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fp-tools

The output of a molecular dynamics simulation is a data file containing properties of the motion of the simulated particles as a function of time (e.g., positions, velocities). From this output, scientists can extract various properties which give insight into the physics of the system; for example, the radial distribution function can be computed from the particle positions, which gives insight into how close the system is to melting or freezing. Many publicly available codes to perform molecular dynamics simulations exist and have been well adopted by the scientific community (e.g., LAMMPS, VASP). However, it remains standard practice for scientists to write their own post-processing scripts to extract various properties of interest from the molecular dynamics simulation data. Since in many cases scientists are interested in the same set of “textbook” properties, there is a large duplication of effort in writing these post-processing scripts. Our proposed code, FP-Tools, is a C++ toolkit designed to help scientists extract and analyze quantities of interest from the output of a molecular dynamics simulation, eliminating the need for them to write these codes themselves and thus reducing this duplication of effort. The quantities which are computed by our code are well documented in the literature (either in publications or textbooks), and the algorithms we implement to compute these properties are also well known in the field. We are not introducing new science or methods here; rather, our primary goal is to provide a useful tool to the community in the form of a well-documented, easy to use package.

Hartman, Leah↗

Shock-Driven Hydrodynamic Instability Growth Near Phase Boundaries and Material Property Transitions: Final Report

Activities for this grant included: 1) Development of dynamic impact experiments to probe strength and phase transition influence on dynamic deformation, 2) development of modern strength and phase aware simulation capabilities, 3) and post-processing of experimental data with simulation and closed form analytical techniques. Two different dynamic experiments were developed to probe material strengths in solid metals (largely copper and iron in this effort). In the first experiment a flyer plate impacts a flat target with an opposite rippled surface that is partially supported by a weaker window material. Post mortem analysis of the target sample showed a strong and repeatable residual plastic deformation dependence on grain orientation. Yield strengths for strain rates near 10 5 s -1 and plastic strains near ~50% were estimated to be around 180 to 240 MPa, varying in this range with grain orientation. Unfortunately dynamic real-time measurements were difficult with this setup due to diagnostic laser scattering; hence, an additional experimental setup was developed to complement these results. In the second set of experiments a rippled surface was ablated by a controlled laser pulsed, which launched a rippled shock front to an opposite initially flat diagnostic surface that was monitored in real-time with spatially resolved velocimetry techniques, e.g., line VISAR in addition to Transient Imaging Displacement Interferometry (TIDI) displacement measurements. This setup limited the displacements at the diagnostic surface to a reasonable level for TIDI measurements (~ less than one micrometer). These experiments coupled with analytical and numerical solutions provided evidence that viscous and elastic deviatoric strength affect shock front perturbation evolution in clearly different ways. Particularly, normalized shock front perturbation amplitudes evolve with viscosity (η) and perturbation wavelength (λ) as η/λ, such that increasing viscosity (or decreasing the initial wavelength) delays the perturbation decay. Conversely our experimental data, analysis and simulations show that for materials with elastic yield strength Y the normalized shock perturbation amplitude evolves with Yλ/A 0 , which shows wavelength increases have the opposite effect as in viscous materials and perturbation decay is also dependent on initial amplitude A 0 (viscous materials are independent of this parameter). Materials where strength had clear strain rate dependence, e.g., such as a PTW material law, behaved similarly to materials with only an effective yield stress (elastic-perfectly plastic) in the shock front perturbation studies obeying a Y eff λA 0 relationship where Y eff was a constant (near ~400 MPa for Cu for strain rates around 10 6 s -1 ). Magnitude changes in strain rate would increase Y eff as would be expected from the PTW behavior, but small perturbations (typical of regions behind the shock front) near a mean had little effect. Additional work based on simulations showed that phase transformation kinetics can affect the behavior of the perturbed shock front as well as the evolution of the RM-like instability that develops due to the imprint of the perturbed shock front on the initially flat surface as the shock breaks out.

