using the parallel transport formalism. RT-TDDFT calculations can thus be significantly accelerated using a combination of the parallel transport gauge and implicit integrators, and the resulting scheme can be used to accelerate any electronic structure software that uses a Schrödinger representation. Here, using absorption spectrum, ultrashort laser pulse, and Ehrenfest dynamics calculations for example, we show that the new method can utilize a time step that is on the order of 10–100 attoseconds using a planewave basis set. Thanks to the significant increase of the size of the time step, we also demonstrate that the new method is more than 10 times faster, in terms of the wall clock time, when compared to the standard explicit fourth-order Runge–Kutta time integrator for silicon systems ranging from 32 to 1024 atoms.

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

Parallel Guanine Duplex and Cytosine Duplex DNA with Uninterrupted Spines of Ag I -Mediated Base Pairs

Here, hydrogen bonding between nucleobases produces diverse DNA structural motifs, including canonical duplexes, guanine (G) quadruplexes, and cytosine (C) i-motifs. Incorporating metal-mediated base pairs into nucleic acid structures can introduce new functionalities and enhanced stabilities. Here we demonstrate, using mass spectrometry (MS), ion mobility spectrometry (IMS), and fluorescence resonance energy transfer (FRET), that parallel-stranded structures consisting of up to 20 G–Ag I –G contiguous base pairs are formed when natural DNA sequences are mixed with silver cations in aqueous solution. FRET indicates that duplexes formed by poly(cytosine) strands with 20 contiguous C–Ag I –C base pairs are also parallel. Silver-mediated G-duplexes form preferentially over G-quadruplexes, and the ability of Ag + to convert G-quadruplexes into silver-paired duplexes may provide a new route to manipulating these biologically relevant structures. IMS indicates that G-duplexes are linear and more rigid than B-DNA. DFT calculations were used to propose structures compatible with the IMS experiments. Such inexpensive, defect-free, and soluble DNA-based nanowires open new directions in the design of novel metal-mediated DNA nanotechnology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Substituent and Heteroatom Effects on π–π Interactions: Evidence That Parallel-Displaced π-Stacking is Not Driven by Quadrupolar Electrostatics

Stacking interactions are a recurring motif in supramolecular chemistry and biochemistry, where a persistent theme is a preference for parallel-displaced aromatic rings rather than face-to-face π-stacking. This is usually explained in terms of quadrupole–quadrupole interactions between the arene moieties but that interpretation is inconsistent with accurate calculations, which reveal that the quadrupolar picture is qualitatively wrong. At typical π-stacking distances, quadrupolar electrostatics may differ in sign from an exact calculation based on charge densities of the interacting arenes. We apply symmetry-adapted perturbation theory to dimers composed of substituted benzene and various aromatic heterocycles, which display a wide range of electrostatic interactions, and we investigate the interplay of Pauli repulsion, dispersion, and electrostatics as it pertains to parallel-displaced π-stacking. Profiles of energy components along cofacial slip-stacking coordinates support a prominent role for the “van der Waals model” (dispersion in competition with Pauli repulsion), even for polar monomers where electrostatic interactions are significant. While electrostatic interactions are necessary to explain the optimal face-to-face π-stacking distance and to account for the relative orientation of one polar arene with respect to another, we find no evidence to support continued invocation of quadrupolar electrostatics as a basis for π-stacking. Our results suggest that a driving force for offset-stacking exists even in the absence of electrostatic interactions. Consequently, tuning electrostatics via functionalization does not guarantee that slip-stacking can be avoided. This has implications for rational design of soft materials and other supramolecular architectures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Cascading parallel fractures on Enceladus

Active eruptions from the south polar region of Saturn’s ~500-km-diameter moon Enceladus are concentrated along a series of lineaments known as the ‘tiger stripes’, thought to be partially open fissures that connect to the liquid water ocean beneath the ice shell. To date, no study simultaneously explains why the tiger stripes should be located only at the south pole, why there are multiple approximately parallel and regularly spaced fractures, what accounts for their spacing of about 35 km, and why similarly active fissures have not been observed on other icy bodies. Here in this paper, we propose that secular cooling, which leads to a thickening of the ice shell and building of global tensile stresses, causes the first fracture to form at one of the poles, where the ice shell is thinnest owing to tidal heating. The tensile stresses are thereby relieved, preventing a similar failure at the opposite pole. The steadily erupting water ice loads the flanks of the open fissure, causing bending in the surrounding elastic plate and further tensile failure in bands parallel to the first fracture—a process that may be unique to Enceladus, where the gravity is too weak for compressive stresses to prevent fracture propagation through the thin ice shell. The sequence of fissures then cascades outwards until the loading becomes too weak or the background shell thickness becomes too great to permit through-going fractures.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Parallel IO Libraries for Managing HEP Experimental Data

