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At least 379 records · Page 21

Development of neural network force fields for corrosion studies

To fully understand the chemistry and physics of corrosion, novel methods of simulation must be developed. One approach is designing machine learning (ML) algorithms integrated with density functional theory to develop adaptive force fields to gain insight into corrosion behavior namely at the surface of metal oxides. Current methods of modeling corrosion are slow due to the computational cost of resolving both reaction mechanics and mass transport processes. Machine learning methods can be implemented to obtain structure-activity relationships at both the molecular and bulk scale while still retaining the accuracy of density functional theory (DFT) and significantly decreasing the time needed for simulations of complex chemical processes in the various environments of corrosion. Multiscale models are needed for corrosion studies to fully understand its processes not only at the atomic length scale (chemical bonding, energies, and forces), but also at the nano and meso length scales (solid-state physics and material science processes). Current methods of study include DFT, molecular dynamics, and Monte Carlo. The limitation of DFT is that only a small number of atoms or molecules can be simulated at that level of theory. Density functional theory is used to study the electronic structure of atoms and molecules, and calculate the force component of each atom. However, these calculations are limited to about 1000 atoms. Custom periodic boundary conditions (PBC) can be used to describe the various environments and defects that affect the atomic forces to produce a large data set from which a training set can be derived. Machine learning can be utilized to overcome the barrier of modeling macroscopic and multi-scale processes from ab initio calculations through the development of adaptive force fields. Local environments determine the atomic forces of a given system, therefore adaptive force fields must be created to produce reliable quantum mechanical calculations. This can be achieved by developing a learning algorithm that uses the mapped atomic forces or fingerprint as an input to produce energies and magnetic moments as output. A systematic approach was used to begin to build a data set in order to accurately describe the atomic forces in various environments. In Figure 4 below, a simple PBC cell of Fe{sub 2}O{sub 3} was first optimized. A surface optimization was performed next, followed by a hydroxylated surface optimization. Once this calculation has converged, the adsorption of halide species to the hydroxylated surface will be investigated. TensorFlow is an open source platform for machine learning developed by Google. Using a high level application program interface (API) such as Keras allows for building and training ML models easily in a number of different environments and languages. For this project, a neural network was developed within Anaconda in Python. Future Work: Further development of reference data set; Refining neural network and learning algorithm; Fingerprinting atomic environment to enable mapping of atomic force components; Choosing appropriate training set from reference data; Learning from training set and enabling non-linear mapping of training set fingerprints and the atomic forces; Estimation of uncertainty to identify ranges of outside applicability; Testing and analysis of molecular dynamic simulations.

36 MATERIALS SCIENCE↗

Differentiable lagrangian shock hydrodynamics with application to stable shock acceleration of density interfaces

We develop a gradient based optimization approach for the equations of compressible, Lagrangian hydrodynamics and demonstrate how it can be employed to automatically uncover strategies to control hydrodynamic instabilities arising from shock acceleration of density interfaces. Strategies for controlling the Richtmyer-Meshkov instability (RMI) are of great benefit for inertial confinement fusion (ICF) where shock interactions with many small imperfections in the density interface lead to instabilities which rapidly grow over time. These instabilities lead to mixing which, in the case of laser driven ICF, quenches the runaway fusion process ruining the potential for positive energy return. Here, we demonstrate that control of these instabilities can be achieved by optimization of initial conditions with ( > 100) parameters. Optimizing over a large parameter space like this is not possible with gradient-free optimization strategies. This requires computation of the gradient of the outputs of a numerical solution to the equations of Lagrangian hydrodynamics with respect to the inputs. We show that the efficient computation of these gradients is made possible via a judicious application of (i) adjoint methods, the exact formal representation of sensitivities involving partial differential equations, and (ii) automatic differentiation (AD), the algorithmic calculation of derivatives of functions. Careful regularization of multiple operators including artificial viscosity and timestep control is required. We perform design optimization of > 100 parameter energy field driving the Richtmyer Meshkov instability showing significant suppression while simultaneously enhancing the acceleration of the interface relative to a nominal baseline case.