36 MATERIALS SCIENCE↗

The Open-source Data Inventory for Anthropogenic CO 2 , version 2016 (ODIAC2016): a global monthly fossil fuel CO 2 gridded emissions data product for tracer transport simulations and surface flux inversions

The Open-source Data Inventory for Anthropogenic CO 2 (ODIAC) is a global high-spatial-resolution gridded emissions data product that distributes carbon dioxide (CO 2 ) emissions from fossil fuel combustion. The emissions spatial distributions are estimated at a 1 × 1 km spatial resolution over land using power plant profiles (emissions intensity and geographical location) and satellite-observed nighttime lights. This work describes the year 2016 version of the ODIAC emissions data product (ODIAC2016) and presents analyses that help guide data users, especially for atmospheric CO 2 tracer transport simulations and flux inversion analysis. Since the original publication in 2011, we have made modifications to our emissions modeling framework in order to deliver a comprehensive global gridded emissions data product. Major changes from the 2011 publication are (1) the use of emissions estimates made by the Carbon Dioxide Information Analysis Center (CDIAC) at the Oak Ridge National Laboratory (ORNL) by fuel type (solid, liquid, gas, cement manufacturing, gas flaring, and international aviation and marine bunkers); (2) the use of multiple spatial emissions proxies by fuel type such as (a) nighttime light data specific to gas flaring and (b) ship/aircraft fleet tracks; and (3) the inclusion of emissions temporal variations. Using global fuel consumption data, we extrapolated the CDIAC emissions estimates for the recent years and produced the ODIAC2016 emissions data product that covers 2000–2015. Our emissions data can be viewed as an extended version of CDIAC gridded emissions data product, which should allow data users to impose global fossil fuel emissions in a more comprehensive manner than the original CDIAC product. Our new emissions modeling framework allows us to produce future versions of the ODIAC emissions data product with a timely update. Such capability has become more significant given the CDIAC/ORNL's shutdown. The ODIAC data product could play an important role in supporting carbon cycle science, especially modeling studies with space-based CO 2 data collected in near real time by ongoing carbon observing missions such as the Japanese Greenhouse gases Observing SATellite (GOSAT), NASA's Orbiting Carbon Observatory-2 (OCO-2), and upcoming future missions. The ODIAC emissions data product including the latest version of the ODIAC emissions data (ODIAC2017, 2000–2016) is distributed from http://db.cger.nies.go.jp/dataset/ODIAC/ with a DOI (https://doi.org/10.17595/20170411.001).

54 ENVIRONMENTAL SCIENCES↗

Confronting Large‐Eddy Simulations With Stereo Camera Data by Means of Reconstructed Hemispheric Cloud Size Distributions

High-resolution hemispheric camera images at a meteorological site in western Germany are used to analyze the multi-dimensional spatial characteristics of continental cumulus cloud fields, and to evaluate Large-Eddy Simulations on this aspect. Traditional non-hemispheric cloud-detecting instruments provide additional reference data. The main model-observation comparison focuses on cloud size distributions (CSDs), employing two methods: (a) directly using three-dimensional model fields, direct CSDs, and (b) using rendered hemispheric images of the model fields as produced by a camera simulator based on path-tracing. In the latter method, both the real and rendered images are used to three-dimensionally reconstruct the cloud fields, yielding hemispheric CSDs. Advantages of hemispheric comparisons over more classic approaches include (a) fair comparisons between model and data, and (b) full use of the enhanced resolutions and hemispheric spatial coverage of the camera imagery. Basic evaluation of the simulations demonstrates good agreement on thermodynamic structure and its diurnal cycle. Cloud heights and cloud cover are intercompared between the model, camera data and other instrumentation, providing insight into their structural differences. A consistent alignment is found between the hemispheric CSDs from both the model and the cameras. Power law fits reveal structurally lower exponents in hemispheric CSDs compared to non-hemispheric CSDs, which particularly caution against directly comparing hemispheric CSDs to non-hemispheric distributions. This result is robust for sample size and fitting method. These findings inform future use of hemispheric camera systems for studying cumulus cloud field morphology and model evaluation.

