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At least 523 records · Page 29

Rolex: Resilience-oriented language extensions for extreme-scale systems

Future exascale high-performance computing (HPC) systems will be constructed from VLSI devices that will be less reliable than those used today, and faults will become the norm, not the exception. This will pose significant problems for system designers and programmers, who for half-a-century have enjoyed an execution model that assumed correct behavior by the underlying computing system. The mean time to failure (MTTF) of the system scales inversely to the number of components in the system and therefore faults and resultant system level failures will increase, as systems scale in terms of the number of processor cores and memory modules used. However every error detected need not cause catastrophic failure. Many HPC applications are inherently fault resilient. Yet it is the application programmers who have this knowledge but lack mechanisms to convey it to the system. In this paper, we present new Resilience Oriented Language Extensions (Rolex) which facilitate the incorporation of fault resilience as an intrinsic property of the application code. We describe the syntax and semantics of the language extensions as well as the implementation of the supporting compiler infrastructure and runtime system. Furthermore, our experiments show that an approach that leverages the programmer's insight to reason about the context and significance of faults to the application outcome significantly improves the probability that an application runs to a successful conclusion.

97 MATHEMATICS AND COMPUTING↗

Estimating Energy Market Schedules using Historical Price Data

The global climate crisis is expected to reshape the energy generation landscape in the coming decades. Increasing integration of non-dispatchable renewable energy resources into energy infrastructures and markets creates uncertainty as well as new opportunities for flexible energy systems. To conduct proper economic evaluation of flexible energy systems, such as integrated energy systems (IES), advancements in modelling of market interactions, such as bidding, is crucial. This work presents a shortcut algorithm which uses two mixed integer linear programs to compute dispatch schedules (e.g., hourly power production targets) that are constrained by the resource's bid information and characteristics (e.g., minimum up and down times) based on historical locational marginal price (LMP) data. The proposed algorithm is approximately 100 times faster and uses orders of magnitude less data than a full production cost model (PCM). We find the shortcut simulator recapitulates generator dispatch signals for the Prescient PCM with approximately 4% error for the RTS-GMLC test system.

electricity generation↗

First Principles Nonadiabatic Excited-State Molecular Dynamics in NWChem

Computational simulation of non-adiabatic molecular dynamics is an indispensable tool for understanding complex photoinduced processes such as internal conversion, energy transfer, charge separation, and spatial localization of excitons, to name a few. Here, we report an implementation of the fewest-switches surface hopping algorithm in the NWChem computational chemistry program. Here the surface hopping method is combined with linear-response time-dependent density functional theory calculations of adiabatic excited state potential energy surfaces. To treat quantum transitions between arbitrary electronic Born{Oppenheimer states, we have implemented both numerical and analytical differentiation schemes for derivative non-adiabatic couplings. A numerical approach for the time-derivative non-adiabatic couplings together with an analytical method for calculating non-adiabatic coupling vectors is an efficient combination for surface hopping approaches. Additionally, electronic decoherence schemes and a state reassigned unavoided crossings algorithm are also implemented to improve the accuracy of the simulated dynamics and to handle trivial unavoided crossings. We apply our code to study the ultrafast decay of photoexcited benzene, including a detailed analysis of the potential energy surface, population decay time scales, and vibrational coordinates coupled to the excitation dynamics. The development presented in this work is a baseline for future implementations of more sophisticated frameworks for simulating of non-adiabatic molecular dynamics in NWChem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C–H Region of DMSO as a Case Study

Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical identification of hydrocarbons and in vibrational sum-frequency generation (SFG) spectroscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a challenge from a theoretical viewpoint. Here in this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effects in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes challenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show significant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Formation mechanism of the secondary building unit in a chromium terephthalate metal-organic framework

Based on density functional theory calculations and simulation, a detailed mechanism is presented on the formation of the secondary building unit (SBU) of MIL-101, a chromium terephthalate metal-organic framework (MOF). SBU formation is key to MOF nucleation, the rate-limiting step in the formation process of many MOFs. A series of reactions that lead to the formation of the SBU of MIL-101 is proposed in this work. Initial rate-limiting reactions form the metal cluster with three chromium (III) atoms linked to a central bridging oxygen. Terephthalate linkers play a key role as chromium (III) atoms are joined to linker carboxylate groups prior to the placement of the central bridging oxygen. Multiple linker addition reactions, which follow in different paths due to structural isomers, are limited by the removal of water molecules in the first chromium coordination shell. The least energy path is identified were all linkers on one face of the metal center plane are added first. A simple kinetic model based on transition state theory shows the rate of secondary building unit formation similar to the rate metal-organic framework nucleation. The authors are thankful to Dr. R. Rousseau for a critical reading of the manuscript. This research would not have been possible without the support of the Office of Fossil Energy, U.S. Department of Energy. This research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and the PNNL Institutional Computing (PIC) program located at Pacific Northwest National Laboratory.