The computing and storage requirements of the energy and intensity frontiers will grow significantly during the Run 4 & 5 and the HL-LHC era. Similarly, in the intensity frontier, with larger trig ger readouts during supernovae explosions, the Deep Underground Neutrino Experiment (DUNE) will have unique computing challenges that could be addressed by the use of parallel and accelerated dataprocessing capabilities. Most of the requirements of the energy and intensity frontier experiments rely on increasing the role of high performance computing (HPC) in the HEP community. In this presentation, we will describe our ongoing efforts that are focused on using HPC resources for the next generation HEP experiments. The HEPCCE (High Energy Physics-Center for Computational Excellence) IOS (Input/Output and Storage) group has been developing approaches to map HEP data to the HDF5 , an IO library optimized for the HPC platforms to store the intermediate HEP data. The complex HEP data products are serialized using ROOT to allow for experiment independent general mapping approaches of the HEP data to the HDF5 format. The mapping approaches can be optimized for high performance parallel IO. Similarly, simpler data can be directly mapped into the HDF5, which can also be suitable for offloading into the GPUs directly. We will present our works on both complex and simple data model models.

Bashyal, Amit↗
DOE OSTI2012

Parallel resistivity and ohmic heating of laboratory dipole plasmas

The parallel resistivity is calculated in the long-mean-free-path regime for the dipole plasma geometry; this is shown to be a neoclassical transport problem in the limit of a small number of circulating electrons. In this regime, the resistivity is substantially higher than the Spitzer resistivity due to the magnetic trapping of a majority of the electrons. This suggests that heating the outer flux surfaces of the plasma with low-frequency parallel electric fields can be substantially more efficient than might be naively estimated. Such a skin-current heating scheme is analyzed by deriving an equation for diffusion of skin currents into the plasma, from which quantities such as the resistive skin-depth, lumped-circuit impedance, and power deposited in the plasma can be estimated. Numerical estimates indicate that this may be a simple and efficient way to couple power into experiments in this geometry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

Parallel transport studies of high-Z impurities in the core of Alcator C-Mod plasmas

Measurements of poloidal variation, ñ{sub z}/ , in high-Z impurity density have been made using photodiode arrays sensitive to vacuum ultraviolet and soft x-ray emission in Alcator C-Mod plasmas. In/out asymmetries in the range of −0.2 <0.3 are observed for r/a<0.8, and accumulation on both the high-field side, n{sub z,cos}<0, and low-field side, n{sub z,cos}>0, of a flux surface is found to be well described by a combination of centrifugal, poloidal electric field, and ion-impurity friction effects. Up/down asymmetries, −0.05 <0.10, are observed over 0.5 0 corresponding to accumulation opposite the ion ∇B drift direction. Measurements of the up/down asymmetry of molybdenum are found to disagree with predictions from recent neoclassical theory in the trace limit, n{sub z}Z{sup 2}/n{sub i}≪1. Non-trace levels of impurities are expected to modify the main-ion poloidal flow and thus change friction-driven impurity density asymmetries and impurity poloidal rotation, v{sub θ,z}. Artificially modifying main-ion flow in parallel transport simulations is shown to impact both ñ{sub z}/ and v{sub θ,z}, but simultaneous agreement between measured and predicted up/down and in/out asymmetry as well as impurity poloidal rotation is not possible for these C-Mod data. This link between poloidal flow and poloidal impurity density variation outlines a more stringent test for parallel neoclassical transport theory than has previously been performed. Measurement and computational techniques specific to the study of poloidal impurity asymmetry physics are discussed as well.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

A primitive kinetic-fluid model for quasi-parallel propagating magnetohydrodynamic waves

The extension and limitation of the existing one-dimensional kinetic-fluid model (Vlasov-MHD (magnetohydrodynamic) model), which has been used to analyze parametric instabilities of parallel propagating Alfvén waves, are discussed. The inconsistency among the given velocity distribution functions in the past studies is resolved through the systematic derivation of the multi-dimensional Vlasov-MHD model. The linear dispersion analysis of the present model indicates that the collisionless damping of the slow modes is adequately evaluated in low beta plasmas, although the deviation between the present model and the full-Vlasov theory increases with increasing plasma beta and increasing propagation angle. This is because the transit-time damping is not correctly evaluated in the present model. It is also shown that the ponderomotive density fluctuations associated with the envelope-modulated quasi-parallel propagating Alfvén waves derived from the present model is not consistent with those derived from the other models such as the Landau-fluid model, except for low beta plasmas. The result indicates the present model would be useful to understand the linear and nonlinear development of the Alfvénic turbulence in the inner heliosphere, whose condition is relatively low beta, while the existing model and the present model are insufficient to discuss the parametric instabilities of Alfvén waves in high beta plasmas and the obliquely propagating waves.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

Parallel multiplex laser feedback interferometry

We present a parallel multiplex laser feedback interferometer based on spatial multiplexing which avoids the signal crosstalk in the former feedback interferometer. The interferometer outputs two close parallel laser beams, whose frequencies are shifted by two acousto-optic modulators by 2Ω simultaneously. A static reference mirror is inserted into one of the optical paths as the reference optical path. The other beam impinges on the target as the measurement optical path. Phase variations of the two feedback laser beams are simultaneously measured through heterodyne demodulation with two different detectors. Their subtraction accurately reflects the target displacement. Under typical room conditions, experimental results show a resolution of 1.6 nm and accuracy of 7.8 nm within the range of 100 μm.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2013