54 ENVIRONMENTAL SCIENCES↗

The Area Localized Coupled Model for Analytical Mean Flow Prediction in Arbitrary Wind Farm Geometries

This work introduces the area localized coupled (ALC) model, which extends the applicability of approaches that couple classical wake superposition models and atmospheric boundary layer models to wind farms with arbitrary layouts. Coupling wake and top–down boundary layer models is particularly challenging since the latter requires averaging over planform areas associated with turbine-specific regions of the flow that need to be specified. The ALC model uses Voronoi tessellation to define this local area around each turbine. A top–down description of a developing internal boundary layer is then applied over Voronoi cells upstream of each turbine to estimate the local mean velocity profile. Coupling between the velocity at hub-height based on this localized top–down model and a wake model is achieved by enforcing a minimum least-square-error in mean velocity in each cell. The wake model in the present implementation takes into account variations in wind farm inflow velocity and represents the wake profile behind each turbine as a super-Gaussian function that smoothly transitions between a top-hat shape in the region immediately following the turbine to a Gaussian profile downstream. Detailed comparisons to large-eddy simulation (LES) data from two different wind farms demonstrate the efficacy of the model in accurately predicting both wind farm power output and local turbine hub-height velocity for different wind farm geometries. These validations using data generated from two different LES codes demonstrate the model's versatility with respect to capturing results from different simulation setups and wind farm configurations.

49 EE - Wind and Water Power Program - Wind (EE-4W↗

Active Subspace Methods for Data-Intensive Inverse Problems (Final Report)

Fostered by advances in computing, simulation and data science have emerged as the third and fourth paradigms enabling scientific discovery. Many mathematical challenges arise when integrating these paradigms to produce new knowledge. One of the most important challenges is the inverse or calibration problem: find the inputs of a simulation such that its outputs agree with a given set of measurements. As both the cost of the complex simulations and the volume of measurement data sets increase, intuition-driven trial-and-error methods for calibration quickly become untenable; modern scientists need more computationally efficient and mathematically rigorous methods. When measurements and simulated predictions contain uncertainty, the Bayesian perspective on statistical inference provides a popular mathematical framework for developing computational methods to solve inverse problems. Markov chain Monte Carlo (MCMC) methods are a mainstay of this framework; they characterize a probability distribution on the space of model inputs that is conditioned on the given measurements. However, despite recent advances, MCMC methods remain impractical for expensive simulations with more than a handful of inputs. At its heart, MCMC searches the space of inputs for corresponding outputs that match measurements, and so it is afflicted with the curse of dimensionality. Additionally, MCMC methods become less efficient as the volume of the measurement data increases, particularly if the measurements are redundant. To make MCMC—and Bayesian methods, in general—amenable to today’s computer models with millions of inputs and terabytes of measurement data, one must devise methods to reduce the dimension of both the simulation inputs and the measurements. For many models used in practice, the outputs vary primarily on a low-dimensional manifold of the nominally high-dimensional input space. Recently developed active subspace methods discover this low-dimensional manifold and exploit it to enable analyses typically suited for low-dimensional settings (e.g., statistical inversion of complex systems). We hypothesize that active subspace methods can provide the necessary dimension reduction, enabling existing Bayesian methods to find solutions for a large class of otherwise intractable statistical inverse problems. We will test the hypothesis with a series of mathematical analyses and computational experiments that will proceed along three research veins: (i) integrating active subspace methods into methods for statistical inversion, (ii) addressing current challenges in active subspace methods, and (iii) incorporating methods for nonlinear dimensionality reduction into active subspace methods. We will apply the methods we develop to real inverse problems in chemical kinetics and turbulent flame modeling. Our team combines expertise in methods for inverse problems, dimension reduction, and reduced order modeling. With a history of active collaboration and thoughtful engagement, we bring enthusiasm and fresh perspectives to a well studied subject. We are excited by the potential opportunity to work together to extend and apply active subspace methods to data-intensive inverse problems.

97 MATHEMATICS AND COMPUTING↗

Electronic structure simulations in the cloud computing environment

The transformative impact of modern computational paradigms and technologies, such as high-performance computing, quantum computing, and cloud computing, has opened up profound new opportunities for scientific simulations. Scalable computational chemistry is one beneficiary of this technological progress. The main focus of this paper is on the performance of various quantum chemical formulations, ranging from low-order methods to high-accuracy approaches, implemented in different computational chemistry packages, such as NWChem, NWChemEx, SPEC, ExaChem, and FLOSIC codes on the Azure Quantum Element (AQE) Microsoft cloud services. We pay particular attention to the intricate workflows for performing composite chemistry simulations, associated data curation, and mechanisms for accuracy assessment, as defined by the enabling cloud Computational Chemistry as a Service (CCaaS). Our focus also extends to Arrows' automated workflow for high throughput simulations. Finally, we provide a perspective on the role of cloud computing in supporting the mission of leadership computational facilities (LCFs).