Hydrophysics↗

Nonintuitive Surface Self-Assembly of Functionalized Molecules on Ag(111)

The fabrication of nanomaterials involves selfordering processes of functional molecules on inorganic surfaces. To obtain specific molecular arrangements, a common strategy is to equip molecules with functional groups. However, focusing on the functional groups alone does not provide a comprehensive picture. Especially at interfaces, processes that govern self-ordering are complex and involve various physical and chemical effects, often leading to unexpected structures, as we showcase here on the example of a homologous series of quinones on Ag(111). Naively, one could expect that such quinones, which all bear the same functionalization, form similar motifs. In salient contrast, our joint theoretical and experimental study shows that profoundly different structures are formed. Using a machine-learning-based structure search algorithm, we find that this is due to a shift of the balance of three antagonizing driving forces: adsorbate-substrate interactions governing adsorption sites, adsorbate-adsorbate interactions favoring close packing, and steric hindrance inhibiting certain otherwise energetically beneficial molecular arrangements. The theoretical structures show excellent agreement with our experimental characterizations of the organic/ inorganic interfaces, both for the unit cell sizes and the orientations of the molecules within. The nonintuitive interplay of similarly important interaction mechanisms will continue to be a challenging aspect for the design of functional interfaces. With a detailed examination of all driving forces, we are, however, still able to devise a design principle for self-assembly of functionalized molecules.

structure prediction↗

TriC: Distributed-memory Triangle Counting by Exploiting the Graph Structure

Graph analytics has emerged as an important tool in the analysis of large scale data from diverse application domains such as social networks, cyber security and bioinformatics. Counting the number of triangles in a graph is a fundamental kernel with several applications such as detecting the community structure of a graph or in identifying important vertices in a graph. The ubiquity of massive datasets is driving the need to scale graph analytics on parallel systems. However, numerous challenges exist in efficiently parallelizing graph algorithms, especially on distributed-memory systems. Irregular memory accesses and communication patterns, low computation to communication ratios, and the need for frequent synchronization are some of the leading challenges. In this paper, we present TriC, our distributed-memory implementation of triangle counting in graphs using the Message Passing Interface (MPI), as a submission to the 2020 GraphChallenge competition. Using a set of synthetic and real-world inputs from the challenge, we demonstrate a speedup of up to 90x relative to previous work on 32 processor-cores of a NERSC Cori node. We also provide details from distributed runs with up to8192 processes along with strong scaling results. The observations presented in this work provide an understanding of the system-level bottlenecks at scale that specifically impact sparse-irregular workloads and will therefore benefit other efforts to parallelize graph algorithms.

Halappanavar, Mahantesh↗

Development of a CPU/GPU portable software library for Lagrangian–Eulerian simulations of liquid sprays

The Lagrangian–Eulerian method is widely used for simulations of fuel sprays in turbulent combustion because of the advantage of treating the spray droplets as discrete points. One challenge of the Lagrangian–Eulerian method is the intense computational requirement when tracking the large number of Lagrangian particles needed for high fidelity. We have developed a performance-portable library, Grit, to track the Lagrangian particles in parallel on central processing unit (CPU) and graphics processing unit (GPU) accelerated high performance computing (HPC) architectures. Grit is a C++ library which employs Message Passing Interface (MPI) for distributed memory parallelism and Kokkos programming model for on-node shared memory parallelism with performance portability across different architectures of GPUs and multi-core/manycore CPUs. The parallel algorithms, key parallel kernels, and their performances on the pre-exascale supercomputer, Summit, are presented. Grit is coupled with a direct numerical simulation (DNS) solver, S3D, for multiphase simulations. A conservative formulation has been developed and implemented in Grit for phase coupling with thermodynamic consistency. The formulation separates the conservation of mass, momentum and energy from the physical models to prevent accidental violation of conservation laws due to inconsistent models. The formulation also enforces consistent definitions of enthalpies of the fuel for both phases and the latent heat of evaporation. Finally, simulations of turbulent particle-laden flow and the evaporation of dilute turbulent spray jet are performed to verify the software implementation, and to demonstrate the scalability of Grit for large-scale multiphase simulations.