Depletion of parallel conducting layers in high mobility In{sub 0.53}Ga{sub 0.47}As/In{sub 0.52}Al{sub 0.48}As modulation doped field effect transistors

Self-consistent calculations for solving the Poisson and Schrödinger equations were performed in order to study parallel conduction in the In{sub 0.52}Al{sub 0.48}As barrier layer in In{sub 0.53}Ga{sub 0.47}As/In{sub 0.52}Al{sub 0.48}As Modulation Doped Field Effect Transistors. It is shown that the parallel conducting layer occupied sub-bands can be entirely depleted by wet chemical etching of the upper part of the un-doped In{sub 0.52}Al{sub 0.48}As Schottky layer without affecting the total carrier concentration at the In{sub 0.53}Ga{sub 0.47}As quantum well.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Spin wave based parallel logic operations for binary data coded with domain walls

We numerically investigate the feasibility of spin wave (SW) based parallel logic operations, where the phase of SW packet (SWP) is exploited as a state variable and the phase shift caused by the interaction with domain wall (DW) is utilized as a logic inversion functionality. A designed functional element consists of parallel ferromagnetic nanowires (6 nm-thick, 36 nm-width, 5120 nm-length, and 200 nm separation) with the perpendicular magnetization and sub-μm scale overlaid conductors. The logic outputs for binary data, coded with the existence (“1”) or absence (“0”) of the DW, are inductively read out from interferometric aspect of the superposed SWPs, one of them propagating through the stored data area. A practical exclusive-or operation, based on 2π periodicity in the phase logic, is demonstrated for the individual nanowire with an order of different output voltage V{sub out}, depending on the logic output for the stored data. The inductive output from the two nanowires exhibits well defined three different signal levels, corresponding to the information distance (Hamming distance) between 2-bit data stored in the multiple nanowires.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Nano-optical observation of cascade switching in a parallel superconducting nanowire single photon detector

The device physics of parallel-wire superconducting nanowire single photon detectors is based on a cascade process. Using nano-optical techniques and a parallel wire device with spatially separate pixels, we explicitly demonstrate the single- and multi-photon triggering regimes. We develop a model for describing efficiency of a detector operating in the arm-trigger regime. We investigate the timing response of the detector when illuminating a single pixel and two pixels. We see a change in the active area of the detector between the two regimes and find the two-pixel trigger regime to have a faster timing response than the one-pixel regime.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2014

Formation of electron kappa distributions due to interactions with parallel propagating whistler waves

In space plasmas, charged particles are frequently observed to possess a high-energy tail, which is often modeled by a kappa-type distribution function. In this work, the formation of the electron kappa distribution in generation of parallel propagating whistler waves is investigated using fully nonlinear particle-in-cell (PIC) simulations. A previous research concluded that the bi-Maxwellian character of electron distributions is preserved in PIC simulations. We now demonstrate that for interactions between electrons and parallel propagating whistler waves, a non-Maxwellian high-energy tail can be formed, and a kappa distribution can be used to fit the electron distribution in time-asymptotic limit. The κ-parameter is found to decrease with increasing initial temperature anisotropy or decreasing ratio of electron plasma frequency to cyclotron frequency. The results might be helpful to understanding the origin of electron kappa distributions observed in space plasmas.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Hydration of non-polar anti-parallel β-sheets

In this work we focus on anti-parallel β-sheets to study hydration of side chains and polar groups of the backbone using all-atom molecular dynamics simulations. We show that: (i) water distribution around the backbone does not depend significantly on amino acid sequence, (ii) more water molecules are found around oxygen than nitrogen atoms of the backbone, and (iii) water molecules around nitrogen are highly localized in the planed formed by peptide backbones. To study hydration around side chains we note that anti-parallel β-sheets exhibit two types of cross-strand pairing: Hydrogen-Bond (HB) and Non-Hydrogen-Bond (NHB) pairing. We show that distributions of water around alanine, leucine, and valine side chains are very different at HB compared to NHB faces. For alanine pairs, the space between side chains has a higher concentration of water if residues are located in the NHB face of the β-sheet as opposed to the HB face. For leucine residues, the HB face is found to be dry while the space between side chains at the NHB face alternates between being occupied and non-occupied by water. Surprisingly, for valine residues the NHB face is dry, whereas the HB face is occupied by water. We postulate that these differences in water distribution are related to context dependent propensities observed for β-sheets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Parallel parametric amplification of coherently excited propagating spin waves in a microscopic Ni{sub 81}Fe{sub 19} waveguide

We present parallel parametric amplification of coherently excited, propagating spin waves in a microstructured magnonic Ni{sub 81}Fe{sub 19} waveguide. Amplification is achieved by the pumping field generated by a microwave current flowing through a Cu micro-stripline underneath the waveguide. By employing microfocussed Brillouin light scattering spectroscopy, we investigate the spatial decay of the propagating spin waves and their amplification by means of parallel pumping. We analyze the dependence of the intensity of the amplified spin waves on the spin-wave excitation power, pumping power, and pumping duration, revealing the most efficient working point for a noise-free amplification. This paves the way for a frequency selective amplification of spin waves in microstructured magnonic circuits.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