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At least 541 records · Page 30

Storage Systems and Input/Output: Organizing, Storing, and Accessing Data for Scientific Discovery. Report for the DOE ASCR Workshop on Storage Systems and I/O. [Summary Brief]

In September, 2018, the Department of Energy, Office of Science, Advanced Scientific Computing Research Program convened a workshop to identify key challenges and define research directions that will advance the field of storage systems and I/O over the next 5-7 years.The workshop concluded that addressing these combined challenges and opportunities requires tools and techniques that greatly extend traditional approaches and require new research directions. Key research opportunities were identified. This summary brief highlights three areas: The Impact of Storage and I/O, Research Opportunities, and, A new and productive Storage and I/O Environment. The full report from the workshop can be viewed at DOI: 10.2172/1491994.

97 MATHEMATICS AND COMPUTING↗

Radiation Hydrodynamics in the Lagrangian Application Project’s LUMOS code

Starting in 2019, the Lagrangian Applications Project (LAP) and the Transport Project set out to develop a new ALE/Lagrangian radiation-hydrodynamics (RH) capability in a new code product named LUMOS. This work was done under the guidance of the Advanced Simulation and Computing (ASC) program with the goal of producing software capable of leveraging the high-order thermal radiative transfer (TRT) solvers provided by the Jayenne and Capsaicin software projects. This capability supplements the existing gray diffusion solver that is currently available in LAP’s FLAG code [1, 2, 3] for RH. The remainder of this memo describes the coupling of the radiation and hydrodynamics solvers within LAP’s LUMOS code. Initially delivered in 2020 as part of an L2 milestone [4], this capability continues to mature in FY21 with more efficient and robust algorithms, new support for ALE, and support for mixed materials per cell. Today, LUMOS is provided as a standard end-user product in the suite of LAP tools provided in each release cycle. Code access can be requested at https://asc.lanl.gov.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A Computer Model to Study the Response of Energetic Materials to a Range of Dynamic Loads

Over the past decade we developed a model to enable computer simulation of the mechanical and subsequent energetic response of explosives and propellants to mechanical insults such as impacts, perforations, drops, and falls. The model is embedded in computer simulation programs that solve the non-linear, large deformation equations of compressible solid and fluid flow in space and time. It is implemented as a user-defined model, which returns the updated stress tensor and composition that result from the simulation supplied strain tensor change. Although it is multi-phase, in that gas and solid species are present, it is single-velocity, in that the gas does not flow through the porous solid. More than 70 time-dependent variables are made available for additional analyses and plotting. The model encompasses a broad range of possible responses: mechanical damage with no energetic response, and a continuous spectrum of degrees of violence including delayed and prompt detonation. This work describes the basic workings of the model.

36 MATERIALS SCIENCE↗

Theory, Solution Methods, and Implementation of the HERMES Model

The HERMES (high explosive response to mechanical stimulus) model was developed over the past decade to enable computer simulation of the mechanical and subsequent energetic response of explosives and propellants to mechanical insults such as impacts, perforations, drops, and falls. The model is embedded in computer simulation programs that solve the non-linear, large deformation equations of compressible solid and fluid flow in space and time. It is implemented as a user-defined model, which returns the updated stress tensor and composition that result from the simulation supplied strain tensor change. Although it is multi-phase, in that gas and solid species are present, it is single-velocity, in that the gas does not flow through the porous solid. More than 70 time-dependent variables are made available for additional analyses and plotting. The model encompasses a broad range of possible responses: mechanical damage with no energetic response, and a continuous spectrum of degrees of violence including delayed and prompt detonation. This paper describes the basic workings of the model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

XtalCAMP: a comprehensive program for the analysis and visualization of scanning Laue X-ray micro-/nanodiffraction data

XtalCAMP is a software package based on the MATLAB platform, which is suitable for, but not limited to, the analysis and visualization of scanning Laue X-ray micro-/nanodiffraction data. The main objective of the software is to provide complementary functionalities to the Laue indexing software packages used at several synchrotron beamlines. Here, the graphical user interfaces allow the easy analysis of characteristic microstructure features, including real-time intensity mapping for a quick examination of phase, grain and defect distribution, 2D color-coded mapping of microstructural properties from the output of other Laue indexing software, crystal orientation visualization, grain boundary characterization based on orientation/misorientation calculation, principal strain/stress analysis, and strain ellipsoid representation, as well as a series of additional toolkits. As an example, XtalCAMP is applied to the microstructural investigation of a solution-heat-treated Ni-based superalloy manufactured using a laser 3D-printing technique, and a deformed natural quartzite from Val Bregaglia in the Central Alps.