97 MATHEMATICS AND COMPUTING↗

Prototype hardware design and testing of the global common module for the global trigger subsystem of the ATLAS phase-II upgrade

We report the High-Luminosity Large Hadron Collider (HL-LHC) will deliver more than ten times the integrated luminosity of the previous runs combined. Meeting its stricter throughput requirements poses new challenges to the Trigger and Data Acquisition (TDAQ) systems of the LHC experiments. Introduced in the framework of the ATLAS experiment’s HL upgrade, the Global Trigger (GT) is a new subsystem which will perform offline-like algorithms on full-granularity calorimeter data. The implementation of the GT’s functionality is firmware-focused and is composed of three layers: multiplexing (or data aggregating), global event processing, and demultiplexing interface to the central trigger processor. Each layer will be composed of several, similar nodes, hosted on replicas of identical hardware, the Global Common Module (GCM), an ATCA front board which is designed to be adopted throughout the entire GT subsystem. This article proceeds from the TWEPP 2021 conference and presents the GCM hardware design, performed in 2020, and focuses on some key results of its extensive testing performed in 2021.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

The drivers and predictability of wildfire re-burns in the western United States (US)

Evidence is mounting that the effectiveness of using prescribed burns as a management tactic may be diminishing due to the higher incidence of wildfire re-burns. The development of predictive models of re-burns is thus essential to better understand their primary drivers so that forest management practices can be updated to account for these events. First, we assess the potential for human activity as a driver of re-burns by evaluating re-burn trends both within and outside of the wildland–urban interface (WUI) of the western US. Next, we investigate the predictability of re-burns through the application of both random forest and the explanatory machine learning non-negative matrix factorization using k-means clustering (NMFk) algorithms to predict re-burn occurrence over California based on a number of climate factors. Our findings indicate that while most states showed increasing trends within the WUI when trends were conducted over longer moving windows (e.g. 20 years), California was the only state where the rate of increase was consistently higher in the WUI, indicating a stronger potential for human activity as a driver in that location. Furthermore, we find model performance was found to be robust over most of California (Testing F1 scores = 0.688), although results were highly variable based on EPA level III Ecoregion (F1 scores = 0.0–0.778). Insights provided from this study will lead to a better understanding of climate and human activity drivers of re-burns and how these vary at broad spatial scales so that improvements in forest management practices can be tuned according to the level of change that is expected for a given region.

54 ENVIRONMENTAL SCIENCES↗

Tracking materials science data lineage to manage millions of materials experiments and analyses

Abstract In an era of rapid advancement of algorithms that extract knowledge from data, data and metadata management are increasingly critical to research success. In materials science, there are few examples of experimental databases that contain many different types of information, and compared with other disciplines, the database sizes are relatively small. Underlying these issues are the challenges in managing and linking data across disparate synthesis and characterization experiments, which we address with the development of a lightweight data management framework that is generally applicable for experimental science and beyond. Five years of managing experiments with this system has yielded the Materials Experiment and Analysis Database (MEAD) that contains raw data and metadata from millions of materials synthesis and characterization experiments, as well as the analysis and distillation of that data into property and performance metrics via software in an accompanying open source repository. The unprecedented quantity and diversity of experimental data are searchable by experiment and analysis attributes generated by both researchers and data processing software. The search web interface allows users to visualize their search results and download zipped packages of data with full annotations of their lineage. The enormity of the data provides substantial challenges and opportunities for incorporating data science in the physical sciences, and MEAD’s data and algorithm management framework will foster increased incorporation of automation and autonomous discovery in materials and chemistry research.