36 MATERIALS SCIENCE↗

Author Correction: Perspectives on ENCODE

In the original article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) were mistakenly omitted from the ENCODE Project Consortium author list. The original Article has been corrected online.

99 GENERAL AND MISCELLANEOUS↗

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) are now included in the author list. These errors have been corrected in the online version of the article.

59 BASIC BIOLOGICAL SCIENCES↗

A survey of pulse shape options for a revised plastic ablator ignition design

Recent experimental results using the “high foot” pulse shape for inertial confinement fusion ignition experiments on the National Ignition Facility (NIF) [Moses et al., Phys. Plasmas 16, 041006 (2009)] have shown encouraging progress compared to earlier “low foot” experiments. These results strongly suggest that controlling ablation front instability growth can significantly improve implosion performance even in the presence of persistent, large, low-mode distortions. Simultaneously, hydrodynamic growth radiography experiments have confirmed that ablation front instability growth is being modeled fairly well in NIF experiments. It is timely then to combine these two results and ask how current ignition pulse shapes could be modified to improve one-dimensional implosion performance while maintaining the stability properties demonstrated with the high foot. This paper presents such a survey of pulse shapes intermediate between the low and high foot extremes in search of an intermediate foot optimum. Of the design space surveyed, it is found that a higher picket version of the low foot pulse shape shows the most promise for improved compression without loss of stability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Assessment of ion kinetic effects in shock-driven inertial confinement fusion implosions using fusion burn imaging

The significance and nature of ion kinetic effects in D{sup 3}He-filled, shock-driven inertial confinement fusion implosions are assessed through measurements of fusion burn profiles. Over this series of experiments, the ratio of ion-ion mean free path to minimum shell radius (the Knudsen number, N{sub K}) was varied from 0.3 to 9 in order to probe hydrodynamic-like to strongly kinetic plasma conditions; as the Knudsen number increased, hydrodynamic models increasingly failed to match measured yields, while an empirically-tuned, first-step model of ion kinetic effects better captured the observed yield trends [Rosenberg et al., Phys. Rev. Lett. 112, 185001 (2014)]. Here, spatially resolved measurements of the fusion burn are used to examine kinetic ion transport effects in greater detail, adding an additional dimension of understanding that goes beyond zero-dimensional integrated quantities to one-dimensional profiles. In agreement with the previous findings, a comparison of measured and simulated burn profiles shows that models including ion transport effects are able to better match the experimental results. In implosions characterized by large Knudsen numbers (N{sub K} ∼ 3), the fusion burn profiles predicted by hydrodynamics simulations that exclude ion mean free path effects are peaked far from the origin, in stark disagreement with the experimentally observed profiles, which are centrally peaked. In contrast, a hydrodynamics simulation that includes a model of ion diffusion is able to qualitatively match the measured profile shapes. Therefore, ion diffusion or diffusion-like processes are identified as a plausible explanation of the observed trends, though further refinement of the models is needed for a more complete and quantitative understanding of ion kinetic effects.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Three-dimensional equilibria and island energy transport due to resonant magnetic perturbation edge localized mode suppression on DIII-D

In this research, we conducted experiments in the DIII-D tokamak that show that the plasma responds to resonant magnetic perturbations (RMPs) with toroidalmode numbers of n=2 and n=3 without field line reconnection, consistent with resistive magnetohydrodynamic predictions, while a strong nonlinear bifurcation is apparent when edge localized modes(ELMs) are suppressed. The magnetic response associated with this bifurcation is localized to the high field side of the machine and exhibits a dominant n=1 component despite the application of a constant amplitude, slowly toroidally rotating, n=2 applied field. The n=1 mode is born locked to the vacuum vessel wall, while the n=2 mode is entrained to the rotating field. Based on these magnetic response measurements and Thomson scattering measurements of flattening of the electron temperature profile, it is likely that these modes are magnetic island chains near the H-mode pedestal. The reduction in ∇Te occurs near the q=4 and 5 rational surfaces, suggesting five unique islands are possible (m=8, 9, or 10 for n=2) and (m=4 or 5 for n=1). In all cases, the island width is estimated to be 2–3 cm. The Chang-Callen calculated confinement degradation due to the presence of an individual island of this size is 8%–12%, which is close to the 13%–14% measured between the ELMs and suppressed states. In conclusion, this suggests that edge tearing modes may alter the pedestal causing peeling-ballooning stability during RMP induced ELM suppression.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Hybrid simulations of fishbone instabilities and Alfvén eigenmodes in DIII-D tokamak

