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DOE OSTI2021

hls4ml: An Open-Source Codesign Workflow to Empower Scientific Low-Power Machine Learning Devices

Accessible machine learning algorithms, software, and diagnostic tools for energy-efficient devices and systems are extremely valuable across a broad range of application domains. In scientific domains, real-time near-sensor processing can drastically improve experimental design and accelerate scientific discoveries. To support domain scientists, we have developed hls4ml, an open-source software-hardware codesign workflow to interpret and translate machine learning algorithms for implementation with both FPGA and ASIC technologies. We expand on previous hls4ml work by extending capabilities and techniques towards low-power implementations and increased usability: new Python APIs, quantization-aware pruning, end-to-end FPGA workflows, long pipeline kernels for low power, and new device backends include an ASIC workflow. Taken together, these and continued efforts in hls4ml will arm a new generation of domain scientists with accessible, efficient, and powerful tools for machine-learning-accelerated discovery.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

HQ-Tracer

HQ-Tracer is a software plugin related to the open-source project Ghidra. It is used for taking an emulation instruction trace from open source platforms and displaying inside of Ghidra. It allows for software debugging, reverse engineering, and enables interactive forward and backward stepping and searching through the execution traces. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-4552 O

Wright, ChristopherM.↗

DOE OSTI2022

Tsdat: An Open-Source Data Standardization Framework for Marine Energy and Beyond: Preprint

Many organizations are tasked with the collection and processing of large quantities of data from various measurement devices. Data reported from these sources are often not interoperable with datasets and software used by analysts and other organizations in the same field, introducing barriers for collaboration on large-scale projects. This poses a particular problem for cross-device comparisons and machine learning applications. To address these challenges, the open source Time-Series Data Pipelines (Tsdat) software was developed by a joint collaboration between Pacific Northwest National Laboratory, the National Renewable Energy Laboratory, and Sandia National Laboratories to facilitate collaboration and accelerate advancements in the Marine Energy domain through the development of an open-source ecosystem of tools. This paper will describe the Tsdat software and the data standards within which the framework operates. A beta version of the framework has been released and is currently being used by several projects in marine energy, wind energy, and building energy systems.

big data↗

DOE OSTI2022

SALT3-NIR: Taking the Open-source Type Ia Supernova Model to Longer Wavelengths for Next-generation Cosmological Measurements

Abstract A large fraction of Type Ia supernova (SN Ia) observations over the next decade will be in the near-infrared (NIR), at wavelengths beyond the reach of the current standard light-curve model for SN Ia cosmology, SALT3 (∼2800–8700 Å central filter wavelength). To harness this new SN Ia sample and reduce future light-curve standardization systematic uncertainties, we train SALT3 at NIR wavelengths (SALT3-NIR) up to 2 μ m with the open-source model-training software SALTshaker , which can easily accommodate future observations. Using simulated data, we show that the training process constrains the NIR model to ∼2%–3% across the phase range (−20 to 50 days). We find that Hubble residual (HR) scatter is smaller using the NIR alone or optical+NIR compared to optical alone, by up to ∼30% depending on filter choice (95% confidence). There is significant correlation between NIR light-curve stretch measurements and luminosity, with stretch and color corrections often improving HR scatter by up to ∼20%. For SN Ia observations expected from the Roman Space Telescope, SALT3-NIR increases the amount of usable data in the SALT framework by ∼20% at redshift z ≲ 0.4 and by ∼50% at z ≲ 0.15. The SALT3-NIR model is part of the open-source SNCosmo and SNANA SN Ia cosmology packages.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2014

SU-E-T-210: Independent MU Dose Calculation Software for S and S IMRT Using Modified Clarkson Integration Sector