Soedarmadji, Edwin↗

A combined kinetic Monte Carlo and phase field approach to model thermally activated dislocation motion

In this work, a kinetic Monte Carlo (KMC) scheme is integrated into a phase field dislocation dynamics (PFDD) model to account for thermal activation. While the implementation is general and could be applied to many different thermally activated processes, we apply the model to simulate a dislocation transmitting through an interface. Two cases are analyzed: a dislocation transmitting through a strong interface, and a dislocation transmitting through a more realistic grain boundary in tungsten. In conclusion, results and trends for both cases are discussed in detail, and ultimately show that the combined KMC-PFDD algorithm is effective in capturing thermally activated dislocation processes.

36 MATERIALS SCIENCE↗

UPS: Unified PMU-Data Storage System to Enhance T+D PMU Data Usability

The emerging distribution-level phasor measurement unit (D-PMU) is expected to play an important role in enhancing distribution system observability and situational-awareness. It is a demanding yet challenging task to develop advanced D-PMU data management and analytics tools to improve D-PMU data usability and further promote D-PMU projects deployment. This paper focuses on D-PMU data processing and storage. It presents a brief review of existing D-PMU data storage systems and points out their limitations on high-performance, flexibility, and scalability. To overcome the limitations, a unified PMU-data storage system (UPS) is proposed. Specifically, a unified I/O interface between storage servers and computing jobs is developed to effectively reduce the overhead of managing various computing jobs and data analytics over multiple storage infrastructures; and PMUCache with PMUCache partitioning and PMUCache replacement algorithms are designed to support in-situ data processing and shared distributed data storage and further serve the computing jobs/queries with different Quality of Service (QoS) requirements. Through a series of experiments, it is demonstrated that UPS achieves high performance on fast and big data processing and storage, and efficiently increases the flexibility and scalability of PMU data management systems.

42 ENGINEERING↗

CACTI Radar b1 Processing: Corrections, Calibrations, and Processing Report

The U.S. Department of Energy’s (DOE) Atmospheric Radiation Measurement (ARM) user facility deployed a large number of instruments to a region nearby the Sierra de Córdobas mountains in Argentina as part of the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) field campaign (1). During this campaign, four radars were installed at a site outside of Villa Yacanto as shown in Figure 1. As part of a post-campaign effort to improve the usability of these data, a significant activity was undertaken towards the calibration, correction, and improvement of the data quality of these radar datastreams. This process in ARM nomenclature is referred to as generating a “b1” datastream. While these “b1” standards may imply different corrections or standards for various ARM instruments, for radars it refers to a datastream that has been calibrated (and cross-calibrated), including a serious effort to deliver the highest-quality (well-characterized) data possible. This report details (i) the status/quality of the original “a1” (raw) data, (ii) the corrections and calibrations that are applied to generate these b1 datastreams, (iii) the details of the applied algorithms and how radar offset/calibration numbers were determined for the eventual corrections, and (iv) the new and flexible plug-in-based processing system designed during CACTI for radar b1 activities (current, future) that interfaces with ARM’s Data Integrator (ADI) and high-performance computing (HPC) system.

47 OTHER INSTRUMENTATION↗

A gradient-based optimization approach for the detection of partially connected surfaces using vibration tests