In DIII-D hybrid discharges, the intense Alfvén eigenmode (AE) activity driven by Neutral Beam Injection (NBI) that is typically observed can be suppressed and replaced by fishbone modes when Electron Cyclotron Current Drive (ECCD) is centrally applied. Simulations have been carried out with the kinetic/magnetohydrodynamic (MHD) hybrid code M3D-K based on DIII-D discharges #161401 and #161403 without and with ECCD, respectively. In both cases unstable modes are found – the mode frequency and mode structure indicate the instability excited in #161403 is of fishbone type, while that in #161401 is identified as the beta-induced Alfvén eigenmode (BAE)-like mode. Moreover, we find that the calculated mode frequencies of these two shots are consistent with experimental observations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Axisymmetric simulations of vertical displacement events in tokamaks: A benchmark of M3D-C 1 , NIMROD, and JOREK

A benchmark exercise for the modeling of vertical displacement events (VDEs) is presented and applied to the 3D nonlinear magnetohydrodynamic codes M3D-C 1 , JOREK, and NIMROD. The simulations are based on a vertically unstable NSTX equilibrium enclosed by an axisymmetric resistive wall with a rectangular cross section. A linear dependence of the linear VDE growth rates on the resistivity of the wall is recovered for sufficiently large wall conductivity and small temperatures in the open field line region. We report the benchmark results show good agreement between the VDE growth rates obtained from linear NIMROD and M3D-C 1 simulations and from the linear phase of axisymmetric nonlinear JOREK, NIMROD, and M3D-C 1 simulations. Axisymmetric nonlinear simulations of a full VDE performed with the three codes are compared, and an excellent agreement is found regarding the plasma location and plasma currents, as well as eddy and halo currents in the wall.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Gyrokinetic understanding of the edge pedestal transport driven by resonant magnetic perturbations in a realistic divertor geometry

Self-consistent simulations of neoclassical and electrostatic turbulent transport in a DIII-D H-mode edge plasma under resonant magnetic perturbations (RMPs) have been performed using the global total-f gyrokinetic particle-in-cell code x-point gyrokinetic code (XGC), in order to study density pump-out and electron heat confinement. The RMP field is imported from the extended magneto-hydrodynamics code M3D-C1, taking into account the linear two-fluid plasma response. With both neoclassical and turbulence physics considered together, the XGC simulation reproduces two key features of experimentally observed edge transport under RMPs: increased radial particle transport in the pedestal region that is sufficient to account for the experimental pump-out rate and suppression of the electron heat flux in the steepest part of the edge pedestal. In the simulation, the density fluctuation amplitude of modes moving in the electron diamagnetic direction increases due to interaction with RMPs in the pedestal shoulder and outward, while the electron temperature fluctuation amplitude decreases.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Validation of heat transport modeling using directly driven beryllium spheres

Recent experiments involving directly driven beryllium spheres are reported. Plasma conditions are measured using Thomson scattering with the probe beam pointed 200, 300, and 400 μ m from the surface of the sphere. Laser coupling is assessed using calorimeters that collect scattered light placed at various locations within the target chamber. Laser intensities of 1 0 14 W / c m 2 and 2.5 × 1 0 14 W / c m 2 are chosen to minimize unmodeled laser-plasma interactions (LPIs) that lead to laser-target decoupling. Two-dimensional simulations are compared to the interpreted data using the radiation-hydrodynamics code Lasnex. Heat transport is simulated using flux-limited Spitzer–Harm with both high ( f = 0.15) and low ( f = 0.03) flux limiters and the Schurtz–Nicolai-Busquet (SNB) model. At 1 0 14 W / c m 2 , all three heat transport models agree well with the measurement, demonstrating that the heat flux is local at low intensities near the measurement locations. At 2.5 × 1 0 14 W / c m 2 , the SNB and high flux model roughly match the plasma conditions but predict 2% uncoupled light compared to 10% measured. Additionally, the use of drive multipliers to match the measured coupled light does not alter the agreement between measured and simulated plasma conditions, suggesting that decoupling due to LPI is unlikely to alter this agreement. The low flux model cannot match the plasma conditions and results in 19% scattered light. The use of a resonant absorption model can be used to bring the simulated scattered light into agreement, but the simulated plasma conditions are still in disagreement with the measurement. For this reason, the low flux model is rejected.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Deficiencies in compression and yield in x-ray-driven implosions