Purpose: The purpose of this work was to develop and validate an open source independent MU dose calculation software for S and S IMRT based in the algorithm proposed by Kung et.al. Methods: Treatment plans were done using Iplan v4.5 BrainLAB TPS and S and S IMRT modality. A 6MV photon beam produced by a Primus linear accelerator equipped with an Optifocus MLC was used. TPS dose calculation algorithms were pencil beam and Monte Carlo. 230 IMRT treatments plans were selected for the study. The software was written under MALTLAB environment. Treatment plans were imported by the software using RTP format. Field fluences were reconstructed adding all segments.The algorithm implemented in the software calculates the dose at a reference point as the sum of primary and scatter dose. The primary dose is obtained by masking the fluence map with a circle of radius 1cm. The scatter dose is obtained through a shaped ring mask around the previous circle with a thickness of 0.5cm; the rings are increased one after another with constant thickness until cover the entire map of influence. The dosimetric parameters Sc, Sp and TPR vary depending on radio, the transmission effect of the MLC, inverse square law and dose profile are used for the calculation. Results: The average difference between measured and independent calculated dose was 0.4% ± 2.2% [−6.8%, 6.4%]. For 91% of the studied plans the difference was less than 3%. The difference between the measured and TPS dose with pencilbeam algorithm was 2.6% ± 1.41% [−2.0%, 5.6%] and Monte Carlo algorithm was 0.4% ± 1.5% [−4.9%, 3.7%]. The differences obtained are comparable to that obtained with the ionization chamber and TPS. Conclusion: The developed software is suitable for use in S and S IMRT dose calculation. This application is open and can be downloading under request.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2016

TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data

In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. However, existing pipelines for GBS and RAD-seq do not provide read counts in formats that are both accurate and easy to access. Additionally, although existing pipelines allow previously-mined SNPs to be genotyped on new samples, they do not allow the user to manually specify a subset of loci to examine. Pipelines that do not use a reference genome assign arbitrary names to SNPs, making meta-analysis across projects difficult. We created the software TagDigger, which includes three programs for analyzing GBS and RAD-seq data. The first script, tagdigger_interactive.py, rapidly extracts read counts and genotypes from FASTQ files using user supplied sets of barcodes and tags. Input and output is in CSV format so that it can be opened by spreadsheet software. Tag sequences can also be imported from the Stacks, TASSEL-GBSv2, TASSEL-UNEAK, or pyRAD pipelines, and a separate file can be imported listing the names of markers to retain. A second script, tag_manager.py, consolidates marker names and sequences across multiple projects. A third script, barcode_splitter.py, assists with preparing FASTQ data for deposit in a public archive by splitting FASTQ files by barcode and generating MD5 checksums for the resulting files. TagDigger is open-source and freely available software written in Python 3. It uses a scalable, rapid search algorithm that can process over 100 million FASTQ reads per hour. TagDigger will run on a laptop with any operating system, does not consume hard drive space with intermediate files, and does not require programming skill to use.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Towards exact finite temperature electronic structure in solids and molecules (Final Technical Report)

This report describes the University of Iowa portion of a project that is now continuing at Michigan State University. We are developing novel methods, algorithms, and software to enable simulations of molecules and materials at high temperature. This is a key challenge in chemistry and materials science. By refining an approach called Density Matrix Quantum Monte Carlo (DMQMC), we developed faster and more accurate ways to conduct these simulations. These advances will help us understand how temperature affects the behavior of electrons, chemical bonds, and phase transitions in solids and molecules. These breakthroughs are especially important for applications where light and heat drive chemical reactions, superconductivity, and materials used in energy and sensing. In addition, this project involved the development of the open-source HANDE-QMC software package, supporting the broader community in benchmarking and developing finite-temperature electronic structure methods.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Effects of overlapping sources on cosmic shear estimation: Statistical sensitivity and pixel-noise bias

The next generation of dark-energy imaging surveys — so called “Stage-IV” surveys, such as that of the Rubin Observatory Legacy Survey of Space and Time (LSST) — will cross a threshold in the number density of detected sources on the sky that requires qualitatively different image analysis and measurement techniques compared to the current generation of Stage-III surveys. In Stage-IV surveys, a significant amount of the cosmologically useful information is due to sources whose images overlap with those of other sources on the sky. Here, we focus on the weak gravitational lensing probe, for which we expect the largest impact since the cosmic shear signal is primarily encoded in the estimated shapes of observed galaxies and thus directly impacted by overlaps. We introduce a framework based on the Fisher formalism to analyze the effect of the overlapping sources (“blending”) on the estimation of cosmic shear. This method gives concrete predictions for the minimum loss of information due to noise and blending for any choice of “deblending” scheme and shape-measurement algorithm. Our studies account for undetected sources but do not address their full effects and biases they may introduce. We use simulated images and predict this impact of blending for three surveys: the Dark Energy Survey (DES), the Hyper-Suprime Cam Subaru Strategic Program (HSC-SSP), and the Rubin LSST. Our methodology successfully estimates the statistical sensitivity to weak lensing for DES and HSC early results. For LSST, we present the expected loss in statistical sensitivity for the ten-year survey due to blending. We find that for approximately 62% of galaxies that are likely to be detected in full-depth LSST images, at least 1% of the flux in their pixels is from overlapping sources. We also find that the statistical correlations between measures of overlapping galaxies and, to a much lesser extent (0.2%) the higher shot noise level due to their presence, decrease the effective number density of galaxies, N eff , by ~ 18%. We calculate an upper limit on N eff of 39.4 galaxies per arcmin 2 in r band. We study the impact of stars on as a function of stellar density and illustrate the diminishing returns of extending the survey into lower Galactic latitudes. We extend the simulation-based Fisher formalism to predict the expected increase in pixel-noise bias due to blending for maximum-likelihood (ML) shape estimators. We find that noise bias depends sensitively on the particular shape estimator and measure of ensemble-average shape that is used, and properties of the galaxy that include redshift-dependent quantities such as size and luminosity. The source code for these studies is available online.[The documented software developed for the catalog-level studies are available in the open-source LSST DESC github repository https://github.com/LSSTDESC/WeakLensingDeblending. The software for analyzing one or two galaxies with user-defined parameters is in the open-source github repository https://github.com/ismael-mendoza/ShapeMeasurementFisherFormalism.]