36 MATERIALS SCIENCE↗

Performance Portable Graphics Processing Unit Acceleration of a High-Order Finite Element Multiphysics Application

The Lawrence Livermore National Laboratory (LLNL) will soon have in place the El Capitan exascale supercomputer, based on advanced micro devices (AMD) graphics processing units (GPUs). As part of a multiyear effort under the National Nuclear Security Administration (NNSA) Advanced Simulation and Computing (ASC) program, we have been developing marbl, a next generation, performance portable multiphysics application based on high-order finite elements. In previous years, we successfully ported the Arbitrary Lagrangian–Eulerian (ALE), multimaterial, compressible flow capabilities of marbl to nvidia GPUs as described in Vargas et al. Here, in this paper, we describe our ongoing effort in extending marbl's GPU capabilities with additional physics, including multigroup radiation diffusion and thermonuclear burn for high energy density physics (HEDP) and fusion modeling. We also describe how our portability abstraction approach based on the raja Portability Suite and the mfem finite element discretization library has enabled us to achieve high performance on AMD based GPUs with minimal effort in hardware-specific porting. Throughout this work, we highlight numerical and algorithmic developments that were required to achieve GPU performance.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Final Report: Performance Engineering Research Institute

This document is a final report about the work performed for cooperative agreement DE-FC02-06ER25764, the Rice University effort of Performance Engineering Research Institute (PERI). PERI was an Enabling Technologies Institute of the Scientific Discovery through Advanced Computing (SciDAC-2) program supported by the Department of Energy's Office of Science Advanced Scientific Computing Research (ASCR) program. The PERI effort at Rice University focused on (1) research and development of tools for measurement and analysis of application program performance, and (2) engagement with SciDAC-2 application teams.

97 MATHEMATICS AND COMPUTING↗

An Ab Initio Multiple Cloning Method for Non-Adiabatic Excited-State Molecular Dynamics in NWChem

The recently developed ab-initio multiple cloning (AIMC) approach based on the multicongurational Ehrenfest (MCE) method provides a powerful and accurate way of describing the excited-state dynamics of molecular systems. The AIMC method is a controlled approximation to non-adiabatic dynamics with a particular strength in the proper description of decoherence effects due to branching of vibrational wavepackets at a level crossing. In this work, we report a new implementation of the AIMC algorithm in the open source NWChem computational chemistry program. The framework combines linear-response time-dependent density functional theory with Ehrenfest mean-eld theory to determine the equations of motion for classical trajectories. The multi-dimensional wave function is decomposed into a superposition of Gaussian coherent states guided by Ehrenfest trajectories (i.e., MCE approach), which can clone with fully quantum mechanical amplitudes and phases. By using an efficient time-derivative based non-adiabatic coupling approach within the AIMC method, all observable are calculated on-the-y in the non-adiabatic molecular dynamics process. As a representative example, we apply our implementation to study the ultrafast photoinduced electronic and vibrational energy transfer in a pyridine molecule. The effects of the cloning procedure on electronic and vibrational coherence, relaxation and unidirectional energy transfer are discussed. This new AIMC implementation provides a high-level non-adiabatic molecular dynamics framework for simulating photoexcited dynamics in complex molecular systems and experimentally relevant ultrafast spectroscopic probes, such as nonlinear coherent optical and X-ray signals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Principles of water oxidation and O2-based hydrocarbon transformation by multinuclear catalytic sites