This paper analyzes x-ray–driven implosions that are designed to be less sensitive to 2-D and 3-D effects in hohlraum and capsule physics. Key performance metrics including the burn-averaged ion temperature, hot-spot areal density, and fusion yield are found to agree with simulations where the design adiabat (internal pressure) is multiplied by a factor of 1.4. Furthermore, these results motivate the development of a simple model for interpreting experimental data, which is then used to quantify how improvements in compression could help achieve ignition.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

3D simulations of vertical displacement events in tokamaks: A benchmark of M3D-C 1 , NIMROD, and JOREK

In recent years, the nonlinear 3D magnetohydrodynamic codes JOREK, M3D-C1, and NIMROD developed the capability of modeling realistic 3D vertical displacement events (VDEs) including resistive walls. In this paper, a comprehensive 3D VDE benchmark is presented between these state-of-the-art codes. The simulated case is based on an experimental NSTX plasma but with a simplified rectangular wall. There are differences between the physics models and numerical methods, and the VDE evolution leads to sensitivities on the initial conditions that cannot be avoided as can be done in edge localized modes (ELM) and sawtooth simulations (due to the non-cyclical nature of VDEs). Nonetheless, the comparison serves to quantify the level of agreement in the relevant quantities used to characterize disruptions, such as the 3D wall forces and energy decay. The results bring confidence regarding the use of the mentioned codes for disruption studies, and they distinguish aspects that are specific to the models used (e.g., reduced vs full MHD models). Here, the simulations show important 3D fea- tures for a NSTX plasma, such as the self-consistent evolution of the halo current and the origin of the wall forces. In contrast to other reduced MHD models based on an ordering in the aspect ratio, the ansatz-based JOREK reduced MHD model allows capturing many aspects of the 3D dynamics even in the spherical tokamak limit considered here.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

ITER cold VDEs in the limit of perfectly conducting walls

Recently, it has been shown that a vertical displacement event (VDE) can occur in ITER even when the walls are perfect conductors, as a consequence of the current quench (CQ) [A. H. Boozer, Phys. Plasmas 26, 114501 (2019)]. We used the extended-MHD code M3D-C1 with an ITER-like equilibrium and induced a CQ to explore cold VDEs in the limit of perfectly conducting walls, using different wall geometries. In the case of a rectangular first wall with the side walls far away from the plasma, we obtained very good agreement with the analytical model developed by Boozer that considers a top/bottom flat-plates wall. We show that the solution in which the plasma remains at the initial equilibrium position is improved when bringing the side walls closer to the plasma. When approximating the ITER first wall as a perfect conductor, the plasma remains stable at the initial equilibrium position far beyond the value predicted by the flat-plates wall limit. When considering an opposite limit in which only the inner shell of the ITER vacuum vessel acts as a perfect conductor, the plasma is displaced during the CQ, but the edge safety factor remains above 2 longer in the current decay compared to the flat-plates wall limit. In all the simulated cases, the VDE is found to be strongly dependent on the plasma current, in agreement with a similar finding in the flat-plates wall limit, showing an important difference with hot VDEs in which the CQ is not a necessary condition.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Sodium tracer measurements of an expanded dense aluminum plasma from e-beam isochoric heating

Spatially and temporally resolved visible absorption spectroscopy is performed on sodium D-lines present as surface contaminants on an expanded dense aluminum plasma plume. An 80-ns FWHM, intense, relativistic electron beam deposits 5.4 J into a 100- μ m-thick Al foil, which isochorically heats and subsequently hydrodynamically expands the material through the warm dense matter state and into a classical-like plasma state, with a coupling parameter of approximately 0.2 and a degeneracy parameter of approximately 270. The Na contamination, carried along with the expanding plume, shows saturated absorption features in the dense Al continuum for λ > 450 nm. X-ray photoelectron spectroscopy and laser-induced breakdown spectroscopy confirm Na is a surface contaminant with an atomic concentration of ~ 0.1 % when interrogating identical foil samples. Additioanlly, a spectroscopic-quality radiation transport model is used to post-process 2D hydrodynamic simulations to interpret the plasma conditions based on the measured Na 3p-3s doublet line profiles. A sodium number density of 3 × 10 15 cm -3 best matches the experimental spectra, which originate from a dense surface plasma with n e = 3.0 ± 0.8 × 10 18 cm -3 .

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