computational chemistry, electronic structure, Clo↗

Union: An Automatic Workload Manager for Accelerating Network Simulation

With the rapid growth of the machine learning applications, the workloads of future HPC systems are anticipated to be a mix of scientific simulation, big data analytics, and machine learning applications. Simulation is a great research vehicle to understand the performance implications of co-running scientific applications with big data and machine learning workloads on large-scale systems. In this paper, we present Union, a workload manager that provides an automatic framework to facilitate hybrid workload simulation in CODES. Furthermore, we use Union, along with CODES, to investigate various hybrid workloads composed of traditional simulation applications and emerging learning applications on two dragonfly systems. The experiment results show that both message latency and communication time are important performance metrics to evaluate network interference. Network interference on HPC applications is more reflected by the message latency variation, whereas ML application performance depends more on the communication time.

heterogeneous workloads↗

Advancements on Multi-Fidelity Random Fourier Neural Networks: Application to Hurricane Modeling for Wind Energy

Multi-fidelity approaches are emerging as effective strategies in computational science to handle otherwise intractable tasks like Uncertainty Quantification (UQ), training of Machine Learning (ML) models, and optimization, for expensive high-fidelity applications in which the amount of available simulations or data is limited. The main idea is simple: large datasets generated for low-fidelity approximations of the problem at hand are fused with a much sparser dataset for the target (high-fidelity) system. In this paper, we build on our recent success in designing random Fourier Neural Networks (rFNNs) [1] to target problems arising in wind energy applications and in particular problems of interest for hurricane modeling. In this context, data for the high-fidelity models are limited and lower fidelity alternatives are needed. In this work, we introduce a novel multi-fidelity training approach for our rFNNs and demonstrate its use on a simple verification problem and on a hurricane modeling problem in which high-fidelity data are generated via Large-Eddy Simulations (LES), while low-fidelity data are given by a mesoscale model. Initial results demonstrate how the multi-fidelity training approach can improve the quality of the resulting surrogate.

Fourier Neural Networks↗

A Gigaparsec-scale Hydrodynamic Volume Reconstructed with Deep Learning

The next generation of spectroscopic surveys will map the large-scale structure of the Universe at high redshifts (2 ≤ z ≤ 5) using millions of quasar spectra, enabling major advances in constraining both the standard cosmological model and its extensions. Robust cosmological analyses of these data sets require numerical simulations that both cover gigaparsec volumes and resolve features on ∼10 kpc scales and smaller. However, running such large-volume, high-resolution hydrodynamic simulations is computationally prohibitive. We present a generative deep learning model that enhances a low-resolution, gigaparsec-scale (960 h −1 Mpc) hydrodynamic simulation using a smaller (80 h −1 Mpc) high-resolution input hydrodynamic simulation as training data. The resulting enhanced simulation reproduces the line-of-sight power spectrum to within ∼10% and the three-dimensional power spectrum at the ∼20% level at intermediate to small scales (k ≲ 2 h Mpc −1 ). Our method shows strong promise for producing realistic simulations for cosmological analyses with current surveys such as the Dark Energy Spectroscopic Instrument and upcoming next-generation experiments, but further improvements are needed to accurately recover the large-scale modes. We publicly release the enhanced hydrodynamic simulation, along with a halo catalog from a companion N-body dark matter simulation to support the calibration of data analysis pipelines for these large-scale surveys.

Convolutional neural networks↗

Photonuclear production of 47 Ca for 47 Ca/ 47 Sc generator from natural CaCO 3 targets

Here this work investigated the indirect production of 47 Sc from natural Ca targets via 48 Ca(γ,n) 47 Ca → 47 Sc +β - +$\bar{\nu}_e$ with incident electron energies of 30, 35, and 40 MeV. The 47 Ca production yields were simulated using the PHITS Monte Carlo simulation code and compared to experimental data. The simulated production rates for all three irradiations are in good agreement with experimental data within uncertainties. As a demonstration of the 47 Ca/ 47 Sc generator system, one of the irradiated CaCO 3 targets was dissolved in nitric acid, and 47 Sc was isolated from the target material using commercially available Eichrom DGA resin. The 47 Sc was allowed to grow in, and the purification process was repeated with promising 47 Sc and Ca recovery yields.