The integrity of engineering structures is often compromised by embedded surfaces that result from incomplete bonding during the manufacturing process, or initiation of damage from fatigue or impact processes. Examples include delaminations in composite materials, incomplete weld bonds when joining two components, and internal crack planes that may form when a structure is damaged. In many cases the areas of the structure in question may not be easily accessible, thus precluding the direct assessment of structural integrity. In this paper, we present a gradient-based, partial differential equation (PDE)-constrained optimization approach for solving the inverse problem of interface detection in the context of steady-state dynamics. An objective function is defined that represents the difference between the model predictions of structural response at a set of spatial locations, and the experimentally measured responses. One of the contributions of our work is a novel representation of the design variables using a density field that takes values in the range [0, 1] and raised to an integer exponent that promotes solutions to be near the extrema of the range. The density field is combined with the penalty method for enforcing a zero gap condition and realizing partially bonded surfaces. Furthermore the use of the penalty method with a density field representation leads to objective functions that are continuously differentiable with respect to the unknown parameters, enabling the use of efficient gradient-based optimization algorithms. Numerical examples of delaminated plates are presented to demonstrate the feasibility of the approach.

42 ENGINEERING↗

Conservative explicit local time-stepping schemes for the shallow water equations

Here we develop explicit local time-stepping (LTS) schemes with second and third order accuracy for the shallow water equations. The system is discretized in space by a C-grid staggering method, namely the TRiSK scheme adopted in MPAS-Ocean, a global ocean model with the capability of resolving multiple resolutions within a single simulation. The time integration is designed based on the strong stability preserving Runge–Kutta (SSP-RK) methods, but different time step sizes can be used in different regions of the domain through the coupling of coarse-fine time discretizations on the interface, and are only restricted by respective local CFL conditions. The proposed LTS schemes are of predictor–corrector type in which the predictors are constructed based on Taylor series expansions and SSP-RK stepping algorithms. The schemes preserve some important physical quantities in the discrete sense, such as exact conservation of the mass and potential vorticity and conservation of the total energy within time truncation errors. Moreover, they inherit the natural parallelism of the original explicit global time-stepping schemes. Extensive numerical tests are presented to illustrate the performance of the proposed algorithms.

58 GEOSCIENCES↗

Hybrid Entanglement Distribution between Remote Microwave Quantum Computers Empowered by Machine Learning

Superconducting microwave circuits with Josephson junctions, the major platform for quantum computing, can only reach the full capability when connected. This requires an efficient protocol to distribute microwave entanglement. While quantum computers typically use discrete-variable (DV) methods for information encoding, the entire continuous-variable (CV) degree of freedom in electromagnetic fields must be utilized to achieve the highest entanglement distribution rate. Here, we propose a hybrid protocol to resolve the incompatibility between DV microwave quantum computers and CV quantum communications. CV microwave entanglement is distributed using optical swapping of optical-microwave entanglement pairs. To interface with DV microwave quantum computers, we further design a hybrid circuit to simultaneously convert and distill high-quality DV entanglement from noisy CV entanglement. The hybrid circuit is trained with machine-learning algorithms, ensuring high entanglement fidelity and generation rate. In conclusion, our work not only provides a practical method to realize efficient quantum links for superconducting microwave quantum computers, but also opens avenues to bridge the gap between DV and CV quantum systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A Magnetoencephalographic/Encephalographic (MEG/EEG) Brain-Computer Interface Driver for Interactive iOS Mobile Videogame Applications Utilizing the Hadoop Ecosystem, MongoDB, and Cassandra NoSQL Databases