Abstract The central thrust of this integrated experimental and computational research program was to obtain an atomistic-level understanding of the structural and dynamic factors underlying the design of catalysts for water oxidation and selective reductant-free O2-based transformations. The focus was on oxidatively robust polyoxometalate (POM) complexes in which a catalytic active site interacts with proximal metal centers in a synergistic manner. Thirty five publications in high-impact journals arose from this grant. I. Developing an oxidatively and hydrolytically stable and fast water oxidation catalyst (WOC), a central need in the production of green fuels using water as a reductant, has proven particularly challenging. During this grant period we have designed and investigated several carbon-free, molecular (homogenous), oxidatively and hydrolytically stable WOCs, including the Rb8K2[{Ru4O4(OH)2(H2O)4}(γ-SiW10O36)2]·25H2O (1) and [Co4(H2O)2(α-PW9O34)2]10- (2). Although complex 1 is fast, oxidatively and hydrolytically stable WOC, Ru is neither abundant nor inexpensive. Therefore, development of a stable and fast carbon-free homogenous WOC, based on earth-abundant elements became our highest priority. In 2010, we reported the first such catalyst, complex 2. This complex is substantially faster than 1 and stable under homogeneous conditions. Recently, we have extended our efforts and reported a V2-analog of the complex 2, i.e. [Co4(H2O)2(α-VW9O34)2]10- (3), which shows an even greater stability and reactivity. We succeeded in: (a) immobilizing catalysts 1 and 2 on the surface of various electrodes, and (b) elucidating the mechanism of O2 formation and release from complex 1, as well as the Mn4O4L6 “cubane” cluster. We have shown that the direct O-O bond formation is the most likely pathway for O2 formation during water oxidation catalyzed by 1. II. Oxo transfer catalysts that contain two proximal and synergistically interacting redox active metal centers in the active site form another part of considerable interest of our grant because species with such sites [including methane monooxygenase (MMO) and more] are some of the most effective oxygenase catalysts known. Our team conducted the following research on γ-M2-Keggin complexes: (a) investigated stability of the trimer [{Fe3(OH)3(H2O)2}3(γ-SiW10O36)3]15-, 4, in water, and developed the chemistry and catalysis of the di-iron centered POM, [γ(1,2)-SiW10{Fe(OH)}2O38]6-, 5, in organic solvents (Figure 2). We also study the thermodynamic and structural stability of γ-M2-Keggin in aqueous media for different M’s (d-electron metals). We have defined two structural classes of POMs with proximally bound d-electron metal centers. We refer to these structural isomers of the {γ-M2SiW10} family of POMs as “in-pocket” and “out-of pocket”. We have elucidated the factors controlling the structure and stability of the V, Fe, Ru, Tc, Mo and Rh derivatives of [(SiO4)M2(OH)2W10O32]4- using a range of computational tools. We have: (a) demonstrated that heteroatom X in these polyanions may function as an “internal switch” for defining the ground electronic states and, consequently, the reactivity of the γ-M2-Keggin POM complexes; (b) elucidated reactivity of divacant lacunary species and polyperoxotungstates (PPTs), {Xn+O4[WO(O2)2]4}n-, which could be degradation products of γ-M2-Keggin complexes in aqueous media; (c) elucidated the role of the POM ligand in stabilization of {Ru2} and {(Ru-oxo)2} fragments in the reactant and product of the reaction of {γ-[(Xn+O4)Ru2(OH)2W10O32]}(8-n)- (where X = Si4+, P5+ and S6+) with O2, and (d) the mechanisms of olefin epoxidation catalyzed by these di-d-transition metal substituted and divacant lacunary γ-M2-Keggin complexes. III. Complementing the efforts presented above was the development of less time-consuming but reasonably accurate computational methods allowing one to explore more deeply large catalytic systems. We developed Reactive Force Field (ReaxFF) to study interaction of the targeted POMs with water, proton and hydroxide ions in the liquid phase. We tested our ReaxFF parameters on the Lindqvist POMs, M6O19n-, where M = Nb and Ta. These parameters are made available as part of the ReaxFF code. In addition, we have developed parameters for Sc, Ti, Fe, Co and Ni in combination with H, C, N, O, as well as the same metal (M-M) for the spin-polarized self-consistent-charge density-functional tight-binding (DFTB) method. Test calculations showed that the DFTB method with the present parameters in most cases reproduces structural properties very well. These parameters are made available as part of the DFTB code. Thus, this DOE BES funded research project has clarified several key areas impacting (a) water oxidation and O2-based hydrocarbon transformation, (b) stabilization of key structures and catalytic intermediates in such processes, (c) immobilization of molecular catalysts on metal oxide surfaces, and (d) application of optimal computational methods to study reaction dynamics in large systems.