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2026

PyJMAK: An Open-Source Python Toolkit for Modeling Solid-State Metallurgical Phase Transformations

Accurate prediction of metallurgical phase transformations is an essential basis for autonomous optimization and rapid part qualification. Several methods can be used to estimate the evolution of phase fractions such as JMAK kinetics-based models, phase-field models, thermodynamic models, and data-driven machine learning models. Thermodynamic and phase-field-based methodologies solve multiphysics equations requiring numerous calibration parameters and significant computational resources. As a result, the computation domain is limited to a point or on order of micron-meters. The data-driven models rely on large datasets from experiments and simulations. While the JMAK model only provides information about phase fraction evolution, it can predict this evolution in near real-time using thermal history and thermodynamic data without restriction on the domain. JMAK models have been popularly used by researchers to model phase transformations occuring during additive manufacturing or over arbitrary temperature profiles. Commercial proprietary software such as Abaqus and Ansys or closed-source in-house implementations offer the ability to model JMAK based kinetics to predict phase transformation. However, these software packages are not open-source or freely available for use and development in conjunction with manufacturing machines, sensors, and machine learning algorithms. In addition, the use of the model is restricted by a license token. In contrast, given temperature profiles at multiple points in the domain, this Python-based PyJMAK model can compute phase evolution in parallel due to its stand-alone modular, voxel-based structure, and it can be executed on high-performance computing resources without any license restrictions.

Prabhune, Bhagya [Oak Ridge National Laboratory (O↗

DOE OSTI2014

SU-E-T-348: Verification MU Calculation for Conformal Radiotherapy with Multileaf Collimator Using Report AAPM TG 114

Purpose: The purpose of this work was to develop and validate an open source independent MU dose calculation software for 3D conformal radiotherapy with multileaf high and low resolution according to the report of AAPM TG 11 Methods: Treatment plans were done using Iplan v4.5 BrainLAB TPS. A 6MV photon beam produced by Primus and Novalis linear accelerators equipped with an Optifocus MLC and HDMLC, respectively. TPS dose calculation algorithms were pencil beam and Monte Carlo. 1082 treatments plans were selected for the study. The algorithm was written in free and open source CodeBlocks C++ platform. Treatment plans were imported by the software using RTP format. Equivalent size field is obtained from the positions of the leaves; the effective depth of calculation can be introduced by TPS's dosimetry report or automatically calculated starting from SSD. The inverse square law is calculated by the 3D coordinates of the isocenter and normalization point of the treatment plan. The dosimetric parameters TPR, Sc, Sp and WF are linearly interpolated. Results: 1082 plans of both machines were analyzed. The average uncertainty between the TPS and the independent calculation was −0.43% ± 2.42% [−7.90%, 7.50%]. Specifically for the Primus the variation obtained was −0.85% ± 2.53% and for the Novalis 0.00% ± 2.23%. Data show that 94.8% of the cases the uncertainty was less than or equal to 5%, while 98.9% is less than or equal to 6%. Conclusion: The developed software is appropriate for use in calculation of UM. This software can be obtained upon request.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2021

Computational framework for behind-the-meter DER techno-economic modeling and optimization: REopt Lite