07 ISOTOPE AND RADIATION SOURCES↗

Bellerophon Environment for Analysis of Materials (BEAM)

Improvements in scientific instrumentation allow imaging at mesoscopic to atomic length scales, many spectroscopic modes, and now--with the rise of multimodal acquisition systems and the associated processing capability--the era of multidimensional, informationally dense data sets has arrived. Technical issues in these combinatorial scientific fields are exacerbated by computational challenges best summarized as a necessity for drastic improvement in the capability to transfer, store, and analyze large volumes of data. The Bellerophon Environment for Analysis of Materials (BEAM) platform provides material scientists the capability to directly leverage the integrated computational and analytical power of High Performance Computing (HPC) to perform scalable data analysis and simulation and manage uploaded data files via an intuitive, cross-platform client user interface. This framework delivers authenticated, "push-button" execution of complex user workflows that deploy data analysis algorithms and computational simulations utilizing compute-and-data cloud infrastructures and HPC environments like Titan at the Oak Ridge Leadershp Computing Facility (OLCF).

Lingerfelt, Eric J↗

Comparing field data using Alpert multi-wavelets

In this paper we introduce a method to compare sets of full-field data using Alpert tree-wavelet transforms. The Alpert tree-wavelet methods transform the data into a spectral space allowing the comparison of all points in the fields by comparing spectral amplitudes. The methods are insensitive to translation, scale and discretization and can be applied to arbitrary geometries. This makes them especially well suited for comparison of field data sets coming from two different sources such as when comparing simulation field data to experimental field data. We have developed both global and local error metrics to quantify the error between two fields. Additionally, we verify the methods on two-dimensional and three-dimensional discretizations of analytical functions. Furthermore, we then deploy the methods to compare full-field strain data from a simulation of elastomeric syntactic foam.

42 ENGINEERING↗

Multiresolution classification of turbulence features in image data through machine learning

During large-scale simulations, intermediate data products such as image databases have become popular due to their low relative storage cost and fast in-situ analysis. Serving as a form of data reduction, these image databases have become more acceptable to perform data analysis on. In this work, we present an image-space detection and classification system for extracting vortices at multiple scales through wavelet-based filtering. A custom image-space descriptor is used to encode a large variety of vortex-types and a machine learning system is trained for fast classification of vortex regions. By combining a radial-based histogram descriptor, a bag of visual words feature descriptor, and a support vector machine, our results show that we are able to detect and classify vortex features at various sizes at multiple scales. Once trained, our framework enables the fast extraction of vortices on new, unknown image datasets for flow analysis.

97 MATHEMATICS AND COMPUTING↗

Active Storage with Analytics Capabilities and I/O Runtime System for Petascale Systems

Computational scientists must understand results from experimental, observational and computational simulation generated data to gain insights and perform knowledge discovery. As systems approach the petascale range, problems that were unimaginable a few years ago are within reach. With the increasing volume and complexity of data produced by ultra-scale simulations and high-throughput experiments, understanding the science is largely hampered by the lack of comprehensive I/O, storage, acceleration of data manipulation, analysis, and mining tools. Scientists require techniques, tools and infrastructure to facilitate better understanding of their data, in particular the ability to effectively perform complex data analysis, statistical analysis and knowledge discovery. The goal of this work is to enable more effective analysis of scientific datasets through the integration of enhancements in the I/O stack, from active storage support at the file system layer to MPI-IO and high-level I/O library layers. We propose to provide software components to accelerate data analytics, mining, I/O, and knowledge discovery for large-scale scientific applications, thereby increasing productivity of both scientists and the systems. Our approaches include 1) design the interfaces in high-level I/O libraries, such as parallel netCDF, for applications to activate data mining operations at the lower I/O layers; 2) Enhance MPI-IO runtime systems to incorporate the functionality developed as a part of the runtime system design; 3) Develop parallel data mining programs as part of runtime library for server-side file system in PVFS file system; and 4) Prototype an active storage cluster, which will utilize multicore CPUs, GPUs, and FPGAs to carry out the data mining workload.

97 MATHEMATICS AND COMPUTING↗