58 GEOSCIENCES↗

Infrastructure for Multiphysics Software Integration in High Performance Computing-Aided Science and Engineering

The project described in this report constructed and exercised an innovative multiphysics coupling toolkit called the Illinois Rocstar MultiPhysics Application Coupling Toolkit (IMPACT). IMPACT is an open source, flexible, natively parallel infrastructure for coupling multiple uniphysics simulation codes into multiphysics computational systems. IMPACT works with codes written in several high-performance-computing (HPC) programming languages, and is designed from the beginning for HPC multiphysics code development. It is designed to be minimally invasive to the individual physics codes being integrated, and has few requirements on those physics codes for integration. The goal of IMPACT is to provide the support needed to enable coupling existing tools together in unique and innovative ways to produce powerful new multiphysics technologies without extensive modification and rewrite of the physics packages being integrated. There are three major outcomes from this project: 1) construction, testing, application, and open-source release of the IMPACT infrastructure, 2) production of example open-source multiphysics tools using IMPACT, and 3) identification and engagement of interested organizations in the tools and applications resulting from the project. This last outcome represents the incipient development of a user community and application echosystem being built using IMPACT. Multiphysics coupling standardization can only come from organizations working together to define needs and processes that span the space of necessary multiphysics outcomes, which Illinois Rocstar plans to continue driving toward. The IMPACT system, including source code, documentation, and test problems are all now available through the public gitHUB.org system to anyone interested in multiphysics code coupling. Many of the basic documents explaining use and architecture of IMPACT are also attached as appendices to this document. Online HTML documentation is available through the gitHUB site. There are over 100 unit tests provided that run through the Illinois Rocstar Application Development (IRAD) lightweight testing infrastructure that is also supplied along with IMPACT. The package as a whole provides an excellent base for developing high-quality multiphysics applications using modern software development practices. To facilitate understanding how to utilize IMPACT effectively, two multiphysics systems have been developed and are available open-source through gitHUB. The simpler of the two systems, named ElmerFoamFSI in the repository, is a multiphysics, fluid-structure-interaction (FSI) coupling of the solid mechanics package Elmer with a fluid dynamics module from OpenFOAM. This coupling illustrates how to combine software packages that are unrelated by either author or architecture and combine them into a robust, parallel multiphysics system. A more complex multiphysics tool is the Illinois Rocstar Rocstar Multiphysics code that was rebuilt during the project around IMPACT. Rocstar Multiphysics was already an HPC multiphysics tool, but now that it has been rearchitected around IMPACT, it can be readily expanded to capture new and different physics in the future. In fact, during this project, the Elmer and OpenFOAM tools were also coupled into Rocstar Multiphysics and demonstrated. The full Rocstar Multiphysics codebase is also available on gitHUB, and licensed for any organization to use as they wish. Finally, the new IMPACT product is already being used in several multiphysics code coupling projects for the Air Force, NASA and the Missile Defense Agency, and initial work on expansion of the IMPACT-enabled Rocstar Multiphysics has begun in support of a commercial company. These initiatives promise to expand the interest and reach of IMPACT and Rocstar Multiphysics, ultimately leading to the envisioned standardization and consortium of users that was one of the goals of this project.

42 ENGINEERING↗

Reflected entropy in random tensor networks. Part III. Triway cuts

For general random tensor network states at large bond dimension, we prove that the integer Rényi reflected entropies (away from phase transitions) are determined by minimal triway cuts through the network. This generalizes the minimal cut description of bipartite entanglement for these states. A natural extrapolation away from integer Rényi parameters, suggested by the triway cut problem, implies the holographic conjecture S R = 2EW, where S R is the reflected entropy and EW is the entanglement wedge cross-section. Minimal triway cuts can be formulated as integer programs which cannot be relaxed to find a dual maximal flow/bit-thread description. This sheds light on the gap between the existence of tripartite entanglement in holographic states and the bipartite entanglement structure motivated by bit-threads. In particular, we prove that the Markov gap that measures tripartite entanglement is lower bounded by the integrality gap of the integer program that computes the triway cut.

AdS-CFT correspondence↗

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↗