The energy system is undergoing a major transformation with the global emphasis on decarbonization. Distributed generation is projected to play a significant role in the new energy system, and energy models are informing how distributed generation can be integrated reliably and economically. In this work, we present an end-to-end computational framework for distributed energy resource (DER) modeling, REopt Lite™, which captures the interface of technology, economics, and policy in the energy modeling process. We describe the problem space, the building blocks of the model, the scaling capabilities of the design, the optimization formulation, and the extensibility of the model. We present a framework for accelerating the techno-economic analysis of behind-the-meter distributed energy resources to enable rapid planning and decision-making, thereby enabling greater renewable energy deployment. This computation framework is open-sourced to facilitate transparency, flexibility, and wider collaboration opportunities within the worldwide energy modeling community.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2018

Numerical and experimental comparison of tracer particle and averaging techniques for particle velocities in a fluidized bed

Particle tracking methods using emitted radiation show potential for following motion in opaque systems such as granular materials. Leading examples are Positron Emission Particle Tracking (PEPT) and Radioactive Particle Tracking (RPT). The application of such techniques sometimes requires the use of tracer particles which differ in size, density and/or shape from the particles of interest. This study investigates the extent to which such differences affect the result of the study by using the open source MFIX-DEM software to model particle motion in the travelling fluidized bed experiments. The results are compared with previously reported experimental studies using both PEPT and RPT. Consistent numerical results were obtained for both PEPT and RPT tracer particles. In determining averaged velocities using such techniques, there is a choice to be made between averaging velocities of particles crossing a virtual plane over a period of time (the “face-average” approach) or those passing through a defined volume over time (the “volume-average” approach). The differences between results obtained with these two methods are shown to be significant in this case, for both computation and experiment.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2015

JP-10 combustion studied with shock tube experiments and modeled with automatic reaction mechanism generation

Our research presents shock tube experiments and kinetic modeling efforts on the pyrolysis and combustion of JP-10. The experiments were performed at 6–8 atm using 2000 ppm of JP-10 over a temperature range of 1000–1600 K for pyrolysis and oxidation equivalence ratios from 0.14 to 1.0. This work distinguishes itself from previous studies as GC/MS was used to identify and quantify the products within the shocked samples, enabling the tracking of product yield dependence on equivalence ratio as well as identifying several new intermediates that form during JP-10’s decomposition. A detailed, comprehensive model of JP-10’s combustion and pyrolysis kinetics was constructed with the help of RMG, an open-source reaction mechanism generation software package. The resulting model, which includes 691 species reacting in 15,518 reactions, was extensively validated against the shock tube experimental dataset as well as newly published flow tube pyrolysis data from Ghent. Most of the significant rate coefficients were computed using quantum chemistry. The model succeeds in identifying all major pyrolysis and combustion products and captures key trends in the product distribution. Simulated ignition delays agree within a factor of 4 with most experimental ignition delay data gathered from literature. The proposed experimental work and modeling efforts yield new insights on JP-10’s complex decomposition and oxidation chemistry and identify key pathways towards aromatics formation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Matminer: An open source toolkit for materials data mining

As materials data sets grow in size and scope, the role of data mining and statistical learning methods to analyze these materials data sets and build predictive models is becoming more important. This manuscript introduces matminer, an open-source, Python-based software platform to facilitate data-driven methods of analyzing and predicting materials properties. Matminer provides modules for retrieving large data sets from external databases such as the Materials Project, Citrination, Materials Data Facility, and Materials Platform for Data Science. It also provides implementations for an extensive library of feature extraction routines developed by the materials community, with 47 featurization classes that can generate thousands of individual descriptors and combine them into mathematical functions. Finally, matminer provides a visualization module for producing interactive, shareable plots. These functions are designed in a way that integrates closely with machine learning and data analysis packages already developed and in use by the Python data science community. We explain the structure and logic of matminer, provide a description of its various modules, and showcase several examples of how matminer can be used to collect data, reproduce data mining studies reported in the literature, and test new methodologies.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Cost optimization of low-salt-rejection reverse osmosis