In Phase I, we collected data on five subjects yielding over 90% positive performance in Magnetoencephalographic (MEG) mid-and post-movement activity. In addition, a driver was developed that substituted the actions of the Brain Computer Interface (BCI) as mouse button presses for real-time use in visual simulations. The process was interfaced to a flight visualization demonstration utilizing left or right brainwave thought movement, the user experiences, the aircraft turning in the chosen direction, or on iOS Mobile Warfighter Videogame application. The BCI’s data analytics of a subject’s MEG brain waves and flight visualization performance videogame analytics were stored and analyzed using the Hadoop Ecosystem as a quick retrieval data warehouse. In Phase II portion of the project involves the Emotiv Encephalographic (EEG) Wireless Brain–Computer interfaces (BCIs) allow for people to establish a novel communication channel between the human brain and a machine, in this case, an iOS Mobile Application(s). The EEG BCI utilizes advanced and novel machine learning algorithms, as well as the Spark Directed Acyclic Graph (DAG), Cassandra NoSQL database environment, and also the competitor NoSQL MongoDB database for housing BCI analytics of subject’s response and users’ intent illustrated for both MEG/EEG brainwave signal acquisition. The wireless EEG signals that were acquired from the OpenVibe and the Emotiv EPOC headset can be connected via Bluetooth to an iPhone utilizing a thin Client architecture. The use of NoSQL databases were chosen because of its schema-less architecture and Map Reduce computational paradigm algorithm for housing a user’s brain signals from each referencing sensor. Thus, in the near future, if multiple users are playing on an online network connection and an MEG/EEG sensor fails, or if the connection is lost from the smartphone and the webserver due to low battery power or failed data transmission, it will not nullify the NoSQL document-oriented (MongoDB) or column-oriented Cassandra databases. Additionally, NoSQL databases have fast querying and indexing methodologies, which are perfect for online game analytics and technology. In Phase II, we collected data on five MEG subjects, yielding over 90% positive performance on iOS Mobile Applications with Objective-C and C++, however on EEG signals utilized on three subjects with the Emotiv wireless headsets and (n < 10) subjects from the OpenVibe EEG database the Variational Bayesian Factor Analysis Algorithm (VBFA) yielded below 60% performance and we are currently pursuing extending the VBFA algorithm to work in the time-frequency domain referred to as VBFA-TF to enhance EEG performance in the near future. The novel usage of NoSQL databases, Cassandra and MongoDB, were the primary main enhancements of the BCI Phase II MEG/EEG brain signal data acquisition, queries, and rapid analytics, with MapReduce and Spark DAG demonstrating future implications for next generation biometric MEG/EEG NoSQL databases.

McClay, Wilbert↗

Reconstruction framework advancements to support streaming for the ePIC detector at the EIC

The ePIC collaboration adopted the JANA2 framework to manage its reconstruction algorithms. This framework has since evolved substantially in response to ePIC’s needs. There have been three main design drivers: integrating cleanly with the Podio-based data models and other layers of the key4hep stack, enabling external configuration of existing components, and supporting timeframe splitting for streaming readout. The result is a unified component model featuring a new declarative interface for specifying inputs, outputs, parameters, services, and resources. This interface enables the user to instantiate, configure, and wire components via an external file. One critical new addition to the component model is a hierarchical decomposition of data boundaries into levels such as Run, Timeframe, PhysicsEvent, and Subevent. Two new component abstractions, Folder and Unfolder, are introduced in order to traverse this hierarchy, e.g. by splitting or merging. The pre-existing components can now operate at different event levels, and JANA2 will automatically construct the corresponding parallel processing topology. This means that a user may write an algorithm once, and configure it at runtime to operate on timeframes or on physics events. Overall, these changes mean that the user requires less knowledge about the framework internals, obtains greater flexibility with configuration, and gains the ability to reuse the existing abstractions in new streaming contexts.

Brei, Nathan [Thomas Jefferson National Accelerato↗

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Towards Rapid Interactive Machine Learning: Evaluating Tradeoffs of Classification without Representation

Our contribution is the design and evaluation of an interac- tive machine learning interface that rapidly provides the user with model feedback after every interaction. To address visual scalability, this interface communicates with the user via a “tip of the iceberg” approach, where the user interacts with a small set of recommended instances for each class. To address computational scalability, we developed an O(n) classification algorithm that incorporates user feedback incrementally, and without consulting the underlying data’s representation matrix. Our computational evaluation showed that this algorithm has similar accuracy to several off-the-shelf classification algo- rithms with small amounts of labeled data. Empirical evalu- ation revealed that users performed better using our design compared to an equivalent active learning setup.

Arendt, Dustin L.↗