Low-salt-rejection reverse osmosis (LSRRO) is an emerging membrane-based desalination technology for concentrating brines with potentially lower energy consumption and cost than thermally driven processes. We assess the technoeconomic performance of LSRRO by using an optimization model that minimizes the levelized cost of water (LCOW). We develop detailed models for the RO module and other equipment using WaterTAP (Water treatment Technoeconomic Assessment Platform), an open-source simulation and optimization software for water treatment. We improve upon previous LSRRO cost optimization studies by optimizing the salt permeability for each stage, which has significant implications for technoeconomic performance. We present the cost-optimal design, operation, and performance for three cases: 35 g/L TDS feed at 70% recovery, 70 g/L at 55%, and 125 g/L at 35%. The cost-optimal LCOW and specific energy consumption (SEC) for these cases are 0.70, 1.89, and 7.41 $/m 3 and 3.9, 8.4, and 30.4 kWh/m 3 , respectively. For each case, we use sensitivity analyses to provide guidance on key factors that impact economic viability. We also present the cost-optimal LCOW and SEC for feed concentrations between 5 and 220 g/L TDS and recoveries between 30 and 90%. So, we compare LSRRO to other high-salinity desalination technologies and find that it may be cost-competitive below feed concentrations of 125 g/L.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

Multiscale modeling of twinning and detwinning behavior of HCP polycrystals

A multiscale scheme is presented here to capture the twinning and detwinning mechanisms during cyclic loading of HCP polycrystals. In the current framework, the crystal plasticity finite element (CPFE) method is employed at the microstructural scale. The response of twinned regions at a material point is calculated using a novel homogenization scheme via a Taylor-type model. The homogenized behavior is then used in the CPFE to obtain the response of a polycrystal. An efficient rate-independent crystal plasticity model that has been incorporated into the open source PRISMS-Plasticity software is introduced here to capture the response of the twinned region. Accordingly, the corresponding algorithmic tangent modulus is derived. Finally, this multiscale scheme is validated against data available for the cyclic response of Mg alloy ZK60A. The results show that the multiscale model can capture the key elements of the sample response observed during the experiment.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Nonintrusive Uncertainty Quantification of Computational Fluid Dynamics Simulations of a Bench-Scale Fluidized-Bed Gasifier

Uncertainty quantification (UQ) analysis is increasingly becoming one of the major requirements of simulation-based engineering to assess the confidence in the results and make better-informed decisions based on the insight derived from the simulations. In an earlier study, Bayesian UQ analysis was applied to existing bench-scale fluidized-bed gasifier experiment results. In the current study, a series of simulations were carried over with the open-source computational fluid dynamics software MFiX to reproduce the experimental conditions, where three operating factors, i.e., coal flow rate, coal particle diameter, and steam-to-oxygen ratio, were systematically varied to understand their effect on the syngas composition. Bayesian UQ analysis was this time performed on the numerical results for comparison purposes. This is part of ongoing research efforts to explore the applicability of advanced UQ methods and processes such as Bayesian methods for large-scale complex multiphase flow simulations. As part of Bayesian UQ analysis, a global sensitivity analysis was performed based on the simulation results, which shows that the predicted syngas composition is strongly affected not only by the steam-to-oxygen ratio (which was observed in experiments as well) but also by variation in the coal flow rate and particle diameter (which was not observed in experiments). The carbon monoxide mole fraction is underpredicted at lower steam-to-oxygen ratios and overpredicted at higher steam-to-oxygen ratios. The opposite trend is observed for the carbon dioxide mole fraction. These discrepancies are attributed to either excessive segregation of the phases that leads to the fuel-rich or -lean regions or alternatively the selection of reaction models, where different reaction models and kinetics can lead to different syngas compositions throughout the gasifier.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2018

Electronic Excitations in Complex Molecular Environments: Many-Body Green’s Functions Theory in VOTCA-XTP

Many-body Green’s functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of electronically excited states in complex molecular environments. Based on Gaussian-type atomic orbitals and making use of resolution of identity techniques, the code is designed specifically for nonperiodic systems. Application to a small molecule reference set successfully validates the methodology and its implementation for a variety of excitation types covering an energy range from 2 to 8 eV in single molecules. Further, embedding each GW-BSE calculation into an atomistically resolved surrounding, typically obtained from Molecular Dynamics, accounts for effects originating from local fields and polarization. Using aqueous DNA as a prototypical system, different levels of electrostatic coupling between the regions in this GW-BSE/MM setup are demonstrated. Particular attention is paid to charge-transfer (CT) excitations in adenine base pairs. It is found that their energy is extremely sensitive to the specific environment and to polarization effects. The calculated redshift of the CT excitation energy compared to a nucelobase dimer treated in vacuum is of the order of 1 eV, which matches expectations from experimental data. Predicted lowest CT energies are below that of a single nucleobase excitation, indicating the possibility of an initial (fast) decay of such an UV excited state into a binucleobase CT exciton. Furthermore, the results show that VOTCA-XTP’s GW-BSE/MM is a powerful tool to study a wide range of types of electronic excitations in complex molecular environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